Table S1. Clinical characteristics of samples. · 8/14/2012 · 1428Actinobacteria Corynebacteriaceae sf_1 AF537604.1 Corynebacterium simulans National Microbiology Laboratory Special

Table S1. Clinical characteristics of samples.

Pneumocystis jiroveci

pneumonia (PCP)

Cytomegalovirus (CMV)

Mycobacterium Avium Complex

(MAC)

SFGH012 + + + + - - - - -SFGH021 + + - - + - - + -SFGH041 + + + + - + + + +SFGH071 +, Hydrocortisone Cream NR NR NR - - - - -SFGH081 Beclomethasone - - - + - - - +SFGH091 - - - - + - - + -SFGH111 - + - + - + + - -SFGH121 - + + - - + - + +SFGH161 + - - - - - + - -SFGH171 - + - - + - - - -SFGH231 + - - - NR - + - -SFGH241 + + - + NR - - - -SFGH251 + + + - - - + + -SFGH271 - + + + - - - - -SFGH291 Triamcinolone Cream - + + + + - - -NR, No recorda +, Prednisone

Microbial Culture

IDSteroid (prednisone)

AdministrationaSmoking History

Alcohol History

Current Drug Use

Prior Pneumonia

Status

Structual Lung

Disease

Table S2. Page 1 of 45

Table S2. Complete list of detected taxa by 16S rRNA PhyloChip in oral and airway samples from HIV-positive patients.

Taxa ID Phylum Family Sub Family

Accession number Representative Sequence

516 Acidobacteria Unclassified sf_1 AJ532721.1 uranium mining waste pile clone JG34-KF-153435 Acidobacteria Unclassified sf_1 AY211077.1 anaerobic VC-degrading enrichment clone VC47 bacterium790 Acidobacteria Unclassified sf_1 Z95709.1 soil clone 11-25

87 Acidobacteria Unclassified sf_1 AF097766.1 activated sludge clone 29516348 Acidobacteria Unclassified sf_1 Z95722.1 soil clone RB416363 Acidobacteria Unclassified sf_1 Z95711.1 soil clone 32-11

523 Acidobacteria Unclassified sf_1 AF245036.1 soil metagenomic library clone 17F9100 Acidobacteria Unclassified sf_1 AJ534631.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-10

1049 Acidobacteria Unclassified sf_1 AF013534.2 soil clone C11213 Acidobacteria Unclassified sf_1 AJ534637.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-202

bacterium350 Acidobacteria Unclassified sf_1 AY221047.1 Mammoth cave clone CCM15a

37 Acidobacteria Unclassified sf_1 AY214904.2 soil clone BAC-14A1500 Acidobacteria Unclassified sf_1 Z95717.1 soil clone RB24642 Acidobacteria Unclassified sf_1 Z95710.1 Holophaga/Acidobacterium phylum clone 32-10834 Acidobacteria Unclassified sf_1 AF280856.1 bioreactor clone mle1-25897 Acidobacteria Unclassified sf_1 AY221071.1 Mammoth cave clone CCM8b588 Acidobacteria Unclassified sf_1 AJ009461.1 TCB-transforming consortium clone SJA-36704 Acidobacteria Unclassified sf_1 AJ347029.1 sponge clone TK29176 Acidobacteria Acidobacteriaceae sf_14 AJ519387.1 uranium mining waste pile clone JG37-AG-112 sp.209 Acidobacteria Acidobacteriaceae sf_14 AJ519367.1 uranium mining waste pile clone JG37-AG-29 sp.274 Acidobacteria Acidobacteriaceae sf_14 AJ519379.1 uranium mining waste pile clone JG37-AG-73 sp.508 Acidobacteria Acidobacteriaceae sf_14 AJ519382.1 uranium mining waste pile clone JG37-AG-81 sp.541 Acidobacteria Acidobacteriaceae sf_14 AJ519667.1 uranium mill tailings soil sample clone GuBH2-AG-47 sp.582 Acidobacteria Acidobacteriaceae sf_14 AY102321.1 heavy metal-contaminated soil clone a13114

6335 Acidobacteria Acidobacteriaceae sf_14 AF523984.1 forested wetland clone FW456350 Acidobacteria Acidobacteriaceae sf_14 AF498719.1 soil isolate Ellin3376356 Acidobacteria Acidobacteriaceae sf_14 AF523985.1 forested wetland clone FW476364 Acidobacteria Acidobacteriaceae sf_14 AY234728.1 Solibacter usitatus Ellin60766366 Acidobacteria Acidobacteriaceae sf_14 AJ292578.1 PCB-polluted soil clone WD2286368 Acidobacteria Acidobacteriaceae sf_14 AF200698.1 soil clone UA26378 Acidobacteria Acidobacteriaceae sf_14 D26171.1 Acidobacterium capsulatum6405 Acidobacteria Acidobacteriaceae sf_14 AJ534632.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-31

bacterium6407 Acidobacteria Acidobacteriaceae sf_146410 Acidobacteria Acidobacteriaceae sf_146412 Acidobacteria Acidobacteriaceae sf_14 AF047646.1 acid mine drainage clone TRB826421 Acidobacteria Acidobacteriaceae sf_14 AJ292576.1 PCB-polluted soil clone WD2176424 Acidobacteria Acidobacteriaceae sf_14 AF524859.1 sphagnum peat bog clone K-5b106425 Acidobacteria Acidobacteriaceae sf_14 AF407719.1 Great Artesian Basin clone B27

89 Acidobacteria Acidobacteriaceae sf_14 AJ519368.1 uranium mining waste pile clone JG37-AG-31 sp.964 Acidobacteria Acidobacteriaceae sf_14 AJ519392.1 uranium mining waste pile clone JG37-AG-145 sp.




994 Acidobacteria Acidobacteriaceae sf_14 AJ519389.1 uranium mining waste pile clone JG37-AG-117 sp.6414 Acidobacteria Acidobacteriaceae sf_16 AF529350.1 PCE-contaminated site clone CLs736345 Acidobacteria Acidobacteriaceae sf_6 AJ534634.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-77

bacterium6359 Acidobacteria Acidobacteriaceae sf_6 AF529322.1 PCE-contaminated site clone CLi1146362 Acidobacteria Acidobacteriaceae sf_6 Y07646.1 grassland soil clone DA0526423 Acidobacteria Acidobacteriaceae sf_6 AF523979.1 coal effluent wetland clone FW926357 Acidobacteria Unclassified sf_1 AY118153.1 anaerobic benzene-degrading clone Cart-N46367 Acidobacteria Unclassified sf_1 AF529104.1 TCE-contaminated site clone FTL2276426 Acidobacteria Unclassified sf_1 AF407714.1 Great Artesian Basin clone B114222 Acidobacteria Unclassified sf_1 AF523991.1 forested wetland clone FW105

572 Acidobacteria Unclassified sf_1 AF523986.1 forested wetland clone FW1441090 Actinobacteria Acidimicrobiaceae sf_11360 Actinobacteria Acidimicrobiaceae sf_1 AF523917.1 forested wetland clone RCP2-1031749 Actinobacteria Acidimicrobiaceae sf_1 AY913475.1 forest soil clone DUNssu275 (-3A) (OTU#188)1856 Actinobacteria Acidimicrobiaceae sf_1 AF523913.1 forested wetland clone RCP2-1052014 Actinobacteria Acidimicrobiaceae sf_1 AY093455.1 marine sediment clone MB-A2-1002030 Actinobacteria Acidimicrobiaceae sf_1 AF523914.1 forested wetland clone RCP1-332031 Actinobacteria Acidimicrobiaceae sf_1 AF523909.1 forested wetland clone RCP1-831576 Actinobacteria Microthrixineae sf_1 AF454307.1 actinobacterium clone ML817J-101964 Actinobacteria Microthrixineae sf_1 AF406548.1 bacterioplankton clone AEGEAN_2471217 Actinobacteria Unclassified sf_1 AJ306762.2 DCP-dechlorinating consortium clone SHA-341666 Actinobacteria Unclassified sf_11399 Actinobacteria Acidothermaceae sf_1 AJ532700.1 uranium mill tailings clone Gitt-KF-1831178 Actinobacteria Actinomycetaceae sf_1 X80414.1 Actinomyces gerencseriae str. DSM 68441227 Actinobacteria Actinomycetaceae sf_1 AB062278.1 Actinomyces naeslundii1368 Actinobacteria Actinomycetaceae sf_1 AJ243893.1 Actinomyces urogenitalis1508 Actinobacteria Actinomycetaceae sf_11649 Actinobacteria Actinomycetaceae sf_1 AJ540309.1 Actinomyces graevenitzii str. CCUG 272941672 Actinobacteria Actinomycetaceae sf_1 AJ234041.1 Actinomyces odontolyticus str. CCUG 280841684 Actinobacteria Actinomycetaceae sf_1 AJ428402.1 Varibaculum cambriense str. CCUG 449981755 Actinobacteria Actinomycetaceae sf_1 X82450.1 Actinomyces israelii str. C.I.P. 103259T1798 Actinobacteria Actinomycetaceae sf_1 X87133.1 Bacterial sp.1801 Actinobacteria Actinomycetaceae sf_1 AF487679.1 Actinobaculum massiliae str. CIP 1074041883 Actinobacteria Actinomycetaceae sf_1 AJ404889.1 Actinomyces funkei str. CCUG 427732039 Actinobacteria Actinomycetaceae sf_1 AJ421779.1 Actinomyces cardiffensis str. CCUG 449972049 Actinobacteria Actinomycetaceae sf_1 AJ234059.1 Arcanobacterium haemolyticum str. CIP 1033701463 Actinobacteria Actinosynnemataceae sf_1 AF114815.1 Saccharothrix texasensis str. NRRL B-16107T1951 Actinobacteria Actinosynnemataceae sf_1 AF114809.1 Saccharothrix longispora str. NRRL B-116116T1745 Actinobacteria Brevibacteriaceae sf_1 X83813.1 Brevibacterium iodinum str. DSM 2062T1240 Actinobacteria Cellulomonadaceae sf_1 AB078847.1 Cellulomonadaceae str. WB91431 Actinobacteria Cellulomonadaceae sf_1 AB078838.1 Cellulomonadaceae str. W61449 Actinobacteria Cellulomonadaceae sf_1 AB078851.1 Cellulomonadaceae str. WB131450 Actinobacteria Cellulomonadaceae sf_1




1489 Actinobacteria Cellulomonadaceae sf_1 M87484.1 Tropheryma whippelii1586 Actinobacteria Cellulomonadaceae sf_1 X83800.1 Cellulomonas gelida str. DSM 20111T1748 Actinobacteria Cellulomonadaceae sf_1 Y18378.1 Beutenbergia cavernosa str. DSM 123331780 Actinobacteria Cellulomonadaceae sf_1 AB023361.2 Cellulomonas sp. IFO16240 str. IFO 162401923 Actinobacteria Cellulomonadaceae sf_1 AJ229245.1 Actinobacteria str. VeCb61089 Actinobacteria Corynebacteriaceae sf_1 AF537600.1 Corynebacterium mucifaciens National Microbiology Laboratory Special identifier 01-01181192 Actinobacteria Corynebacteriaceae sf_1 AJ439344.1 Corynebacterium segmentosum str. CIP107068 (CCUG37878)1338 Actinobacteria Corynebacteriaceae sf_1 X84258.1 Corynebacterium pseudodiphtheriticum str. NCTC 111361374 Actinobacteria Corynebacteriaceae sf_11428 Actinobacteria Corynebacteriaceae sf_1 AF537604.1 Corynebacterium simulans National Microbiology Laboratory Special identifier 00-01861492 Actinobacteria Corynebacteriaceae sf_1 AY677186.1 Corynebacterium tuscaniae str. ISS-53091493 Actinobacteria Corynebacteriaceae sf_1 AJ438045.1 Corynebacterium tuberculostearicum str. CIP1023461517 Actinobacteria Corynebacteriaceae sf_1 X84446.1 Corynebacterium xerosis str. DSM 207431575 Actinobacteria Corynebacteriaceae sf_1 X84443.1 Corynebacterium matruchotii str. DSM 206351803 Actinobacteria Corynebacteriaceae sf_1 AJ429234.1 Corynebacterium spheniscorum str. CCUG 455121820 Actinobacteria Corynebacteriaceae sf_1 U87823.1 Corynebacterium jeikeium str. ATCC 437341504 Actinobacteria Dermabacteraceae sf_1 AJ415380.1 Brachybacterium sacelli str. LMG 203381677 Actinobacteria Dermabacteraceae sf_1 X91030.1 Brachybacterium conglomeratum str. NCIB 98591736 Actinobacteria Dermabacteraceae sf_1 AJ415376.1 Brachybacterium rhamnosum str. LMG 198482053 Actinobacteria Dermabacteraceae sf_1 X91033.1 Brachybacterium nesterenkovii str. DSM 95731716 Actinobacteria Dermacoccaceae sf_1 X87757.1 Dermacoccus nishinomyaensis1216 Actinobacteria Dermatophilaceae sf_1 AY218605.1 penguin droppings sediments clone KD3-1381852 Actinobacteria Dermatophilaceae sf_1 AB096085.1 Tonsillophilus suis str. HT1-191990 Actinobacteria Dermatophilaceae sf_1 AF527583.1 EBPR sludge lab scale clone LPB211872 Actinobacteria Dietziaceae sf_1 X79290.1 Dietzia maris1970 Actinobacteria Dietziaceae sf_1 AF481211.1 Dietzia sp. str. E9_21161 Actinobacteria Frankiaceae sf_1 AJ408876.1 Frankia sp. MRn2-21286 Actinobacteria Frankiaceae sf_1 AJ408875.1 Frankia sp. Sn5-81644 Actinobacteria Frankiaceae sf_1 AJ408870.1 Frankia sp. M164671116 Actinobacteria Gordoniaceae sf_1 X79286.1 Gordona terrae1184 Actinobacteria Gordoniaceae sf_1 AB065369.1 Gordonia alkanivorans1191 Actinobacteria Gordoniaceae sf_1 X80635.1 Gordonia amarae str. DSM433921545 Actinobacteria Gordoniaceae sf_11567 Actinobacteria Gordoniaceae sf_11654 Actinobacteria Gordoniaceae sf_1 AF416719.1 Gordonia polyisoprenivorans str. Y2K1674 Actinobacteria Intrasporangiaceae sf_1 AJ310085.1 Janibacter terrae str. DSM 13953T1087 Actinobacteria Kineosporiaceae sf_1 AB003931.1 Kineosporia aurantiaca str. JCM32301581 Actinobacteria Kineosporiaceae sf_1 AJ293746.1 Cryptosporangium aurantiacum str. IMSNU 221201598 Actinobacteria Kineosporiaceae sf_1 AY250880.1 lichen-dominated Antarctic cryptoendolithic community clone FBP4021893 Actinobacteria Kineosporiaceae sf_1 AF095336.1 Kineosporia aurantiaca str. NRLL B-169131961 Actinobacteria Kineosporiaceae sf_1 X77958.1 Kineococcus aurantiacus str. IFO 152681106 Actinobacteria Microbacteriaceae sf_11135 Actinobacteria Microbacteriaceae sf_1 AJ459101.1 Rhodoglobus vestalii str. LV31186 Actinobacteria Microbacteriaceae sf_1 AF505514.1 Cryocola antiquus str. VKM 103PF




1197 Actinobacteria Microbacteriaceae sf_1 AF468440.1 Arctic sea ice ARK101731241 Actinobacteria Microbacteriaceae sf_1 AJ717353.1 Microbacterium kitamiense CV881404 Actinobacteria Microbacteriaceae sf_1 AJ507468.1 freshwater isolate str. MWH-Ta31437 Actinobacteria Microbacteriaceae sf_1 AJ575522.1 freshwater clone SV1-161513 Actinobacteria Microbacteriaceae sf_1 AF263565.1 Microbacterium gubbeenense str. DPC 52841667 Actinobacteria Microbacteriaceae sf_1 AB007415.1 Microbacterium lacticum1758 Actinobacteria Microbacteriaceae sf_1 AF479358.1 glacial ice isolate str. SB12K-2-11779 Actinobacteria Microbacteriaceae sf_1 AB042083.1 Microbacterium sp. str. VKM Ac-20481804 Actinobacteria Microbacteriaceae sf_1 AY244784.1 Microbacterium resistens str. 2002-591191921 Actinobacteria Microbacteriaceae sf_1 AJ292036.1 Firmicutes isolate str. d81212 Actinobacteria Micrococcaceae sf_1 AB071952.1 Rothia aeria str. GTC 8671213 Actinobacteria Micrococcaceae sf_1 X87756.1 Kocuria roseus1266 Actinobacteria Micrococcaceae sf_1 AF134179.1 Arthrobacter psychrolactophilus1324 Actinobacteria Micrococcaceae sf_1 AF479325.1 glacial ice isolate str. CanDirty11494 Actinobacteria Micrococcaceae sf_1 X80748.1 Arthrobacter agilis str. DSM 205501557 Actinobacteria Micrococcaceae sf_1 X83408.1 Arthrobacter oxydans str. DSM 201191573 Actinobacteria Micrococcaceae sf_1 AJ315492.1 Arthrobacter nicotianae str. SB421582 Actinobacteria Micrococcaceae sf_1 AY053487.1 gas hydrate clone AT425_EubD111593 Actinobacteria Micrococcaceae sf_1 M23411.1 Arthrobacter globiformis1610 Actinobacteria Micrococcaceae sf_1 X86595.1 Arthrobacter sp str. AC-511686 Actinobacteria Micrococcaceae sf_1 AY228479.1 Yania halotolerans str. YIM 700851724 Actinobacteria Micrococcaceae sf_1 X95483.1 Rothia mucilaginosa str. DSM1889 Actinobacteria Micrococcaceae sf_1 AB094464.1 Citricoccus sp. str. 2216.25.221966 Actinobacteria Micrococcaceae sf_1 AY133106.1 TCE-contaminated site clone ccspost22082019 Actinobacteria Micrococcaceae sf_1 AF057289.1 Micrococcus luteus str. HN2-112020 Actinobacteria Micrococcaceae sf_1 AF543278.1 Rothia dentocariosa str. ChDC B2002063 Actinobacteria Micrococcaceae sf_1 M59055.1 Rothia dentocariosa str. ATCC 179311120 Actinobacteria Micromonosporaceae sf_1 AJ277586.1 Actinoplanes violaceus str. IMSNU 221361159 Actinobacteria Micromonosporaceae sf_1 AJ277568.1 Actinoplanes durhamensis str. IMSNU 22124T1395 Actinobacteria Micromonosporaceae sf_1 D14642.1 Catenuloplanes japonicus str. IFO141761488 Actinobacteria Micromonosporaceae sf_1 AJ277574.1 Actinoplanes utahensis str. IMSNU 20044T1542 Actinobacteria Micromonosporaceae sf_1 AJ277575.1 Actinoplanes garbadinensis str. IMSNU 200401615 Actinobacteria Micromonosporaceae sf_1 AB036999.1 Actinoplanes derwentensis str. IFO 14935T1633 Actinobacteria Micromonosporaceae sf_1 AJ277585.1 Actinoplanes tuftoflagellus str. IMSNU 221351641 Actinobacteria Micromonosporaceae sf_1 AB196714.1 Micromonospora marina str. JSM3-11689 Actinobacteria Micromonosporaceae sf_1 AB047516.1 Actinoplanes yunnanensis str. IFO 14459T1750 Actinobacteria Micromonosporaceae sf_1 X93196.1 Dactylosporangium vinaceum str. DSM 438231760 Actinobacteria Micromonosporaceae sf_1 AJ277583.1 Actinoplanes roseosporangius str. IMSNU 221331770 Actinobacteria Micromonosporaceae sf_1 X93194.1 Dactylosporangium roseum str. DSM 439161910 Actinobacteria Micromonosporaceae sf_1 AB013495.2 Actinoplanes capillaceus str. K95-55611931 Actinobacteria Micromonosporaceae sf_1 X80823.1 Actinoplanes utahensis str. ATCC 310441972 Actinobacteria Micromonosporaceae sf_1 AB037011.1 Actinoplanes regularis str. IFO 12514T2051 Actinobacteria Micromonosporaceae sf_1 D85479.1 Couchioplanes subsp. caeruleus str. IFO139391175 Actinobacteria Mycobacteriaceae sf_1 AJ243481.1 Mycobacterium cf. xenopi 'Hymi_Wue Tb_939/99' str. Hymi_Wue Tb_939/99




1180 Actinobacteria Mycobacteriaceae sf_1 AJ308603.1 Mycobacterium palustre str. E8461187 Actinobacteria Mycobacteriaceae sf_1 AF498656.1 Mycobacterium aichiense str. JS6181204 Actinobacteria Mycobacteriaceae sf_1 M95488.1 Mycobacterium sp. 31239 Actinobacteria Mycobacteriaceae sf_1 AJ271863.1 Mycobacterium ratisbonense str. SD41262 Actinobacteria Mycobacteriaceae sf_1 AJ310467.1 Mycobacterium holsaticum str. 14061308 Actinobacteria Mycobacteriaceae sf_1 AJ431371.1 Mycobacterium pyrenivorans str. DSM 446051317 Actinobacteria Mycobacteriaceae sf_1 AF418956.1 USA: Colorado Fort collins Horsetooth Reservoir clone HTDD31365 Actinobacteria Mycobacteriaceae sf_1 AY457072.1 Mycobacterium chelonae str. CIP 104535T1435 Actinobacteria Mycobacteriaceae sf_1 AJ276890.1 Mycobacterium cf. triplex 'isolate 23' 231637 Actinobacteria Mycobacteriaceae sf_1 AF190800.1 Mycobacterium austroafricanum str. IFP21731650 Actinobacteria Mycobacteriaceae sf_1 X58890.1 Mycobacterium tuberculosis str. NCTC 7416 H37Rv1681 Actinobacteria Mycobacteriaceae sf_1 AY227356.1 Mycobacterium sp. str. 1B(CD)1726 Actinobacteria Mycobacteriaceae sf_1 X52925.1 Mycobacterium terrae str. ATCC 157551781 Actinobacteria Mycobacteriaceae sf_1 AF498650.1 Mycobacterium rhodesiae str. JS601860 Actinobacteria Mycobacteriaceae sf_1 AF251565.1 Mycobacterium marinum1885 Actinobacteria Mycobacteriaceae sf_1 AF480593.1 Mycobacterium neoaurum str. ATCC 257951888 Actinobacteria Mycobacteriaceae sf_1 AY012577.2 Mycobacterium brisbanense str. W6743; ATCC 499382034 Actinobacteria Mycobacteriaceae sf_1 X79094.1 Mycobacterium chlorophenolicum str. PCP-I1142 Actinobacteria Nocardiaceae sf_11146 Actinobacteria Nocardiaceae sf_1 AF430068.1 Nocardia otitidiscaviarum str. S6391261 Actinobacteria Nocardiaceae sf_1 AF459443.1 Nocardia caishijiensis str. F8291304 Actinobacteria Nocardiaceae sf_1 AF421564.1 Nocardia sp. str. 99-08-244A1432 Actinobacteria Nocardiaceae sf_1 AF430055.1 Nocardia veterana str. DSM 444451454 Actinobacteria Nocardiaceae sf_1 AB092561.1 Nocardia yamanashiensis str. IFM 02651769 Actinobacteria Nocardiaceae sf_1 AF430064.1 Nocardia sp. str. DSM 460671787 Actinobacteria Nocardiaceae sf_1 AF430046.1 Nocardia pseudovaccinii str. DSM 434061834 Actinobacteria Nocardiaceae sf_1 AF430047.1 Nocardia transvalensis str. DSM 434051917 Actinobacteria Nocardiaceae sf_1 X80611.1 Nocardia otitidiscaviarum str. DSM432421940 Actinobacteria Nocardiaceae sf_1 AB178563.1 Rhodococcus opacus str. B-42048 Actinobacteria Nocardiaceae sf_1 AF430044.1 Nocardia uniformis str. DSM 431361208 Actinobacteria Nocardioidaceae sf_1 AF005021.1 Aeromicrobium erythreum str. NRRL B-33811854 Actinobacteria Nocardioidaceae sf_1 AY166703.1 Aeromicrobium marinum str. T21385 Actinobacteria Nocardiopsaceae sf_1 AF178988.1 Streptomonospora salina str. YIM900021991 Actinobacteria Nocardiopsaceae sf_1 X97887.1 Nocardiopsis listeri str. DSM 40297T1671 Actinobacteria Promicromonosporaceae sf_1 X79453.1 Cellulosimicrobium cellulans str. NCIMB 110251711 Actinobacteria Promicromonosporaceae sf_1 AJ272024.1 Promicromonospora sukumoe str. DSM 441211371 Actinobacteria Propionibacteriaceae sf_1 AJ003057.1 Propionibacterium granulosum str. DSM 207002002 Actinobacteria Propionibacteriaceae sf_1 AB108484.1 Propionibacterium acnes #29292023 Actinobacteria Propionibacteriaceae sf_1 AJ315953.1 Propionibacterium propionicum str. DSM 43307T1119 Actinobacteria Pseudonocardiaceae sf_1 AJ508241.1 Amycolatopsis tolypomycina str. DSM 445441343 Actinobacteria Pseudonocardiaceae sf_1 Z38017.1 Saccharomonospora azurea str. M.Goodfel K161=NA128 (type strain)1402 Actinobacteria Pseudonocardiaceae sf_11594 Actinobacteria Pseudonocardiaceae sf_1 AF466101.1 Amycolatopsis sp. str. GY3071824 Actinobacteria Pseudonocardiaceae sf_1 AJ293756.1 Amycolatopsis sulphurea str. IMSNU 20060T




1849 Actinobacteria Pseudonocardiaceae sf_11863 Actinobacteria Pseudonocardiaceae sf_11695 Actinobacteria Sporichthyaceae sf_1 AY250883.1 lichen-dominated Antarctic cryptoendolithic community clone FBP4171229 Actinobacteria Streptomycetaceae sf_1 AF074412.1 Streptacidiphilus carbonis str. JL 415; DSM 417541274 Actinobacteria Streptomycetaceae sf_1 AB006154.1 Trichotomospora caesia str. IFO145621354 Actinobacteria Streptomycetaceae sf_1 X80825.1 Streptomyces subrutilus str. DSM 404451375 Actinobacteria Streptomycetaceae sf_1 AF423240.1 soil clone 228-11436 Actinobacteria Streptomycetaceae sf_1 AF117304.1 Streptomyces malaysiensis str. ATB-111544 Actinobacteria Streptomycetaceae sf_1 AB022872.1 Kitasatospora cystarginea str. IFO14836T1617 Actinobacteria Streptomycetaceae sf_1 AF423260.1 soil clone 41-11639 Actinobacteria Streptomycetaceae sf_1 X60514.1 Streptomyces coelicolor str. M145 ssp. A3(2)1690 Actinobacteria Streptomycetaceae sf_1 X79325.1 Streptomyces galbus str. DSM404801771 Actinobacteria Streptomycetaceae sf_1 D63872.1 Streptomyces setonii str. ATCC254971786 Actinobacteria Streptomycetaceae sf_1 X79851.1 Streptomyces bikiniensis str. DSM405811983 Actinobacteria Streptomycetaceae sf_1 AJ399487.1 Streptomyces cinnabarinus str. ISP 54671743 Actinobacteria Streptomycetaceae sf_3 AB026214.1 Streptomyces scabiei str. DNK-G011158 Actinobacteria Streptosporangiaceae sf_1 X89947.1 Streptosporangium roseum str. DSM43021T1189 Actinobacteria Streptosporangiaceae sf_1 AF191734.1 Streptosporangium subroseum str. 71131190 Actinobacteria Streptosporangiaceae sf_1 U48977.1 Nonomuraea polychroma str. IFO 143451224 Actinobacteria Streptosporangiaceae sf_1 X89941.1 Acrocarpospora corrugata str. DSM43316T1505 Actinobacteria Streptosporangiaceae sf_1 U48986.1 Microbispora rosea subsp. aerata str. ATCC 270981587 Actinobacteria Streptosporangiaceae sf_1 AB039960.1 Nonomuraea subsp. roseoviolacea str. SF 23031595 Actinobacteria Streptosporangiaceae sf_11546 Actinobacteria Thermomonosporaceae sf_1 AJ420137.1 Actinomadura fulvescens str. DSM 43923T1669 Actinobacteria Thermomonosporaceae sf_1 AF223348.1 Pseudonocardiaceae str. PA1231741 Actinobacteria Thermomonosporaceae sf_1 AJ293710.1 Actinomadura pelletieri str. IMSNU 22169T1130 Actinobacteria Unclassified sf_3 X94155.2 Georgenia muralis str. 1A-C1243 Actinobacteria Unclassified sf_3 AB089076.1 termite gut homogenate clone Rs-M95 bacterium1296 Actinobacteria Unclassified sf_3 AB089080.1 termite gut homogenate clone Rs-M66 bacterium1348 Actinobacteria Unclassified sf_3 AY250882.1 lichen-dominated Antarctic cryptoendolithic community clone FBP4061405 Actinobacteria Unclassified sf_3 X80744.1 Arthrobacter ureafaciens str. DSM 201261486 Actinobacteria Unclassified sf_3 AY093463.1 deep marine sediment clone MB-A2-1081514 Actinobacteria Unclassified sf_31577 Actinobacteria Unclassified sf_3 AB089072.1 termite gut homogenate clone Rs-N91 bacterium1583 Actinobacteria Unclassified sf_3 AB089079.1 termite gut homogenate clone Rs-F20 bacterium1687 Actinobacteria Unclassified sf_3 AJ626896.1 Jonesia quinghaiensis str. DSM 157011822 Actinobacteria Unclassified sf_3 AY145533.1 dilution (10e-7) brackish section Weser estuary isolate str. GP-5 GP-51900 Actinobacteria Unclassified sf_32045 Actinobacteria Unclassified sf_3 AF507852.1 hypersaline lake clone ML602J-441337 Actinobacteria Unclassified sf_4 AF234118.1 Sturt arid-zone soil clone #0425-2M171109 Actinobacteria Bifidobacteriaceae sf_1 AY148470.1 Bifidobacterium thermacidophilum porcinum subsp. suis str. P3-14 subsp.1319 Actinobacteria Bifidobacteriaceae sf_1 D89331.1 Parascardovia denticolens str. DSM101051320 Actinobacteria Bifidobacteriaceae sf_1 D89332.1 Scardovia inopinata str. DSM 101071351 Actinobacteria Bifidobacteriaceae sf_1 AY174108.1 Bifidobacterium psychraerophilum str. T16




1444 Actinobacteria Bifidobacteriaceae sf_1 AY278612.1 Bifidobacteriaceae genomosp. C11835 Actinobacteria Bifidobacteriaceae sf_1 AY513712.1 Bifidobacterium breve str. KB 921875 Actinobacteria Bifidobacteriaceae sf_11915 Actinobacteria Bifidobacteriaceae sf_1 AJ278695.1 Bifidobacterium urinalis1967 Actinobacteria Bifidobacteriaceae sf_1 D86187.1 Bifidobacterium pseudocatenulatum str. JCM12001987 Actinobacteria Bifidobacteriaceae sf_1 AF287758.1 human subgingival plaque clone CX0102040 Actinobacteria Bifidobacteriaceae sf_1 AF275881.1 Bifidobacterium adolescentis str. E-981074T1258 Actinobacteria Coriobacteriaceae sf_1 AJ534678.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-

MN251459 Actinobacteria Coriobacteriaceae sf_1 AB089077.1 termite gut homogenate clone Rs-J59 bacterium1510 Actinobacteria Coriobacteriaceae sf_1 AF292374.2 Olsenella profusa str. D315A-291800 Actinobacteria Coriobacteriaceae sf_1 AJ534681.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-

MN1001924 Actinobacteria Coriobacteriaceae sf_1 AF292371.1 Atopobium rimae str. ATCC496261926 Actinobacteria Coriobacteriaceae sf_1 AB011815.1 Collinsella aerofaciens str. JCM77911298 Actinobacteria Rubrobacteraceae sf_11551 Actinobacteria Rubrobacteraceae sf_1 AF498683.1 soil isolate Ellin3011739 Actinobacteria Rubrobacteraceae sf_11843 Actinobacteria Rubrobacteraceae sf_1 AJ536866.1 uranium mining waste pile soil sample clone JG30-KF-A231901 Actinobacteria Rubrobacteraceae sf_1 AY039806.1 earthworm burrow isolate B33D11367 Actinobacteria Unclassified sf_11370 Actinobacteria Unclassified sf_1 AF523912.1 forested wetland clone RCP1-371676 Actinobacteria Unclassified sf_11898 Actinobacteria Unclassified sf_1 AB089074.1 termite gut homogenate clone Rs-J10 bacterium1233 Actinobacteria Unclassified sf_21652 Actinobacteria Unclassified sf_2 AY193208.1 marine sediment clone Bol72338 AD3 Unclassified sf_1 AJ536867.1 uranium mining waste pile soil clone JG30-KF-C12

737 Aquificae Hydrogenothermaceae sf_1 AF528192.1 Sulfurihydrogenibium azorense2364 Aquificae Unclassified sf_1 AY263403.1 Thermovibrio ammoniificans str. HB-15256 Bacteroidetes Bacteroidaceae sf_12 AB088925.1 termite gut homogenate clone Rs-D38 bacterium5320 Bacteroidetes Bacteroidaceae sf_12 M86695.1 Bacteroides distasonis5474 Bacteroidetes Bacteroidaceae sf_12 AB021159.1 Bacteroides acidofaciens str.A245621 Bacteroidetes Bacteroidaceae sf_12 AY217430.1 TCE-dechlorinating microbial community clone 3G5950 Bacteroidetes Bacteroidaceae sf_125792 Bacteroidetes Bacteroidaceae sf_6 AF513095.1 activated sludge foam clone 475295 Bacteroidetes Porphyromonadaceae sf_1 AF371910.1 swine intestine clone p-987-s962-55429 Bacteroidetes Porphyromonadaceae sf_15454 Bacteroidetes Porphyromonadaceae sf_1 AY643492.1 Dysgonomonas wimpennyi str. ANFA25460 Bacteroidetes Porphyromonadaceae sf_1 AJ400267.2 mouse feces clone F85510 Bacteroidetes Porphyromonadaceae sf_1 AF524856.1 sphagnum peat bog clone 26-4b25652 Bacteroidetes Porphyromonadaceae sf_1 AB088943.1 termite gut homogenate clone Rs-D29 bacterium5664 Bacteroidetes Porphyromonadaceae sf_1 AB088937.1 termite gut homogenate clone Rs-E83 bacterium5680 Bacteroidetes Porphyromonadaceae sf_1 AB100460.1 termite gut clone Rs-1065713 Bacteroidetes Porphyromonadaceae sf_1 X82823.1 Porphyromonas catoniae str. ATCC 51270




