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Corrigendum: The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiotaIlias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz, Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt, Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, Jörg Overmann, Bärbel Stecher and Thomas Clavel

Nature Microbiology 1, 16131 (2016); published 8 August 2016; corrected 17 October 2016

In the original version of this paper, several of the bacterial genus and species names were incorrect or incompatible with formal taxo-nomic validation and have had to be modified. The relevant names and descriptions have been amended in all versions of the Article. In addition, Supplementary Figs 3,4 and Supplementary Tables 1,4,5,11 have been replaced.

ARTICLESNATURE MICROBIOLOGY DOI: 10.1038/NMICROBIOL.2016.219

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The Mouse Intestinal Bacterial Collection (miBC)provides host-specific insight into cultured diversity

and functional potential of the gut microbiota

Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U. Foesel, Jan P. Meier-Kolthoff,

Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux,

Debora Garzetti, Mareike Wenning, Thi P. N. Bui, Jun Wang, Floor Hugenholtz,

Caroline M. Plugge, Daniel A. Peterson, Mathias W. Hornef, John F. Baines, Hauke Smidt,

Jens Walter, Karsten Kristiansen, Henrik B. Nielsen, Dirk Haller, Jörg Overmann,

Bärbel Stecher and Thomas Clavel

SUPPLEMENTARY INFORMATIONARTICLE NUMBER: 16131 | DOI: 10.1038/NMICROBIOL.2016.131

NATURE MICROBIOLOGY | www.nature.com/naturemicrobiology 1

Families (leaf labels):

Sutterellaceae

CoriobacteriaceaeErysipelotrichaceae

Oscillospiraceae

Lactobacillaceae

Porphyromonadaceae

Lachnospiraceae

Eubacteriaceae

Clostridiaceae

Bacteroidaceae

Pasteurellaceae

NA

Ruminococcaceae

Phyla (outer column):

NA

Proteobacteria

Bacteroidetes

Actinobacteria

Firmicutes

0.01

DSM 26109Parasutterella excrementihominisSutterella parvirubraSutterella wadsworthensis

DSM 28627Pasteurella pneumotropica

Haemophilus aegyptiusHaemophilus pittmaniaeAggregatibacter actinomycetemcomitans

Bacteroides faecichinchillae

Bacteroides caccaeBacteroides xylanivoransBacteroides ovatusDSM 26085Bacteroides acidifaciens

Bacteroides faecis

Bacteroides fragilis

DSM 28989

Barnesiella intestinihominisBarnesiella viscericola

Coprobacter