5761 Bacteroidetes Porphyromonadaceae sf_1 AY005072.1 subgingival dental plaque clone AU1265791 Bacteroidetes Porphyromonadaceae sf_1 AF385565.1 crevicular epithelial cells clone BU0455800 Bacteroidetes Porphyromonadaceae sf_1 AY253728.1 Porphyromonas endodontalis str. ATCC 354065817 Bacteroidetes Porphyromonadaceae sf_1 AB088927.2 termite gut homogenate clone Rs-N56 bacterium5932 Bacteroidetes Porphyromonadaceae sf_1 AB088940.1 termite gut homogenate clone Rs-P41 bacterium5943 Bacteroidetes Porphyromonadaceae sf_15961 Bacteroidetes Porphyromonadaceae sf_1 AJ488070.1 chlorobenzene-degrading consortium clone IA-165990 Bacteroidetes Porphyromonadaceae sf_1 AB062826.1 termite gut homogenate clone BCf5-086012 Bacteroidetes Porphyromonadaceae sf_1 AJ400264.1 mouse feces clone L11-66214 Bacteroidetes Porphyromonadaceae sf_1 AB035460.1 Tannerella forsythensis str. ATCC430375249 Bacteroidetes Prevotellaceae sf_1 AY323524.1 Prevotella denticola str. ATCC 353085331 Bacteroidetes Prevotellaceae sf_1 AF385519.1 tongue dorsa clone DO0225398 Bacteroidetes Prevotellaceae sf_1 AY699286.1 Prevotella ruminicola L165403 Bacteroidetes Prevotellaceae sf_1 AJ006457.1 Prevotella bryantii str. B14 (DSM 11371 species )5408 Bacteroidetes Prevotellaceae sf_1 X81876.1 Prevotella dentalis str. DSM 36885426 Bacteroidetes Prevotellaceae sf_1 AF385509.1 tongue dorsa clone DO0145437 Bacteroidetes Prevotellaceae sf_1 AY244919.1 cow rumen clone BE15453 Bacteroidetes Prevotellaceae sf_1 AY005062.1 subgingival dental plaque clone AU0695484 Bacteroidetes Prevotellaceae sf_1 AY134905.1 oral periodontitis clone FX0465646 Bacteroidetes Prevotellaceae sf_1 AF371886.1 swine intestine clone p-219-o55705 Bacteroidetes Prevotellaceae sf_15706 Bacteroidetes Prevotellaceae sf_1 U43698.1 oral cavity clone 3.35718 Bacteroidetes Prevotellaceae sf_1 AF183403.1 Prevotella tannerae str. 29-15720 Bacteroidetes Prevotellaceae sf_1 AF481227.1 Prevotella sp. str. E9_345741 Bacteroidetes Prevotellaceae sf_1 L16473.1 Prevotella veroralis5756 Bacteroidetes Prevotellaceae sf_1 AY689226.1 Prevotella intermedia str. ChDC KB535766 Bacteroidetes Prevotellaceae sf_1 L16483.1 Prevotella disiens5768 Bacteroidetes Prevotellaceae sf_1 AF385564.1 crevicular epithelial cells clone BU0355769 Bacteroidetes Prevotellaceae sf_1 AB081578.1 Bacteroidaceae str. A425834 Bacteroidetes Prevotellaceae sf_1 AY244923.1 cow rumen clone BE65893 Bacteroidetes Prevotellaceae sf_1 AF385515.1 tongue dorsa clone DO0455905 Bacteroidetes Prevotellaceae sf_1 AF371893.1 swine intestine clone p-2443-18B55916 Bacteroidetes Prevotellaceae sf_1 AY244931.1 cow rumen clone BE145926 Bacteroidetes Prevotellaceae sf_1 AY244900.1 cow rumen clone BF225927 Bacteroidetes Prevotellaceae sf_15929 Bacteroidetes Prevotellaceae sf_1 AJ011683.1 Prevotella albensis str. M3845940 Bacteroidetes Prevotellaceae sf_1 AF481226.1 Prevotella sp. str. E7_345946 Bacteroidetes Prevotellaceae sf_1 AF385511.1 tongue dorsa clone DO0276011 Bacteroidetes Prevotellaceae sf_1 AB185583.1 rumen clone F24-B036018 Bacteroidetes Prevotellaceae sf_1 AF371885.1 swine intestine clone p-394-o36045 Bacteroidetes Prevotellaceae sf_1 AY689230.1 Prevotella nigrescens str. ChDC B2706047 Bacteroidetes Prevotellaceae sf_1 AY093462.1 deep marine sediment clone MB-A2-1076066 Bacteroidetes Prevotellaceae sf_1 AY207061.1 human mouth isolate str. P4P_626072 Bacteroidetes Prevotellaceae sf_1 AY005058.1 subgingival dental plaque clone AA016




6091 Bacteroidetes Prevotellaceae sf_1 AY244950.1 cow rumen clone BE346109 Bacteroidetes Prevotellaceae sf_16118 Bacteroidetes Prevotellaceae sf_16152 Bacteroidetes Prevotellaceae sf_1 AF001768.1 rumen clone RF376166 Bacteroidetes Prevotellaceae sf_1 AY278625.1 Prevotella genomosp. C26169 Bacteroidetes Prevotellaceae sf_1 AY005063.1 subgingival dental plaque clone CY0066179 Bacteroidetes Prevotellaceae sf_1 AY005065.1 subgingival dental plaque clone DA0586207 Bacteroidetes Prevotellaceae sf_1 AY244912.1 cow rumen clone BF346239 Bacteroidetes Prevotellaceae sf_1 AF385512.1 tongue dorsa clone DO0336259 Bacteroidetes Prevotellaceae sf_16271 Bacteroidetes Prevotellaceae sf_1 AY244896.1 cow rumen clone BF185356 Bacteroidetes Rikenellaceae sf_5 AJ519404.1 uranium mining waste pile clone JG37-AG-150 sp.5889 Bacteroidetes Rikenellaceae sf_5 AB088945.1 termite gut homogenate clone Rs-F73 bacterium5892 Bacteroidetes Rikenellaceae sf_5 AJ229217.1 anoxic bulk soil flooded rice microcosm clone BSV735947 Bacteroidetes Rikenellaceae sf_5 AJ441218.1 hydrothermal vent polychaete mucous clone P. palm C/A 2216173 Bacteroidetes Rikenellaceae sf_5 AY005071.1 subgingival dental plaque clone DA0645257 Bacteroidetes Unclassified sf_15 AY188307.1 marine? clone KD3-675353 Bacteroidetes Unclassified sf_15 AF529128.1 trichloroethene-contaminated site clone FTLpost3 bacterium5355 Bacteroidetes Unclassified sf_15 AJ306736.1 DCP-dechlorinating consortium clone SHA-55475 Bacteroidetes Unclassified sf_15 AJ249101.1 SHA-25 clone5481 Bacteroidetes Unclassified sf_15 AJ535258.1 marine sediment above hydrate ridge clone Hyd89-72 bacterium5500 Bacteroidetes Unclassified sf_15 AJ535228.1 marine sediment above hydrate ridge clone Hyd24-665511 Bacteroidetes Unclassified sf_15 AJ535256.1 marine sediment above hydrate ridge clone Hyd-B2-1 bacterium5544 Bacteroidetes Unclassified sf_15 AY188304.1 marine? clone KD3-175573 Bacteroidetes Unclassified sf_15 AB088930.1 termite gut homogenate clone Rs-D44 bacterium5578 Bacteroidetes Unclassified sf_15 AJ534685.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-

MN915783 Bacteroidetes Unclassified sf_15 AF507869.2 Mono Lake at depth 35 m station 6 July 2000 clone ML635J-15 bacterium5784 Bacteroidetes Unclassified sf_15 AY838556.1 fruiting body Pleurotus eryngii clone PE015820 Bacteroidetes Unclassified sf_15 AY244902.1 cow rumen clone BF245874 Bacteroidetes Unclassified sf_15 AJ441239.1 hydrothermal vent polychaete mucous clone P. palm A 535890 Bacteroidetes Unclassified sf_15 AY218551.1 penguin droppings sediments clone KD1-1255907 Bacteroidetes Unclassified sf_15 AY244952.1 cow rumen clone BE365957 Bacteroidetes Unclassified sf_15 AJ441217.1 hydrothermal vent polychaete mucous clone P. palm C/A 206046 Bacteroidetes Unclassified sf_15 AJ488097.1 chlorobenzene-degrading consortium clone IIIB-16069 Bacteroidetes Unclassified sf_15 AJ289174.1 corneal ulcer clone E1-K96233 Bacteroidetes Unclassified sf_15 AY134906.1 oral periodontitis clone FX0696324 Bacteroidetes Unclassified sf_15 AY216445.1 temperate estuarine mud clone KM026187 Bacteroidetes Unclassified sf_17 AF323762.2 benzoate-degrading consortium clone BA0295828 Bacteroidetes Blattabacteriaceae sf_1 Z35664.1 Blattabacterium species5267 Bacteroidetes Flavobacteriaceae sf_1 AF406541.1 bacterioplankton clone AEGEAN_1795317 Bacteroidetes Flavobacteriaceae sf_1 AB078057.1 Tenacibaculum maritimum str. IFO 159465352 Bacteroidetes Flavobacteriaceae sf_1 AY871820.2 Riemerella anatipestifer str. H-25655367 Bacteroidetes Flavobacteriaceae sf_1 AY238333.1 patient's bronchoalveolar lavage isolate str. MDA2507 sp.




5401 Bacteroidetes Flavobacteriaceae sf_1 AF543295.1 Capnocytophaga gingivalis str. ChDC OS455423 Bacteroidetes Flavobacteriaceae sf_1 AF170754.1 Aequorivita antarctica str. QSSC9-145434 Bacteroidetes Flavobacteriaceae sf_1 AF543293.1 Capnocytophaga sp. str. ChDC OS435436 Bacteroidetes Flavobacteriaceae sf_1 AF468406.1 Arctic sea ice ARK100045473 Bacteroidetes Flavobacteriaceae sf_15499 Bacteroidetes Flavobacteriaceae sf_1 AJ535222.1 marine sediment above hydrate ridge clone Hyd24-2-2 bacterium5509 Bacteroidetes Flavobacteriaceae sf_1 AF539756.1 Cellulophaga sp. str. E145521 Bacteroidetes Flavobacteriaceae sf_1 AF493689.1 Flavobacteriaceae str. SW2695641 Bacteroidetes Flavobacteriaceae sf_15695 Bacteroidetes Flavobacteriaceae sf_1 AJ535225.1 marine sediment above hydrate ridge clone Hyd24-41 bacterium5726 Bacteroidetes Flavobacteriaceae sf_1 AY008691.1 Bergeyella sp. oral AK152 clone5730 Bacteroidetes Flavobacteriaceae sf_15836 Bacteroidetes Flavobacteriaceae sf_1 U41348.1 Capnocytophaga granulosa str. LMG 12119; FDC SD45906 Bacteroidetes Flavobacteriaceae sf_1 X67609.1 Capnocytophaga sputigena str. ATCC 336125914 Bacteroidetes Flavobacteriaceae sf_1 AY771714.1 Psychroserpens burtonensis str. S2-645915 Bacteroidetes Flavobacteriaceae sf_1 AJ534682.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-

MN27 bacterium5919 Bacteroidetes Flavobacteriaceae sf_1 AF469612.1 Tenacibaculum skagerrakense str. D305942 Bacteroidetes Flavobacteriaceae sf_15955 Bacteroidetes Flavobacteriaceae sf_1 AJ244701.1 Flavobacterium sp. str. V4.MS.29 = MM_27475969 Bacteroidetes Flavobacteriaceae sf_1 U41350.1 Capnocytophaga ochracea str. ATCC 27872 T5971 Bacteroidetes Flavobacteriaceae sf_1 M62799.1 Cytophaga uliginosa5991 Bacteroidetes Flavobacteriaceae sf_1 AB032506.1 Tenacibaculum ovolyticum str. IAM143185997 Bacteroidetes Flavobacteriaceae sf_1 M62797.1 Flavobacterium aquatile6079 Bacteroidetes Flavobacteriaceae sf_1 AB074611.1 synonym: CFB group clone APe4_426104 Bacteroidetes Flavobacteriaceae sf_16140 Bacteroidetes Flavobacteriaceae sf_16200 Bacteroidetes Flavobacteriaceae sf_16246 Bacteroidetes Flavobacteriaceae sf_1 AF385569.1 crevicular epithelial cells clone BU0846248 Bacteroidetes Flavobacteriaceae sf_1 AY005073.1 Capnocytophaga sp. oral strain str. S36252 Bacteroidetes Flavobacteriaceae sf_1 AF449259.1 Riftia pachyptila's tube clone R103-B206269 Bacteroidetes Flavobacteriaceae sf_1 AY080916.1 acidic forest soil clone UC16274 Bacteroidetes Flavobacteriaceae sf_15248 Bacteroidetes Unclassified sf_3 AY274839.1 Delaware River estuary clone 1G125951 Bacteroidetes Unclassified sf_1 AF449785.1 CFB group clone ML615J-45334 Bacteroidetes Crenotrichaceae sf_11 AB117715.1 autotrophic nitrifying biofilm clone NB-115619 Bacteroidetes Crenotrichaceae sf_11 AY211072.1 anaerobic VC-degrading enrichment clone VC10 bacterium5654 Bacteroidetes Crenotrichaceae sf_11 AB088636.1 Saprospira grandis str. ATCC231165888 Bacteroidetes Crenotrichaceae sf_11 AY218661.1 penguin droppings sediments clone KD9-1695987 Bacteroidetes Crenotrichaceae sf_116050 Bacteroidetes Crenotrichaceae sf_11 AF527580.1 EBPR sludge lab scale clone LPB086123 Bacteroidetes Crenotrichaceae sf_11 AB078055.1 Flexibacter japonensis str. IFO 160416143 Bacteroidetes Crenotrichaceae sf_11 AF534433.1 Toolik Lake main station at 3 m depth clone TLM09/TLMdgge12a6249 Bacteroidetes Crenotrichaceae sf_11 M58790.2 Haliscomenobacter hydrossis




6267 Bacteroidetes Crenotrichaceae sf_11 AF316115.1 Cilia- respiratory isolate str. 243-546084 Bacteroidetes Flammeovirgaceae sf_5 AB078078.1 Microscilla arenaria str. IFO 159825307 Bacteroidetes Flexibacteraceae sf_19 AB078082.1 Microscilla sericea str. IFO 165615357 Bacteroidetes Flexibacteraceae sf_19 AB078065.1 Flexibacter ruber str. IFO 166775364 Bacteroidetes Flexibacteraceae sf_19 AJ577142.1 Algoriphagus antarcticus str. LMG 219835366 Bacteroidetes Flexibacteraceae sf_19 AB078061.1 Flexibacter roseolus str. IFO 160305372 Bacteroidetes Flexibacteraceae sf_195545 Bacteroidetes Flexibacteraceae sf_19 AF408309.1 Hymenobacter group clone KL-37-1-85563 Bacteroidetes Flexibacteraceae sf_19 AB073573.2 Cytophaga sp. I-5455566 Bacteroidetes Flexibacteraceae sf_19 AY264838.1 Hongiella mannitolivorans str. IMSNU 14012 JC20505602 Bacteroidetes Flexibacteraceae sf_195667 Bacteroidetes Flexibacteraceae sf_19 AY218749.1 penguin droppings sediments clone KD6-1185728 Bacteroidetes Flexibacteraceae sf_19 AB073564.2 Cytophaga sp. str. MBIC046935994 Bacteroidetes Flexibacteraceae sf_19 AJ549285.1 Hymenobacter sp. str. NS/506124 Bacteroidetes Flexibacteraceae sf_19 AB078054.1 Flexibacter flexilis subsp. pelliculosus str. IFO 16028 subsp.6261 Bacteroidetes Flexibacteraceae sf_19 AF468338.1 Arctic sea ice cryoconite clone ARKCRY-506297 Bacteroidetes Flexibacteraceae sf_19 AF502211.1 EBPR sludge lab scale clone HP1A92

10311 Bacteroidetes Flexibacteraceae sf_20 AJ431236.1 Cytophaga sp. str. BHI60-57B5459 Bacteroidetes Sphingobacteriaceae sf_1 AJ551152.1 Pedobacter sp. An135492 Bacteroidetes Sphingobacteriaceae sf_1 AF492000.1 Sphingobacterium sp. str. HC-61555513 Bacteroidetes Sphingobacteriaceae sf_1 AF385549.1 crevicular epithelial cells clone AZ1235601 Bacteroidetes Sphingobacteriaceae sf_1 AB020205.1 Sphingobacterium multivorum str. OM-A85913 Bacteroidetes Sphingobacteriaceae sf_1 AF409002.1 Sphingobacteriaceae str. Ellin1606158 Bacteroidetes Sphingobacteriaceae sf_1 AF538748.1 municipal wastewater treatment bioreactor isolate str. CAGY106272 Bacteroidetes Sphingobacteriaceae sf_1 M11657.1 Sphingobacterium heparinum6168 Bacteroidetes Unclassified sf_3 AF534435.1 Toolik Lake main station at 3 m depth clone TLM11/TLMdgge046298 Bacteroidetes Unclassified sf_3 AF445661.1 travertine hot spring clone SM1C046030 Bacteroidetes Unclassified sf_4 AF445648.1 travertine hot spring clone SM1A075439 Bacteroidetes Unclassified sf_6 AF507859.1 Mono Lake at depth 35 m station 6 July 2000 clone ML635J-40 bacterium5745 Bacteroidetes Unclassified sf_15637 Bacteroidetes Unclassified sf_45703 Bacteroidetes Unclassified sf_45785 Bacteroidetes Unclassified sf_4 AF507862.1 Mono Lake at depth 35 m station 6 July 2000 clone ML635J-565787 Bacteroidetes Unclassified sf_4 AF507860.1 Mono Lake at depth 35 m station 6 July 2000 clone ML635J-1 bacterium5051 BRC1 Unclassified sf_1 AJ390454.1 soil clone PBS-III-245143 BRC1 Unclassified sf_1 AJ390438.1 soil clone PBS-II-1

118 BRC1 Unclassified sf_2 AY218548.1 penguin droppings sediments clone KD1-12384 Caldithrix Caldithraceae sf_1 AF286032.1 saltmarsh clone LCP-89

91 Caldithrix Caldithraceae sf_2 AF323775.1 benzoate-degrading consortium clone BA0594820 Chlamydiae Chlamydiaceae sf_1 NC_002179.2 Chlamydophila pneumoniae str. AR394964 Chlamydiae Parachlamydiaceae sf_1 AY082465.1 neutral pH mine biofilm clone 44a-B1-344702 Chlamydiae Simkaniaceae sf_1 AY223862.1 Candidatus Rhabdochlamydia porcellionis clone RKPsHep porcellionis

262 Chlorobi Chlorobiaceae sf_1 Y18253.1 Chlorobium ferrooxidans DSM 13031 str. KofoX859 Chlorobi Chlorobiaceae sf_1 Y08105.1 Chlorobium phaeovibrioides str. 2631




995 Chlorobi Chlorobiaceae sf_1 AB054671.1 Chlorobium limicola str. M15294 Chlorobi Unclassified sf_6 AY221073.1 Mammoth cave clone CCM9b

549 Chlorobi Unclassified sf_8 AY118151.1 benzene-degrading nitrate-reducing consortium clone Cart-N2 bacterium5822 Chlorobi Unclassified sf_8 AJ428454.1 Saltmarsh mud clone K-790

636 Chlorobi Unclassified sf_8 AY118152.1 benzene-degrading nitrate-reducing consortium clone Cart-N3 bacterium6146 Chlorobi Unclassified sf_9 AF234699.1 sludge clone A12b

106 Chloroflexi Unclassified sf_1 AJ306798.1 DCP-dechlorinating consortium clone SHD-231159 Chloroflexi Unclassified sf_1 AJ278169.1 anaerobic bioreactor clone SHD-235258 Chloroflexi Unclassified sf_1 AJ306793.1 DCP-dechlorinating consortium clone SHD-14487 Chloroflexi Unclassified sf_1 AB109437.1 thermophilic UASB granular sludge isolate str. IMO-1 bacterium583 Chloroflexi Unclassified sf_1 AJ278171.2 anaerobic bioreactor clone SHD-238

76 Chloroflexi Unclassified sf_1 AJ306749.1 DCP-dechlorinating consortium clone SHA-1471071 Chloroflexi Unclassified sf_1 AJ412677.1 denitrifying reactor clone 131

789 Chloroflexi Unclassified sf_2 AF445676.1 travertine hot spring clone SM1D10765 Chloroflexi Unclassified sf_1 AJ278167.1 anaerobic bioreactor clone SHD-71266 Chloroflexi Unclassified sf_1205 Chloroflexi Unclassified sf_9 AJ532729.1 uranium mining waste pile clone JG34-KF-221

2539 Chloroflexi Unclassified sf_9 AY218649.1 penguin droppings sediments clone KD4-96375 Chloroflexi Unclassified sf_9 AF507690.1 forest soil clone C043576 Chloroflexi Unclassified sf_9 AJ306746.2 DCP-dechlorinating consortium clone SHA-36

72 Chloroflexi Unclassified sf_9 AY221035.1 sediments collected at Charon's Cascade near Echo River October 2000 clone CCD21727 Chloroflexi Unclassified sf_9 AF507692.1 forest soil clone S0208

94 Chloroflexi Unclassified sf_9 AJ306740.1 DCP-dechlorinating consortium clone SHA-2946 Chloroflexi Unclassified sf_9 AY216458.1 temperate estuarine mud clone KM87

2344 Chloroflexi Unclassified sf_2 AF507700.1 forest soil clone C0832532 Chloroflexi Unclassified sf_2 AF529110.1 trichloroethene-contaminated site clone FTL276 bacterium2339 Chloroflexi Unclassified sf_1 AJ519643.1 uranium mill tailings soil sample clone Sh765B-TzT-20 bacterium2367 Chloroflexi Unclassified sf_1 AY093473.1 deep marine sediment clone MB-B2-1132397 Chloroflexi Unclassified sf_1 AY093480.1 deep marine sediment clone MB-C2-1272438 Chloroflexi Unclassified sf_1 AY093464.1 deep marine sediment clone MB-A2-1102485 Chloroflexi Unclassified sf_12497 Chloroflexi Unclassified sf_1 AF524015.1 forested wetland clone FW601041 Chloroflexi Unclassified sf_1 AY250886.1 Antarctic cryptoendolith clone FBP471

652 Chloroflexi Unclassified sf_2 AJ536890.1 uranium mining waste pile soil sample clone JG30-KF-CM452534 Chloroflexi Unclassified sf_1 AF507693.1 forest soil clone S0852523 Chloroflexi Unclassified sf_12 AJ347055.1 sponge clone TK10

818 Chloroflexi Unclassified sf_21051 Chloroflexi Unclassified sf_5 AY913277.1 forest soil clone DUNssu055 (-2B) (OTU#087)

757 Chloroflexi Unclassified sf_7 AJ306741.2 DCP-dechlorinating consortium clone SHA-8751 Coprothermobacteria Unclassified sf_1 AJ431258.1 Coprothermobacter sp. str. Dex80-3

5098 Cyanobacteria Chloroplasts sf_11 AF289245.1 Euglena tripteris str. UW OB5123 Cyanobacteria Chloroplasts sf_11 AF289249.1 Lepocinclis fusiformis str. ACOI 10255000 Cyanobacteria Chloroplasts sf_13 U67742.1 Mitrastema yamamotoi4966 Cyanobacteria Chloroplasts sf_5 AF244549.1 Adiantum pedatum




4967 Cyanobacteria Chloroplasts sf_5 AF534438.1 Toolik Lake main station at 3 m depth clone TLM144976 Cyanobacteria Chloroplasts sf_5 AF244550.1 Calypogeia muelleriana4984 Cyanobacteria Chloroplasts sf_5 U70721.1 Cape Hatteras picoplankton clone OM1645006 Cyanobacteria Chloroplasts sf_55007 Cyanobacteria Chloroplasts sf_5 AF534437.1 Toolik Lake main station at 3 m depth clone TLM13/TLMdgge205039 Cyanobacteria Chloroplasts sf_5 U70723.1 Cape Hatteras picoplankton clone OM2705040 Cyanobacteria Chloroplasts sf_5 Y18934.1 Solanum nigrum5112 Cyanobacteria Chloroplasts sf_5 X52985.1 Cyanidium caldarium str. 14-1-15130 Cyanobacteria Chloroplasts sf_5 AF445714.1 travertine hot spring clone SM2B115147 Cyanobacteria Chloroplasts sf_5 X82156.1 Emiliania huxleyi str. Plymouth Marine Laborator PML 925166 Cyanobacteria Chloroplasts sf_55182 Cyanobacteria Chloroplasts sf_5 M81884.1 Epifagus virginiana -- chloroplast5183 Cyanobacteria Chloroplasts sf_5 M37430.1 Pisum sativum -- chloroplast5192 Cyanobacteria Chloroplasts sf_5 AF244551.1 Cycas revoluta5004 Cyanobacteria Unclassified sf_1 AJ630458.1 Anabaena augstumalis 'SCHMIDKE JAHNKE/4a' str. SCMIDKE JAHNKE/4a5028 Cyanobacteria Unclassified sf_1 AF516732.1 Cylindrospermopsis raciborskii str. 05E5047 Cyanobacteria Unclassified sf_1 AF247573.1 Anabaena circinalis str. AWQC150A5057 Cyanobacteria Unclassified sf_1 AJ781148.1 Nodularia sphaerocarpa str. UTEX B 20935072 Cyanobacteria Unclassified sf_1 AF268023.1 Nodularia spumigena str. PCC731045174 Cyanobacteria Unclassified sf_1 AF516731.1 Cylindrospermopsis raciborskii str. 23B5175 Cyanobacteria Unclassified sf_1 AF516729.1 Cylindrospermopsis raciborskii str. 24C5191 Cyanobacteria Unclassified sf_1 AY038036.1 Cyanospira rippkae str. PCC 95015199 Cyanobacteria Unclassified sf_1 AB074502.1 Anabaena variabilis str. IAM M-2045049 Cyanobacteria Unclassified sf_1 AF420444.1 Oscillatoria spongeliae str. 520bg5077 Cyanobacteria Unclassified sf_1 AB045906.1 Lyngbya var. hieronymusii str. CN4-35184 Cyanobacteria Unclassified sf_1 AB074508.1 Arthrospira platensis str. IAM M-1355189 Cyanobacteria Unclassified sf_1 AB039015.1 Oscillatoria sancta str. PCC 75155010 Cyanobacteria Unclassified sf_1 AF170757.1 LPP-group cyanobacterium isolate str. QSSC5cya QSSC5cya5190 Cyanobacteria Unclassified sf_1 AF091110.1 Plectonema sp. str. F35210 Cyanobacteria Unclassified sf_1 AY250881.1 lichen-dominated Antarctic cryptoendolithic community clone FBP4035001 Cyanobacteria Unclassified sf_1 AJ347056.1 sponge clone TK095008 Cyanobacteria Unclassified sf_1 AF448080.1 Synechococcus sp. str. PCC 75025034 Cyanobacteria Unclassified sf_1 AF329394.1 Spirulina subsalsa str. FACHB3514998 Cyanobacteria Unclassified sf_55015 Cyanobacteria Unclassified sf_5 AB093489.1 Chlorogloeopsis fritschii str. PCC 69125027 Cyanobacteria Unclassified sf_55030 Cyanobacteria Unclassified sf_5 AY034793.1 Hapalosiphon welwitschii5188 Cyanobacteria Unclassified sf_5 AY163573.1 Acaryochloris marina str. MBIC110175186 Cyanobacteria Unclassified sf_6 AY222299.1 silica sinter depositing geothermal power station discharge drain clone ST01-SN2C5206 Cyanobacteria Unclassified sf_85038 Cyanobacteria Unclassified sf_9 AF544207.1 Rumen isolate str. YS25164 Cyanobacteria Unclassified sf_9 AB089123.1 termite gut homogenate clone Rs-H34

563 Deinococcus-Thermus

Unclassified sf_1 AJ507298.1 Vulcanithermus mediatlanticus str. TR





Unclassified sf_1


Unclassified sf_2 AF513964.1 hypersaline pond clone LA7-B27N


Unclassified sf_3

38 DSS1 Unclassified sf_2 AJ306783.1 DCP-dechlorinating consortium clone SHA-1094304 Firmicutes Unclassified sf_1 AF507889.1 Mono Lake at depth 35m station 6 July 2000 clone ML635J-34 G+C3368 Firmicutes Alicyclobacillaceae sf_1 AY529492.1 geothermal site isolate str. G11050 Firmicutes Bacillaceae sf_1 AJ717384.1 Bacillus firmus CV93b

234 Firmicutes Bacillaceae sf_1 AJ293805.1 Bacillus vulcani str. 3S-1246 Firmicutes Bacillaceae sf_1 AJ509006.1 Bacillus sp. 6160m-C1283 Firmicutes Bacillaceae sf_1 Z26926.1 Geobacillus thermocatenulatus str. DSM 730305 Firmicutes Bacillaceae sf_1 M77488.1 Bacillus thermoleovorans

3283 Firmicutes Bacillaceae sf_1 AB021194.1 Bacillus niacini str. IFO155663328 Firmicutes Bacillaceae sf_1 AJ224963.1 Pseudobacillus carolinae3345 Firmicutes Bacillaceae sf_1 AY548955.1 Bacillus pumilus str. S93370 Firmicutes Bacillaceae sf_1 AB020195.1 Bacillus sp. str. TGS4373383 Firmicutes Bacillaceae sf_13385 Firmicutes Bacillaceae sf_1 AY167806.1 Bacillus licheniformis str. SAFN-0313419 Firmicutes Bacillaceae sf_1 AY228462.1 Bacillus algicola str. KMM 37373424 Firmicutes Bacillaceae sf_1 AJ532701.1 uranium mill tailings clone Gitt-KF-763439 Firmicutes Bacillaceae sf_1 AF071856.1 Bacillus siralis str. 1715443460 Firmicutes Bacillaceae sf_1 AY312404.1 Geobacillus jurassicus str. DS13467 Firmicutes Bacillaceae sf_1 AJ419629.1 Bacillus luciferensis str. LMG 184223489 Firmicutes Bacillaceae sf_1 AY167818.1 Bacillus silvestris str. SAFN-0103491 Firmicutes Bacillaceae sf_1 AF326361.1 Bacillus sp. str. MB-123492 Firmicutes Bacillaceae sf_1 AB042061.1 Bacillus subtilis str. IAM 12118T3509 Firmicutes Bacillaceae sf_1 AY043085.1 Bacillus benzoevorans3517 Firmicutes Bacillaceae sf_1 AF500007.1 Planococcus maritimus str. TF-93540 Firmicutes Bacillaceae sf_1 AB034836.1 Geobacillus thermoleovorans str. B233542 Firmicutes Bacillaceae sf_1 AJ277984.1 Bacillus psychrodurans str. DSM 11713 68E33550 Firmicutes Bacillaceae sf_1 AF142677.4 Bacillus megaterium str. QM B15513579 Firmicutes Bacillaceae sf_1 AB020198.1 Bacillus sp. str. TGS7503589 Firmicutes Bacillaceae sf_1 AF519468.1 Bacillus senegalensis str. RS8; CIP 106 6693612 Firmicutes Bacillaceae sf_1 AB042060.1 Bacillus schlegelii str. ATCC 43741T3635 Firmicutes Bacillaceae sf_1 AJ504797.1 Bacillus aeolius str. 4-13650 Firmicutes Bacillaceae sf_13661 Firmicutes Bacillaceae sf_1 AB094471.1 Bacillus sp. str. 2216.25.23675 Firmicutes Bacillaceae sf_1 AY189750.1 Bacillus mojavensis str. M-13688 Firmicutes Bacillaceae sf_1 AY167821.1 Bacillus sp. str. SAFN-0063706 Firmicutes Bacillaceae sf_1 AF302119.1 Bacillus sonorensis str. NRRL B-231553730 Firmicutes Bacillaceae sf_1 AF541965.1 Bacillus baekryungensis str. SW-933763 Firmicutes Bacillaceae sf_1 AY672761.1 Geobacillus stearothermophilus




3818 Firmicutes Bacillaceae sf_1 AF372616.1 Bacillus licheniformis str. Mo13827 Firmicutes Bacillaceae sf_1 AF547209.1 Bacillus acidogenesis str. 105-23831 Firmicutes Bacillaceae sf_1 AY030328.1 Bacillus licheniformis str. KL-0683836 Firmicutes Bacillaceae sf_1 AY682096.1 Geobacillus stearothermophilus str. 463845 Firmicutes Bacillaceae sf_1 AF252326.1 hot synthetic compost clone pPD153848 Firmicutes Bacillaceae sf_1 AB098576.1 Bacillus sp. str. TUT1007

385 Firmicutes Bacillaceae sf_1 X57309.1 Geobacillus stearothermophilus str. T103861 Firmicutes Bacillaceae sf_1 AJ229201.1 anoxic bulk soil flooded rice microcosm clone BSV46 clone3894 Firmicutes Bacillaceae sf_1 AJ514408.1 Sporosarcina macmurdoensis str. CMS 21w3898 Firmicutes Bacillaceae sf_1 AB034710.1 compost clone 4-283900 Firmicutes Bacillaceae sf_1 X68416.1 Bacillus licheniformis str. DSM 133909 Firmicutes Bacillaceae sf_1 D26185.1 Bacillus subtilis subsp. Marburg str. 1683918 Firmicutes Bacillaceae sf_1 AF549498.1 Bacillus subtilis3926 Firmicutes Bacillaceae sf_1 X92160.1 Lake Bogoria isolate 64B4

429 Firmicutes Bacillaceae sf_1 X60616.1 Bacillus firmus str. NCIMB 9366462 Firmicutes Bacillaceae sf_1 Z26927.1 Geobacillus thermodenitrificans str. DSM 466571 Firmicutes Bacillaceae sf_1 Z26922.1 Bacillus caldotenax str. DSM 406829 Firmicutes Bacillaceae sf_1 AY191842.2 Geobacillus sp. str. YMTC1049

3285 Firmicutes Caryophanaceae sf_1 AJ491302.1 Caryophanon latum str. DSM 141513344 Firmicutes Halobacillaceae sf_1 AY881246.1 Halobacillus yeomjeoni str. MSS-4023488 Firmicutes Halobacillaceae sf_1 AF500003.1 Halobacillus salinus str. HSL-33552 Firmicutes Halobacillaceae sf_1 AB087828.1 Paraliobacillus ryukyuensis3633 Firmicutes Halobacillaceae sf_1 AY152839.1 Bacillus clausii str. GMBAE 423702 Firmicutes Halobacillaceae sf_1 AJ496807.1 Amphibacillus xylanus str. DSM 66263756 Firmicutes Halobacillaceae sf_1 AY121439.1 Salibacillus sp. str. YIM-kkny163758 Firmicutes Halobacillaceae sf_1 AY121435.1 Amphibacillus sp. str. YIM-kkny103769 Firmicutes Halobacillaceae sf_1 AY121437.1 Gracilibacillus sp. str. YIM-kkny133299 Firmicutes Paenibacillaceae sf_1 AF378230.1 Brevibacillus borstelensis str. LMG 155363415 Firmicutes Paenibacillaceae sf_1 AF480937.1 Paenibacillus nematophilus str. NEM1b3559 Firmicutes Paenibacillaceae sf_1 AF378696.1 Paenibacillus turicensis str. MOL7223595 Firmicutes Paenibacillaceae sf_1 AY257871.1 Paenibacillus sp. str. MB 20393630 Firmicutes Paenibacillaceae sf_13641 Firmicutes Paenibacillaceae sf_1 AJ313027.1 Brevibacillus sp. MN 47.2a3651 Firmicutes Paenibacillaceae sf_1 AJ011323.1 Paenibacillus borealis KK203922 Firmicutes Paenibacillaceae sf_1 AJ320490.1 Paenibacillus thiaminolyticus str. DSM 72623365 Firmicutes Sporolactobacillaceae sf_1 AF454300.1 Bacillus sp. clone ML615J-193747 Firmicutes Sporolactobacillaceae sf_1 AB043848.1 Bacillus sp. str. C-59-23879 Firmicutes Sporolactobacillaceae sf_1 X92161.1 Lake Elmenteita isolate WE43258 Firmicutes Staphylococcaceae sf_1 D83358.1 Staphylococcus auricularis str. MAFF911484 ATCC33753T3284 Firmicutes Staphylococcaceae sf_13432 Firmicutes Staphylococcaceae sf_1 AY188939.1 deep-sea sediment isolate str. P_wp02253494 Firmicutes Staphylococcaceae sf_1 AB079788.1 Micrococcus luteus B-P 263524 Firmicutes Staphylococcaceae sf_1 L14326.1 Gemella haemolysans3545 Firmicutes Staphylococcaceae sf_1




3569 Firmicutes Staphylococcaceae sf_1 L37596.1 Staphylococcus saprophyticus3592 Firmicutes Staphylococcaceae sf_1 Y12593.1 Staphylococcus caprae str. DSM 206083605 Firmicutes Staphylococcaceae sf_13628 Firmicutes Staphylococcaceae sf_1 X66100.1 Staphylococcus haemolyticus str. CCM27373638 Firmicutes Staphylococcaceae sf_1 X86641.1 Staphylococcus sp str. AG-303654 Firmicutes Staphylococcaceae sf_1 AF322002.1 Staphylococcus pettenkoferi str. B31173684 Firmicutes Staphylococcaceae sf_1 S83569.1 Staphylococcus sciuri3794 Firmicutes Staphylococcaceae sf_13822 Firmicutes Staphylococcaceae sf_1 AJ320272.1 Staphylococcus succinus str. SB723865 Firmicutes Staphylococcaceae sf_1 AY119687.1 Macrococcus lamae str. CCM 48153301 Firmicutes Thermoactinomycetaceae sf_1 AB088361.1 Thermoactinomyces sp. str. 7003753743 Firmicutes Unclassified sf_33323 Firmicutes Aerococcaceae sf_1 Y17301.1 Trichococcus flocculiformis str. DSM 20943326 Firmicutes Aerococcaceae sf_1 AF255736.1 Nostocoida limicola I str. Ben2063386 Firmicutes Aerococcaceae sf_1 AF317386.1 feedlot manure clone B873435 Firmicutes Aerococcaceae sf_1 AF275700.1 cf. Alkalibacterium sp. isolate str. F13504 Firmicutes Aerococcaceae sf_1 AB083413.1 Marinilactibacillus psychrotolerans str. O213522 Firmicutes Aerococcaceae sf_1 M58797.2 Aerococcus viridans3553 Firmicutes Aerococcaceae sf_1 Y17300.1 Desemzia incerta str. DSM 205813561 Firmicutes Aerococcaceae sf_1 AJ387905.1 Carnobacterium gallinarum str. DSM 4847(T) NCFB 2766(T)3631 Firmicutes Aerococcaceae sf_1 D50541.1 Abiotrophia defectiva str. GIFU12707 (ATCC49176)3682 Firmicutes Aerococcaceae sf_1 X70907.1 Dolosigranulum pigrum str. NCFB 29753736 Firmicutes Aerococcaceae sf_1 Y14650.1 Desemzia incerta str. DSM 205813833 Firmicutes Aerococcaceae sf_1 L08623.1 Carnobacterium alterfunditum3840 Firmicutes Aerococcaceae sf_1 X87150.1 Trichococcus pasteurii str. KoTa23870 Firmicutes Aerococcaceae sf_1 AB022027.1 Abiotrophia para-adiacens str. TKT13536 Firmicutes Carnobacteriaceae sf_13792 Firmicutes Carnobacteriaceae sf_1 AF451271.1 Carnobacterium sp. str. D353261 Firmicutes Enterococcaceae sf_1 AJ301836.1 Enterococcus mundtii str. LMG 107483288 Firmicutes Enterococcaceae sf_1 AY167946.1 Isolation and identification hyper-ammonia producing swine storage pits manure3298 Firmicutes Enterococcaceae sf_1 AJ301839.1 Enterococcus saccharolyticus str. LMG 114273318 Firmicutes Enterococcaceae sf_1 AF539705.1 Enterococcus ratti str. ATCC 7009143382 Firmicutes Enterococcaceae sf_13392 Firmicutes Enterococcaceae sf_1 Y17152.2 Vagococcus lutrae str. m1134/97/1; CCUG 391873433 Firmicutes Enterococcaceae sf_1 D88824.1 Tetragenococcus muriaticus3598 Firmicutes Enterococcaceae sf_1 AJ301840.1 Enterococcus solitarius str. DSM 56343680 Firmicutes Enterococcaceae sf_1 X75752.1 Melissococcus plutonius str. NCDO 24403713 Firmicutes Enterococcaceae sf_1 AF061009.1 Enterococcus cecorum str. ATCC431983881 Firmicutes Enterococcaceae sf_1 AJ301829.1 Enterococcus dispar str. LMG 135213278 Firmicutes Lactobacillaceae sf_1 AB205055.1 Lactobacillus buchneri str. JCM11153330 Firmicutes Lactobacillaceae sf_1 AB107637.1 Lactobacillus kitasatonis str. KM92123342 Firmicutes Lactobacillaceae sf_1 Y17362.1 Lactobacillus crispatus str. DSM 20584 T3366 Firmicutes Lactobacillaceae sf_1 AY255802.1 Lactobacillus saerimneri str. GDA154 LMG 22087 DSM 16049 (T); CCUG 48462 (T)3381 Firmicutes Lactobacillaceae sf_1 AF371486.1 swine intestine clone p-4312-4Wa3




3395 Firmicutes Lactobacillaceae sf_1 X76328.1 Lactobacillus reuteri str. DSM 20016 T3418 Firmicutes Lactobacillaceae sf_1 AB001836.2 Lactobacillus subsp. aviarius3459 Firmicutes Lactobacillaceae sf_1 AF371475.1 swine intestine clone p-4729-2Wb23478 Firmicutes Lactobacillaceae sf_1 AF257096.1 Lactobacillus crispatus str. ATCC331973490 Firmicutes Lactobacillaceae sf_1 AY675248.1 Lactobacillus suntoryeus str. LH3521 Firmicutes Lactobacillaceae sf_1 AJ271383.1 Pediococcus inopinatus str. DSM 202853526 Firmicutes Lactobacillaceae sf_1 AF401673.1 Lactobacillus sakei3547 Firmicutes Lactobacillaceae sf_1 AJ250074.1 Lactobacillus frumenti str. TMW 1.6663566 Firmicutes Lactobacillaceae sf_1 X76329.1 Lactobacillus pontis str. LTH 25873599 Firmicutes Lactobacillaceae sf_1 AJ242968.1 Lactobacillus gallinarum str. ATCC 331993600 Firmicutes Lactobacillaceae sf_1 AJ242969.1 Lactobacillus crispatus str. NCTC 43604 Firmicutes Lactobacillaceae sf_13618 Firmicutes Lactobacillaceae sf_1 AF243159.1 Lactobacillus jensenii str. KC36b3634 Firmicutes Lactobacillaceae sf_1 AJ417738.1 Lactobacillus letivazi str. JCL39943678 Firmicutes Lactobacillaceae sf_1 Y18654.1 Lactobacillus fornicalis str. TV10183696 Firmicutes Lactobacillaceae sf_1 AY253657.1 Lactobacillus kalixensis str. Kx127A2; LMG 22115T; DSM 16043T; CCUG 48459T3703 Firmicutes Lactobacillaceae sf_1 AY389803.1 Lactobacillus salivarius str. RA21153767 Firmicutes Lactobacillaceae sf_1 AJ575744.1 Lactobacillus suebicus str. CECT 5917T3768 Firmicutes Lactobacillaceae sf_1 Y19167.1 Lactobacillus perolens str. L5323798 Firmicutes Lactobacillaceae sf_1 AY373589.1 Lactobacillus fermentum str. MD-93821 Firmicutes Lactobacillaceae sf_1 M23928.1 Lactobacillus casei3829 Firmicutes Lactobacillaceae sf_1 AJ417500.1 Lactobacillus paralimentarius str. DSM 132383842 Firmicutes Lactobacillaceae sf_1 Y19168.1 Lactobacillus perolens str. L5343885 Firmicutes Lactobacillaceae sf_1 M58834.1 Pediococcus pentosaceus3887 Firmicutes Lactobacillaceae sf_1 AJ292530.2 Lactobacillus coleohominis3914 Firmicutes Lactobacillaceae sf_1 AJ251560.1 Lactobacillus cypricasei str. LMK33497 Firmicutes Leuconostocaceae sf_1 AY035892.1 Weissella koreensis S-56733573 Firmicutes Leuconostocaceae sf_1 AF360736.1 Leuconostoc ficulneum str. FS-13250 Firmicutes Streptococcaceae sf_1 AF396920.1 Streptococcus bovis str. B3153251 Firmicutes Streptococcaceae sf_1 AY188347.1 Streptococcus cristatus str. ATCC 511003253 Firmicutes Streptococcaceae sf_1 AF349918.1 derived cheese sample clone 32CR3287 Firmicutes Streptococcaceae sf_1 AF432137.1 tongue dorsum scrapings clone FP0153290 Firmicutes Streptococcaceae sf_1 AY518677.1 Streptococcus mitis str. Sm913313 Firmicutes Streptococcaceae sf_1 AY188352.1 Streptococcus salivarius str. ATCC 70733397 Firmicutes Streptococcaceae sf_1 Z94012.1 Streptococcus macedonicus str. ACA-DC 206 LAB6173422 Firmicutes Streptococcaceae sf_1 X68418.1 Streptococcus thermophilus str. DSM 206173446 Firmicutes Streptococcaceae sf_1 AY173079.1 Streptococcus bovis str. HJ503499 Firmicutes Streptococcaceae sf_1 AF104676.1 Streptococcus constellatus str. ATCC278233543 Firmicutes Streptococcaceae sf_13560 Firmicutes Streptococcaceae sf_1 AJ307888.1 Streptococcus gallinaceus str. CCUG 426923588 Firmicutes Streptococcaceae sf_1 AY188350.1 Streptococcus downei str. ATCC 337483629 Firmicutes Streptococcaceae sf_1 AF139600.1 Streptococcus mutans str. UA963637 Firmicutes Streptococcaceae sf_1 AF227836.1 str. 372363685 Firmicutes Streptococcaceae sf_1 AF003931.1 Streptococcus gordonii str. ATCC 10558




3722 Firmicutes Streptococcaceae sf_1 NC_002662.1 Lactococcus Il1403 subsp. lactis str. IL14033753 Firmicutes Streptococcaceae sf_1 AF009482.1 Streptococcus suis str. 80743846 Firmicutes Streptococcaceae sf_1 AB002516.1 Streptococcus equi subsp. zooepidemicus str. ATCC 430793869 Firmicutes Streptococcaceae sf_1 AB104843.1 Streptococcus equi subsp. zooepidemicus str. Tokyo1291 subsp.3906 Firmicutes Streptococcaceae sf_1 AF104114.1 Streptococcus bovis str.ATCC 431433907 Firmicutes Streptococcaceae sf_1 U87830.1 aortic heart valve patient with endocarditis clone v63289 Firmicutes Unclassified sf_1 AJ302648.1 Isobaculum melis CCUG 37660T3481 Firmicutes Unclassified sf_14261 Firmicutes Unclassified sf_1 AB089006.1 termite gut homogenate clone Rs-G04 bacterium4293 Firmicutes Unclassified sf_1 AB089008.1 termite gut homogenate clone Rs-Q01 bacterium2716 Firmicutes Unclassified sf_4 AB089010.1 termite gut homogenate clone Rs-F76 bacterium3023 Firmicutes Unclassified sf_4 AY197417.1 Guaymas Basin hydrothermal vent sediments clone B04R0164325 Firmicutes Unclassified sf_4 AB088963.1 termite gut homogenate clone Rs-K21 bacterium4503 Firmicutes Unclassified sf_4 AB088976.1 termite gut homogenate clone Rs-H83 bacterium4526 Firmicutes Unclassified sf_4 AY133082.1 TCE-contaminated site clone ccslm210

132 Firmicutes Clostridiaceae sf_12 AB089019.1 termite gut homogenate clone Rs-J36 bacterium206 Firmicutes Clostridiaceae sf_12 AB089017.1 termite gut homogenate clone Rs-P50 bacterium252 Firmicutes Clostridiaceae sf_12 AB089014.1 termite gut homogenate clone Rs-A28 bacterium

2736 Firmicutes Clostridiaceae sf_12 AY137848.1 Alkaliphilus metalliredigenes str. QYMF2764 Firmicutes Clostridiaceae sf_122786 Firmicutes Clostridiaceae sf_12 AY007244.1 Clostridium glycolicum str. CIN52790 Firmicutes Clostridiaceae sf_12 AF224675.1 Clostridium sp. str. FL42915 Firmicutes Clostridiaceae sf_12 AY158079.1 Tepidibacter thalassicus str. SC 5623004 Firmicutes Clostridiaceae sf_12 AB023973.1 Clostridium hylemonae str. TN-2723019 Firmicutes Clostridiaceae sf_12 AY245527.1 Tepidibacter formicigenes str. DV11843021 Firmicutes Clostridiaceae sf_12 AF458779.1 Clostridium caminithermale str. DVird33049 Firmicutes Clostridiaceae sf_12 Z69929.1 Clostridium paradoxum str. DSM 7308T3077 Firmicutes Clostridiaceae sf_12 X76750.1 Clostridium glycolicum str. DSM 12883108 Firmicutes Clostridiaceae sf_12 Z69940.1 Clostridium paradoxum str. DSM 7308T3219 Firmicutes Clostridiaceae sf_12 AF407695.1 Great Artesian Basin clone R824154 Firmicutes Clostridiaceae sf_12 AY187622.1 Clostridium tunisiense str. DSM 152064156 Firmicutes Clostridiaceae sf_12 AF407388.1 MCB-contaminated groundwater-treating reactor clone RA9C14157 Firmicutes Clostridiaceae sf_12 AB089043.1 termite gut homogenate clone Rs-A15 bacterium4169 Firmicutes Clostridiaceae sf_124177 Firmicutes Clostridiaceae sf_12 AF241842.1 Clostridium subterminale DSM 26364180 Firmicutes Clostridiaceae sf_12 AB089028.1 termite gut homogenate clone Rs-M23 bacterium4187 Firmicutes Clostridiaceae sf_12 AF538854.1 Clostridiales oral clone P4PB_122 P34225 Firmicutes Clostridiaceae sf_12 AB100486.1 termite gut clone Rs-1164229 Firmicutes Clostridiaceae sf_124244 Firmicutes Clostridiaceae sf_12 AB089011.1 termite gut homogenate clone Rs-K46 bacterium4253 Firmicutes Clostridiaceae sf_124265 Firmicutes Clostridiaceae sf_12 AB088969.1 termite gut homogenate clone Rs-N70 bacterium4266 Firmicutes Clostridiaceae sf_12 AB088951.1 termite gut homogenate clone Rs-M86 bacterium4267 Firmicutes Clostridiaceae sf_12 AB100485.1 termite gut clone Rs-114




4272 Firmicutes Clostridiaceae sf_12 AB088965.1 termite gut homogenate clone Rs-M34 bacterium4275 Firmicutes Clostridiaceae sf_12 M59087.1 Clostridium botulinum str. type G4278 Firmicutes Clostridiaceae sf_12 AF482434.1 granular sludge clone R1p164296 Firmicutes Clostridiaceae sf_12 AB081585.1 Clostridiaceae str. A4d4297 Firmicutes Clostridiaceae sf_124299 Firmicutes Clostridiaceae sf_12 AB100466.1 termite gut clone Rs-L024300 Firmicutes Clostridiaceae sf_12 AB100493.1 termite gut clone Rs-0604306 Firmicutes Clostridiaceae sf_12 AY261814.1 UASB reactor granular sludge clone PD-UASB-4 bacterium4310 Firmicutes Clostridiaceae sf_12 AB100478.1 termite gut clone Rs-0564321 Firmicutes Clostridiaceae sf_12 AB089045.1 termite gut homogenate clone Rs-C76 bacterium4326 Firmicutes Clostridiaceae sf_12 AB040497.1 Oscillospira guilliermondii4339 Firmicutes Clostridiaceae sf_12 U51843.1 Clostridium chauvoei str. ATCC 10092T4341 Firmicutes Clostridiaceae sf_12 AB041865.1 Clostridium novyi subsp. type C str. ATCC273234357 Firmicutes Clostridiaceae sf_12 AF550610.1 Lachnospiraceae bacterium 19gly44359 Firmicutes Clostridiaceae sf_12 AB089047.1 termite gut homogenate clone Rs-C69 bacterium4364 Firmicutes Clostridiaceae sf_12 AF481208.1 oral endodontic infection clone MCE3_94369 Firmicutes Clostridiaceae sf_12 AB089032.1 termite gut homogenate clone Rs-N73 bacterium4378 Firmicutes Clostridiaceae sf_124406 Firmicutes Clostridiaceae sf_12 AB088977.1 termite gut homogenate clone Rs-J39 bacterium4415 Firmicutes Clostridiaceae sf_12 AB089041.1 termite gut homogenate clone Rs-K32 bacterium4418 Firmicutes Clostridiaceae sf_12 AB088966.2 termite gut homogenate clone Rs-H18 bacterium4424 Firmicutes Clostridiaceae sf_12 AB088982.1 termite gut homogenate clone Rs-M05 bacterium4427 Firmicutes Clostridiaceae sf_12 L08062.1 Clostridium tyrobutyricum str. NIZO 514459 Firmicutes Clostridiaceae sf_12 AB100469.1 termite gut clone Rs-1094461 Firmicutes Clostridiaceae sf_12 AJ488075.1 chlorobenzene-degrading consortium clone IA-244475 Firmicutes Clostridiaceae sf_12 AB089035.1 termite gut homogenate clone Rs-N02 bacterium4477 Firmicutes Clostridiaceae sf_12 AB089042.1 termite gut homogenate clone Rs-N85 bacterium4497 Firmicutes Clostridiaceae sf_12 AB089033.1 termite gut homogenate clone Rs-N16 bacterium4502 Firmicutes Clostridiaceae sf_124507 Firmicutes Clostridiaceae sf_12 AB088984.1 termite gut homogenate clone Rs-N21 bacterium4524 Firmicutes Clostridiaceae sf_12 AB100476.1 termite gut clone Rs-0934548 Firmicutes Clostridiaceae sf_12 AB089029.1 termite gut homogenate clone Rs-Q69 bacterium4550 Firmicutes Clostridiaceae sf_12 AF371790.1 swine intestine clone p-320-a34551 Firmicutes Clostridiaceae sf_12 X78070.1 Clostridium acetobutylicum str. ATCC 824 (T)4554 Firmicutes Clostridiaceae sf_12 AB100479.1 termite gut clone Rs-0684555 Firmicutes Clostridiaceae sf_12 M59113.1 Clostridium tyrobutyricum4559 Firmicutes Clostridiaceae sf_12 AY244908.1 cow rumen clone BF304560 Firmicutes Clostridiaceae sf_12 X68180.1 Clostridium beijerinckii str. NCIMB93624566 Firmicutes Clostridiaceae sf_12 AF371796.1 swine intestine clone p-2657-65A54574 Firmicutes Clostridiaceae sf_12 NC_003030.1 Clostridium acetobutylicum str. ATCC 8244575 Firmicutes Clostridiaceae sf_12 X68451.1 Clostridium subterminale str. NCIMB 107464582 Firmicutes Clostridiaceae sf_12 AF371783.1 swine intestine clone p-2600-9F54584 Firmicutes Clostridiaceae sf_12 X71852.1 Clostridium papyrosolvens str. DSM 27824589 Firmicutes Clostridiaceae sf_12 X68176.1 Clostridium butyricum str. ATCC43755




4598 Firmicutes Clostridiaceae sf_12 AB161372.1 Clostridium sardiniense str. DSM 6004607 Firmicutes Clostridiaceae sf_12 X68188.1 Clostridium novyi str. NCTC5384610 Firmicutes Clostridiaceae sf_12 AF127024.1 Clostridium putrefaciens str. DSM 12914614 Firmicutes Clostridiaceae sf_12 AB093546.1 Clostridium sp. str. JC34620 Firmicutes Clostridiaceae sf_12 AF371805.1 swine intestine clone p-1877-s962-34622 Firmicutes Clostridiaceae sf_12 AB100475.1 termite gut clone Rs-L364627 Firmicutes Clostridiaceae sf_12 AB089030.1 termite gut homogenate clone Rs-A13 bacterium4632 Firmicutes Clostridiaceae sf_124637 Firmicutes Clostridiaceae sf_12 AB100473.1 termite gut clone Rs-0884638 Firmicutes Clostridiaceae sf_124471 Firmicutes Clostridiaceae sf_21 AB100483.1 termite gut clone Rs-0581045 Firmicutes Eubacteriaceae sf_1 AF371692.1 swine intestine clone p-3402-SwA21053 Firmicutes Eubacteriaceae sf_1 AB036759.1 Pseudoramibacter alactolyticus str. 23263T

28 Firmicutes Eubacteriaceae sf_1 AB088988.1 termite gut homogenate clone Rs-H81 bacterium423 Firmicutes Eubacteriaceae sf_1 AY082466.1 neutral pH mine biofilm clone 44a-B1-37687 Firmicutes Eubacteriaceae sf_1 X96955.1 Acetobacterium wieringae str. DSM 1911

2668 Firmicutes Lachnospiraceae sf_5 AB088998.1 termite gut homogenate clone Rs-G40 bacterium2673 Firmicutes Lachnospiraceae sf_5 AF287771.1 human subgingival plaque clone AO0682681 Firmicutes Lachnospiraceae sf_5 AB088974.1 termite gut homogenate clone Rs-K41 bacterium2693 Firmicutes Lachnospiraceae sf_5 AB008552.1 ruminantium str. GA1952698 Firmicutes Lachnospiraceae sf_5 AB088950.1 termite gut homogenate clone Rs-B88 bacterium2708 Firmicutes Lachnospiraceae sf_5 AF275914.2 anaerobic digester clone AA022709 Firmicutes Lachnospiraceae sf_5 AY916314.1 human stool clone B0652726 Firmicutes Lachnospiraceae sf_5 AF371597.1 swine intestine clone p-1561-b52733 Firmicutes Lachnospiraceae sf_5 AF349421.1 pig feces clone2737 Firmicutes Lachnospiraceae sf_5 AF001754.1 rumen clone RF222745 Firmicutes Lachnospiraceae sf_5 AF385562.1 crevicular epithelial cells clone BS0912747 Firmicutes Lachnospiraceae sf_5 AF371559.1 swine intestine clone p-3075-SwA52756 Firmicutes Lachnospiraceae sf_5 AY804149.1 Roseburia faecalis str. M6/12784 Firmicutes Lachnospiraceae sf_5 AJ408993.1 human colonic clone HuCB122793 Firmicutes Lachnospiraceae sf_5 AF357572.1 mpn-isolate group 242801 Firmicutes Lachnospiraceae sf_5 AY169412.1 Butyrivibrio fibrisolvens2804 Firmicutes Lachnospiraceae sf_5 AY353957.1 Clostridium amygdalinum str. BR-102815 Firmicutes Lachnospiraceae sf_5 AF399956.1 Shuttleworthia satelles str. VPI D143K-132825 Firmicutes Lachnospiraceae sf_5 AF105403.1 Butyrivibrio fibrisolvens str. LP12652830 Firmicutes Lachnospiraceae sf_5 AF132278.1 adult human fecal matter clone adhufec682834 Firmicutes Lachnospiraceae sf_5 U41168.1 Butyrivibrio fibrisolvens str. OB1562844 Firmicutes Lachnospiraceae sf_5 AF202260.1 Pseudobutyrivibrio ruminis str. pC-XS22849 Firmicutes Lachnospiraceae sf_5 X89975.1 Butyrivibrio fibrisolvens str. NCDO 24352893 Firmicutes Lachnospiraceae sf_5 AY169411.1 Ruminococcus obeum2931 Firmicutes Lachnospiraceae sf_5 AB088994.1 termite gut homogenate clone Rs-G77 bacterium2937 Firmicutes Lachnospiraceae sf_5 AF371541.1 swine intestine clone p-2482-18B52943 Firmicutes Lachnospiraceae sf_5 AF527773.1 human thigh wound isolate str. MDA24772961 Firmicutes Lachnospiraceae sf_5 AB088989.1 termite gut homogenate clone Rs-F92 bacterium




2965 Firmicutes Lachnospiraceae sf_5 AF481221.1 oral endodontic infection clone MCE9_1732971 Firmicutes Lachnospiraceae sf_5 X87152.1 Johnsonella ignava str. ATCC 512762991 Firmicutes Lachnospiraceae sf_5 AB034063.1 rumen clone 3C3d-82994 Firmicutes Lachnospiraceae sf_5 AB100463.1 termite gut clone Rs-L153001 Firmicutes Lachnospiraceae sf_5 AJ408972.1 human colonic clone HuCA203007 Firmicutes Lachnospiraceae sf_53017 Firmicutes Lachnospiraceae sf_5 AB088993.1 termite gut homogenate clone Rs-D48 bacterium3033 Firmicutes Lachnospiraceae sf_5 AJ408968.1 human colonic clone HuCA153036 Firmicutes Lachnospiraceae sf_5 AB088990.1 termite gut homogenate clone Rs-F27 bacterium3038 Firmicutes Lachnospiraceae sf_5 AF371648.1 swine intestine clone p-1594-c53042 Firmicutes Lachnospiraceae sf_5 AF371584.1 swine intestine clone p-2876-6C53059 Firmicutes Lachnospiraceae sf_5 X89978.1 Butyrivibrio fibrisolvens str. NCDO 22493060 Firmicutes Lachnospiraceae sf_5 AB089002.1 termite gut homogenate clone Rs-B14 bacterium3066 Firmicutes Lachnospiraceae sf_5 AF067965.1 Clostridium methoxybenzovorans str. SR3; DSM 121823075 Firmicutes Lachnospiraceae sf_5 AJ312385.1 Roseburia intestinalis str. L1-823076 Firmicutes Lachnospiraceae sf_5 AY169415.1 Clostridium nexile3087 Firmicutes Lachnospiraceae sf_5 AY178635.1 Butyrivibrio hungatei str. Su63088 Firmicutes Lachnospiraceae sf_5 X73449.1 Clostridium sphenoides str. DSM 6323089 Firmicutes Lachnospiraceae sf_5 AY169419.1 Ruminococcus obeum3105 Firmicutes Lachnospiraceae sf_5 AF287774.1 human subgingival plaque clone CK0513107 Firmicutes Lachnospiraceae sf_5 AF202259.1 oxidoreducens str. G2-23109 Firmicutes Lachnospiraceae sf_5 X87151.1 Catonella morbi str. ATCC 512713111 Firmicutes Lachnospiraceae sf_5 AB034059.1 rumen clone 6C3d-113152 Firmicutes Lachnospiraceae sf_5 AF385510.1 tongue dorsa clone DO0163154 Firmicutes Lachnospiraceae sf_5 AF287773.1 human subgingival plaque clone CK0303171 Firmicutes Lachnospiraceae sf_5 AY169414.1 Lachnospira pectinoschiza3218 Firmicutes Lachnospiraceae sf_5 AB089000.1 termite gut homogenate clone Rs-N533236 Firmicutes Lachnospiraceae sf_5 AF287770.1 Firmicutes sp. oral strain str. FTB414164 Firmicutes Lachnospiraceae sf_5 AF376226.1 ckncm322-B3-7 clone4167 Firmicutes Lachnospiraceae sf_5 AB089038.1 termite gut homogenate clone Rs-D76 bacterium4212 Firmicutes Lachnospiraceae sf_5 AB100488.1 termite gut clone Rs-0614273 Firmicutes Lachnospiraceae sf_5 AB089044.1 termite gut homogenate clone Rs-M14 bacterium4281 Firmicutes Lachnospiraceae sf_5 AF332721.1 granular sludge clone UASB_brew_B864289 Firmicutes Lachnospiraceae sf_5 AB100487.1 termite gut clone Rs-0394301 Firmicutes Lachnospiraceae sf_5 AF287779.1 human subgingival plaque clone F0584315 Firmicutes Lachnospiraceae sf_5 AB089040.1 termite gut homogenate clone Rs-N94 bacterium4331 Firmicutes Lachnospiraceae sf_5 AF332720.1 granular sludge clone UASB_brew_B844335 Firmicutes Lachnospiraceae sf_5 AB088952.1 termite gut homogenate clone Rs-N86 bacterium4381 Firmicutes Lachnospiraceae sf_5 AF376205.1 ckncm301-B3-28 clone4434 Firmicutes Lachnospiraceae sf_5 AB089036.1 termite gut homogenate clone Rs-K11 bacterium4443 Firmicutes Lachnospiraceae sf_5 AF371775.1 swine intestine clone p-3567-9F34510 Firmicutes Lachnospiraceae sf_5 AB089034.1 termite gut homogenate clone Rs-Q53 bacterium4511 Firmicutes Lachnospiraceae sf_5 AF376218.1 ckncm314-B7-17 clone4512 Firmicutes Lachnospiraceae sf_5 AF332711.1 granular sludge clone UASB_brew_B25




4514 Firmicutes Lachnospiraceae sf_5 AB088983.2 termite gut homogenate clone Rs-B34 bacterium4525 Firmicutes Lachnospiraceae sf_5 AB088991.1 termite gut homogenate clone Rs-Q18 bacterium4533 Firmicutes Lachnospiraceae sf_5 AB088980.1 termite gut homogenate clone Rs-N06 bacterium4535 Firmicutes Lachnospiraceae sf_5 AF376201.1 ckncm297-B1-1 clone4539 Firmicutes Lachnospiraceae sf_5 AB089046.1 termite gut homogenate clone Rs-C61 bacterium4540 Firmicutes Lachnospiraceae sf_5 AB088968.1 termite gut homogenate clone Rs-M18 bacterium4567 Firmicutes Lachnospiraceae sf_5 AJ408989.1 human colonic clone HuCB54571 Firmicutes Lachnospiraceae sf_5 X85022.1 Faecalibacterium prausnitzii str. ATCC 277664572 Firmicutes Lachnospiraceae sf_5 AF349415.1 pig feces clone4613 Firmicutes Lachnospiraceae sf_5 AB034003.1 rumen clone 3C0d-34623 Firmicutes Lachnospiraceae sf_5 AJ408957.1 human colonic clone HuCA11036 Firmicutes Peptococc/Acidaminococc sf_11 AF407698.1 Great Artesian Basin clone G07

126 Firmicutes Peptococc/Acidaminococc sf_11 AY134907.1 oral periodontitis clone FY011131 Firmicutes Peptococc/Acidaminococc sf_11 AF349425.1 pig feces clone150 Firmicutes Peptococc/Acidaminococc sf_11181 Firmicutes Peptococc/Acidaminococc sf_11 AF548373.1 Allisonella histaminiformans str. MR2191 Firmicutes Peptococc/Acidaminococc sf_11 AF287796.1 human subgingival plaque clone CS024242 Firmicutes Peptococc/Acidaminococc sf_11 AJ493052.1 Desulfosporosinus orientis str. DSMZ 7493300 Firmicutes Peptococc/Acidaminococc sf_11 AY214183.1 benzene-contaminated groundwater clone ZZ12C8304 Firmicutes Peptococc/Acidaminococc sf_11 AB003379.1 Selenomonas ruminantium str.JCM6582

31 Firmicutes Peptococc/Acidaminococc sf_11 Y10164.1 Dehalobacter restrictus str. TEA362 Firmicutes Peptococc/Acidaminococc sf_11 AF287792.1 human subgingival plaque isolate str. FNA3 oral377 Firmicutes Peptococc/Acidaminococc sf_11 AF385502.1 subgingival plaque clone EW079

39 Firmicutes Peptococc/Acidaminococc sf_11 AF523919.1 forested wetland clone RCP2-71392 Firmicutes Peptococc/Acidaminococc sf_11 AF481210.1 oral endodontic infection clone MCE7_134428 Firmicutes Peptococc/Acidaminococc sf_11 AJ488090.1 chlorobenzene-degrading consortium clone IIIA-1534 Firmicutes Peptococc/Acidaminococc sf_11 AJ488084.1 chlorobenzene-degrading consortium clone IIA-26556 Firmicutes Peptococc/Acidaminococc sf_11 AY244971.1 cow rumen clone BS17562 Firmicutes Peptococc/Acidaminococc sf_11 AF481224.1 oral endodontic infection clone MCE10_265

59 Firmicutes Peptococc/Acidaminococc sf_11 AF371694.1 swine intestine clone p-1941-s962-3657 Firmicutes Peptococc/Acidaminococc sf_11 AY278628.1 Selenomonas genomosp. C2709 Firmicutes Peptococc/Acidaminococc sf_11 AB017195.1 Selenomonas ruminantium str.S20

71 Firmicutes Peptococc/Acidaminococc sf_11 AY218598.1 penguin droppings sediments clone KD2-97710 Firmicutes Peptococc/Acidaminococc sf_11 AF458222.1 Centipeda periodontii str. HB-2761 Firmicutes Peptococc/Acidaminococc sf_11 AF338413.1 Anaeroglobus geminatus str. AIP313.00; CIP 106856; CCUG 44773771 Firmicutes Peptococc/Acidaminococc sf_11 X82500.1 Dialister pneumosintes str. ATCC 33048794 Firmicutes Peptococc/Acidaminococc sf_11 AF366273.1 derived supragingival plaque on tooth surfaces clone DS051 sp.

80 Firmicutes Peptococc/Acidaminococc sf_11 AF287799.1 Selenomonas noxia str. ATCC 43541800 Firmicutes Peptococc/Acidaminococc sf_11 AJ289179.1 corneal ulcer clone E1-K16862 Firmicutes Peptococc/Acidaminococc sf_11 AF473834.1 Megasphaera micronuciformis str. AIP 412.00; CIP 107280863 Firmicutes Peptococc/Acidaminococc sf_11 AY162469.1 Dialister invisus str. E7_25865 Firmicutes Peptococc/Acidaminococc sf_11 AF287793.1 Selenomonas sputigena str. ATCC 35185940 Firmicutes Peptococc/Acidaminococc sf_11 X84006.1 Veillonella dispar str. DSM 20735975 Firmicutes Peptococc/Acidaminococc sf_11 AF357557.1 mpn-isolate group 9




986 Firmicutes Peptococc/Acidaminococc sf_11 AF385501.1 subgingival plaque clone EW076992 Firmicutes Peptococc/Acidaminococc sf_11 AJ229198.1 anoxic bulk soil flooded rice microcosm clone BSV43 clone999 Firmicutes Peptococc/Acidaminococc sf_11 AF287791.1 human subgingival plaque clone CS015

1037 Firmicutes Peptostreptococcaceae sf_5 AY169425.1 Finegoldia magna140 Firmicutes Peptostreptococcaceae sf_5 AY134899.1 oral periodontitis clone EX153

17 Firmicutes Peptostreptococcaceae sf_5 AF538859.1 Peptostreptococcus sp. oral clone P4PA_156 P4 oral224 Firmicutes Peptostreptococcaceae sf_5 AB109771.1 Finegoldia magna str. ATCC 29328

2679 Firmicutes Peptostreptococcaceae sf_5 AB062845.1 termite gut homogenate clone BCf9-132694 Firmicutes Peptostreptococcaceae sf_5 AY134903.1 oral periodontitis clone FX0282701 Firmicutes Peptostreptococcaceae sf_5 AB034093.1 rumen clone 4C3d-122710 Firmicutes Peptostreptococcaceae sf_5 AJ306755.1 DCP-dechlorinating consortium clone SHA-742714 Firmicutes Peptostreptococcaceae sf_5 AB088954.2 termite gut homogenate clone Rs-N27 bacterium2721 Firmicutes Peptostreptococcaceae sf_5 AB088971.1 termite gut homogenate clone Rs-N71 bacterium2722 Firmicutes Peptostreptococcaceae sf_5 AB088987.2 termite gut homogenate clone Rs-E61 bacterium2729 Firmicutes Peptostreptococcaceae sf_5 AJ306754.1 DCP-dechlorinating consortium clone SHA-582738 Firmicutes Peptostreptococcaceae sf_5 AB037875.1 Mogibacterium neglectum str. ATCC 700924 (=P9a-h)2751 Firmicutes Peptostreptococcaceae sf_5 AF287762.1 human subgingival plaque clone CK0472792 Firmicutes Peptostreptococcaceae sf_5 Z36275.1 minutum str. NCTC 129412796 Firmicutes Peptostreptococcaceae sf_5 AF287764.1 human subgingival plaque clone BB1422797 Firmicutes Peptostreptococcaceae sf_5 AY167963.1 Isolation and identification hyper-ammonia producing swine storage pits manure2800 Firmicutes Peptostreptococcaceae sf_5 Z36296.1 Mogibacterium timidum str. ATCC 330932805 Firmicutes Peptostreptococcaceae sf_5 AY134904.1 oral periodontitis clone FX0332913 Firmicutes Peptostreptococcaceae sf_5 AB088960.2 termite gut homogenate clone Rs-N82 bacterium2946 Firmicutes Peptostreptococcaceae sf_5 AB034148.1 rumen clone 3C28d-42988 Firmicutes Peptostreptococcaceae sf_5 AB100461.1 termite gut clone Rs-0502993 Firmicutes Peptostreptococcaceae sf_5 AF538856.1 oral clone P2PB_46 P33080 Firmicutes Peptostreptococcaceae sf_5 AB088986.1 termite gut homogenate clone Rs-F43 bacterium3112 Firmicutes Peptostreptococcaceae sf_5 CR933145.1 Evry municipal wastewater treatment plant clone 012C11_B_SD_P153131 Firmicutes Peptostreptococcaceae sf_5 U65987.1 saphenum str. ATCC 499893153 Firmicutes Peptostreptococcaceae sf_5 U13039.1 infirmum str. W 14713182 Firmicutes Peptostreptococcaceae sf_5 AB088970.1 termite gut homogenate clone Rs-Q64 bacterium3193 Firmicutes Peptostreptococcaceae sf_5 Z36274.1 nodatum str. ATCC 330993220 Firmicutes Peptostreptococcaceae sf_5 AJ488072.1 chlorobenzene-degrading consortium clone IA-193237 Firmicutes Peptostreptococcaceae sf_5

393 Firmicutes Peptostreptococcaceae sf_5 AF542229.1 Anaerococcus vaginalis str. CCUG 31349436 Firmicutes Peptostreptococcaceae sf_5 AF550609.1 Peptostreptococcaceae bacterium 19gly3

58 Firmicutes Peptostreptococcaceae sf_5 AF481225.1 Peptostreptococcus sp. str. E3_32616 Firmicutes Peptostreptococcaceae sf_5 AF542230.1 Peptoniphilus lacrimalis str. CCUG 31350619 Firmicutes Peptostreptococcaceae sf_5 AY217429.1 TCE-dechlorinating microbial community clone 1G668 Firmicutes Peptostreptococcaceae sf_5 AY221992.1 Sedimentibacter sp. str. BRS2861 Firmicutes Peptostreptococcaceae sf_5 AY244779.1 Peptoniphilus sp. str. 2002-2300004919 Firmicutes Peptostreptococcaceae sf_5 AF542234.1 Anaerococcus tetradius str. CCUG 46590

2456 Firmicutes Syntrophomonadaceae sf_5 AF482440.1 granular sludge clone R4b142483 Firmicutes Syntrophomonadaceae sf_5 AF529116.1 trichloroethene-contaminated site clone FTLM142 bacterium




2324 Firmicutes Unclassified sf_172432 Firmicutes Unclassified sf_172675 Firmicutes Unclassified sf_172680 Firmicutes Unclassified sf_173476 Firmicutes Unclassified sf_174168 Firmicutes Unclassified sf_174307 Firmicutes Unclassified sf_17

926 Firmicutes Unclassified sf_172373 Firmicutes Unclassified sf_34280 Firmicutes Unclassified sf_32398 Firmicutes Unclassified sf_4 AY093477.1 deep marine sediment clone MB-C2-1064216 Firmicutes Unclassified sf_7

198 Firmicutes Unclassified sf_1 AB091323.1 Pelotomaculum sp. str. JT2351 Firmicutes Unclassified sf_1 Y11574.1 Desulfotomaculum thermobenzoicum str. DSM 61932359 Firmicutes Unclassified sf_1 AB091324.1 UASB granular sludge clone JP2443 Firmicutes Unclassified sf_1 Y11573.1 Desulfotomaculum thermoacetoxidans str. DSM 58132490 Firmicutes Unclassified sf_1 AY084078.1 Desulfotomaculum solfataricum str. V212541 Firmicutes Unclassified sf_1 AB091328.1 UASB granular sludge clone UT-2

894 Firmicutes Unclassified sf_1 AF351222.1 coal tar waste-contaminated groundwater clone 36-22 G+C4298 Firmicutes Unclassified sf_1 AY207065.1 human mouth clone P4PA_664616 Firmicutes Unclassified sf_1 AB185532.1 rumen clone F23-C123955 Firmicutes Acholeplasmataceae sf_1 AF521672.1 Weeping tea tree witches'-broom phytoplasma tree3961 Firmicutes Acholeplasmataceae sf_1 L33766.1 Clover yellow edge mycoplasma-like organism3975 Firmicutes Acholeplasmataceae sf_1 AF302841.1 Black raspberry witches'-broom phytoplasma str. BRWB witches'-broom3976 Firmicutes Acholeplasmataceae sf_14044 Firmicutes Acholeplasmataceae sf_14045 Firmicutes Acholeplasmataceae sf_1 AY081817.1 Chinaberry yellows phytoplasma4046 Firmicutes Acholeplasmataceae sf_1 L33735.1 Pigeon pea witches'-broom mycoplasma-like organism4064 Firmicutes Acholeplasmataceae sf_1 AJ542542.1 Malus domestica isolate str. AT1/934092 Firmicutes Acholeplasmataceae sf_1 AY083605.1 Australia isolate str. BVGY

144 Firmicutes Erysipelotrichaceae sf_3 L34616.1 Eubacterium cylindroides3943 Firmicutes Erysipelotrichaceae sf_3 AB030218.1 Coprobacillus cateniformis str. JCM 106033952 Firmicutes Erysipelotrichaceae sf_3 AB055907.1 Erysipelothrix rhusiopathiae str. Pecs 563965 Firmicutes Erysipelotrichaceae sf_3 AY133091.1 TCE-contaminated site clone ccslm2383981 Firmicutes Erysipelotrichaceae sf_3 AY128088.1 phototrophic sludge clone PSB-M-34038 Firmicutes Erysipelotrichaceae sf_3 AB031058.1 Bulleidia moorei str. JCM 10647 RCA59-77

768 Firmicutes Erysipelotrichaceae sf_34074 Firmicutes Entomoplasmataceae sf_1 AF371522.1 swine intestine clone p-2013-s959-54112 Firmicutes Entomoplasmataceae sf_2 AY157871.1 Entomoplasma somnilux str. ATCC 491943929 Firmicutes Mycoplasmataceae sf_1 AY191226.1 Mycoplasma gypsbengalensis str. Gb-V333970 Firmicutes Mycoplasmataceae sf_1 U44769.1 Mycoplasma canadense str. 275c3997 Firmicutes Mycoplasmataceae sf_1 AF125583.1 Mycoplasma salivarium str. PG20(T)4014 Firmicutes Mycoplasmataceae sf_1 NC_002771.1 Mycoplasma pulmonis str. UAB CTIP4037 Firmicutes Mycoplasmataceae sf_1 AJ002265.1 Mycoplasma hominis str. PG21




4102 Firmicutes Mycoplasmataceae sf_1 AF493543.1 Mycoplasma zalophus str. 4296C149 Firmicutes Unclassified sf_6 M23730.1 Streptococcus pleomorphus

2388 Firmicutes Unclassified sf_1 AF465653.1 G+C Gram-positive clone YNPRH70A77 Firmicutes Unclassified sf_1 AF391988.1 thermal soil clone YNPFFP9

3508 Firmicutes Unclassified sf_3 AF190460.1 Symbiobacterium toebii str. SC-1141 Firmicutes Unclassified sf_8 AF407393.1 MCB-contaminated groundwater-treating reactor clone RB9C2

2433 Firmicutes Unclassified sf_8 AF282252.1 Ferribacter thermoautotrophicus str. JW/JH-Fiji-24536 Firmicutes Unclassified sf_8 AF507891.1 Mono Lake at depth 35m station 6 July 2000 clone ML635J-14 G+C

546 Firmicutes Unclassified sf_8 AF282254.1 Ferribacter thermoautotrophicus488 Fusobacteria Fusobacteriaceae sf_1 NZ_AABF020 Fusobacterium nucleatum subsp. vincentii str. ATCC 49256

1081 Fusobacteria Fusobacteriaceae sf_13 AF189244.1 Leptotrichia sp.1034 Fusobacteria Fusobacteriaceae sf_3 AJ307982.1 Ilyobacter tartaricus str. DSM 2382 T

116 Fusobacteria Fusobacteriaceae sf_3 AF287814.1 human subgingival plaque clone F138285 Fusobacteria Fusobacteriaceae sf_3 AF366276.1 supragingival plaque on tooth surfaces clone DT031

35 Fusobacteria Fusobacteriaceae sf_3 AF385571.1 crevicular epithelial cells clone EI013367 Fusobacteria Fusobacteriaceae sf_3 AY078425.1 Leptotrichia amnionii str. AMN-1387 Fusobacteria Fusobacteriaceae sf_3 AY029802.1 Leptotrichia wadeii str. LB16558 Fusobacteria Fusobacteriaceae sf_3 AJ344093.1 Sneathia sanguinegens str. CCUG 41628T644 Fusobacteria Fusobacteriaceae sf_3 AJ307981.1 Ilyobacter polytropus str. DSM 2926 T694 Fusobacteria Fusobacteriaceae sf_3 AF385518.1 tongue dorsa clone DR011721 Fusobacteria Fusobacteriaceae sf_3 AY207053.1 human mouth clone P2PB_51779 Fusobacteria Fusobacteriaceae sf_3 AY029803.1 Leptotrichia hofstadii str. LB23

10112 Gemmatimonadetes Unclassified sf_5 AF432607.1 forest soil clone NOS7.157WL1127 Gemmatimonadetes Unclassified sf_5 AJ519396.1 uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-211149 Gemmatimonadetes Unclassified sf_5 AF432618.1 lodgepole pine rhizosphere soil clone C17.11WL1238 Gemmatimonadetes Unclassified sf_5 AB072735.1 Gemmatimonas aurantiaca1565 Gemmatimonadetes Unclassified sf_5 AJ532728.1 uranium mining waste pile clone JG34-KF-4182047 Gemmatimonadetes Unclassified sf_5 AF234148.1 soil clone #0319-7G21

227 Gemmatimonadetes Unclassified sf_5 AJ519397.1 uranium mining waste pile clone JG37-AG-36317 Gemmatimonadetes Unclassified sf_5 AY218696.1 penguin droppings sediments clone KD8-87442 Gemmatimonadetes Unclassified sf_5 AF507712.1 forest soil clone S0134

9464 Gemmatimonadetes Unclassified sf_5 AF432648.1 lodgepole pine rhizosphere soil British Columbia Ministry Forests Long-Term Soil Productivity

2554 Gemmatimonadetes Unclassified sf_6 AJ347028.1 sponge symbiont clone TK1910118 LD1PA group Unclassified sf_1 AY114324.1 anoxic marine sediment clone LD1-PA3810027 Lentisphaerae Unclassified sf_5 AJ431234.1 Cytophaga sp. str. Dex80-4310330 Lentisphaerae Unclassified sf_5 AF507900.1 Mono lake clone ML635J-589704 Lentisphaerae Unclassified sf_5 AJ431235.1 Cytophaga sp. str. Dex80-646408 marine group A Unclassified sf_1 AACY010941

30.1Sargasso Sea

6454 marine group A Unclassified sf_1 U34043.1 marine clone SAR4066344 marine group A Unclassified sf_1 AF382142.1 bacterioplankton clone ZA3648c2437 Natronoanaerobium Unclassified sf_1 AF507879.2 Mono Lake at depth 23m station 6 July 2000 clone ML623J-193570 Natronoanaerobium Unclassified sf_1 AF454298.1 Bacillus sp. clone ML1228J-1




3745 Natronoanaerobium Unclassified sf_1 AF507877.1 Mono Lake at depth 35m station 6 July 2000 clone ML635J-454377 Natronoanaerobium Unclassified sf_1 AF507888.1 Mono Lake at depth 35m station 6 July 2000 clone ML635J-65 G+C

769 Natronoanaerobium Unclassified sf_1 AJ431345.1 fjord ikaite column clone un-c23452 NC10 Unclassified sf_1 AY177763.1 vadose clone 5G01536 NC10 Unclassified sf_1 AJ519669.1 uranium mill tailings clone GuBH2-AD-8

10254 NC10 Unclassified sf_1 AJ519650.1 uranium mill tailings soil sample clone Sh765B-TzT-352516 NC10 Unclassified sf_1 AF529103.1 TCE-contaminated site clone FTL22

179 Nitrospira Nitrospiraceae sf_1 AF407702.1 Great Artesian Basin clone G19864 Nitrospira Nitrospiraceae sf_1 Y14644.1 nitrifying sludge clone GC86984 Nitrospira Nitrospiraceae sf_1 AJ519405.1 uranium mining waste pile clone JG37-AG-131 sp.542 Nitrospira Nitrospiraceae sf_2 AF524005.1 forested wetland clone FW19681 Nitrospira Nitrospiraceae sf_2697 Nitrospira Nitrospiraceae sf_2 AF524003.1 forested wetland clone FW118833 Nitrospira Nitrospiraceae sf_3 AF225448.1 acid mine drainage clone BA29515 OD1 Unclassified sf_1326 OP10 Unclassified sf_1 AY222300.1 geothermal clone ST01-SN3H514 OP10 Unclassified sf_1 AF368184.1 sludge clone SBRA136

8413 OP10 Unclassified sf_1 AJ306784.1 DCP-dechlorinating consortium clone SHA-37484 OP10 Unclassified sf_4 AF524022.1 forested wetland clone FW68

9782 OP10 Unclassified sf_5 AY192275.1 Rocky Mountain alpine soil clone S1a-1H349 OP3 Unclassified sf_2 AJ390463.1 soil clone PBS-25

1015 OP3 Unclassified sf_3 AY013695.1 polluted aquifer clone BVC56628 OP3 Unclassified sf_4 AY050598.1 CB-contaminated groundwater clone GOUTB15598 OP8 Unclassified sf_3 AF419671.1 Guaymas Basin hydrothermal sediment clone a2b010

2380 OP9/JS1 Unclassified sf_1 AY197406.1 Guaymas Basin hydrothermal vent sediments clone B03R0122489 OP9/JS1 Unclassified sf_1 AY197377.1 Guaymas Basin hydrothermal vent sediments clone B01R0052491 OP9/JS1 Unclassified sf_1 AY093469.1 deep marine sediment clone MB-B2-103

726 OP9/JS1 Unclassified sf_1 AF027086.1 hot spring clone OPB72969 OP9/JS1 Unclassified sf_1 AJ306782.1 DCP-dechlorinating consortium clone SHA-1

4683 Planctomycetes Anammoxales sf_2 BX294785.1 anoxic basin clone CY0ARA028B094694 Planctomycetes Anammoxales sf_4 AF418968.1 USA: Colorado Fort collins Horsetooth Reservoir clone HT2F114695 Planctomycetes Anammoxales sf_4 AF316773.1 Crater Lake clone CL500-159662 Planctomycetes Anammoxales sf_4 AF407728.1 Great Artesian Basin clone B834670 Planctomycetes Pirellulae sf_34677 Planctomycetes Pirellulae sf_3 BX294863.1 aerobic basin clone CY0ARA032A034692 Planctomycetes Pirellulae sf_3 BX294733.1 aerobic basin clone CY0ARA026G044704 Planctomycetes Pirellulae sf_3 BX294700.1 aerobic basin clone CY0ARA025E114803 Planctomycetes Pirellulae sf_3 X86388.1 Pirellula sp. str. ACM 31814652 Planctomycetes Planctomycetaceae sf_3 BX294789.1 anoxic basin clone CY0ARA028C044818 Planctomycetes Planctomycetaceae sf_3 AY328733.1 drinking water system simulator clone DSSD344831 Planctomycetes Planctomycetaceae sf_3 AJ231190.1 Planctomyces brasiliensis4855 Planctomycetes Planctomycetaceae sf_3 BX294726.1 aerobic basin clone CY0ARA026D104948 Planctomycetes Planctomycetaceae sf_3 BX294756.1 anoxic basin clone CY0ARA027D014897 Planctomycetes Unclassified sf_1 AY093476.1 deep marine sediment clone MB-C2-105




7529 Proteobacteria Acetobacteraceae sf_1 AJ012698.1 Gluconacetobacter europaeus str. ZIM B028 V37600 Proteobacteria Acetobacteraceae sf_1 AJ001632.1 Acetobacter pomorum str. LTH24587500 Proteobacteria Roseococcaceae sf_1 AF407720.1 Great Artesian Basin clone B357028 Proteobacteria Unclassified sf_16959 Proteobacteria Azospirillaceae sf_1 AF523824.1 Rhodocista pekingensis str. 3-p7171 Proteobacteria Azospirillaceae sf_1 Z29623.1 Azospirillum species7539 Proteobacteria Azospirillaceae sf_1 AJ401217.1 Rhodocista sp. AR21076922 Proteobacteria Magnetospirillaceae sf_1 AY171615.1 Dechlorospirillum sp. str. SN16732 Proteobacteria Unclassified sf_1 AF426002.1 Anabaena circinalis AWQC118C isolate str. UNSW77400 Proteobacteria Unclassified sf_1 AF524861.1 sphagnum peat bog clone K-5b56651 Proteobacteria Beijerinck/Rhodoplan/Methylo

cystsf_3 AB119196.1 Beijerinckia indica

6762 Proteobacteria Beijerinck/Rhodoplan/Methylocyst

sf_3 AY080913.1 acidic forest soil clone UP8


sf_3 AJ563928.1 Methylocella tundrae str. Y1


sf_3 M95665.1 Methylosinus sporium


sf_3 AF359545.1 Scrippsiella trochoidea NEPCC 15


sf_3 AF150804.1 Methylosinus trichosporium

6636 Proteobacteria Bradyrhizobiaceae sf_1 U35000.3 Bradyrhizobium elkanii str. USDA 766768 Proteobacteria Bradyrhizobiaceae sf_1 M59068.1 Rhodopseudomonas palustris str. GH6799 Proteobacteria Bradyrhizobiaceae sf_1 D12700.1 Rhodopseudomonas palustris str. ATCC 170016867 Proteobacteria Bradyrhizobiaceae sf_1 AY102327.1 heavy metal-contaminated soil clone a131316878 Proteobacteria Bradyrhizobiaceae sf_1 AF530467.1 Bradyrhizobium japonicum SD56887 Proteobacteria Bradyrhizobiaceae sf_1 AB067729.1 Bradyrhizobium str. YB26917 Proteobacteria Bradyrhizobiaceae sf_1 D11345.1 Bradyrhizobium japonicum str. IAM 126086927 Proteobacteria Bradyrhizobiaceae sf_1 L11663.1 Nitrobacter hamburgensis str. X146941 Proteobacteria Bradyrhizobiaceae sf_1 AB087719.1 Rhodopseudomonas rhenobacensis str. Klemme Rb7044 Proteobacteria Bradyrhizobiaceae sf_1 U87765.1 Afipia genosp. 2 str. G44387078 Proteobacteria Bradyrhizobiaceae sf_1 M69186.1 Afipia clevelandensis7087 Proteobacteria Bradyrhizobiaceae sf_1 AF530468.1 Bradyrhizobium japonicum HA17126 Proteobacteria Bradyrhizobiaceae sf_1 AJ534670.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-7316 Proteobacteria Bradyrhizobiaceae sf_17333 Proteobacteria Bradyrhizobiaceae sf_1 U87768.1 Afipia genosp. 4 str. G36447353 Proteobacteria Bradyrhizobiaceae sf_1 AY216437.1 temperate estuarine mud clone HC657390 Proteobacteria Bradyrhizobiaceae sf_1 U87781.1 Afipia genosp. 10 str. G89967398 Proteobacteria Bradyrhizobiaceae sf_1 AF208514.1 Bradyrhizobium japonicum str. USDA 387403 Proteobacteria Bradyrhizobiaceae sf_1 AB099659.1 Oligotropha carboxidovorans str. S237438 Proteobacteria Bradyrhizobiaceae sf_1 AY055798.1 Nitrobacter sp. str. KB2127477 Proteobacteria Bradyrhizobiaceae sf_1 AY904744.1 Bradyrhizobium elkanii str. SEMIA 60287522 Proteobacteria Bradyrhizobiaceae sf_1 AF509906.1 Bradyrhizobium sp. str. KKI14




7646 Proteobacteria Hyphomicrobiaceae sf_1 Y14304.1 Hyphomicrobium aestuarii str. DSM 15647585 Proteobacteria Methylobacteriaceae sf_1 U58018.1 Methylobacterium thiocyanatum str. ALL/SCN-P6711 Proteobacteria Unclassified sf_1 AY078053.1 Microvirga subterranea str. FaiI4; ATCC BAA-295; DSM 143647067 Proteobacteria Unclassified sf_1 AB033757.1 Blastochloris sulfoviridis str. GN17199 Proteobacteria Unclassified sf_1 AJ532683.1 uranium mill tailings clone Gitt-KF-1947264 Proteobacteria Unclassified sf_1 AF508112.1 Bosea thiooxidans TJ17306 Proteobacteria Unclassified sf_1 AF358017.1 peat soil microcosm clone LO13.36660 Proteobacteria Xanthobacteraceae sf_1 D11342.1 Azorhizobium caulinodans str. ORS 5716781 Proteobacteria Caulobacteraceae sf_1 AB023784.1 Brevundimonas intermedia str. MBIC2712 ATCC152626904 Proteobacteria Caulobacteraceae sf_1 AB021414.1 Brevundimonas vesicularis str. IAM 12105T6909 Proteobacteria Caulobacteraceae sf_1 X87274.1 Brevundimonas diminuta str. DSM 16356968 Proteobacteria Caulobacteraceae sf_1 AB021415.1 Brevundimonas diminuta str. IAM 12691T7257 Proteobacteria Caulobacteraceae sf_1 AJ459874.1 larval intestine clone D7359 Proteobacteria Caulobacteraceae sf_1 AJ227782.1 Brevundimonas bacteroides str. CB77366 Proteobacteria Caulobacteraceae sf_1 AJ227784.1 Brevundimonas subvibrioides str. CB817436 Proteobacteria Caulobacteraceae sf_1 AJ227797.1 Brevundimonas sp. str. FWC407010 Proteobacteria Caedibacteraceae sf_3 AJ428412.1 periodontal pocket clone 10B67157 Proteobacteria Caedibacteraceae sf_4 AF533506.1 acid mine drainage clone ASL456947 Proteobacteria Caedibacteraceae sf_5 AB089084.2 termite gut homogenate clone Rs-B60 proteobacterium6810 Proteobacteria Unclassified sf_4 AY033325.1 marine bacterioplankton clone MB13F017105 Proteobacteria Unclassified sf_4 AB186982.1 Mariana trough hydrothermal vent water 0.2micro-m filterable fraction clone MT-NB256735 Proteobacteria Unclassified sf_5 AF510192.1 Candidatus Pelagibacter ubique str. HTCC10027123 Proteobacteria Unclassified sf_1 AJ518774.1 uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-1027222 Proteobacteria Unclassified sf_1 AF407727.1 Great Artesian Basin clone B796945 Proteobacteria Unclassified sf_1 AB081581.3 Rhizobiales str. A487194 Proteobacteria Unclassified sf_1 AF498744.1 soil isolate Ellin3627384 Proteobacteria Bartonellaceae sf_1 U87831.1 aortic heart valve patient with endocarditis clone v97415 Proteobacteria Bartonellaceae sf_1 NC_005955.1 Bartonella quintana str. Toulouse7029 Proteobacteria Bradyrhizobiaceae sf_17392 Proteobacteria Hyphomicrobiaceae sf_16692 Proteobacteria Phyllobacteriaceae sf_1 AY786080.1 Phyllobacterium trifolii str. PETP026857 Proteobacteria Phyllobacteriaceae sf_1 AY195844.1 Mesorhizobium mediterraneum str. PECA207009 Proteobacteria Phyllobacteriaceae sf_17216 Proteobacteria Phyllobacteriaceae sf_1 D88524.1 Ahrensia kielensis str. IAM126187300 Proteobacteria Phyllobacteriaceae sf_1 AY007683.1 marine isolate JP577381 Proteobacteria Phyllobacteriaceae sf_1 AJ011759.1 Aminobacter aminovorans str. DSM7048T7497 Proteobacteria Phyllobacteriaceae sf_1 AJ294416.1 Pseudaminobacter salicylatoxidans str. KTC0017543 Proteobacteria Phyllobacteriaceae sf_1 AJ318199.1 Waste-gas biofilter clone BIwii16683 Proteobacteria Rhizobiaceae sf_1 D14516.1 Sinorhizobium fredii str. ATCC354236770 Proteobacteria Rhizobiaceae sf_1 X67234.2 Rhizobium tropici str. LMG 95176964 Proteobacteria Rhizobiaceae sf_1 AE008265.2 Agrobacterium tumefaciens str. C58 Cereon6972 Proteobacteria Rhizobiaceae sf_1 AY040360.1 Ensifer adhaerens str. LMG 205827051 Proteobacteria Rhizobiaceae sf_1 D12786.1 Mycoplana dimorpha str. IAM 131547568 Proteobacteria Rhizobiaceae sf_1 U47303.1 Rhizobium etli str. USDA 2667 ATCC 14483 SEMIA 043




6756 Proteobacteria Unclassified sf_16789 Proteobacteria Unclassified sf_1 X74915.1 Shinella zoogloeoides str. ATCC 196237060 Proteobacteria Unclassified sf_17323 Proteobacteria Unclassified sf_16652 Proteobacteria Rhodobacteraceae sf_1 AF353235.1 marine clone Arctic96A-16701 Proteobacteria Rhodobacteraceae sf_1 AF245632.1 Roseobacter clone NAC11-36980 Proteobacteria Rhodobacteraceae sf_1 AJ582226.1 Loktanella vestfoldensis str. LMG 220036991 Proteobacteria Rhodobacteraceae sf_1 X53853.1 Rhodobacter sphaeroides str. 2.4.17026 Proteobacteria Rhodobacteraceae sf_1 AY005463.1 Leisingera methylohalidivorans str. MB27040 Proteobacteria Rhodobacteraceae sf_1 D32238.1 Paracoccus alcaliphilus str. JCM 73647084 Proteobacteria Rhodobacteraceae sf_1 AF359546.1 Scrippsiella trochoidea NEPCC 157237 Proteobacteria Rhodobacteraceae sf_1 AF368183.1 non-EBPR sludge clone SBRT1557263 Proteobacteria Rhodobacteraceae sf_17433 Proteobacteria Rhodobacteraceae sf_1 AF359537.1 Scrippsiella trochoidea NEPCC 157536 Proteobacteria Rhodobacteraceae sf_17025 Proteobacteria Unclassified sf_5 AF382105.1 bacterioplankton clone ZA2526c7471 Proteobacteria Unclassified sf_5 AJ347025.1 sponge clone TK036628 Proteobacteria Anaplasmataceae sf_3 U23709.1 Wolbachia pipientis6648 Proteobacteria Anaplasmataceae sf_3 AF035160.1 Wolbachia sp6803 Proteobacteria Anaplasmataceae sf_3 AY007547.1 Wolbachia sp. Dlem16SWol6908 Proteobacteria Anaplasmataceae sf_3 M85267.1 Rhinocyllus conicus endosymbiont7481 Proteobacteria Anaplasmataceae sf_3 AF179630.1 Wolbachia pipientis6809 Proteobacteria Rickettsiaceae sf_1 U11021.1 Rickettsia rickettsii str. Sawtooth7556 Proteobacteria Rickettsiaceae sf_1 U11014.1 Rickettsia bellii str. strains 369-C and G2D427156 Proteobacteria Unclassified sf_1 AB089097.1 termite gut homogenate clone Rs-M62 proteobacterium6639 Proteobacteria Unclassified sf_26650 Proteobacteria Sphingomonadaceae sf_1 AY563441.1 Sphingomonas phyllosphaerae str. FA16663 Proteobacteria Sphingomonadaceae sf_1 AY554010.1 Sphingopyxis flavimaris str. SW-1516690 Proteobacteria Sphingomonadaceae sf_1 AY048657.1 Porphyrobacter tepidarius str. OK5APO7016 Proteobacteria Sphingomonadaceae sf_1 AY167834.1 Sphingomonas sp. str. SAFR-0277036 Proteobacteria Sphingomonadaceae sf_1 AY026916.1 Lutibacterium anuloederans str. LC87075 Proteobacteria Sphingomonadaceae sf_1 AJ000920.2 Novosphingobium sp. str. K167090 Proteobacteria Sphingomonadaceae sf_1 AB024288.1 Blastomonas natatoria str. DSM 3183T7100 Proteobacteria Sphingomonadaceae sf_1 D16147.1 Novosphingobium capsulatum str. GIFU115267215 Proteobacteria Sphingomonadaceae sf_1 AF445712.1 travertine hot spring clone SM2B067319 Proteobacteria Sphingomonadaceae sf_1 AF425996.1 Anabaena circinalis AWQC118C isolate str. UNSW17440 Proteobacteria Sphingomonadaceae sf_1 AF159257.2 Sphingobium chungbukense str. DJ777528 Proteobacteria Sphingomonadaceae sf_1 D16145.1 Sphingobium yanoikuyae str. GIFU98827535 Proteobacteria Sphingomonadaceae sf_1 D16144.1 Sphingomonas paucimobilis str. GIFU23957537 Proteobacteria Sphingomonadaceae sf_1 AY250869.1 lichen-dominated Antarctic cryptoendolithic community clone FBP255 proteobacterium7548 Proteobacteria Sphingomonadaceae sf_1 U87784.1 Afipia genosp. 13 str. G89917576 Proteobacteria Sphingomonadaceae sf_1 AB025013.1 Novosphingobium stygium str. IFO 160857035 Proteobacteria Sphingomonadaceae sf_15 Y09639.1 Sphingomonas asaccharolytica str. IFO 10564-T6653 Proteobacteria Unclassified sf_1 AY785128.1 Kaistobacter koreensis str. PB229




6697 Proteobacteria Unclassified sf_2 AB089090.1 termite gut homogenate clone Rs-D84 proteobacterium7188 Proteobacteria Unclassified sf_2 AB089085.1 termite gut homogenate clone Rs-B50 proteobacterium6665 Proteobacteria Unclassified sf_6 AF143830.1 hydrocarbon-degrading consortium clone 4-Org2-226694 Proteobacteria Unclassified sf_6 AF523879.1 forested wetland clone RCP2-926918 Proteobacteria Unclassified sf_6 AJ581616.1 soil near uranium mill tailings clone KCM-C-456920 Proteobacteria Unclassified sf_6 AY486423.1 Pseudovibrio denitrificans str. DN346987 Proteobacteria Unclassified sf_67013 Proteobacteria Unclassified sf_6 AF143823.1 hydrocarbon-degrading consortium clone 4-Org1-367312 Proteobacteria Unclassified sf_67340 Proteobacteria Unclassified sf_6 AJ536878.1 uranium mining waste pile soil sample clone JG30-KF-AS507377 Proteobacteria Unclassified sf_6 AY192273.1 Rocky Mountain alpine soil clone W2b-8C7572 Proteobacteria Unclassified sf_67575 Proteobacteria Unclassified sf_68780 Proteobacteria Unclassified sf_6 AJ296549.1 uranium mining mill tailing clone GR-296.II.89 GR-296.II.897737 Proteobacteria Alcaligenaceae sf_1 AY081977.1 atrazine-catabolizing microbial presence methanol clone KRA30+06A7768 Proteobacteria Alcaligenaceae sf_1 AF371864.1 swine intestine clone p-861-a57788 Proteobacteria Alcaligenaceae sf_1 AY081994.1 atrazine-catabolizing microbial absence methanol clone KRA30-587838 Proteobacteria Alcaligenaceae sf_1 AB195161.1 Alcaligenes defragrans str. PD-197902 Proteobacteria Alcaligenaceae sf_1 AF155147.1 Alcaligenes faecalis str. M3A7932 Proteobacteria Alcaligenaceae sf_1 AJ278451.1 Achromobacter subsp. denitrificans str. DSM 30026 (T)7984 Proteobacteria Alcaligenaceae sf_1 AJ318125.1 Waste-gas biofilter clone BIfciii387992 Proteobacteria Alcaligenaceae sf_1 AJ509012.1 Alcaligenes faecalis 5659-H8062 Proteobacteria Alcaligenaceae sf_1 AJ277742.1 Brackiella oedipodis str. LMG 1945 R88468094 Proteobacteria Alcaligenaceae sf_1 AF430122.1 Alcaligenes sp. str. VKM B-2263 dcm67720 Proteobacteria Burkholderiaceae sf_1 AY218566.1 penguin droppings sediments clone KD1-797747 Proteobacteria Burkholderiaceae sf_17771 Proteobacteria Burkholderiaceae sf_1 AB021374.1 Burkholderia glathei str. ATCC 29195T7782 Proteobacteria Burkholderiaceae sf_1 AY040365.1 Burkholderia hospita str. LMG 20598T7914 Proteobacteria Burkholderiaceae sf_1 AB021422.1 Burkholderia andropogonis str. ATCC 19311T7963 Proteobacteria Burkholderiaceae sf_1 AF476084.1 Erium globosum symbiont7969 Proteobacteria Burkholderiaceae sf_1 U37342.1 Burkholderia sp.8011 Proteobacteria Burkholderiaceae sf_1 U96941.1 Burkholderia graminis str. AUS358068 Proteobacteria Burkholderiaceae sf_1 X67039.1 Burkholderia caryophylli str. ATCC 254188097 Proteobacteria Burkholderiaceae sf_1 AB091761.1 Burkholderia cepacia7704 Proteobacteria Comamonadaceae sf_1 AF289169.1 freshwater clone PRD01b009B7705 Proteobacteria Comamonadaceae sf_1 AY218644.1 penguin droppings sediments clone KD4-77718 Proteobacteria Comamonadaceae sf_1 AY291119.1 Lampropedia hyalina str. DSM 153367719 Proteobacteria Comamonadaceae sf_1 AY218585.1 penguin droppings sediments clone KD2-467725 Proteobacteria Comamonadaceae sf_1 AF534428.1 Toolik Lake main station at 3 m depth clone TLM04/TLMdgge03 proteobacterium7801 Proteobacteria Comamonadaceae sf_1 AF534429.1 Toolik Lake main station at 3 m depth clone TLM05/TLMdgge10 proteobacterium7807 Proteobacteria Comamonadaceae sf_1 Y18618.1 Aquaspirillum metamorphum str. DSM 18377822 Proteobacteria Comamonadaceae sf_1 AY166684.1 Polaromonas naphthalenivorans str. CJ27827 Proteobacteria Comamonadaceae sf_17829 Proteobacteria Comamonadaceae sf_1 AF078758.1 Xylophilus ampelinus str. ATCC 33914




7847 Proteobacteria Comamonadaceae sf_1 AY218568.1 penguin droppings sediments clone KD2-1047856 Proteobacteria Comamonadaceae sf_1 AY169431.1 Variovorax paradoxus7884 Proteobacteria Comamonadaceae sf_1 AJ421915.2 Germany:Elbe River clone Elb377888 Proteobacteria Comamonadaceae sf_1 AB021420.1 Hydrogenophaga flava str. DSM 619T7919 Proteobacteria Comamonadaceae sf_1 AB021339.1 strain isolate str. rM47928 Proteobacteria Comamonadaceae sf_1 AY218738.1 penguin droppings sediments clone KD5-437929 Proteobacteria Comamonadaceae sf_1 AF068803.1 hydrothermal vent clone VC2.1 Bac297941 Proteobacteria Comamonadaceae sf_1 AF407397.1 MCB-contaminated groundwater-treating reactor clone RB9C107943 Proteobacteria Comamonadaceae sf_1 AF035052.1 Aquabacterium parvum str. B67949 Proteobacteria Comamonadaceae sf_1 AF508103.1 Variovorax paradoxus TG277964 Proteobacteria Comamonadaceae sf_1 AY250104.1 napthalene-contaminated sediment clone 767965 Proteobacteria Comamonadaceae sf_1 X72724.1 Anoxobacterium dechloraticum7971 Proteobacteria Comamonadaceae sf_1 AF502222.1 EBPR sludge lab scale clone HP1B337978 Proteobacteria Comamonadaceae sf_1 D30793.1 Variovorax paradoxus str. IAM 123737986 Proteobacteria Comamonadaceae sf_1 AF468446.1 Arctic sea ice ARK102817987 Proteobacteria Comamonadaceae sf_1 AB076844.1 Acidovorax sp. str. OS-67990 Proteobacteria Comamonadaceae sf_1 AF236010.1 isolate str. A06407995 Proteobacteria Comamonadaceae sf_1 AJ537466.1 Ottowia thiooxydans str. K118003 Proteobacteria Comamonadaceae sf_1 AF143840.1 hydrocarbon-degrading consortium clone AF1-88009 Proteobacteria Comamonadaceae sf_1 AJ412678.1 denitrifying reactor clone 818012 Proteobacteria Comamonadaceae sf_1 AJ420325.1 Acidovorax konjaci str. DSM 74818018 Proteobacteria Comamonadaceae sf_1 AF078764.1 Acidovorax delafieldii str. ATCC 175058021 Proteobacteria Comamonadaceae sf_1 AF078765.1 Acidovorax facilis str. CCUG 21138022 Proteobacteria Comamonadaceae sf_1 AF078762.1 Acidovorax avenae subsp. cattleyae str. NCPPB 961 subsp.8031 Proteobacteria Comamonadaceae sf_1 AB021328.1 strain isolate str. rJ108046 Proteobacteria Comamonadaceae sf_1 Y18616.1 Acidovorax defluvii str. BSB4118067 Proteobacteria Comamonadaceae sf_1 AY218607.1 penguin droppings sediments clone KD3-1418079 Proteobacteria Comamonadaceae sf_1 AJ543439.1 nephridia Eisenia foetida clone8112 Proteobacteria Comamonadaceae sf_1 AF336312.1 Comamonas testosteroni str. SMCC B3298138 Proteobacteria Comamonadaceae sf_1 AB021390.1 Pseudomonas lanceolata str. ATCC 14669T8139 Proteobacteria Comamonadaceae sf_1 AY899912.1 Delftia tsuruhatensis str. AD98140 Proteobacteria Comamonadaceae sf_1 AY538706.1 Schlegelella sp. str. KB1a8152 Proteobacteria Comamonadaceae sf_1 AJ543434.1 nephridia Octolasion lacteum clone Ol2-27843 Proteobacteria Oxalobacteraceae sf_1 U54470.1 Massilia timonae timone7845 Proteobacteria Oxalobacteraceae sf_1 AB038368.1 Diaphorina citri symbiont7866 Proteobacteria Oxalobacteraceae sf_1 AB021375.1 Paucimonas lemoignei str. ATCC 17989T7878 Proteobacteria Oxalobacteraceae sf_1 AY250094.1 napthalene-contaminated sediment clone 297921 Proteobacteria Oxalobacteraceae sf_1 AY593479.1 Collimonas fungivorans str. Ter3317968 Proteobacteria Oxalobacteraceae sf_1 U49757.2 Oxalobacter formigenes str. OXB ovinen rumen8013 Proteobacteria Oxalobacteraceae sf_1 AF236013.1 isolate str. A10208032 Proteobacteria Oxalobacteraceae sf_1 AB074523.1 Aquaspirillum arcticum str. IAM 149638034 Proteobacteria Oxalobacteraceae sf_1 Y08845.1 Janthinobacterium agaricidamnosum str. W1r3T8058 Proteobacteria Oxalobacteraceae sf_1 Y10146.1 Herbaspirillum seropedicae str. DSM 6445 ATCC 358927761 Proteobacteria Ralstoniaceae sf_1 AF280433.1 Ralstonia detusculanense str. APF11




7778 Proteobacteria Ralstoniaceae sf_1 AJ539233.1 Ralstonia insidiosa str. CCUG 463887823 Proteobacteria Ralstoniaceae sf_1 AF312022.1 Wautersia basilensis str. DSM 118538110 Proteobacteria Ralstoniaceae sf_1 AF085226.1 Wautersia paucula str. LMG 34138128 Proteobacteria Ralstoniaceae sf_1 M32021.1 Cupriavidus necator8035 Proteobacteria Unclassified sf_18087 Proteobacteria Unclassified sf_17766 Proteobacteria Unclassified sf_18050 Proteobacteria Methylophilaceae sf_1 AJ318156.1 Waste-gas biofilter clone BIki28137 Proteobacteria Methylophilaceae sf_1 AF289159.1 freshwater clone PRD01a011B7750 Proteobacteria Unclassified sf_1 AJ518782.1 uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-357808 Proteobacteria Unclassified sf_1 AY221081.1 Mammoth cave clone CCU257818 Proteobacteria Unclassified sf_1 AJ534623.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-215

proteobacterium7993 Proteobacteria Unclassified sf_1 AF423222.1 soil clone 1326-28023 Proteobacteria Unclassified sf_1 AF293006.1 ferromanganous micronodule clone MND17675 Proteobacteria Neisseriaceae sf_1 AY157705.1 Neisseria sp. str. CCUG 469107945 Proteobacteria Neisseriaceae sf_1 AB074518.1 Aquaspirillum serpens str. IAM 139448092 Proteobacteria Neisseriaceae sf_1 AF487709.1 Neisseria dentiae str. V338143 Proteobacteria Neisseriaceae sf_1 AY005029.1 subgingival dental plaque clone AK1058037 Proteobacteria Unclassified sf_1 AY323827.2 Chitinimonas taiwanensis str. cf7682 Proteobacteria Nitrosomonadaceae sf_1 AF363291.1 Nitrosovibrio sp. str. RY6A7770 Proteobacteria Nitrosomonadaceae sf_1 BX321856.1 Nitrosomonas europaea str. ATCC 197187789 Proteobacteria Nitrosomonadaceae sf_17796 Proteobacteria Nitrosomonadaceae sf_1 AF080256.1 Nitrosospira sp. str. TYM97805 Proteobacteria Nitrosomonadaceae sf_1 AY123800.1 Nitrosospira briensis str. Nsp107858 Proteobacteria Nitrosomonadaceae sf_17865 Proteobacteria Nitrosomonadaceae sf_17931 Proteobacteria Nitrosomonadaceae sf_1 L35509.1 Nitrosospira multiformis8145 Proteobacteria Nitrosomonadaceae sf_1 AY123795.1 Nitrosomonas eutropha str. Nm578136 Proteobacteria Procabacteriaceae sf_1 AF177426.1 Acanthamoeba sp. UWC6 symbiont7762 Proteobacteria Rhodocyclaceae sf_1 AF150698.1 Elbe River snow isolate Iso18 Iso18_14117800 Proteobacteria Rhodocyclaceae sf_1 AY013692.1 sample taken upstream landfill clone BVC77 landfill7817 Proteobacteria Rhodocyclaceae sf_1 AY133064.1 TCE-contaminated site clone ccs2657824 Proteobacteria Rhodocyclaceae sf_1 AB089101.1 termite gut homogenate clone Rs-B77 proteobacterium7907 Proteobacteria Rhodocyclaceae sf_1 AJ315680.1 Thauera aromatica str. LG3567925 Proteobacteria Rhodocyclaceae sf_1 Y17591.1 Thauera selenatis str. ATCC 55363T7956 Proteobacteria Rhodocyclaceae sf_18156 Proteobacteria Rhodocyclaceae sf_1 AY098637.2 industrial-phenol-degrading community clone MM1 sp.7974 Proteobacteria Unclassified sf_37997 Proteobacteria Unclassified sf_38007 Proteobacteria Unclassified sf_38036 Proteobacteria Unclassified sf_3 AJ519624.1 Uranium mill tailings soil sample clone Sh765B-TzT-132 proteobacterium8045 Proteobacteria Unclassified sf_38114 Proteobacteria Unclassified sf_3




10084 Proteobacteria Unclassified sf_1 AF543496.1 acid mine drainage clone AS63084 Proteobacteria Unclassified sf_1 AF523884.1 coal effluent wetland clone RCP2166830 Proteobacteria Unclassified sf_1 AF523882.1 coal effluent wetland clone RCP1249678 Proteobacteria Unclassified sf_1 AF523883.1 coal effluent wetland clone RCP1859945 Proteobacteria Unclassified sf_1 AF225446.1 acid mine drainage clone BA18

10010 Proteobacteria Bdellovibrionaceae sf_1 AJ518802.1 uranium mining waste pile clone JG37-AG-139 proteobacterium7382 Proteobacteria Unclassified sf_1 AF355039.1 marine clone Arctic95C-59959 Proteobacteria Unclassified sf_1 AF523965.1 forested wetland clone FW110

10227 Proteobacteria Desulfoarculaceae sf_2 AY193132.1 marine sediment clone Bol1110031 Proteobacteria Desulfobacteraceae sf_5 AY177795.1 Antarctic sediment clone SB1_4910046 Proteobacteria Desulfobacteraceae sf_5 AJ237603.1 Desulfobacterium cetonicum str. DSM 7267 oil recovery water10136 Proteobacteria Desulfobacteraceae sf_5 AY197382.1 Guaymas Basin hydrothermal vent sediments clone B01R01110267 Proteobacteria Desulfobacteraceae sf_5 AJ535249.1 marine sediment above hydrate ridge clone Hyd89-61 proteobacterium10268 Proteobacteria Desulfobacteraceae sf_510319 Proteobacteria Desulfobacteraceae sf_5 AY083017.1 sulfate-reducing habitat clone SLM-CP-1169666 Proteobacteria Desulfobacteraceae sf_5 AJ535229.1 marine sediment above hydrate ridge clone Hyd89-13 proteobacterium9777 Proteobacteria Desulfobacteraceae sf_5 AY197376.1 Guaymas Basin hydrothermal vent sediments clone B01R0049800 Proteobacteria Desulfobacteraceae sf_5 AF523960.1 forested wetland clone FW579818 Proteobacteria Desulfobacteraceae sf_5 AY216453.1 temperate estuarine mud clone KM629875 Proteobacteria Desulfobacteraceae sf_5 AF420354.1 hydrothermal sediment clone AF4203549939 Proteobacteria Desulfobacteraceae sf_5 AF354163.1 marine methane seep clone 14279940 Proteobacteria Desulfobacteraceae sf_5 AY177800.1 Antarctic sediment clone SB2_56

10047 Proteobacteria Desulfobulbaceae sf_1 AY355301.2 epibiontic clone C11-D310062 Proteobacteria Desulfobulbaceae sf_1 AJ535241.1 marine sediment above hydrate ridge clone Hyd24-11 proteobacterium10107 Proteobacteria Desulfobulbaceae sf_1 AJ535243.1 marine sediment above hydrate ridge clone Hyd24-30 proteobacterium10172 Proteobacteria Desulfobulbaceae sf_1 AY005036.1 subgingival dental plaque clone CH03110187 Proteobacteria Desulfobulbaceae sf_1 AF507840.1 Mono Lake at depth 23 m station 6 July 2000 clone ML623J-57 proteobacterium10332 Proteobacteria Desulfobulbaceae sf_1 AF099059.1 Psychrophilic sulfate-reducing isolate str. LSv23 bacterium9705 Proteobacteria Desulfobulbaceae sf_1 AJ535237.1 marine sediment above hydrate ridge clone Hyd01-n proteobacterium9734 Proteobacteria Desulfobulbaceae sf_1 AF449229.1 Riftia pachyptila's tube clone R103-B139739 Proteobacteria Desulfobulbaceae sf_1 AJ535252.1 gas hydrate clone Hyd89-51

594 Proteobacteria Nitrospinaceae sf_2 AJ296568.1 uranium mining mill tailing clone GR-296.II.52 GR-296.I.52468 Proteobacteria Unclassified sf_3 AJ241004.1 marine sediment clone Sva0515

9813 Proteobacteria Unclassified sf_3 AF420340.1 hydrothermal sediment clone AF4203409951 Proteobacteria Unclassified sf_4 AF523973.1 forested wetland clone FW13

10069 Proteobacteria Desulfohalobiaceae sf_19894 Proteobacteria Desulfohalobiaceae sf_1 AF524933.1 Desulfonauticus submarinus str. 6N

10079 Proteobacteria Desulfomicrobiaceae sf_1 AJ277896.1 Desulfomicrobium baculatum str. DSM 174210225 Proteobacteria Desulfomicrobiaceae sf_1 AJ251624.1 Desulfomicrobium orale str. NY67910016 Proteobacteria Desulfovibrionaceae sf_1 AB089110.1 termite gut homogenate clone Rs-N35 proteobacterium10071 Proteobacteria Desulfovibrionaceae sf_1 M34113.1 Desulfovibrio desulfuricans10075 Proteobacteria Desulfovibrionaceae sf_1 AF056090.1 Desulfovibrio sp. str. ABHU2SB10189 Proteobacteria Desulfovibrionaceae sf_110212 Proteobacteria Desulfovibrionaceae sf_1




10244 Proteobacteria Desulfovibrionaceae sf_110248 Proteobacteria Desulfovibrionaceae sf_1 AF418170.1 Desulfovibrio giganteus str. DSM 437010262 Proteobacteria Desulfovibrionaceae sf_1 AF228127.2 Desulfovibrio sp. str. Ac5.210263 Proteobacteria Desulfovibrionaceae sf_1 AJ544687.2 Desulfovibrio brasiliensis str. LVform110361 Proteobacteria Desulfovibrionaceae sf_1 U42221.1 Desulfovibrio fairfieldensis9709 Proteobacteria Desulfovibrionaceae sf_1 AB089104.1 termite gut homogenate clone Rs-N31 proteobacterium9711 Proteobacteria Desulfovibrionaceae sf_1 AF418172.1 Desulfovibrio profundus str. DSM 113849826 Proteobacteria Desulfovibrionaceae sf_1 AB089108.2 termite gut homogenate clone Rs-M72 proteobacterium9828 Proteobacteria Unclassified sf_1 AB089109.1 termite gut homogenate clone Rs-M89 proteobacterium

10020 Proteobacteria Desulfuromonaceae sf_1 AJ519664.1 uranium mill tailings soil sample clone GuBH2-AG-114 proteobacterium10171 Proteobacteria Geobacteraceae sf_1

482 Proteobacteria Geobacteraceae sf_1 AF529120.1 trichloroethene-contaminated site clone FTLM205 proteobacterium9956 Proteobacteria Geobacteraceae sf_1 AF523968.1 forested wetland clone FW140

10076 Proteobacteria Unclassified sf_1 AF407700.1 Great Artesian Basin clone G1310024 Proteobacteria Unclassified sf_4 AF420338.1 hydrothermal sediment clone AF4203388169 Proteobacteria Unclassified sf_4 AF523886.1 forested wetland clone RCP2-549741 Proteobacteria Unclassified sf_4 AJ518791.1 uranium mining waste pile clone JG37-AG-30 proteobacterium9884 Proteobacteria Unclassified sf_4 AF523885.1 forested wetland clone RCP2-62

10358 Proteobacteria Myxococcaceae sf_1 AJ233917.1 Myxococcus fulvus str. Mx f210082 Proteobacteria Polyangiaceae sf_3 AJ518792.1 uranium mining waste pile clone JG37-AG-33 proteobacterium10249 Proteobacteria Polyangiaceae sf_3 AJ534629.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-168

proteobacterium10298 Proteobacteria Polyangiaceae sf_3 AY193162.1 marine tidal mat clone BTM3610309 Proteobacteria Polyangiaceae sf_3 AJ233947.1 Nannocystis exedens str. Na e57110353 Proteobacteria Polyangiaceae sf_3 AF234747.1 sludge clone A99671 Proteobacteria Polyangiaceae sf_3 AF420357.1 hydrothermal sediment clone AF4203579735 Proteobacteria Polyangiaceae sf_3 AJ518790.1 uranium mining waste pile clone JG37-AG-15 proteobacterium9755 Proteobacteria Polyangiaceae sf_3 AF382126.1 bacterioplankton clone ZA3704c9874 Proteobacteria Polyangiaceae sf_3 AJ532714.1 uranium mining waste pile clone JG34-KF-243 proteobacterium9900 Proteobacteria Polyangiaceae sf_3 AF280857.1 bioreactor clone mle1-279912 Proteobacteria Polyangiaceae sf_3 AJ532713.1 uranium mining waste pile clone JG34-KF-14 proteobacterium9733 Proteobacteria Polyangiaceae sf_4 AF382143.1 bacterioplankton clone ZA3735c

10092 Proteobacteria Unclassified sf_1 AY102330.1 heavy metal-contaminated soil clone a1313410259 Proteobacteria Unclassified sf_110067 Proteobacteria Syntrophaceae sf_3 AF323766.1 benzoate-degrading consortium clone BA0449665 Proteobacteria Syntrophaceae sf_3 X85132.1 Syntrophus gentianae str. HQgoe1

10013 Proteobacteria Syntrophobacteraceae sf_1 AF420341.2 hydrothermal sediment clone AF42034110021 Proteobacteria Syntrophobacteraceae sf_1 AJ519630.1 uranium mill tailings soil sample clone Sh765B-TzT-29 proteobacterium10184 Proteobacteria Syntrophobacteraceae sf_1 AF482435.1 granular sludge clone R1p3210221 Proteobacteria Syntrophobacteraceae sf_1 AF482439.1 granular sludge clone R3p410294 Proteobacteria Syntrophobacteraceae sf_1 AF170417.1 Desulfacinum hydrothermale str. MT-969661 Proteobacteria Syntrophobacteraceae sf_1 AJ306805.1 DCP-dechlorinating consortium clone SHD-19731 Proteobacteria Syntrophobacteraceae sf_1 AJ518795.1 uranium mining waste pile clone JG37-AG-90 proteobacterium9845 Proteobacteria Syntrophobacteraceae sf_1 AJ518800.1 uranium mining waste pile clone JG37-AG-128 proteobacterium




9864 Proteobacteria Syntrophobacteraceae sf_1 AJ518801.1 uranium mining waste pile clone JG37-AG-133 proteobacterium10048 Proteobacteria Unclassified sf_710049 Proteobacteria Unclassified sf_9 AJ306774.1 DCP-dechlorinating consortium clone SHA-72

244 Proteobacteria Unclassified sf_9 AY093483.1 deep marine sediment clone MB-C2-1529760 Proteobacteria Unclassified sf_9 AY093467.1 deep marine sediment clone MB-A2-1379784 Proteobacteria Unclassified sf_9 AY177804.1 Antarctic sediment clone LH5_309798 Proteobacteria Unclassified sf_9 AJ519663.1 uranium mill tailings soil sample clone GuBH2-AD/TzT-67 proteobacterium9876 Proteobacteria Unclassified sf_9 AY093471.1 deep marine sediment clone MB-B2-1069890 Proteobacteria Unclassified sf_9 AB089106.1 termite gut homogenate clone Rs-K70 proteobacterium

10397 Proteobacteria Campylobacteraceae sf_3 AB030592.1 groundwater clone 100610434 Proteobacteria Campylobacteraceae sf_3 L37787.1 Campylobacter gracilis10446 Proteobacteria Campylobacteraceae sf_310447 Proteobacteria Campylobacteraceae sf_3 Y13671.1 Sulfurospirillum deleyianum str. Spirillum 517510456 Proteobacteria Campylobacteraceae sf_3 L06975.1 Campylobacter showae10463 Proteobacteria Campylobacteraceae sf_3 AF482990.1 Campylobacter subsp. fetus10464 Proteobacteria Campylobacteraceae sf_3 AY135395.1 Campylobacter sp. str. NO2B10474 Proteobacteria Campylobacteraceae sf_3 AB013833.1 NB1-l clone NB1-l10484 Proteobacteria Campylobacteraceae sf_3 U03022.1 Campylobacter helveticus10508 Proteobacteria Campylobacteraceae sf_3 AY005038.1 subgingival dental plaque clone BB12010532 Proteobacteria Campylobacteraceae sf_3 AF219235.1 Campylobacter hyointestinalis MGH 97-265210538 Proteobacteria Campylobacteraceae sf_3 L14624.1 Arcobacter cryaerophilus10540 Proteobacteria Campylobacteraceae sf_3 AF550655.1 Campylobacter showae str. LMG 1263610549 Proteobacteria Campylobacteraceae sf_3 AF497805.1 Campylobacter upsaliensis str. LMG 885010563 Proteobacteria Campylobacteraceae sf_3 AF144694.2 Campylobacter sp. str. DSM 80610443 Proteobacteria Helicobacteraceae sf_23 U00679.1 Helicobacter pylori str. 85D0810385 Proteobacteria Helicobacteraceae sf_310411 Proteobacteria Helicobacteraceae sf_3 AB089112.2 termite gut homogenate clone Rs-P71 proteobacterium10417 Proteobacteria Helicobacteraceae sf_3 AY216452.1 temperate estuarine mud clone KM6110425 Proteobacteria Helicobacteraceae sf_3 AB088432.1 Sulfurimonas autotrophica str. OK510428 Proteobacteria Helicobacteraceae sf_3 AF034135.1 Flexispira rappini FH 970224810430 Proteobacteria Helicobacteraceae sf_3 AF506783.1 Helicobacter heilmannii str. MM210432 Proteobacteria Helicobacteraceae sf_3 AF449246.1 Riftia pachyptila's tube clone R76-B5110436 Proteobacteria Helicobacteraceae sf_3 AF297868.1 Helicobacter aurati str. MIT 97-5075c10438 Proteobacteria Helicobacteraceae sf_3 AF154101.1 hydrocarbon seep clone GCA01410442 Proteobacteria Helicobacteraceae sf_3 AF292378.1 Helicobacter cetorum str. MIT 99-565610444 Proteobacteria Helicobacteraceae sf_3 AB006148.1 Helicobacter suncus str. Kaz-210448 Proteobacteria Helicobacteraceae sf_3 U51870.1 Helicobacter felis str. Dog-110451 Proteobacteria Helicobacteraceae sf_3 AF506779.1 Helicobacter heilmannii str. C4S10454 Proteobacteria Helicobacteraceae sf_3 L36143.1 Helicobacter pullorum str. NCTC 1282610462 Proteobacteria Helicobacteraceae sf_3 U96297.1 Helicobacter rodentium str. MIT 96-131210467 Proteobacteria Helicobacteraceae sf_310507 Proteobacteria Helicobacteraceae sf_3 AB089111.2 termite gut homogenate clone Rs-M59 proteobacterium10518 Proteobacteria Helicobacteraceae sf_3 X67854.1 Helicobacter pylori str. ATCC 49396T10520 Proteobacteria Helicobacteraceae sf_3 AJ249858.1 Helicobacter sp. blood isolate 964




10534 Proteobacteria Helicobacteraceae sf_3 U01329.1 Helicobacter pylori10548 Proteobacteria Helicobacteraceae sf_3 AF286052.1 Helicobacter rappini W.Tee-Bat10552 Proteobacteria Helicobacteraceae sf_3 AF363062.1 Helicobacter winghamensis str. NLEP 97-161110562 Proteobacteria Helicobacteraceae sf_3 AF286053.1 Helicobacter rappini W.Tee-Yu10572 Proteobacteria Helicobacteraceae sf_3 AF057163.1 Helicobacter sp10576 Proteobacteria Helicobacteraceae sf_3 AF142585.1 Helicobacter sp. 'liver 3' str. liver 310590 Proteobacteria Helicobacteraceae sf_3 AB089113.1 termite gut homogenate clone Rs-H40 proteobacterium10602 Proteobacteria Helicobacteraceae sf_310407 Proteobacteria Unclassified sf_1 AF420342.1 hydrothermal sediment clone AF42034210414 Proteobacteria Unclassified sf_1 AY218582.1 penguin droppings sediments clone KD2-3410427 Proteobacteria Unclassified sf_1 AY672515.1 hydrothermal vent 9 degrees North East Rise Pacific Ocean clone 10475 Proteobacteria Unclassified sf_1 AF420359.1 hydrothermal sediment clone AF42035910480 Proteobacteria Unclassified sf_1 AJ441204.1 hydrothermal vent polychaete mucous clone P. palm C 8410489 Proteobacteria Unclassified sf_1 AF299121.1 S17sBac16 complete clone10497 Proteobacteria Unclassified sf_1 AY261811.1 UASB reactor granular sludge clone PD-UASB-2 proteobacterium10530 Proteobacteria Unclassified sf_1 AY672531.1 hydrothermal vent 9 degrees North East Rise Pacific Ocean clone

CH5_6_BAC_16SrRNA_9N_EPR10543 Proteobacteria Unclassified sf_1 U15103.1 hydrothermal vent clone PVB_108340 Proteobacteria Aeromonadaceae sf_1 X71120.1 Aeromonas ichthiosmia8364 Proteobacteria Aeromonadaceae sf_1 S39232.1 Aeromonas allosaccharophila str. CECT 41998621 Proteobacteria Aeromonadaceae sf_1 AF427150.1 Aeromonas sp. PAR2A9000 Proteobacteria Aeromonadaceae sf_1 AF170914.4 Aeromonas culicicola str. MTCC 32499026 Proteobacteria Aeromonadaceae sf_1 AJ009860.1 Haemophilus piscium str. NCIMB 19529245 Proteobacteria Aeromonadaceae sf_1 AB105442.1 Batch reactor filled with cyanobacterial bloom and lake water clone -89294 Proteobacteria Aeromonadaceae sf_1 AJ557849.1 Arctic deep sea Isolation common chemoorganotrophic oxygen-respiring polar current d

1210 (50 m above sediment Hakon Mosby Mud Vulcano (HMMV 72N 14E)) via serial dilution series applying 2 g/l yeast or meat extract artifical seawater

9440 Proteobacteria Aeromonadaceae sf_1 X60412.1 Aeromonas sobria str. NCIMB 120659494 Proteobacteria Aeromonadaceae sf_1 AY532691.1 Aeromonas molluscorum str. 849T8822 Proteobacteria Succinivibrionaceae sf_1 AF497809.1 Anaerobiospirillum sp. str. 3J1028172 Proteobacteria Alteromonadaceae sf_1 AB055791.1 Pseudoalteromonas sp. str. Bdeep-18174 Proteobacteria Alteromonadaceae sf_1 AF114499.1 attached marine recovered surface clone 17 proteobacterium8196 Proteobacteria Alteromonadaceae sf_18211 Proteobacteria Alteromonadaceae sf_1 AB002630.1 Colwellia maris str. ABE-18222 Proteobacteria Alteromonadaceae sf_18318 Proteobacteria Alteromonadaceae sf_1 AY207502.1 Aestuariibacter salexigens str. JC20428336 Proteobacteria Alteromonadaceae sf_1 AF237977.1 Alteromonas sp. str. MS238348 Proteobacteria Alteromonadaceae sf_1 AF468388.1 Arctic sea ice ARK100388368 Proteobacteria Alteromonadaceae sf_1 AJ507251.1 Pseudoalteromonas mariniglutinosa str. KMM 36358374 Proteobacteria Alteromonadaceae sf_1 AB076560.1 Agarivorans albus str. MKT 898484 Proteobacteria Alteromonadaceae sf_1 AF513454.1 Alteromonadaceae isolate str. LA508503 Proteobacteria Alteromonadaceae sf_1 AF468401.1 Arctic sea ice ARK102448533 Proteobacteria Alteromonadaceae sf_18578 Proteobacteria Alteromonadaceae sf_1 AY147906.1 Marinobacter lipolyticus str. SM-19




8579 Proteobacteria Alteromonadaceae sf_1 AJ416756.1 Psychromonas profunda str. 28258580 Proteobacteria Alteromonadaceae sf_1 AJ295713.1 Arctic seawater isolate str. R70768643 Proteobacteria Alteromonadaceae sf_1 AY771715.1 Pseudoalteromonas porphyrae str. S2-658695 Proteobacteria Alteromonadaceae sf_1 AF468296.1 Arctic pack ice; northern Fram Strait; 80 31.1 N; 01 deg 59.7 min E clone ARKIA-348753 Proteobacteria Alteromonadaceae sf_1 AY553079.1 Idiomarina loihiensis str. GSP378863 Proteobacteria Alteromonadaceae sf_1 AF529060.1 Alteromonas marina str. SW-478916 Proteobacteria Alteromonadaceae sf_1 U91545.1 Shewanella algae str. 439408932 Proteobacteria Alteromonadaceae sf_1 AF045560.1 Pseudoalteromonas antarctica str. N-18970 Proteobacteria Alteromonadaceae sf_1 AJ295716.1 Arctic seawater isolate str. R98798975 Proteobacteria Alteromonadaceae sf_1 AB016268.1 Alteromonas sp. str. NIBH P1M38978 Proteobacteria Alteromonadaceae sf_1 AF468393.1 Arctic sea ice ARK101089035 Proteobacteria Alteromonadaceae sf_1 AB124836.1 Microbulbifer sp. str. JAMB-A949058 Proteobacteria Alteromonadaceae sf_1 X82136.1 Pseudoalteromonas carrageenovora str. ATCC 12662T9067 Proteobacteria Alteromonadaceae sf_1 AF006669.1 Shewanella algae str. ACM 47339111 Proteobacteria Alteromonadaceae sf_1 AF539773.1 Pseudoalteromonas sp. str. E369143 Proteobacteria Alteromonadaceae sf_1 AJ417594.1 Pseudoalteromonas agarivorans str. KMM 2559205 Proteobacteria Alteromonadaceae sf_1 AF354597.1 marine clone Arctic96B-179218 Proteobacteria Alteromonadaceae sf_1 X67024.1 Pseudoalteromonas haloplanktis str. ATCC 143939222 Proteobacteria Alteromonadaceae sf_1 X82132.1 Shewanella hanedai str. CIP 103207T9230 Proteobacteria Alteromonadaceae sf_1 AY165576.1 Antarctic pack ice Lasarev Sea Southern Ocean clone ANTXI/4_14-62 sea9236 Proteobacteria Alteromonadaceae sf_1 AF114501.1 attached marine recovered surface clone 18 proteobacterium9239 Proteobacteria Alteromonadaceae sf_1 AF468400.1 Arctic sea ice ARK102289288 Proteobacteria Alteromonadaceae sf_1 AJ295715.1 Alteromonas stellipolaris str. LMG 218619292 Proteobacteria Alteromonadaceae sf_19324 Proteobacteria Alteromonadaceae sf_1 AF316891.1 Pseudoalteromonas ruthenica str. KMM3009364 Proteobacteria Alteromonadaceae sf_1 U85855.1 Pseudoalteromonas prydzensis str. MB8-119369 Proteobacteria Alteromonadaceae sf_1 X82144.1 Pseudoalteromonas luteoviolacea str. NCIMB 1893T9384 Proteobacteria Alteromonadaceae sf_1 AJ132226.1 Moritella viscosa str. NVI 88/478T9386 Proteobacteria Alteromonadaceae sf_1 AB016267.1 Alteromonas sp. str. NIBH P2M119411 Proteobacteria Alteromonadaceae sf_1 AY170366.1 Shewanella waksmanii str. KMM 38239416 Proteobacteria Alteromonadaceae sf_1 AF539786.1 marine isolate str. R89486 Proteobacteria Alteromonadaceae sf_1 AF406617.1 Marine isolate str. GK-20019501 Proteobacteria Alteromonadaceae sf_1 AB086226.1 sea water isolate str. BP-PH9562 Proteobacteria Alteromonadaceae sf_1 AF513941.2 Alteromonadaceae clone PH-B55N9640 Proteobacteria Alteromonadaceae sf_1 AY028205.1 exposed to diatom detritus isolate str. Tw-10 Tw-109627 Proteobacteria Pseudoalteromonadaceae sf_1 AF218245.1 Pseudoalteromonas sp8201 Proteobacteria Shewanellaceae sf_1 AB094597.1 Shewanella surugaensis str. c9598581 Proteobacteria Shewanellaceae sf_1 AB008796.1 Shewanella benthica str. DB21MT-28641 Proteobacteria Shewanellaceae sf_1 AJ252022.1 Moritella abyssi str. 26938662 Proteobacteria Shewanellaceae sf_19081 Proteobacteria Shewanellaceae sf_1 AB059264.1 Shewanella sp. str. MTW-18483 Proteobacteria Unclassified sf_1 AJ002006.1 Rheinheimera baltica str. OS140 Baltic # 1668839 Proteobacteria Unclassified sf_1 AJ400349.1 f cytometric sorted marine sample subpopulation 3 clone ZD0408 bacterium8957 Proteobacteria Unclassified sf_1 AF354614.1 marine clone Arctic97C-5




9246 Proteobacteria Unclassified sf_1 AY221036.1 Mammoth Cave sediment clone CCD248536 Proteobacteria Cardiobacteriaceae sf_1 M35014.1 Cardiobacterium hominis9453 Proteobacteria Cardiobacteriaceae sf_1 AF506987.1 Cardiobacterium valvarum str. MDA30798408 Proteobacteria Chromatiaceae sf_1 Y12368.2 Thiorhodovibrio winogradskyi8546 Proteobacteria Chromatiaceae sf_1 AJ242772.1 Thiocapsa litoralis8697 Proteobacteria Chromatiaceae sf_1 AJ401211.1 Thiococcus sp. AT22049370 Proteobacteria Chromatiaceae sf_1 AB010860.1 isolate str. HTB0199598 Proteobacteria Ectothiorhodospiraceae sf_1 AF507818.1 Mono Lake at depth 2 m station 6 July 2000 clone ML602J-47 proteobacterium9282 Proteobacteria Unclassified sf_18532 Proteobacteria Unclassified sf_19458 Proteobacteria Unclassified sf_1 AJ518786.1 uranium mining waste pile clone JG37-AG-94 proteobacterium1206 Proteobacteria Enterobacteriaceae sf_1 AY265343.1 Dermacentor variabilis symbiont8173 Proteobacteria Enterobacteriaceae sf_1 Z76752.1 Photorhabdus asymbiotica str. ATCC 439498182 Proteobacteria Enterobacteriaceae sf_1 X07652.1 Proteus vulgaris str. IFAM 17318225 Proteobacteria Enterobacteriaceae sf_18236 Proteobacteria Enterobacteriaceae sf_1 AF476110.1 Vryburgia amaryllidis symbiont8251 Proteobacteria Enterobacteriaceae sf_1 AF214640.1 Nitrogen-fixing isolate str. CANF38282 Proteobacteria Enterobacteriaceae sf_1 AF476101.1 Antonina pretiosa symbiont8283 Proteobacteria Enterobacteriaceae sf_1 AF263562.1 Heteropsylla texana symbiont8286 Proteobacteria Enterobacteriaceae sf_1 AF476102.1 Cyphonococcus alpinus symbiont8362 Proteobacteria Enterobacteriaceae sf_1 AF453251.1 Klebsiella pneumoniae str. ASR18379 Proteobacteria Enterobacteriaceae sf_1 AF289542.1 Erwinia amylovora EA G-58467 Proteobacteria Enterobacteriaceae sf_1 AB061685.1 Serratia marcescens subsp. sakuensis str. KRED subsp.8473 Proteobacteria Enterobacteriaceae sf_1 M59155.1 Hafnia alvei8504 Proteobacteria Enterobacteriaceae sf_1 AF476104.1 Dysmicoccus neobrevipes symbiont8505 Proteobacteria Enterobacteriaceae sf_1 AJ233406.1 Buttiauxella warmboldiae str. DSM 94048510 Proteobacteria Enterobacteriaceae sf_1 AJ233420.1 Klebsiella pneumoniae str. DSM 301048528 Proteobacteria Enterobacteriaceae sf_1 Y17665.1 Enterobacter cloacae Nr. 38529 Proteobacteria Enterobacteriaceae sf_1 AF181574.1 Raoultella planticola 78530 Proteobacteria Enterobacteriaceae sf_1 AJ489826.1 Enterobacteriaceae CF01Ent-18554 Proteobacteria Enterobacteriaceae sf_1 AJ627202.1 Kluyvera ascorbata 698564 Proteobacteria Enterobacteriaceae sf_1 X79939.1 Rahnella aquatilis str. ATCC 339898603 Proteobacteria Enterobacteriaceae sf_1 AF476106.1 Melanococcus albizziae symbiont8607 Proteobacteria Enterobacteriaceae sf_1 AF476100.1 Amonostherium lichtensioides symbiont8627 Proteobacteria Enterobacteriaceae sf_1 AF476099.1 Australicoccus grevilleae symbiont8640 Proteobacteria Enterobacteriaceae sf_18642 Proteobacteria Enterobacteriaceae sf_1 AF373202.1 Erwinia chrysanthemi str. 5808693 Proteobacteria Enterobacteriaceae sf_1 AF130912.1 Pantoea agglomerans str. A408700 Proteobacteria Enterobacteriaceae sf_1 AF489427.1 Baumannia cicadellinicola8739 Proteobacteria Enterobacteriaceae sf_1 AJ233427.1 Serratia entomophila str. DSM 123588742 Proteobacteria Enterobacteriaceae sf_1 AF084835.1 USA:New York isolate str. KN48770 Proteobacteria Enterobacteriaceae sf_18773 Proteobacteria Enterobacteriaceae sf_18775 Proteobacteria Enterobacteriaceae sf_1




8864 Proteobacteria Enterobacteriaceae sf_18885 Proteobacteria Enterobacteriaceae sf_1 AB089246.1 Morganella morganii str. AP288886 Proteobacteria Enterobacteriaceae sf_1 AF170176.1 Salmonella typhimurium LT2 str. SGSC14128890 Proteobacteria Enterobacteriaceae sf_1 X93216.1 Raoultella planticola str. DR38892 Proteobacteria Enterobacteriaceae sf_1 U93263.1 Aranicola proteolyticus8934 Proteobacteria Enterobacteriaceae sf_1 AF373188.1 Pectobacterium subsp. carotovorum str. E155 subsp.8936 Proteobacteria Enterobacteriaceae sf_1 AF543283.1 Klebsiella oxytoca str. ChDC OS319060 Proteobacteria Enterobacteriaceae sf_1 AJ853891.1 Enterobacter ludwigii str. EN-119 = DSMZ 166889142 Proteobacteria Enterobacteriaceae sf_1 AJ233410.1 Erwinia amylovora str. DSM 301659157 Proteobacteria Enterobacteriaceae sf_1 AF293618.1 Secondary symbiont type-U Acyrthosiphon pisum (rrs) clone 5B type-U9274 Proteobacteria Enterobacteriaceae sf_1 AJ550468.1 Enterobacter sp. CC19290 Proteobacteria Enterobacteriaceae sf_1 AF465797.1 Baumannia cicadellinicola9293 Proteobacteria Enterobacteriaceae sf_1 AJ245598.1 USA clone 14/79302 Proteobacteria Enterobacteriaceae sf_1 AF373198.1 Pantoea subsp. stewartii str. GSPB 26269309 Proteobacteria Enterobacteriaceae sf_1 AJ417833.1 Buchnera sp9337 Proteobacteria Enterobacteriaceae sf_1 U90758.1 Rahnella genosp. 3 str. DSM 300789345 Proteobacteria Enterobacteriaceae sf_1 AF141891.1 Erwinia amylovora str. BC199(=Ea528)9358 Proteobacteria Enterobacteriaceae sf_1 U92194.1 Salmonella subsp. enterica serovar Waycross str. Swy1 subsp.9361 Proteobacteria Enterobacteriaceae sf_1 AB004747.1 Enterobacter intermedius str. JCM12389363 Proteobacteria Enterobacteriaceae sf_1 AF025365.1 Citrobacter freundii str. CDC 621-649385 Proteobacteria Enterobacteriaceae sf_1 AY264673.1 Australiococcus greville symbiont9390 Proteobacteria Enterobacteriaceae sf_1 Z96077.1 Enterobacter nimipressuralis str. LMG 10245-T9420 Proteobacteria Enterobacteriaceae sf_19496 Proteobacteria Enterobacteriaceae sf_1

433 Proteobacteria Enterobacteriaceae sf_6 AF523903.1 coal effluent wetland clone RCP2-6646 Proteobacteria Enterobacteriaceae sf_6 AY695840.1 Opitutus sp. str. SA-9

8430 Proteobacteria Unclassified sf_1 AF029226.1 Salmonella bongori str. JEO 41628980 Proteobacteria Unclassified sf_1 AY098909.1 activated sludge clone SBRL2_199008 Proteobacteria Unclassified sf_1 AF361092.1 activated sludge clone SBRQ1579059 Proteobacteria Unclassified sf_1 AF361096.1 activated sludge clone SBRH107893 Proteobacteria Coxiellaceae sf_3 AJ252651.1 agricultural soil clone SC-I-718457 Proteobacteria Coxiellaceae sf_3 AJ240918.1 5' clone CHAB-XI-278969 Proteobacteria Coxiellaceae sf_3 AJ536861.1 uranium mining waste pile soil sample clone JG30-KF-C15 proteobacterium9198 Proteobacteria Coxiellaceae sf_3 AJ295651.1 uranium mining waste pile clone KF-JG30-B15 KF-JG30-B159444 Proteobacteria Coxiellaceae sf_3 AF523974.1 forested wetland clone FW238865 Proteobacteria Legionellaceae sf_1 AF468229.1 Arctic pack ice; northern Fram Strait; 80 31.1 N; 01 deg 59.7 min E clone ARKCH2Br2-239617 Proteobacteria Legionellaceae sf_1 X73406.1 Legionella feeleii subsp. sgp 2 str. ATCC 358499418 Proteobacteria Unclassified sf_1 AJ518784.1 uranium mining waste pile clone JG37-AG-14 proteobacterium8587 Proteobacteria Unclassified sf_3 AF526927.2 Mars Odyssey Orbiter and encapsulation facility clone T5-38243 Proteobacteria Methylococcaceae sf_1 AF521582.1 isolate str. IR8645 Proteobacteria Methylococcaceae sf_1 AF307138.1 Methylomicrobium buryatense str. 5B8821 Proteobacteria Methylococcaceae sf_1 AF152597.1 Methylobacter psychrophilus str. Z-00219438 Proteobacteria Methylococcaceae sf_1 AJ535221.1 marine sediment above hydrate ridge clone Hyd24-01 proteobacterium8335 Proteobacteria Alcanivoraceae sf_1 AB055205.1 Alcanivorax sp. str. K3-3 (MBIC 4323)




9658 Proteobacteria Alcanivoraceae sf_1 AB053127.1 Alcanivorax sp. str. Haw18514 Proteobacteria Halomonadaceae sf_1 AJ295144.1 Chromohalobacter israelensis str. ATCC 43985 T8596 Proteobacteria Oceanospirillaceae sf_1 AF353238.1 marine clone Arctic95B-79351 Proteobacteria Oceanospirillaceae sf_1 AF382102.1 bacterioplankton clone ZA2333c8889 Proteobacteria Saccharospirillaceae sf_1 AF452603.1 hypersaline Mono Lake clone ML110J-58327 Proteobacteria Unclassified sf_3 AF468398.1 Arctic sea ice ARK101488961 Proteobacteria Unclassified sf_3 M99446.1 Calyptogena magnifica symbiont8195 Proteobacteria Pasteurellaceae sf_1 NZ_AADP010 Haemophilus influenzae str. R28668228 Proteobacteria Pasteurellaceae sf_1 AF268964.1 Actinobacillus indolicus str. H14198409 Proteobacteria Pasteurellaceae sf_1 AF499896.1 human colonic mucosal biopsy clone ABLCf18432 Proteobacteria Pasteurellaceae sf_18555 Proteobacteria Pasteurellaceae sf_1 AY613451.1 Haemophilus influenzae str. M97418614 Proteobacteria Pasteurellaceae sf_1 AF359941.1 Acidithiobacillus thiooxidans str. KCTC 8928P8848 Proteobacteria Pasteurellaceae sf_1 AF227858.1 str. 863558861 Proteobacteria Pasteurellaceae sf_1 AB004031.1 Haemophilus parasuis 4278876 Proteobacteria Pasteurellaceae sf_1 AF053894.1 Mannheimia sp. R19.2 str. R19.2; CCUG 38463 R19.28952 Proteobacteria Pasteurellaceae sf_1 M75068.1 Actinobacillus lignieresii9213 Proteobacteria Pasteurellaceae sf_1 AF224307.1 Haemophilus quentini str. MCCM 020269237 Proteobacteria Pasteurellaceae sf_19263 Proteobacteria Pasteurellaceae sf_1 M75067.1 Actinobacillus capsulatus9349 Proteobacteria Pasteurellaceae sf_1 AF227861.1 Pasteurella sp. str. 919859360 Proteobacteria Pasteurellaceae sf_1 AF224297.1 Pasteurella multocida subsp. gallicida str. MCCM 00021 subsp.9477 Proteobacteria Pasteurellaceae sf_1 AY613549.1 Haemophilus influenzae str. M111059533 Proteobacteria Pasteurellaceae sf_1 AF224299.1 Haemophilus segnis str. MCCM 003379628 Proteobacteria Pasteurellaceae sf_1 AF549390.1 Histophilus somni str. CCUG 128398366 Proteobacteria Moraxellaceae sf_3 AJ609556.1 Psychrobacter frigidicola str. DSM 124118604 Proteobacteria Moraxellaceae sf_3 AB087260.2 Moraxella oblonga str. IAM 149718727 Proteobacteria Moraxellaceae sf_3 AY251390.1 Alkanindiges hongkongensis str. HKU98838 Proteobacteria Moraxellaceae sf_3 AJ748267.1 Psychrobacter psychrophilus CMS 289359 Proteobacteria Moraxellaceae sf_3 AB101444.1 Acinetobacter junii str. S339428 Proteobacteria Moraxellaceae sf_3 AF143841.1 hydrocarbon-degrading consortium clone AF2-1D9466 Proteobacteria Moraxellaceae sf_3 AF509830.1 Acinetobacter tandoii str. 4N139641 Proteobacteria Moraxellaceae sf_3 X81662.1 Acinetobacter haemolyticus8209 Proteobacteria Pseudomonadaceae sf_1 AJ518787.1 uranium mining waste pile clone JG37-AG-122 proteobacterium8288 Proteobacteria Pseudomonadaceae sf_18338 Proteobacteria Pseudomonadaceae sf_1 AF267911.1 Pseudomonas synxantha str. DSM 13080 G8344 Proteobacteria Pseudomonadaceae sf_1 AF425998.1 Anabaena circinalis AWQC118C isolate str. UNSW38433 Proteobacteria Pseudomonadaceae sf_1 AB001441.1 Pseudomonas syringae pv. broussonetiae str. KOZ 8101 pv.8474 Proteobacteria Pseudomonadaceae sf_1 AJ534672.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN7

proteobacterium8508 Proteobacteria Pseudomonadaceae sf_1 AF530073.1 Pseudomonas citronellolis str. TERIDB268513 Proteobacteria Pseudomonadaceae sf_1 AF064458.1 Pseudomonas monteilii str. CIP 1048838553 Proteobacteria Pseudomonadaceae sf_1 AB046997.1 Pseudomonas fulva str. IAM 15878561 Proteobacteria Pseudomonadaceae sf_1 AF332541.1 Pseudomonas sp. B65




8601 Proteobacteria Pseudomonadaceae sf_1 AB021401.1 Pseudomonas marginalis str. ATCC 10844T8687 Proteobacteria Pseudomonadaceae sf_1 AF094738.1 Pseudomonas putida str. ATCC 174728691 Proteobacteria Pseudomonadaceae sf_1 AE004501.1 Pseudomonas aeruginosa str. PAO18708 Proteobacteria Pseudomonadaceae sf_18725 Proteobacteria Pseudomonadaceae sf_1 AJ419674.1 Pseudomonas sp. str. 2N1-18755 Proteobacteria Pseudomonadaceae sf_1 AJ288146.1 Pseudomonas sp. SK-1-3-18777 Proteobacteria Pseudomonadaceae sf_1 AB095005.1 Pseudomonas sp. str. KNA6-58813 Proteobacteria Pseudomonadaceae sf_1 AY150184.1 Lyrodus pedicellatus symbiont8852 Proteobacteria Pseudomonadaceae sf_1 AF063219.1 Pseudomonas stutzeri str. KC9005 Proteobacteria Pseudomonadaceae sf_1 AJ278108.1 Pseudomonas sp. str. KY9028 Proteobacteria Pseudomonadaceae sf_1 AF468452.1 Pseudomonas koreensis str. Ps 9-149056 Proteobacteria Pseudomonadaceae sf_1 AB037546.1 Pseudomonas aeruginosa str. #479068 Proteobacteria Pseudomonadaceae sf_1 AF143245.1 Pseudomonas stutzeri str. A15019172 Proteobacteria Pseudomonadaceae sf_1 AB041885.1 Pseudomonas psychrophila str. E-39175 Proteobacteria Pseudomonadaceae sf_1 AF405328.1 Pseudomonas extremorientalis str. KMM34479219 Proteobacteria Pseudomonadaceae sf_1 AF181576.1 Pseudomonas cf. monteilii 99221 Proteobacteria Pseudomonadaceae sf_1 AJ492830.1 Pseudomonas fulgida str. DSM 14938 = LMG 2146 P 515/129228 Proteobacteria Pseudomonadaceae sf_1 AJ297767.1 Pseudomonas stutzeri HY-1059238 Proteobacteria Pseudomonadaceae sf_19240 Proteobacteria Pseudomonadaceae sf_1 AJ278812.1 Pseudomonas fluorescens str. CHA09243 Proteobacteria Pseudomonadaceae sf_1 Z76670.1 Pseudomonas tolaasii str. LMG 2342T ()9267 Proteobacteria Pseudomonadaceae sf_1 AB001450.1 Pseudomonas syringae pv. theae str. PT19295 Proteobacteria Pseudomonadaceae sf_19300 Proteobacteria Pseudomonadaceae sf_1 AY150183.1 Lyrodus pedicellatus symbiont9310 Proteobacteria Pseudomonadaceae sf_1 AJ519791.1 Pseudomonas sp. str. AC-1679343 Proteobacteria Pseudomonadaceae sf_1 AF448515.1 Cellvibrio subsp. mixtus str. ACM 26019366 Proteobacteria Pseudomonadaceae sf_1 AJ293826.1 Arctic seawater isolate str. R73669469 Proteobacteria Pseudomonadaceae sf_1 AF290486.1 cf. Pseudomonas sp. clone Llangefni 529493 Proteobacteria Pseudomonadaceae sf_1 AF430125.1 Pseudomonas sp. str. dcm7B9613 Proteobacteria Pseudomonadaceae sf_1 U01916.1 Pseudomonas flavescens str. B628962 Proteobacteria Unclassified sf_1 AF406526.1 bacterioplankton clone AEGEAN_2349344 Proteobacteria Unclassified sf_1 AF005249.1 Shewanella algae str. ATCC 511928605 Proteobacteria Unclassified sf_1 AF382104.1 bacterioplankton clone ZA2525c8654 Proteobacteria Unclassified sf_1 AB099939.1 inactive deep-sea hydrothermal vent chimneys clone IheB2-318403 Proteobacteria Unclassified sf_1 AF432146.1 Selenate-reducing isolate str. KE4OH19128 Proteobacteria Unclassified sf_1 X95229.1 Lucina nassula gill symbiont9556 Proteobacteria Unclassified sf_1 AY129087.1 Seepiophila jonesi symbiont9554 Proteobacteria Francisellaceae sf_1 AF206675.1 Tilapia parasite TPT-5418664 Proteobacteria Piscirickettsiaceae sf_3 AJ237758.1 Thiomicrospira sp. str. Milos-T28845 Proteobacteria Piscirickettsiaceae sf_3 AF513949.1 Piscirickettsia group clone LA7-B48N9291 Proteobacteria Piscirickettsiaceae sf_3 AF384373.1 Methylophaga alcalica str. M399557 Proteobacteria Piscirickettsiaceae sf_3 AF449225.1 Riftia pachyptila's tube clone R76-B238321 Proteobacteria Thiotrichaceae sf_3 AF532769.1 Wadden Sea sediment clone Dangast A98477 Proteobacteria Thiotrichaceae sf_3 AF532774.1 marine sediment clone Limfjorden L8




8559 Proteobacteria Thiotrichaceae sf_3 L40998.1 Thioploca ingrica8703 Proteobacteria Thiotrichaceae sf_3 AF110275.1 Beggiatoa sp. str. AA5A8741 Proteobacteria Thiotrichaceae sf_3 AF532771.1 marine sediment clone Limfjorden L108752 Proteobacteria Thiotrichaceae sf_3 AF110276.1 Beggiatoa sp. str. MS-81-1c9015 Proteobacteria Thiotrichaceae sf_3 AF110274.1 Beggiatoa alba str. B18LD; ATCC 335559321 Proteobacteria Thiotrichaceae sf_3 AB108786.1 marine sediment clone Tokyo Bay D8245 Proteobacteria Unclassified sf_38339 Proteobacteria Unclassified sf_3 AY212729.1 water 5 m downstream manure clone 35ds58488 Proteobacteria Unclassified sf_38566 Proteobacteria Unclassified sf_38606 Proteobacteria Unclassified sf_38646 Proteobacteria Unclassified sf_38668 Proteobacteria Unclassified sf_38676 Proteobacteria Unclassified sf_38714 Proteobacteria Unclassified sf_3 AB021372.1 Marinobacter hydrocarbonoclasticus str. ATCC 27132T8815 Proteobacteria Unclassified sf_38874 Proteobacteria Unclassified sf_3 AF420367.1 hydrothermal sediment clone AF4203678926 Proteobacteria Unclassified sf_3 AB099937.1 inactive deep-sea hydrothermal vent chimneys clone IheB2-138959 Proteobacteria Unclassified sf_3 AF406527.1 bacterioplankton clone AEGEAN_1339044 Proteobacteria Unclassified sf_3 AF420370.1 hydrothermal sediment clone AF4203709105 Proteobacteria Unclassified sf_39124 Proteobacteria Unclassified sf_3 AY145601.1 10e-6 dilution marine samples Weser estuary clone DC8-80-1 proteobacterium9269 Proteobacteria Unclassified sf_39367 Proteobacteria Unclassified sf_3 AF387348.1 USA: Pacific Ocean seawater Naha Vents Hawaii isolate str. PV-49498 Proteobacteria Unclassified sf_39568 Proteobacteria Unclassified sf_3 AF523888.1 forested wetland clone RCP2-968855 Proteobacteria Unclassified sf_48747 Proteobacteria Unclassified sf_1 AJ536882.1 uranium waste soil clone JG30-KF-CM358999 Proteobacteria Vibrionaceae sf_1 AY292944.1 Photobacterium leiognathi str. LN1018577 Proteobacteria Xanthomonadaceae sf_3 AF442743.1 Xanthomonas axonopodis pv. citri str. MA8689 Proteobacteria Xanthomonadaceae sf_3 AB110496.1 Dyemonas todaii str. XD108983 Proteobacteria Xanthomonadaceae sf_3 AF012541.1 Iron oxidising strain ES-19167 Proteobacteria Xanthomonadaceae sf_3 AB074619.1 pea aphid symbiont clone APe4_389211 Proteobacteria Xanthomonadaceae sf_3 AY218694.1 penguin droppings sediments clone KD8-809270 Proteobacteria Xanthomonadaceae sf_3 AJ293463.1 Stenotrophomonas rhizophila str. e-p109286 Proteobacteria Xanthomonadaceae sf_3 AJ131912.1 Stenotrophomonas maltophilia str. LMG 111049320 Proteobacteria Xanthomonadaceae sf_3 AJ318204.1 Waste-gas biofilter clone BIyi39332 Proteobacteria Xanthomonadaceae sf_3 AY096032.1 wetland ecosystem constructed to remediate mine drainage isolate str. WJ2 WJ22520 Proteobacteria Unclassified sf_208509 Proteobacteria Unclassified sf_21

10091 Proteobacteria Unclassified sf_288247 Proteobacteria Unclassified sf_89558 Proteobacteria Unclassified sf_8

705 SPAM Unclassified sf_1 AJ519639.1 uranium tailings soil clone Sh765B-AG-45




738 SPAM Unclassified sf_1 AJ532725.1 uranium mining waste clone JG34-KF-2526470 Spirochaetes Leptospiraceae sf_3 AY082470.1 neutral pH mine biofilm clone 44a-B1-486496 Spirochaetes Leptospiraceae sf_3 NC_005823.1 Leptospira interrogans serovar Copenhageni str. Fiocruz L1-1306458 Spirochaetes Spirochaetaceae sf_1 AB084961.1 termite gut clone NkS346459 Spirochaetes Spirochaetaceae sf_1 AJ431240.1 Spirochaeta sp. str. BHI80-1586460 Spirochaetes Spirochaetaceae sf_1 AB088907.1 termite gut homogenate clone Rs-B69 sp.6463 Spirochaetes Spirochaetaceae sf_1 AB088901.1 termite gut homogenate clone Rs-C91 sp.6473 Spirochaetes Spirochaetaceae sf_1 AB088891.1 termite gut homogenate clone Rs-B29 sp.6476 Spirochaetes Spirochaetaceae sf_1 AB084965.1 termite gut clone NkS506477 Spirochaetes Spirochaetaceae sf_1 AJ458945.1 Mixotricha paradoxa is flagellate hindgut Mastotermes darwiniensis clone mp3 of6479 Spirochaetes Spirochaetaceae sf_1 Y08893.1 Treponema sp6484 Spirochaetes Spirochaetaceae sf_1 Y09959.1 Treponema amylovorum HA2P6487 Spirochaetes Spirochaetaceae sf_1 AB088866.1 termite gut homogenate clone Rs-D52 sp.6488 Spirochaetes Spirochaetaceae sf_1 AF093251.1 Treponema primitia str. ZAS-16489 Spirochaetes Spirochaetaceae sf_1 AJ458944.1 Mixotricha paradoxa is flagellate hindgut Mastotermes darwiniensis clone mp1 of6490 Spirochaetes Spirochaetaceae sf_1 AB062823.1 termite gut homogenate clone BCf4-146491 Spirochaetes Spirochaetaceae sf_1 AB062840.1 termite gut homogenate clone BCf8-036494 Spirochaetes Spirochaetaceae sf_1 AB088890.1 termite gut homogenate clone Rs-C47 sp.6502 Spirochaetes Spirochaetaceae sf_1 AF139203.1 Treponema denticola str. ATCC354056503 Spirochaetes Spirochaetaceae sf_1 AY570600.1 biodegraded Canadian oil reservoir clone PL-16B96505 Spirochaetes Spirochaetaceae sf_1 AF363634.1 Treponema sp. str. G1796506 Spirochaetes Spirochaetaceae sf_1 AB088911.1 termite gut homogenate clone Rs-J58 sp.6507 Spirochaetes Spirochaetaceae sf_1 AB085161.1 termite gut clone NkS-Ste26508 Spirochaetes Spirochaetaceae sf_1 X89050.1 termite hindgut clone mpsp26523 Spirochaetes Spirochaetaceae sf_1 AB088912.1 termite gut homogenate clone Rs-J64 sp.6526 Spirochaetes Spirochaetaceae sf_1 AY230217.1 Treponema sp. str. 7CPL2086529 Spirochaetes Spirochaetaceae sf_1 AB062806.1 termite gut homogenate clone BCf10-216531 Spirochaetes Spirochaetaceae sf_1 AF023044.1 Treponema sp. str. V:19:D366532 Spirochaetes Spirochaetaceae sf_1 AB084963.1 termite gut clone NkS396540 Spirochaetes Spirochaetaceae sf_1 AF182835.1 Treponema sp. str. 3:G:BB0036546 Spirochaetes Spirochaetaceae sf_1 AF302939.1 Treponema parvum str. OMZ8436549 Spirochaetes Spirochaetaceae sf_1 AF523927.1 forested wetland clone RCP1-646554 Spirochaetes Spirochaetaceae sf_1 AB088889.1 termite gut homogenate clone Rs-A43 sp.6557 Spirochaetes Spirochaetaceae sf_1 AF454308.1 spirochete clone ML320J-136562 Spirochaetes Spirochaetaceae sf_1 AF523928.1 forested wetland clone RCP1-966565 Spirochaetes Spirochaetaceae sf_1 AB085166.1 termite gut clone NkS-Oxy256568 Spirochaetes Spirochaetaceae sf_1 AJ419821.1 Spirochaeta sp6570 Spirochaetes Spirochaetaceae sf_1 X87140.1 Treponema maltophilum periodontitis patient BR6571 Spirochaetes Spirochaetaceae sf_1 AJ458946.1 Mixotricha paradoxa is flagellate hindgut Mastotermes darwiniensis clone mp4 of6573 Spirochaetes Spirochaetaceae sf_1 AB084955.1 termite gut clone NkS76575 Spirochaetes Spirochaetaceae sf_1 AY133079.1 TCE-contaminated site clone ccslm2266579 Spirochaetes Spirochaetaceae sf_1 AB084968.1 termite gut clone NkS836580 Spirochaetes Spirochaetaceae sf_1 AF056341.1 Treponema sp. str. III:C:BA2136583 Spirochaetes Spirochaetaceae sf_1 AB088875.1 termite gut homogenate clone Rs-J42 sp.




6604 Spirochaetes Spirochaetaceae sf_1 AY369255.1 Treponema socranskii subsp. buccale str. OMZ 8846623 Spirochaetes Spirochaetaceae sf_1 AB088865.1 termite gut homogenate clone Rs-D46 sp.6514 Spirochaetes Spirochaetaceae sf_3 AB088897.1 termite gut homogenate clone Rs-B68 sp.6558 Spirochaetes Spirochaetaceae sf_3 AF166259.1 Spironema culicis str. BR912900 SR1 Unclassified sf_1

117 Synergistes Unclassified sf_3 AB089065.2 termite gut homogenate clone Rs-D89272 Synergistes Unclassified sf_3 AB089066.1 termite gut homogenate clone Rs-C88353 Synergistes Unclassified sf_3 AY261810.1 UASB reactor granular sludge clone PD-UASB-13 G+C

60 Synergistes Unclassified sf_3 AF481216.1 Flexistipes sp. str. E3_33601 Synergistes Unclassified sf_3 AF229792.1 terephthalate-degrading consortium clone TA19719 Synergistes Unclassified sf_3 AY207056.1 Synergistes sp. P1 str. P4G_18740 Synergistes Unclassified sf_3 AF371930.1 swine intestine clone p-4292-4Wa3808 Synergistes Unclassified sf_3 AF125199.2 oral cavity clone BH017437 Termite group 1 Unclassified sf_2 AB089050.2 termite gut homogenate clone Rs-D43 group722 Termite group 1 Unclassified sf_2 AB089051.1 termite gut homogenate clone Rs-H93 group667 Thermodesulfobacteri

aThermodesulfobacteriaceae sf_1 AF411013.1 Geothermobacterium ferrireducens

51 Thermotogae Thermotogaceae sf_4 AJ419874.1 Thermosipho sp. str. MV106310203 TM6 Unclassified sf_1 AY043739.1 forest soil clone NOS7.2WL9803 TM6 Unclassified sf_1 AF507715.1 forest soil clone S12042697 TM7 Unclassified sf_1 AJ576410.1 midgut homogenate Pachnoda ephippiata larva clone PeM472917 TM7 Unclassified sf_1 AF507686.1 arid soil clone C0262985 TM7 Unclassified sf_1 AY005448.1 oral cavity clone BS0033044 TM7 Unclassified sf_1 AF513103.1 activated sludge foam clone 7343081 TM7 Unclassified sf_1 AF445701.1 travertine hot spring clone SM1G123145 TM7 Unclassified sf_1 AF385520.1 tongue dorsa clone DR0343151 TM7 Unclassified sf_1 AF513102.1 activated sludge foam clone 718040 TM7 Unclassified sf_1 AY005446.1 oral cavity clone BE1098155 TM7 Unclassified sf_1 AY134895.1 oral periodontitis clone EW0862472 TM7 Unclassified sf_1 AF125206.1 oral cavity clone I0252935 TM7 Unclassified sf_1 AF385568.1 crevicular epithelial cells clone BU0803025 TM7 Unclassified sf_15061 TM7 Unclassified sf_15177 TM7 Unclassified sf_1

243 Unclassified Unclassified sf_106 AF027097.1 hot spring clone OPB256355 Unclassified Unclassified sf_1405022 Unclassified Unclassified sf_148 AF454327.1 plastid clone ML310M-375062 Unclassified Unclassified sf_1485235 Unclassified Unclassified sf_1484291 Unclassified Unclassified sf_156 AF507892.1 Mono Lake at depth 35m station 6 July 2000 clone ML635J-21 G+C

10012 Unclassified Unclassified sf_1601914 Unclassified Unclassified sf_160






4410 Unclassified Unclassified sf_160485 Unclassified Unclassified sf_160 AY193179.1 thermal spring mat clone O1aA90

6337 Unclassified Unclassified sf_1606360 Unclassified Unclassified sf_1606430 Unclassified Unclassified sf_1606456 Unclassified Unclassified sf_160

651 Unclassified Unclassified sf_1607767 Unclassified Unclassified sf_1604668 Unclassified Unclassified sf_349999 Unclassified Unclassified sf_92 AB089068.1 termite gut homogenate clone Rs-J96

925 Unclassified Unclassified sf_93 AF254404.1 4MB-degrading consortium clone UASB_TL262545 Unclassified Unclassified sf_95 AB106352.1 anaerobic sludge isolate str. JE

40 Verrucomicrobia Unclassified sf_3 AJ401121.1 Elbe river clone DEV055486 Verrucomicrobia Unclassified sf_3 AJ401113.1 Elbe river clone DEV045288 Verrucomicrobia Unclassified sf_4 U60012.1 Prosthecobacter dejongeii686 Verrucomicrobia Unclassified sf_5 AF419674.1 Guaymas Basin hydrothermal sediment clone a2b018

11 Verrucomicrobia Unclassified sf_3 AF234711.1 sludge clone H2792 Verrucomicrobia Unclassified sf_3 AB089122.1 termite gut homogenate clone Rs-P07 bacterium530 Verrucomicrobia Verrucomicrobia subdivision 5 sf_1 AY114334.1 anoxic marine sediment clone LD1-PB20533 Verrucomicrobia Verrucomicrobia subdivision 5 sf_1 AY114330.1 anoxic marine sediment clone LD1-PB12547 Verrucomicrobia Verrucomicrobia subdivision 5 sf_1 AY114329.1 anoxic marine sediment clone LD1-PB1629 Verrucomicrobia Verrucomicrobia subdivision 5 sf_1 AY114328.1 anoxic marine sediment clone LD1-PA50885 Verrucomicrobia Verrucomicrobia subdivision 5 sf_1 AJ390455.1 soil clone PBS-III-26446 Verrucomicrobia Verrucomicrobia subdivision 7 sf_1 AY114322.1 anoxic marine sediment clone LD1-PA34559 Verrucomicrobia Verrucomicrobia subdivision 7 sf_1 AY114314.1 anoxic marine sediment clone LD1-PA20760 Verrucomicrobia Verrucomicrobia subdivision 7 sf_1 AF454310.2 Mono lake clone ML316M-1

1024 Verrucomicrobia Verrucomicrobiaceae sf_1 AY244959.1 rumen clone BS5203 Verrucomicrobia Verrucomicrobiaceae sf_6 AY271254.1 Akkermansia muciniphila613 Verrucomicrobia Verrucomicrobiaceae sf_6 AJ441222.1 hydrothermal vent polychaete mucous clone P. palm C 85888 Verrucomicrobia Xiphinematobacteraceae sf_3 AF217462.1 Candidatus Xiphinematobacter brevicolli

2537 WS3 Unclassified sf_1 AY114325.1 anoxic marine sediment clone LD1-PA3995 WS3 Unclassified sf_3 AJ535231.1 marine sediment above hydrate ridge clone Hyd24-32

8119 WS5 Unclassified sf_2 AF419661.1 Guaymas Basin hydrothermal sediment clone a2b013

Table S3. Primers used for PhyloChip validation

Taxa ID Target Family Sample used for

amplification Primer Sequence (5'-3') Annealing Temperature

Product Length

5249 Prevotellaceae SFGH012-O 5249_2F CGC GTA TCC AAC CTT CCC GTT ACT G 65 °C 1110 bp5249_4R GTA ACA CGT GTG TAG CCC CGG ACG T

5249_5F AAG GCA GAC TAA TAC CGC ATG TTC T 60 °C 900 bp5249_6R ACC ATG CAG CAC CTT CAC AGG AGT C

11 paired samples 5249_qR GCT AAT CAG ACG CAT CCC CCT CCG T 60 °C 132 bp

3446 Streptococcaceae SFGH081-A 3446_1F AAC TAT TGG AAA CGA TAG CTA ATA C 58 °C 1344 bp3446_1R CCC AAT CAT CTA TCC CAC CTT AGG C

3446_3F TGG TGG GGT AAC GGC TCA CCA AGG C 67 °C 1063 bp3446_3R CAG CCT ACA ATC CGA ACT GAG ACT G

3446_1F-3446_1R amplified products

5249_2F-5249_4R amplified products

Table S4. BLAST results

Target family PrimersIdentity to taxon representative sequence

BLAST closest hita Accession number

Identity to BLAST closest hit

Prevotellaceae 5249_2F-5249_4R 758/761 (99%) AB547679.1 759/761 (99%) and5249_5F-5249_6R

Streptococcaceae 3446_1F-3446_1R 917/946 (97%) GU561390.1 943/946 (99%)and3446_3F-3446_3R AY281078.1 943/946 (99%)

a BLAST search was performed against non-redundant nucleotide collection (nr/nt) excluding uncultured/environmental sample sequences

Prevotella denticola gene for 16S ribosomal RNA, partial sequence, strain: JCM 13449

Streptococcus parasanguinis strain PTO10 16S ribosomal RNA gene, partial sequenceStreptococcus mitis ATCC 903 16S ribosomal RNA gene, partial sequence


Taxa ID Phylum Family Sub

Family p-value q-valuea Accession number Representative Sequence

Taxa detected significantly higher in oral samples5621 Bacteroidetes Bacteroidaceae sf_12 0.0195 0.01241 AY217430.1 TCE-dechlorinating microbial community clone 3G5429 Bacteroidetes Porphyromonadaceae sf_1 0.0012 0.018985510 Bacteroidetes Porphyromonadaceae sf_1 0.0189 0.04651 AF524856.1 sphagnum peat bog clone 26-4b25664 Bacteroidetes Porphyromonadaceae sf_1 0.0121 0.04041 AB088937.1 termite gut homogenate clone Rs-E83 bacterium5932 Bacteroidetes Porphyromonadaceae sf_1 0.0085 0.03261 AB088940.1 termite gut homogenate clone Rs-P41 bacterium5331 Bacteroidetes Prevotellaceae sf_1 0.0022 0.01898 AF385519.1 tongue dorsa clone DO0225398 Bacteroidetes Prevotellaceae sf_1 0.0191 0.01601 AY699286.1 Prevotella ruminicola L165408 Bacteroidetes Prevotellaceae sf_1 <0.001 0.04225 X81876.1 Prevotella dentalis str. DSM 36885453 Bacteroidetes Prevotellaceae sf_1 0.0016 0.04795 AY005062.1 subgingival dental plaque clone AU0695484 Bacteroidetes Prevotellaceae sf_1 0.0147 0.03968 AY134905.1 oral periodontitis clone FX0465741 Bacteroidetes Prevotellaceae sf_1 <0.001 0.02125 L16473.1 Prevotella veroralis5768 Bacteroidetes Prevotellaceae sf_1 0.0013 0.04548 AF385564.1 crevicular epithelial cells clone BU0355769 Bacteroidetes Prevotellaceae sf_1 0.0333 0.03017 AB081578.1 Bacteroidaceae str. A425834 Bacteroidetes Prevotellaceae sf_1 0.0082 0.01695 AY244923.1 cow rumen clone BE65893 Bacteroidetes Prevotellaceae sf_1 0.0036 0.01727 AF385515.1 tongue dorsa clone DO0455905 Bacteroidetes Prevotellaceae sf_1 0.0128 0.01241 AF371893.1 swine intestine clone p-2443-18B55916 Bacteroidetes Prevotellaceae sf_1 0.0277 0.03746 AY244931.1 cow rumen clone BE145927 Bacteroidetes Prevotellaceae sf_1 0.0017 0.039695929 Bacteroidetes Prevotellaceae sf_1 0.0273 0.03453 AJ011683.1 Prevotella albensis str. M3845940 Bacteroidetes Prevotellaceae sf_1 0.0104 0.02301 AF481226.1 Prevotella sp. str. E7_345946 Bacteroidetes Prevotellaceae sf_1 0.021 0.03968 AF385511.1 tongue dorsa clone DO0276011 Bacteroidetes Prevotellaceae sf_1 0.025 0.02116 AB185583.1 rumen clone F24-B036066 Bacteroidetes Prevotellaceae sf_1 0.0099 0.01727 AY207061.1 human mouth isolate str. P4P_626118 Bacteroidetes Prevotellaceae sf_1 0.0167 0.029096152 Bacteroidetes Prevotellaceae sf_1 <0.001 0.04737 AF001768.1 rumen clone RF376169 Bacteroidetes Prevotellaceae sf_1 0.0083 0.04232 AY005063.1 subgingival dental plaque clone CY0066207 Bacteroidetes Prevotellaceae sf_1 0.0055 0.02362 AY244912.1 cow rumen clone BF345889 Bacteroidetes Rikenellaceae sf_5 0.0401 0.02746 AB088945.1 termite gut homogenate clone Rs-F73 bacterium

5353 Bacteroidetes Unclassified sf_15 0.0158 0.03484 AF529128.1 trichloroethene-contaminated site clone FTLpost3 bacterium

5784 Bacteroidetes Unclassified sf_15 0.0214 0.01727 AY838556.1 fruiting body Pleurotus eryngii clone PE015874 Bacteroidetes Unclassified sf_15 0.0309 0.02683 AJ441239.1 hydrothermal vent polychaete mucous clone P. palm A 53

Table S5. Complete taxa exhibiting a significant (p<0.05) difference in abundance between oral and airway samples. Greatest difference with ≥1,000 fluorescence intensity units were highlighted.




5267 Bacteroidetes Flavobacteriaceae sf_1 0.0037 0.01695 AF406541.1 bacterioplankton clone AEGEAN_1795317 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.03261 AB078057.1 Tenacibaculum maritimum str. IFO 159465367 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.01727 AY238333.1 patient's bronchoalveolar lavage isolate str. MDA2507 sp.5423 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.02404 AF170754.1 Aequorivita antarctica str. QSSC9-145436 Bacteroidetes Flavobacteriaceae sf_1 0.0343 0.04232 AF468406.1 Arctic sea ice ARK100045473 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.035115521 Bacteroidetes Flavobacteriaceae sf_1 0.0016 0.02317 AF493689.1 Flavobacteriaceae str. SW2695641 Bacteroidetes Flavobacteriaceae sf_1 0.0234 0.01727

5695 Bacteroidetes Flavobacteriaceae sf_1 0.0027 0.02301 AJ535225.1 marine sediment above hydrate ridge clone Hyd24-41 bacterium

5836 Bacteroidetes Flavobacteriaceae sf_1 0.0021 0.01727 U41348.1 Capnocytophaga granulosa str. LMG 121195914 Bacteroidetes Flavobacteriaceae sf_1 0.0042 0.01727 AY771714.1 Psychroserpens burtonensis str. S2-64

5915 Bacteroidetes Flavobacteriaceae sf_1 0.0031 0.01695 AJ534682.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN27 bacterium

5942 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.018985955 Bacteroidetes Flavobacteriaceae sf_1 0.0012 0.01727 AJ244701.1 Flavobacterium sp. str. V4.MS.29 = MM_27475969 Bacteroidetes Flavobacteriaceae sf_1 0.0446 0.02215 U41350.1 Capnocytophaga ochracea str. ATCC 27872 T5991 Bacteroidetes Flavobacteriaceae sf_1 0.022 0.01695 AB032506.1 Tenacibaculum ovolyticum str. IAM143185997 Bacteroidetes Flavobacteriaceae sf_1 <0.001 0.02909 M62797.1 Flavobacterium aquatile6140 Bacteroidetes Flavobacteriaceae sf_1 0.0019 0.021166252 Bacteroidetes Flavobacteriaceae sf_1 0.0105 0.03028 AF449259.1 Riftia pachyptila's tube clone R103-B206269 Bacteroidetes Flavobacteriaceae sf_1 0.0023 0.02301 AY080916.1 acidic forest soil clone UC15566 Bacteroidetes Flexibacteraceae sf_19 0.0136 0.01857 AY264838.1 Hongiella mannitolivorans str. IMSNU 14012 JC20505602 Bacteroidetes Flexibacteraceae sf_19 0.0058 0.049245728 Bacteroidetes Flexibacteraceae sf_19 <0.001 0.04867 AB073564.2 Cytophaga sp. str. MBIC046935994 Bacteroidetes Flexibacteraceae sf_19 <0.001 0.03504 AJ549285.1 Hymenobacter sp. str. NS/50

10311 Bacteroidetes Flexibacteraceae sf_20 0.03 0.01241 AJ431236.1 Cytophaga sp. str. BHI60-57B

6168 Bacteroidetes Unclassified sf_3 0.0188 0.02404 AF534435.1 Toolik Lake main station at 3 m depth clone TLM11/TLMdgge04

6030 Bacteroidetes Unclassified sf_4 0.0011 0.04109 AF445648.1 travertine hot spring clone SM1A07995 Chlorobi Chlorobiaceae sf_1 0.0293 0.01727 AB054671.1 Chlorobium limicola str. M1

2539 Chloroflexi Unclassified sf_9 0.0231 0.04072 AY218649.1 penguin droppings sediments clone KD4-961041 Chloroflexi Unclassified sf_1 0.0466 0.03906 AY250886.1 Antarctic cryptoendolith clone FBP471757 Chloroflexi Unclassified sf_7 0.0489 0.04867 AJ306741.2 DCP-dechlorinating consortium clone SHA-8

4976 Cyanobacteria Chloroplasts sf_5 0.0041 0.03746 AF244550.1 Calypogeia muelleriana5192 Cyanobacteria Chloroplasts sf_5 <0.001 0.02641 AF244551.1 Cycas revoluta




5004 Cyanobacteria Unclassified sf_1 0.0135 0.04867 AJ630458.1 Anabaena augstumalis 'SCHMIDKE JAHNKE/4a' str. SCMIDKE JAHNKE/4a

5028 Cyanobacteria Unclassified sf_1 0.0237 0.04678 AF516732.1 Cylindrospermopsis raciborskii str. 05E5047 Cyanobacteria Unclassified sf_1 0.0334 0.02116 AF247573.1 Anabaena circinalis str. AWQC150A5174 Cyanobacteria Unclassified sf_1 0.0201 0.02317 AF516731.1 Cylindrospermopsis raciborskii str. 23B5175 Cyanobacteria Unclassified sf_1 0.0438 0.04867 AF516729.1 Cylindrospermopsis raciborskii str. 24C5199 Cyanobacteria Unclassified sf_1 0.0472 0.03022 AB074502.1 Anabaena variabilis str. IAM M-2045015 Cyanobacteria Unclassified sf_5 0.0318 0.01241 AB093489.1 Chlorogloeopsis fritschii str. PCC 69125206 Cyanobacteria Unclassified sf_8 0.0122 0.040723588 Firmicutes Streptococcaceae sf_1 0.0206 0.04596 AY188350.1 Streptococcus downei str. ATCC 337483907 Firmicutes Streptococcaceae sf_1 0.0057 0.02746 U87830.1 aortic heart valve patient with endocarditis clone v64503 Firmicutes Unclassified sf_4 0.0043 0.03511 AB088976.1 termite gut homogenate clone Rs-H83 bacterium4526 Firmicutes Unclassified sf_4 0.0045 0.02362 AY133082.1 TCE-contaminated site clone ccslm2102786 Firmicutes Clostridiaceae sf_12 0.0484 0.01898 AY007244.1 Clostridium glycolicum str. CIN54244 Firmicutes Clostridiaceae sf_12 0.016 0.03217 AB089011.1 termite gut homogenate clone Rs-K46 bacterium4266 Firmicutes Clostridiaceae sf_12 0.0035 0.01727 AB088951.1 termite gut homogenate clone Rs-M86 bacterium4272 Firmicutes Clostridiaceae sf_12 0.0256 0.03022 AB088965.1 termite gut homogenate clone Rs-M34 bacterium4300 Firmicutes Clostridiaceae sf_12 0.019 0.03746 AB100493.1 termite gut clone Rs-0604364 Firmicutes Clostridiaceae sf_12 0.0016 0.02301 AF481208.1 oral endodontic infection clone MCE3_94369 Firmicutes Clostridiaceae sf_12 0.0234 0.01727 AB089032.1 termite gut homogenate clone Rs-N73 bacterium4418 Firmicutes Clostridiaceae sf_12 0.0177 0.01898 AB088966.2 termite gut homogenate clone Rs-H18 bacterium4424 Firmicutes Clostridiaceae sf_12 0.0277 0.02301 AB088982.1 termite gut homogenate clone Rs-M05 bacterium4475 Firmicutes Clostridiaceae sf_12 0.0114 0.04225 AB089035.1 termite gut homogenate clone Rs-N02 bacterium4548 Firmicutes Clostridiaceae sf_12 0.0127 0.04199 AB089029.1 termite gut homogenate clone Rs-Q69 bacterium4550 Firmicutes Clostridiaceae sf_12 0.0019 0.03746 AF371790.1 swine intestine clone p-320-a34627 Firmicutes Clostridiaceae sf_12 0.0018 0.03746 AB089030.1 termite gut homogenate clone Rs-A13 bacterium2693 Firmicutes Lachnospiraceae sf_5 <0.001 0.03603 AB008552.1 ruminantium str. GA1952698 Firmicutes Lachnospiraceae sf_5 0.033 0.03571 AB088950.1 termite gut homogenate clone Rs-B88 bacterium2801 Firmicutes Lachnospiraceae sf_5 0.0195 0.02301 AY169412.1 Butyrivibrio fibrisolvens4164 Firmicutes Lachnospiraceae sf_5 0.01 0.04232 AF376226.1 ckncm322-B3-7 clone4331 Firmicutes Lachnospiraceae sf_5 <0.001 0.01695 AF332720.1 granular sludge clone UASB_brew_B844535 Firmicutes Lachnospiraceae sf_5 0.0178 0.03746 AF376201.1 ckncm297-B1-1 clone126 Firmicutes Peptococc/Acidaminococcsf_11 0.0025 0.03968 AY134907.1 oral periodontitis clone FY011181 Firmicutes Peptococc/Acidaminococcsf_11 0.0177 0.01727 AF548373.1 Allisonella histaminiformans str. MR2771 Firmicutes Peptococc/Acidaminococcsf_11 <0.001 0.04232 X82500.1 Dialister pneumosintes str. ATCC 33048

2701 Firmicutes Peptostreptococcaceae sf_5 0.0278 0.03722 AB034093.1 rumen clone 4C3d-12




2710 Firmicutes Peptostreptococcaceae sf_5 0.0249 0.03746 AJ306755.1 DCP-dechlorinating consortium clone SHA-742729 Firmicutes Peptostreptococcaceae sf_5 0.0288 0.05 AJ306754.1 DCP-dechlorinating consortium clone SHA-582946 Firmicutes Peptostreptococcaceae sf_5 0.0368 0.04558 AB034148.1 rumen clone 3C28d-44307 Firmicutes Unclassified sf_17 <0.001 0.04041514 OP10 Unclassified sf_1 0.037 0.04651 AF368184.1 sludge clone SBRA136

4683 Planctomycetes Anammoxales sf_2 0.0229 0.04528 BX294785.1 anoxic basin clone CY0ARA028B094692 Planctomycetes Pirellulae sf_3 0.0077 0.04678 BX294733.1 aerobic basin clone CY0ARA026G044948 Planctomycetes Planctomycetaceae sf_3 0.0272 0.04232 BX294756.1 anoxic basin clone CY0ARA027D01

7123 Proteobacteria Unclassified sf_1 0.0176 0.04232 AJ518774.1 uranium mining waste pile near Johanngeorgenstadt soil clone JG37-AG-102

7415 Proteobacteria Bartonellaceae sf_1 0.0399 0.03746 NC_005955.1Bartonella quintana str. Toulouse6701 Proteobacteria Rhodobacteraceae sf_1 0.0062 0.04225 AF245632.1 Roseobacter clone NAC11-37319 Proteobacteria Sphingomonadaceae sf_1 <0.001 0.04737 AF425996.1 Anabaena circinalis AWQC118C isolate str. UNSW17440 Proteobacteria Sphingomonadaceae sf_1 0.0237 0.04109 AF159257.2 Sphingobium chungbukense str. DJ77

7818 Proteobacteria Unclassified sf_1 0.0331 0.03746 AJ534623.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-215 proteobacterium

6473 Spirochaetes Spirochaetaceae sf_1 0.0186 0.01695 AB088891.1 termite gut homogenate clone Rs-B29 sp.6476 Spirochaetes Spirochaetaceae sf_1 0.006 0.01695 AB084965.1 termite gut clone NkS506487 Spirochaetes Spirochaetaceae sf_1 0.0026 0.01727 AB088866.1 termite gut homogenate clone Rs-D52 sp.6488 Spirochaetes Spirochaetaceae sf_1 0.0013 0.01695 AF093251.1 Treponema primitia str. ZAS-16490 Spirochaetes Spirochaetaceae sf_1 0.0046 0.01727 AB062823.1 termite gut homogenate clone BCf4-146506 Spirochaetes Spirochaetaceae sf_1 0.0041 0.04528 AB088911.1 termite gut homogenate clone Rs-J58 sp.6523 Spirochaetes Spirochaetaceae sf_1 0.0172 0.01695 AB088912.1 termite gut homogenate clone Rs-J64 sp.

6571 Spirochaetes Spirochaetaceae sf_1 0.0098 0.04737 AJ458946.1 Mixotricha paradoxa is flagellate hindgut Mastotermes darwiniensis clone mp4 of

6573 Spirochaetes Spirochaetaceae sf_1 0.0161 0.02215 AB084955.1 termite gut clone NkS76623 Spirochaetes Spirochaetaceae sf_1 0.0469 0.02292 AB088865.1 termite gut homogenate clone Rs-D46 sp.2917 TM7 Unclassified sf_1 0.0418 0.02215 AF507686.1 arid soil clone C0263151 TM7 Unclassified sf_1 0.0021 0.03484 AF513102.1 activated sludge foam clone 718155 TM7 Unclassified sf_1 <0.001 0.02909 AY134895.1 oral periodontitis clone EW0864410 Unclassified Unclassified sf_160 0.0037 0.03134

Taxa detected significantly higher in airway samples

6345 Acidobacteria Acidobacteriaceae sf_6 0.017 0.03484 AJ534634.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-77 bacterium

484 OP10 Unclassified sf_4 0.0056 0.03927 AF524022.1 forested wetland clone FW68




6959 Proteobacteria Azospirillaceae sf_1 0.0094 0.03484 AF523824.1 Rhodocista pekingensis str. 3-p

7126 Proteobacteria Bradyrhizobiaceae sf_1 0.0229 0.03968 AJ534670.1 ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN96 proteobacterium

8062 Proteobacteria Alcaligenaceae sf_1 0.0081 0.01727 AJ277742.1 Brackiella oedipodis str. LMG 1945 R88467827 Proteobacteria Comamonadaceae sf_1 0.0267 0.04225

10332 Proteobacteria Desulfobulbaceae sf_1 0.007 0.04737 AF099059.1 Psychrophilic sulfate-reducing isolate str. LSv23 bacterium10538 Proteobacteria Campylobacteraceae sf_3 0.0174 0.03968 L14624.1 Arcobacter cryaerophilus10563 Proteobacteria Campylobacteraceae sf_3 0.0468 0.04528 AF144694.2 Campylobacter sp. str. DSM 8068196 Proteobacteria Alteromonadaceae sf_1 0.0104 0.016018374 Proteobacteria Alteromonadaceae sf_1 0.0097 0.04213 AB076560.1 Agarivorans albus str. MKT 899058 Proteobacteria Alteromonadaceae sf_1 0.027 0.02301 X82136.1 Pseudoalteromonas carrageenovora str. ATCC 12662T9364 Proteobacteria Alteromonadaceae sf_1 0.027 0.04737 U85855.1 Pseudoalteromonas prydzensis str. MB8-119384 Proteobacteria Alteromonadaceae sf_1 0.0369 0.02923 AJ132226.1 Moritella viscosa str. NVI 88/478T9640 Proteobacteria Alteromonadaceae sf_1 0.0289 0.03746 AY028205.1 exposed to diatom detritus isolate str. Tw-10 Tw-108641 Proteobacteria Shewanellaceae sf_1 0.0368 0.04072 AJ252022.1 Moritella abyssi str. 26938662 Proteobacteria Shewanellaceae sf_1 0.0316 0.042258546 Proteobacteria Chromatiaceae sf_1 0.0228 0.04232 AJ242772.1 Thiocapsa litoralis8697 Proteobacteria Chromatiaceae sf_1 0.0209 0.03307 AJ401211.1 Thiococcus sp. AT2204

9458 Proteobacteria Unclassified sf_1 0.0287 0.01898 AJ518786.1 uranium mining waste pile clone JG37-AG-94 proteobacterium

8251 Proteobacteria Enterobacteriaceae sf_1 0.0308 0.02923 AF214640.1 Nitrogen-fixing isolate str. CANF38510 Proteobacteria Enterobacteriaceae sf_1 0.0425 0.04095 AJ233420.1 Klebsiella pneumoniae str. DSM 301048529 Proteobacteria Enterobacteriaceae sf_1 0.0273 0.04867 AF181574.1 Raoultella planticola 78554 Proteobacteria Enterobacteriaceae sf_1 0.044 0.03484 AJ627202.1 Kluyvera ascorbata 698742 Proteobacteria Enterobacteriaceae sf_1 0.0419 0.02317 AF084835.1 USA:New York isolate str. KN48934 Proteobacteria Enterobacteriaceae sf_1 0.0433 0.01898 AF373188.1 Pectobacterium subsp. carotovorum str. E155 subsp.8936 Proteobacteria Enterobacteriaceae sf_1 0.0378 0.01719 AF543283.1 Klebsiella oxytoca str. ChDC OS319060 Proteobacteria Enterobacteriaceae sf_1 0.0431 0.01241 AJ853891.1 Enterobacter ludwigii str. EN-119 = DSMZ 166889142 Proteobacteria Enterobacteriaceae sf_1 0.0274 0.01241 AJ233410.1 Erwinia amylovora str. DSM 301659293 Proteobacteria Enterobacteriaceae sf_1 0.0114 0.03571 AJ245598.1 USA clone 14/79302 Proteobacteria Enterobacteriaceae sf_1 0.0251 0.02301 AF373198.1 Pantoea subsp. stewartii str. GSPB 26269345 Proteobacteria Enterobacteriaceae sf_1 0.0319 0.02048 AF141891.1 Erwinia amylovora str. BC199(=Ea528)9390 Proteobacteria Enterobacteriaceae sf_1 0.0263 0.02923 Z96077.1 Enterobacter nimipressuralis str. LMG 10245-T8645 Proteobacteria Methylococcaceae sf_1 0.0163 0.01241 AF307138.1 Methylomicrobium buryatense str. 5B

9438 Proteobacteria Methylococcaceae sf_1 0.0206 0.03401 AJ535221.1 marine sediment above hydrate ridge clone Hyd24-01 proteobacterium




8432 Proteobacteria Pasteurellaceae sf_1 0.0126 0.035118952 Proteobacteria Pasteurellaceae sf_1 0.0339 0.03657 M75068.1 Actinobacillus lignieresii9237 Proteobacteria Pasteurellaceae sf_1 0.0314 0.02301

9360 Proteobacteria Pasteurellaceae sf_1 0.0322 0.02301 AF224297.1 Pasteurella multocida subsp. gallicida str. MCCM 00021 subsp.

8727 Proteobacteria Moraxellaceae sf_3 0.0187 0.01727 AY251390.1 Alkanindiges hongkongensis str. HKU99068 Proteobacteria Pseudomonadaceae sf_1 0.0256 0.03571 AF143245.1 Pseudomonas stutzeri str. A15019238 Proteobacteria Pseudomonadaceae sf_1 0.0123 0.034849295 Proteobacteria Pseudomonadaceae sf_1 0.0114 0.041099344 Proteobacteria Unclassified sf_1 0.027 0.02116 AF005249.1 Shewanella algae str. ATCC 511929291 Proteobacteria Piscirickettsiaceae sf_3 0.0116 0.03261 AF384373.1 Methylophaga alcalica str. M39

9124 Proteobacteria Unclassified sf_3 0.0071 0.03028 AY145601.1 10e-6 dilution marine samples Weser estuary clone DC8-80-1 proteobacterium

9367 Proteobacteria Unclassified sf_3 0.0159 0.02909 AF387348.1 USA: Pacific Ocean seawater Naha Vents Hawaii isolate str. PV-4

9568 Proteobacteria Unclassified sf_3 0.0317 0.04228 AF523888.1 forested wetland clone RCP2-969558 Proteobacteria Unclassified sf_8 0.0325 0.02858

60 Synergistes Unclassified sf_3 0.0272 0.03511 AF481216.1 Flexistipes sp. str. E3_33719 Synergistes Unclassified sf_3 0.0414 0.01898 AY207056.1 Synergistes sp. P1 str. P4G_18

Table S6. Relationships between clinical variables and community profiles.

Clinical Variables r2 P-valueVector variables

Age 0.1849 0.2887

Days on antimicrobial therapy prior to sampling 0.1374 0.4735

CD4 cell count 0.0116 0.935

HIV RNA level 0.1604 0.3556

Factor variablesAnti-pseudomonal therapies (cefepime, piperacillin/tazobactam, levaquin) use 0.1439 0.1299

Antimicrobial therapy for drug-resistant anti-gram positives (vancomycin) 0.1439 0.1179

ART administration 0.0733 0.3367

Steroid (prednisone) administration 0.1116 0.5624

Smoking history 0.0739 0.7043

Alohol history 0.0317 0.8871

Current cocaine, crack or heroin use 0.0339 0.8871

Prior pneumonia status 0.1323 0.4675

Stuructural lung disease 0.0584 0.4456

Microbial culture, Pneumocystis jirovecii pneumonia (PCP) 0.0655 0.4086

Microbial culture, Cytomegalovirus (CMV) 0.004 0.957

Microbial culture, Mycobacterium Avium Complex (MAC) 0.0149 0.8472


Taxa ID

Phylum Family Sub Family

p-value q-valuea Accession number

Representative Sequence

Taxa detected higher in HIV-infected patients1049 Acidobacteria Unclassified sf_1 0.0342 0.04856 AF013534.2 soil clone C112350 Acidobacteria Unclassified sf_1 0.0015 0.01249 AY221047.1 Mammoth cave clone CCM15a588 Acidobacteria Unclassified sf_1 0.0052 0.02468 AJ009461.1 TCB-transforming consortium clone SJA-36508 Acidobacteria Acidobacteriaceae sf_14 0.0099 0.0313 AJ519382.1 uranium mining waste pile clone JG37-AG-81 sp.

1227 Actinobacteria Actinomycetaceae sf_1 0.0311 0.04662 AB062278.1 Actinomyces naeslundii1745 Actinobacteria Brevibacteriaceae sf_1 <0.001 0.00963 X83813.1 Brevibacterium iodinum str. DSM 2062T1431 Actinobacteria Cellulomonadaceae sf_1 <0.001 0.00725 AB078838.1 Cellulomonadaceae str. W61450 Actinobacteria Cellulomonadaceae sf_1 0.0199 0.04071586 Actinobacteria Cellulomonadaceae sf_1 0.0157 0.03694 X83800.1 Cellulomonas gelida str. DSM 20111T1748 Actinobacteria Cellulomonadaceae sf_1 0.0025 0.01738 Y18378.1 Beutenbergia cavernosa str. DSM 123331923 Actinobacteria Cellulomonadaceae sf_1 0.0138 0.03541 AJ229245.1 Actinobacteria str. VeCb62053 Actinobacteria Dermabacteraceae sf_1 0.0134 0.03524 X91033.1 Brachybacterium nesterenkovii str. DSM 95731654 Actinobacteria Gordoniaceae sf_1 0.0198 0.0407 AF416719.1 Gordonia polyisoprenivorans str. Y2K1087 Actinobacteria Kineosporiaceae sf_1 0.0101 0.03175 AB003931.1 Kineosporia aurantiaca str. JCM32301581 Actinobacteria Kineosporiaceae sf_1 0.0358 0.04979 AJ293746.1 Cryptosporangium aurantiacum str. IMSNU 22120

1598 Actinobacteria Kineosporiaceae sf_1 0.0179 0.04007 AY250880.1 lichen-dominated Antarctic cryptoendolithic community clone FBP402

1961 Actinobacteria Kineosporiaceae sf_1 0.023 0.04214 X77958.1 Kineococcus aurantiacus str. IFO 152681106 Actinobacteria Microbacteriaceae sf_1 0.033 0.047821135 Actinobacteria Microbacteriaceae sf_1 0.0236 0.04251 AJ459101.1 Rhodoglobus vestalii str. LV31197 Actinobacteria Microbacteriaceae sf_1 0.0067 0.02738 AF468440.1 Arctic sea ice ARK101731804 Actinobacteria Microbacteriaceae sf_1 0.0112 0.03369 AY244784.1 Microbacterium resistens str. 2002-591191213 Actinobacteria Micrococcaceae sf_1 <0.001 0.00853 X87756.1 Kocuria roseus1266 Actinobacteria Micrococcaceae sf_1 0.008 0.02922 AF134179.1 Arthrobacter psychrolactophilus1494 Actinobacteria Micrococcaceae sf_1 0.0106 0.03296 X80748.1 Arthrobacter agilis str. DSM 205501557 Actinobacteria Micrococcaceae sf_1 0.0069 0.02749 X83408.1 Arthrobacter oxydans str. DSM 201191593 Actinobacteria Micrococcaceae sf_1 0.0089 0.0302 M23411.1 Arthrobacter globiformis2019 Actinobacteria Micrococcaceae sf_1 0.0201 0.0407 AF057289.1 Micrococcus luteus str. HN2-112020 Actinobacteria Micrococcaceae sf_1 0.0197 0.0407 AF543278.1 Rothia dentocariosa str. ChDC B2001120 Actinobacteria Micromonosporaceae sf_1 0.0228 0.04214 AJ277586.1 Actinoplanes violaceus str. IMSNU 221361395 Actinobacteria Micromonosporaceae sf_1 0.0212 0.04179 D14642.1 Catenuloplanes japonicus str. IFO141761142 Actinobacteria Nocardiaceae sf_1 0.0264 0.045271146 Actinobacteria Nocardiaceae sf_1 0.0229 0.04214 AF430068.1 Nocardia otitidiscaviarum str. S639

Table S7. Complete taxa exhibiting a significant (p<0.05, q<0.05) difference in abundance between HIV-infected and HIV-uninfected samples. Greatest difference with ≥1,000 fluorescence intensity units were highlighted.


Taxa ID




1917 Actinobacteria Nocardiaceae sf_1 0.0334 0.04782 X80611.1 Nocardia otitidiscaviarum str. DSM432421940 Actinobacteria Nocardiaceae sf_1 0.0218 0.04179 AB178563.1 Rhodococcus opacus str. B-42048 Actinobacteria Nocardiaceae sf_1 0.035 0.04907 AF430044.1 Nocardia uniformis str. DSM 431361854 Actinobacteria Nocardioidaceae sf_1 0.0109 0.03308 AY166703.1 Aeromicrobium marinum str. T21711 Actinobacteria Promicromonosporaceae sf_1 0.0253 0.0442 AJ272024.1 Promicromonospora sukumoe str. DSM 44121

1695 Actinobacteria Sporichthyaceae sf_1 0.0225 0.04203 AY250883.1 lichen-dominated Antarctic cryptoendolithic community clone FBP417

1354 Actinobacteria Streptomycetaceae sf_1 0.0216 0.04179 X80825.1 Streptomyces subrutilus str. DSM 404451617 Actinobacteria Streptomycetaceae sf_1 0.0304 0.04658 AF423260.1 soil clone 41-11690 Actinobacteria Streptomycetaceae sf_1 0.0059 0.02593 X79325.1 Streptomyces galbus str. DSM404801771 Actinobacteria Streptomycetaceae sf_1 0.0362 0.04981 D63872.1 Streptomyces setonii str. ATCC254971786 Actinobacteria Streptomycetaceae sf_1 0.0052 0.02468 X79851.1 Streptomyces bikiniensis str. DSM405811224 Actinobacteria Streptosporangiaceae sf_1 0.0214 0.04179 X89941.1 Acrocarpospora corrugata str. DSM43316T1741 Actinobacteria Thermomonosporaceae sf_1 0.013 0.03524 AJ293710.1 Actinomadura pelletieri str. IMSNU 22169T1130 Actinobacteria Unclassified sf_3 0.0235 0.04246 X94155.2 Georgenia muralis str. 1A-C1405 Actinobacteria Unclassified sf_3 0.0126 0.03487 X80744.1 Arthrobacter ureafaciens str. DSM 201261577 Actinobacteria Unclassified sf_3 0.0034 0.02033 AB089072.1 termite gut homogenate clone Rs-N91 bacterium1687 Actinobacteria Unclassified sf_3 0.0051 0.02468 AJ626896.1 Jonesia quinghaiensis str. DSM 15701

1822 Actinobacteria Unclassified sf_3 0.0175 0.03967 AY145533.1 dilution (10e-7) brackish section Weser estuary isolate str. GP-5 GP-5

1900 Actinobacteria Unclassified sf_3 0.0135 0.035242338 AD3 Unclassified sf_1 0.015 0.03654 AJ536867.1 uranium mining waste pile soil clone JG30-KF-C125680 Bacteroidetes Porphyromonadaceae sf_1 0.0234 0.04246 AB100460.1 termite gut clone Rs-1066012 Bacteroidetes Porphyromonadaceae sf_1 0.0329 0.04782 AJ400264.1 mouse feces clone L11-65249 Bacteroidetes Prevotellaceae sf_1 0.0304 0.04658 AY323524.1 Prevotella denticola str. ATCC 353085403 Bacteroidetes Prevotellaceae sf_1 0.0218 0.04179 AJ006457.1 Prevotella bryantii str. B14 (DSM 11371 species )5720 Bacteroidetes Prevotellaceae sf_1 0.0307 0.04658 AF481227.1 Prevotella sp. str. E9_345741 Bacteroidetes Prevotellaceae sf_1 0.0285 0.04576 L16473.1 Prevotella veroralis5926 Bacteroidetes Prevotellaceae sf_1 0.0306 0.04658 AY244900.1 cow rumen clone BF225946 Bacteroidetes Prevotellaceae sf_1 0.0063 0.02669 AF385511.1 tongue dorsa clone DO0276118 Bacteroidetes Prevotellaceae sf_1 0.028 0.045376152 Bacteroidetes Prevotellaceae sf_1 0.0279 0.04537 AF001768.1 rumen clone RF37

5353 Bacteroidetes Unclassified sf_15 <0.001 0.00725 AF529128.1 trichloroethene-contaminated site clone FTLpost3 bacterium

5307 Bacteroidetes Flexibacteraceae sf_19 0.0096 0.03064 AB078082.1 Microscilla sericea str. IFO 16561

5566 Bacteroidetes Flexibacteraceae sf_19 0.0195 0.0407 AY264838.1 Hongiella mannitolivorans str. IMSNU 14012 JC2050


Taxa ID




5602 Bacteroidetes Flexibacteraceae sf_19 0.0287 0.045765667 Bacteroidetes Flexibacteraceae sf_19 0.0197 0.0407 AY218749.1 penguin droppings sediments clone KD6-1186297 Bacteroidetes Flexibacteraceae sf_19 0.0144 0.03588 AF502211.1 EBPR sludge lab scale clone HP1A925601 Bacteroidetes Sphingobacteriaceae sf_1 0.0361 0.04981 AB020205.1 Sphingobacterium multivorum str. OM-A84964 Chlamydiae Parachlamydiaceae sf_1 0.0299 0.04645 AY082465.1 neutral pH mine biofilm clone 44a-B1-34789 Chloroflexi Unclassified sf_2 0.0078 0.02922 AF445676.1 travertine hot spring clone SM1D10205 Chloroflexi Unclassified sf_9 <0.001 0.00853 AJ532729.1 uranium mining waste pile clone JG34-KF-221

2539 Chloroflexi Unclassified sf_9 0.0226 0.04203 AY218649.1 penguin droppings sediments clone KD4-96375 Chloroflexi Unclassified sf_9 0.0161 0.03752 AF507690.1 forest soil clone C043576 Chloroflexi Unclassified sf_9 0.0287 0.04576 AJ306746.2 DCP-dechlorinating consortium clone SHA-36946 Chloroflexi Unclassified sf_9 0.0273 0.04537 AY216458.1 temperate estuarine mud clone KM87

2339 Chloroflexi Unclassified sf_1 0.0242 0.04331 AJ519643.1 uranium mill tailings soil sample clone Sh765B-TzT-20 bacterium

751 Coprothermobacteria Unclassified sf_1 0.0227 0.04203 AJ431258.1 Coprothermobacter sp. str. Dex80-3

4976 Cyanobacteria Chloroplasts sf_5 0.0317 0.04697 AF244550.1 Calypogeia muelleriana5183 Cyanobacteria Chloroplasts sf_5 0.0178 0.03996 M37430.1 Pisum sativum -- chloroplast5192 Cyanobacteria Chloroplasts sf_5 0.0095 0.03064 AF244551.1 Cycas revoluta5001 Cyanobacteria Unclassified sf_1 0.0194 0.0407 AJ347056.1 sponge clone TK095008 Cyanobacteria Unclassified sf_1 <0.001 0.00857 AF448080.1 Synechococcus sp. str. PCC 75025164 Cyanobacteria Unclassified sf_9 0.034 0.04843 AB089123.1 termite gut homogenate clone Rs-H343542 Firmicutes Bacillaceae sf_1 0.02 0.0407 AJ277984.1 Bacillus psychrodurans str. DSM 11713 68E33926 Firmicutes Bacillaceae sf_1 0.0208 0.04136 X92160.1 Lake Bogoria isolate 64B43415 Firmicutes Paenibacillaceae sf_1 0.0132 0.03524 AF480937.1 Paenibacillus nematophilus str. NEM1b3595 Firmicutes Paenibacillaceae sf_1 0.0042 0.02272 AY257871.1 Paenibacillus sp. str. MB 20393630 Firmicutes Paenibacillaceae sf_1 0.0028 0.018853651 Firmicutes Paenibacillaceae sf_1 0.0059 0.02593 AJ011323.1 Paenibacillus borealis KK203922 Firmicutes Paenibacillaceae sf_1 0.0295 0.04621 AJ320490.1 Paenibacillus thiaminolyticus str. DSM 7262

3258 Firmicutes Staphylococcaceae sf_1 0.0328 0.04782 D83358.1 Staphylococcus auricularis str. MAFF911484 ATCC33753T

3553 Firmicutes Aerococcaceae sf_1 0.0123 0.03444 Y17300.1 Desemzia incerta str. DSM 20581

3366 Firmicutes Lactobacillaceae sf_1 0.0291 0.04612 AY255802.1 Lactobacillus saerimneri str. GDA154 LMG 22087 DSM 16049 (T); CCUG 48462 (T)

3521 Firmicutes Lactobacillaceae sf_1 0.029 0.04603 AJ271383.1 Pediococcus inopinatus str. DSM 202853703 Firmicutes Lactobacillaceae sf_1 0.0347 0.04898 AY389803.1 Lactobacillus salivarius str. RA21154325 Firmicutes Unclassified sf_4 0.0064 0.02685 AB088963.1 termite gut homogenate clone Rs-K21 bacterium4526 Firmicutes Unclassified sf_4 0.0055 0.02515 AY133082.1 TCE-contaminated site clone ccslm210


Taxa ID




132 Firmicutes Clostridiaceae sf_12 0.0218 0.04179 AB089019.1 termite gut homogenate clone Rs-J36 bacterium4177 Firmicutes Clostridiaceae sf_12 0.0308 0.04658 AF241842.1 Clostridium subterminale DSM 26364180 Firmicutes Clostridiaceae sf_12 0.0148 0.03654 AB089028.1 termite gut homogenate clone Rs-M23 bacterium4187 Firmicutes Clostridiaceae sf_12 0.0319 0.0471 AF538854.1 Clostridiales oral clone P4PB_122 P34265 Firmicutes Clostridiaceae sf_12 0.0013 0.01127 AB088969.1 termite gut homogenate clone Rs-N70 bacterium4266 Firmicutes Clostridiaceae sf_12 0.0184 0.0407 AB088951.1 termite gut homogenate clone Rs-M86 bacterium4272 Firmicutes Clostridiaceae sf_12 0.0245 0.04356 AB088965.1 termite gut homogenate clone Rs-M34 bacterium4278 Firmicutes Clostridiaceae sf_12 0.0019 0.01478 AF482434.1 granular sludge clone R1p164296 Firmicutes Clostridiaceae sf_12 0.0355 0.0496 AB081585.1 Clostridiaceae str. A4d4297 Firmicutes Clostridiaceae sf_12 0.0118 0.034424310 Firmicutes Clostridiaceae sf_12 0.0139 0.03541 AB100478.1 termite gut clone Rs-0564321 Firmicutes Clostridiaceae sf_12 0.0121 0.03442 AB089045.1 termite gut homogenate clone Rs-C76 bacterium4369 Firmicutes Clostridiaceae sf_12 0.0278 0.04537 AB089032.1 termite gut homogenate clone Rs-N73 bacterium4418 Firmicutes Clostridiaceae sf_12 0.0276 0.04537 AB088966.2 termite gut homogenate clone Rs-H18 bacterium4477 Firmicutes Clostridiaceae sf_12 0.0187 0.0407 AB089042.1 termite gut homogenate clone Rs-N85 bacterium4575 Firmicutes Clostridiaceae sf_12 0.0141 0.03556 X68451.1 Clostridium subterminale str. NCIMB 107464610 Firmicutes Clostridiaceae sf_12 0.0133 0.03524 AF127024.1 Clostridium putrefaciens str. DSM 12914614 Firmicutes Clostridiaceae sf_12 0.0051 0.02468 AB093546.1 Clostridium sp. str. JC34637 Firmicutes Clostridiaceae sf_12 0.0309 0.04662 AB100473.1 termite gut clone Rs-0882698 Firmicutes Lachnospiraceae sf_5 0.0021 0.01535 AB088950.1 termite gut homogenate clone Rs-B88 bacterium2709 Firmicutes Lachnospiraceae sf_5 0.0127 0.03493 AY916314.1 human stool clone B0652937 Firmicutes Lachnospiraceae sf_5 0.0194 0.0407 AF371541.1 swine intestine clone p-2482-18B53089 Firmicutes Lachnospiraceae sf_5 0.0091 0.0302 AY169419.1 Ruminococcus obeum4281 Firmicutes Lachnospiraceae sf_5 0.0357 0.04973 AF332721.1 granular sludge clone UASB_brew_B864335 Firmicutes Lachnospiraceae sf_5 0.0116 0.03418 AB088952.1 termite gut homogenate clone Rs-N86 bacterium4511 Firmicutes Lachnospiraceae sf_5 0.007 0.02749 AF376218.1 ckncm314-B7-17 clone4514 Firmicutes Lachnospiraceae sf_5 0.035 0.04907 AB088983.2 termite gut homogenate clone Rs-B34 bacterium4525 Firmicutes Lachnospiraceae sf_5 0.0208 0.04136 AB088991.1 termite gut homogenate clone Rs-Q18 bacterium4567 Firmicutes Lachnospiraceae sf_5 0.0126 0.03487 AJ408989.1 human colonic clone HuCB54571 Firmicutes Lachnospiraceae sf_5 0.011 0.03308 X85022.1 Faecalibacterium prausnitzii str. ATCC 27766131 Firmicutes Peptococc/Acidaminococc sf_11 0.0261 0.04482 AF349425.1 pig feces clone242 Firmicutes Peptococc/Acidaminococc sf_11 0.0329 0.04782 AJ493052.1 Desulfosporosinus orientis str. DSMZ 7493428 Firmicutes Peptococc/Acidaminococc sf_11 0.0197 0.0407 AJ488090.1 chlorobenzene-degrading consortium clone IIIA-1940 Firmicutes Peptococc/Acidaminococc sf_11 0.0362 0.04981 X84006.1 Veillonella dispar str. DSM 20735

1037 Firmicutes Peptostreptococcaceae sf_5 0.0272 0.04537 AY169425.1 Finegoldia magna3182 Firmicutes Peptostreptococcaceae sf_5 0.0199 0.0407 AB088970.1 termite gut homogenate clone Rs-Q64 bacterium393 Firmicutes Peptostreptococcaceae sf_5 0.0193 0.0407 AF542229.1 Anaerococcus vaginalis str. CCUG 31349


Taxa ID




619 Firmicutes Peptostreptococcaceae sf_5 0.0314 0.04683 AY217429.1 TCE-dechlorinating microbial community clone 1G4216 Firmicutes Unclassified sf_7 0.0343 0.04861198 Firmicutes Unclassified sf_1 0.0078 0.02922 AB091323.1 Pelotomaculum sp. str. JT

2359 Firmicutes Unclassified sf_1 0.0082 0.02922 AB091324.1 UASB granular sludge clone JP3952 Firmicutes Erysipelotrichaceae sf_3 0.0143 0.03579 AB055907.1 Erysipelothrix rhusiopathiae str. Pecs 564074 Firmicutes Entomoplasmataceae sf_1 <0.001 0.00887 AF371522.1 swine intestine clone p-2013-s959-5

77 Firmicutes Unclassified sf_1 0.0294 0.04621 AF391988.1 thermal soil clone YNPFFP9

10112 Gemmatimonadetes Unclassified sf_5 0.0082 0.02922 AF432607.1 forest soil clone NOS7.157WL

1565 Gemmatimonadetes Unclassified sf_5 0.015 0.03654 AJ532728.1 uranium mining waste pile clone JG34-KF-418

9464 Gemmatimonadetes Unclassified sf_5 0.0021 0.01539 AF432648.1 lodgepole pine rhizosphere soil British Columbia

Ministry Forests Long-Term Soil Productivity10027 Lentisphaerae Unclassified sf_5 <0.001 0.00725 AJ431234.1 Cytophaga sp. str. Dex80-4310330 Lentisphaerae Unclassified sf_5 <0.001 0.00725 AF507900.1 Mono lake clone ML635J-589704 Lentisphaerae Unclassified sf_5 0.0363 0.04982 AJ431235.1 Cytophaga sp. str. Dex80-646454 marine group A Unclassified sf_1 0.0011 0.01026 U34043.1 marine clone SAR406

2437 Natronoanaerobium Unclassified sf_1 0.0167 0.03838 AF507879.2 Mono Lake at depth 23m station 6 July 2000 clone

ML623J-19

10254 NC10 Unclassified sf_1 0.032 0.0471 AJ519650.1 uranium mill tailings soil sample clone Sh765B-TzT-35

4695 Planctomycetes Anammoxales sf_4 0.0165 0.03808 AF316773.1 Crater Lake clone CL500-159662 Planctomycetes Anammoxales sf_4 0.0275 0.04537 AF407728.1 Great Artesian Basin clone B834704 Planctomycetes Pirellulae sf_3 0.003 0.01928 BX294700.1 aerobic basin clone CY0ARA025E114818 Planctomycetes Planctomycetaceae sf_3 0.0032 0.01942 AY328733.1 drinking water system simulator clone DSSD344895 Planctomycetes Unclassified sf_1 0.0075 0.02891 AY093482.1 deep marine sediment clone MB-C2-1474897 Planctomycetes Unclassified sf_1 0.0076 0.02922 AY093476.1 deep marine sediment clone MB-C2-1056922 Proteobacteria Magnetospirillaceae sf_1 0.0095 0.03064 AY171615.1 Dechlorospirillum sp. str. SN16917 Proteobacteria Bradyrhizobiaceae sf_1 0.0364 0.04982 D11345.1 Bradyrhizobium japonicum str. IAM 126087078 Proteobacteria Bradyrhizobiaceae sf_1 0.0278 0.04537 M69186.1 Afipia clevelandensis7646 Proteobacteria Hyphomicrobiaceae sf_1 0.006 0.02622 Y14304.1 Hyphomicrobium aestuarii str. DSM 15647323 Proteobacteria Unclassified sf_1 0.0217 0.041797263 Proteobacteria Rhodobacteraceae sf_1 0.0136 0.035246648 Proteobacteria Anaplasmataceae sf_3 0.031 0.04662 AF035160.1 Wolbachia sp6639 Proteobacteria Unclassified sf_2 0.0109 0.03308

10227 Proteobacteria Desulfoarculaceae sf_2 0.0039 0.02178 AY193132.1 marine sediment clone Bol119800 Proteobacteria Desulfobacteraceae sf_5 0.0058 0.0258 AF523960.1 forested wetland clone FW57


Taxa ID




9818 Proteobacteria Desulfobacteraceae sf_5 0.0025 0.01738 AY216453.1 temperate estuarine mud clone KM629813 Proteobacteria Unclassified sf_3 0.0132 0.03524 AF420340.1 hydrothermal sediment clone AF420340

10020 Proteobacteria Desulfuromonaceae sf_1 0.0157 0.03694 AJ519664.1 uranium mill tailings soil sample clone GuBH2-AG-114 proteobacterium

10171 Proteobacteria Geobacteraceae sf_1 0.0032 0.01942

482 Proteobacteria Geobacteraceae sf_1 0.0044 0.02307 AF529120.1 trichloroethene-contaminated site clone FTLM205 proteobacterium

244 Proteobacteria Unclassified sf_9 0.0012 0.01088 AY093483.1 deep marine sediment clone MB-C2-1529760 Proteobacteria Unclassified sf_9 0.0031 0.01928 AY093467.1 deep marine sediment clone MB-A2-1379876 Proteobacteria Unclassified sf_9 0.0015 0.01253 AY093471.1 deep marine sediment clone MB-B2-1068533 Proteobacteria Alteromonadaceae sf_1 0.0115 0.034189292 Proteobacteria Alteromonadaceae sf_1 0.0191 0.04079562 Proteobacteria Alteromonadaceae sf_1 0.0296 0.04621 AF513941.2 Alteromonadaceae clone PH-B55N

10091 Proteobacteria Unclassified sf_28 0.0267 0.045346458 Spirochaetes Spirochaetaceae sf_1 0.0032 0.01942 AB084961.1 termite gut clone NkS34243 Unclassified Unclassified sf_106 0.0256 0.04436 AF027097.1 hot spring clone OPB25

5022 Unclassified Unclassified sf_148 0.0175 0.03967 AF454327.1 plastid clone ML310M-374410 Unclassified Unclassified sf_160 0.0039 0.02178

95 WS3 Unclassified sf_3 0.0092 0.0302 AJ535231.1 marine sediment above hydrate ridge clone Hyd24-32

Taxa detected higher in HIV-uninfected patients6414 Acidobacteria Acidobacteriaceae sf_16 0.0238 0.04276 AF529350.1 PCE-contaminated site clone CLs73

6345 Acidobacteria Acidobacteriaceae sf_6 0.0088 0.0302 AJ534634.1 soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-77 bacterium

6359 Acidobacteria Acidobacteriaceae sf_6 0.0056 0.02533 AF529322.1 PCE-contaminated site clone CLi1146362 Acidobacteria Acidobacteriaceae sf_6 0.0326 0.04782 Y07646.1 grassland soil clone DA0526423 Acidobacteria Acidobacteriaceae sf_6 0.014 0.03541 AF523979.1 coal effluent wetland clone FW921337 Actinobacteria Unclassified sf_4 0.0269 0.04537 AF234118.1 Sturt arid-zone soil clone #0425-2M17

1843 Actinobacteria Rubrobacteraceae sf_1 0.0155 0.03694 AJ536866.1 uranium mining waste pile soil sample clone JG30-KF-A23

5511 Bacteroidetes Unclassified sf_15 0.0023 0.01654 AJ535256.1 marine sediment above hydrate ridge clone Hyd-B2-1 bacterium

6046 Bacteroidetes Unclassified sf_15 0.0065 0.02704 AJ488097.1 chlorobenzene-degrading consortium clone IIIB-15828 Bacteroidetes Blattabacteriaceae sf_1 0.019 0.0407 Z35664.1 Blattabacterium species5509 Bacteroidetes Flavobacteriaceae sf_1 0.0196 0.0407 AF539756.1 Cellulophaga sp. str. E14


Taxa ID




5619 Bacteroidetes Crenotrichaceae sf_11 0.0293 0.04621 AY211072.1 anaerobic VC-degrading enrichment clone VC10 bacterium

6050 Bacteroidetes Crenotrichaceae sf_11 0.0251 0.04413 AF527580.1 EBPR sludge lab scale clone LPB085459 Bacteroidetes Sphingobacteriaceae sf_1 0.0103 0.03212 AJ551152.1 Pedobacter sp. An132497 Chloroflexi Unclassified sf_1 0.0028 0.0188 AF524015.1 forested wetland clone FW604551 Firmicutes Clostridiaceae sf_12 0.0044 0.02307 X78070.1 Clostridium acetobutylicum str. ATCC 824 (T)4366 Firmicutes Lachnospiraceae sf_5 0.009 0.0302 AJ488078.1 chlorobenzene-degrading consortium clone IB-182433 Firmicutes Unclassified sf_8 0.0045 0.02307 AF282252.1 Ferribacter thermoautotrophicus str. JW/JH-Fiji-2546 Firmicutes Unclassified sf_8 0.0232 0.04245 AF282254.1 Ferribacter thermoautotrophicus

7529 Proteobacteria Acetobacteraceae sf_1 0.0029 0.019 AJ012698.1 Gluconacetobacter europaeus str. ZIM B028 V37600 Proteobacteria Acetobacteraceae sf_1 0.0146 0.03613 AJ001632.1 Acetobacter pomorum str. LTH24586945 Proteobacteria Unclassified sf_1 0.0015 0.01249 AB081581.3 Rhizobiales str. A486692 Proteobacteria Phyllobacteriaceae sf_1 0.0194 0.0407 AY786080.1 Phyllobacterium trifolii str. PETP026857 Proteobacteria Phyllobacteriaceae sf_1 0.0054 0.02506 AY195844.1 Mesorhizobium mediterraneum str. PECA207433 Proteobacteria Rhodobacteraceae sf_1 0.0206 0.04136 AF359537.1 Scrippsiella trochoidea NEPCC 157319 Proteobacteria Sphingomonadaceae sf_1 0.0161 0.03752 AF425996.1 Anabaena circinalis AWQC118C isolate str. UNSW16987 Proteobacteria Unclassified sf_6 <0.001 0.008577312 Proteobacteria Unclassified sf_6 0.0048 0.024087377 Proteobacteria Unclassified sf_6 0.0122 0.03442 AY192273.1 Rocky Mountain alpine soil clone W2b-8C7572 Proteobacteria Unclassified sf_6 0.0315 0.046867768 Proteobacteria Alcaligenaceae sf_1 0.0254 0.0442 AF371864.1 swine intestine clone p-861-a58094 Proteobacteria Alcaligenaceae sf_1 0.0057 0.0258 AF430122.1 Alcaligenes sp. str. VKM B-2263 dcm67720 Proteobacteria Burkholderiaceae sf_1 0.0045 0.02307 AY218566.1 penguin droppings sediments clone KD1-797782 Proteobacteria Burkholderiaceae sf_1 0.0045 0.02307 AY040365.1 Burkholderia hospita str. LMG 20598T7914 Proteobacteria Burkholderiaceae sf_1 0.0063 0.02669 AB021422.1 Burkholderia andropogonis str. ATCC 19311T7705 Proteobacteria Comamonadaceae sf_1 0.0079 0.02922 AY218644.1 penguin droppings sediments clone KD4-77943 Proteobacteria Comamonadaceae sf_1 0.035 0.04907 AF035052.1 Aquabacterium parvum str. B67808 Proteobacteria Unclassified sf_1 0.0252 0.0442 AY221081.1 Mammoth cave clone CCU25

7818 Proteobacteria Unclassified sf_1 <0.001 0.00857 AJ534623.1soil sample uranium mining waste pile near town Johanngeorgenstadt clone JG36-TzT-215 proteobacterium

7993 Proteobacteria Unclassified sf_1 0.0122 0.03442 AF423222.1 soil clone 1326-28037 Proteobacteria Unclassified sf_1 0.004 0.02214 AY323827.2 Chitinimonas taiwanensis str. cf7382 Proteobacteria Unclassified sf_1 0.0267 0.04534 AF355039.1 marine clone Arctic95C-5

10079 Proteobacteria Desulfomicrobiaceae sf_1 0.0246 0.04356 AJ277896.1 Desulfomicrobium baculatum str. DSM 1742

9735 Proteobacteria Polyangiaceae sf_3 0.0298 0.04638 AJ518790.1 uranium mining waste pile clone JG37-AG-15 proteobacterium


Taxa ID




9900 Proteobacteria Polyangiaceae sf_3 0.0135 0.03524 AF280857.1 bioreactor clone mle1-2710092 Proteobacteria Unclassified sf_1 0.0334 0.04782 AY102330.1 heavy metal-contaminated soil clone a1313410538 Proteobacteria Campylobacteraceae sf_3 0.0273 0.04537 L14624.1 Arcobacter cryaerophilus10454 Proteobacteria Helicobacteraceae sf_3 0.0312 0.04674 L36143.1 Helicobacter pullorum str. NCTC 1282610407 Proteobacteria Unclassified sf_1 0.0268 0.04534 AF420342.1 hydrothermal sediment clone AF4203428552 Proteobacteria Acidithiobacillaceae sf_1 0.0276 0.04537 AJ278723.1 Acidithiobacillus ferrooxidans str. D28621 Proteobacteria Aeromonadaceae sf_1 0.007 0.02749 AF427150.1 Aeromonas sp. PAR2A9026 Proteobacteria Aeromonadaceae sf_1 0.0185 0.0407 AJ009860.1 Haemophilus piscium str. NCIMB 1952

9294 Proteobacteria Aeromonadaceae sf_1 <0.001 0.00725 AJ557849.1

Arctic deep sea Isolation common chemoorganotrophic oxygen-respiring polar current d 1210 (50 m above sediment Hakon Mosby Mud Vulcano (HMMV 72N 14E)) via serial dilution series applying 2 g/l yeast or meat extract artifical seawater

9440 Proteobacteria Aeromonadaceae sf_1 0.0332 0.04782 X60412.1 Aeromonas sobria str. NCIMB 120658196 Proteobacteria Alteromonadaceae sf_1 0.0121 0.034428336 Proteobacteria Alteromonadaceae sf_1 0.0154 0.03694 AF237977.1 Alteromonas sp. str. MS238374 Proteobacteria Alteromonadaceae sf_1 0.0094 0.03064 AB076560.1 Agarivorans albus str. MKT 898578 Proteobacteria Alteromonadaceae sf_1 <0.001 0.00857 AY147906.1 Marinobacter lipolyticus str. SM-198580 Proteobacteria Alteromonadaceae sf_1 0.0108 0.03308 AJ295713.1 Arctic seawater isolate str. R70768753 Proteobacteria Alteromonadaceae sf_1 0.0275 0.04537 AY553079.1 Idiomarina loihiensis str. GSP378932 Proteobacteria Alteromonadaceae sf_1 0.0174 0.03967 AF045560.1 Pseudoalteromonas antarctica str. N-19035 Proteobacteria Alteromonadaceae sf_1 0.0015 0.01253 AB124836.1 Microbulbifer sp. str. JAMB-A94

9058 Proteobacteria Alteromonadaceae sf_1 0.0119 0.03442 X82136.1 Pseudoalteromonas carrageenovora str. ATCC 12662T

9143 Proteobacteria Alteromonadaceae sf_1 0.0122 0.03442 AJ417594.1 Pseudoalteromonas agarivorans str. KMM 2559218 Proteobacteria Alteromonadaceae sf_1 0.0082 0.02922 X67024.1 Pseudoalteromonas haloplanktis str. ATCC 143939239 Proteobacteria Alteromonadaceae sf_1 0.0019 0.01478 AF468400.1 Arctic sea ice ARK102289324 Proteobacteria Alteromonadaceae sf_1 0.0028 0.0188 AF316891.1 Pseudoalteromonas ruthenica str. KMM300

9369 Proteobacteria Alteromonadaceae sf_1 0.0258 0.04448 X82144.1 Pseudoalteromonas luteoviolacea str. NCIMB 1893T

9384 Proteobacteria Alteromonadaceae sf_1 0.0197 0.0407 AJ132226.1 Moritella viscosa str. NVI 88/478T9386 Proteobacteria Alteromonadaceae sf_1 0.0092 0.0302 AB016267.1 Alteromonas sp. str. NIBH P2M119411 Proteobacteria Alteromonadaceae sf_1 0.0307 0.04658 AY170366.1 Shewanella waksmanii str. KMM 38239416 Proteobacteria Alteromonadaceae sf_1 0.0044 0.02307 AF539786.1 marine isolate str. R89640 Proteobacteria Alteromonadaceae sf_1 0.008 0.02922 AY028205.1 exposed to diatom detritus isolate str. Tw-10 Tw-108641 Proteobacteria Shewanellaceae sf_1 0.0222 0.04195 AJ252022.1 Moritella abyssi str. 2693


Taxa ID




9081 Proteobacteria Shewanellaceae sf_1 0.0218 0.04179 AB059264.1 Shewanella sp. str. MTW-19246 Proteobacteria Unclassified sf_1 0.0019 0.01478 AY221036.1 Mammoth Cave sediment clone CCD249450 Proteobacteria Ectothiorhodospiraceae sf_1 0.0035 0.02039 AJ318526.1 Halorhodospira neutrophila str. SG 3304

9598 Proteobacteria Ectothiorhodospiraceae sf_1 0.0092 0.0302 AF507818.1 Mono Lake at depth 2 m station 6 July 2000 clone ML602J-47 proteobacterium

9316 Proteobacteria Unclassified sf_1 0.0191 0.0407

9458 Proteobacteria Unclassified sf_1 0.0135 0.03524 AJ518786.1 uranium mining waste pile clone JG37-AG-94 proteobacterium

8251 Proteobacteria Enterobacteriaceae sf_1 0.0302 0.04658 AF214640.1 Nitrogen-fixing isolate str. CANF38282 Proteobacteria Enterobacteriaceae sf_1 0.0156 0.03694 AF476101.1 Antonina pretiosa symbiont8286 Proteobacteria Enterobacteriaceae sf_1 0.0223 0.042 AF476102.1 Cyphonococcus alpinus symbiont8528 Proteobacteria Enterobacteriaceae sf_1 0.0201 0.0407 Y17665.1 Enterobacter cloacae Nr. 38742 Proteobacteria Enterobacteriaceae sf_1 0.0281 0.04537 AF084835.1 USA:New York isolate str. KN48886 Proteobacteria Enterobacteriaceae sf_1 0.0219 0.04179 AF170176.1 Salmonella typhimurium LT2 str. SGSC14128890 Proteobacteria Enterobacteriaceae sf_1 0.0234 0.04246 X93216.1 Raoultella planticola str. DR39151 Proteobacteria Enterobacteriaceae sf_1 <0.001 0.007259496 Proteobacteria Enterobacteriaceae sf_1 0.0087 0.03028457 Proteobacteria Coxiellaceae sf_3 0.022 0.04179 AJ240918.1 5' clone CHAB-XI-27

9198 Proteobacteria Coxiellaceae sf_3 0.028 0.04537 AJ295651.1 uranium mining waste pile clone KF-JG30-B15 KF-JG30-B15

8587 Proteobacteria Unclassified sf_3 0.0116 0.03418 AF526927.2 Mars Odyssey Orbiter and encapsulation facility clone T5-3

9438 Proteobacteria Methylococcaceae sf_1 0.019 0.0407 AJ535221.1 marine sediment above hydrate ridge clone Hyd24-01 proteobacterium

8335 Proteobacteria Alcanivoraceae sf_1 0.0011 0.0103 AB055205.1 Alcanivorax sp. str. K3-3 (MBIC 4323)9658 Proteobacteria Alcanivoraceae sf_1 0.0119 0.03442 AB053127.1 Alcanivorax sp. str. Haw18514 Proteobacteria Halomonadaceae sf_1 0.022 0.04179 AJ295144.1 Chromohalobacter israelensis str. ATCC 43985 T8889 Proteobacteria Saccharospirillaceae sf_1 0.0212 0.04179 AF452603.1 hypersaline Mono Lake clone ML110J-58327 Proteobacteria Unclassified sf_3 0.0155 0.03694 AF468398.1 Arctic sea ice ARK101488366 Proteobacteria Moraxellaceae sf_3 0.0246 0.04356 AJ609556.1 Psychrobacter frigidicola str. DSM 124118604 Proteobacteria Moraxellaceae sf_3 0.0204 0.04107 AB087260.2 Moraxella oblonga str. IAM 149718727 Proteobacteria Moraxellaceae sf_3 0.0068 0.02738 AY251390.1 Alkanindiges hongkongensis str. HKU99428 Proteobacteria Moraxellaceae sf_3 0.0063 0.02669 AF143841.1 hydrocarbon-degrading consortium clone AF2-1D9466 Proteobacteria Moraxellaceae sf_3 0.0303 0.04658 AF509830.1 Acinetobacter tandoii str. 4N139641 Proteobacteria Moraxellaceae sf_3 0.0052 0.02468 X81662.1 Acinetobacter haemolyticus

8209 Proteobacteria Pseudomonadaceae sf_1 0.0136 0.03524 AJ518787.1 uranium mining waste pile clone JG37-AG-122 proteobacterium


Taxa ID




8288 Proteobacteria Pseudomonadaceae sf_1 0.0091 0.03028338 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF267911.1 Pseudomonas synxantha str. DSM 13080 G8344 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF425998.1 Anabaena circinalis AWQC118C isolate str. UNSW3

8433 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB001441.1 Pseudomonas syringae pv. broussonetiae str. KOZ 8101 pv.

8474 Proteobacteria Pseudomonadaceae sf_1 0.0019 0.01476 AJ534672.1ground water deep-well injection disposal site radioactive wastes Tomsk-7 clone S15A-MN7 proteobacterium

8508 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF530073.1 Pseudomonas citronellolis str. TERIDB268513 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF064458.1 Pseudomonas monteilii str. CIP 1048838553 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00857 AB046997.1 Pseudomonas fulva str. IAM 15878561 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF332541.1 Pseudomonas sp. B658601 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB021401.1 Pseudomonas marginalis str. ATCC 10844T8635 Proteobacteria Pseudomonadaceae sf_1 0.0133 0.035248687 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00734 AF094738.1 Pseudomonas putida str. ATCC 174728691 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AE004501.1 Pseudomonas aeruginosa str. PAO18708 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.007258725 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AJ419674.1 Pseudomonas sp. str. 2N1-18755 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AJ288146.1 Pseudomonas sp. SK-1-3-18777 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB095005.1 Pseudomonas sp. str. KNA6-58813 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AY150184.1 Lyrodus pedicellatus symbiont8852 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF063219.1 Pseudomonas stutzeri str. KC9002 Proteobacteria Pseudomonadaceae sf_1 0.0067 0.02738 AJ316016.1 Paederus fuscipes endosymbiont9005 Proteobacteria Pseudomonadaceae sf_1 0.002 0.0153 AJ278108.1 Pseudomonas sp. str. KY9028 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF468452.1 Pseudomonas koreensis str. Ps 9-14

9049 Proteobacteria Pseudomonadaceae sf_1 0.0033 0.01954 AJ296559.1 uranium mining mill tailing clone GR-Sh2-34 GR-Sh2-34

9050 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF139998.1 Pseudomonas sp. str. ML-1249056 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB037546.1 Pseudomonas aeruginosa str. #479068 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF143245.1 Pseudomonas stutzeri str. A15019172 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB041885.1 Pseudomonas psychrophila str. E-39175 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF405328.1 Pseudomonas extremorientalis str. KMM34479219 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF181576.1 Pseudomonas cf. monteilii 9

9221 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AJ492830.1 Pseudomonas fulgida str. DSM 14938 = LMG 2146 P 515/12

9228 Proteobacteria Pseudomonadaceae sf_1 0.0012 0.01088 AJ297767.1 Pseudomonas stutzeri HY-1059238 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725


Taxa ID




9240 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AJ278812.1 Pseudomonas fluorescens str. CHA09243 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 Z76670.1 Pseudomonas tolaasii str. LMG 2342T ()9267 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AB001450.1 Pseudomonas syringae pv. theae str. PT19295 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.007259300 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AY150183.1 Lyrodus pedicellatus symbiont9310 Proteobacteria Pseudomonadaceae sf_1 0.0039 0.02178 AJ519791.1 Pseudomonas sp. str. AC-1679343 Proteobacteria Pseudomonadaceae sf_1 0.0029 0.019 AF448515.1 Cellvibrio subsp. mixtus str. ACM 26019366 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00857 AJ293826.1 Arctic seawater isolate str. R73669469 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF290486.1 cf. Pseudomonas sp. clone Llangefni 529493 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF430125.1 Pseudomonas sp. str. dcm7B9588 Proteobacteria Pseudomonadaceae sf_1 <0.001 0.00725 AF530072.1 Pseudomonas citronellolis str. TERIDB189613 Proteobacteria Pseudomonadaceae sf_1 0.0086 0.0302 U01916.1 Pseudomonas flavescens str. B629344 Proteobacteria Unclassified sf_1 0.0333 0.04782 AF005249.1 Shewanella algae str. ATCC 511928605 Proteobacteria Unclassified sf_1 0.0139 0.03541 AF382104.1 bacterioplankton clone ZA2525c9128 Proteobacteria Unclassified sf_1 0.0226 0.04203 X95229.1 Lucina nassula gill symbiont9291 Proteobacteria Piscirickettsiaceae sf_3 <0.001 0.00725 AF384373.1 Methylophaga alcalica str. M399015 Proteobacteria Thiotrichaceae sf_3 0.0091 0.0302 AF110274.1 Beggiatoa alba str. B18LD; ATCC 335558606 Proteobacteria Unclassified sf_3 0.0051 0.024688646 Proteobacteria Unclassified sf_3 0.007 0.02749

8714 Proteobacteria Unclassified sf_3 <0.001 0.00954 AB021372.1 Marinobacter hydrocarbonoclasticus str. ATCC 27132T

8926 Proteobacteria Unclassified sf_3 0.0256 0.04436 AB099937.1 inactive deep-sea hydrothermal vent chimneys clone IheB2-13

9124 Proteobacteria Unclassified sf_3 0.0016 0.01314 AY145601.1 10e-6 dilution marine samples Weser estuary clone DC8-80-1 proteobacterium

9367 Proteobacteria Unclassified sf_3 0.0082 0.02922 AF387348.1 USA: Pacific Ocean seawater Naha Vents Hawaii isolate str. PV-4

8855 Proteobacteria Unclassified sf_4 0.0082 0.029228747 Proteobacteria Unclassified sf_1 0.0053 0.02493 AJ536882.1 uranium waste soil clone JG30-KF-CM358689 Proteobacteria Xanthomonadaceae sf_3 0.0036 0.02083 AB110496.1 Dyemonas todaii str. XD109270 Proteobacteria Xanthomonadaceae sf_3 0.0331 0.04782 AJ293463.1 Stenotrophomonas rhizophila str. e-p10

9332 Proteobacteria Xanthomonadaceae sf_3 0.0151 0.03654 AY096032.1 wetland ecosystem constructed to remediate mine drainage isolate str. WJ2 WJ2

9558 Proteobacteria Unclassified sf_8 0.0098 0.03101719 Synergistes Unclassified sf_3 0.0287 0.04576 AY207056.1 Synergistes sp. P1 str. P4G_18

667 Thermodesulfobacteria Thermodesulfobacteriaceae sf_1 0.015 0.03654 AF411013.1 Geothermobacterium ferrireducens


Taxa ID




8155 TM7 Unclassified sf_1 0.0048 0.02408 AY134895.1 oral periodontitis clone EW0866355 Unclassified Unclassified sf_140 0.0075 0.02891

10012 Unclassified Unclassified sf_160 0.0172 0.03953a It should be noted that following correction for false discovery, reported q-values ranged from 0.007-0.049, indicating that these taxa that exhibited a significant p-value (p<0.05) had a ~0.7-5% chance of being a random event.

Documents

Table S1. Clinical characteristics of samples. · 8/14/2012 · 1428Actinobacteria Corynebacteriaceae sf_1 AF537604.1 Corynebacterium simulans National Microbiology Laboratory Special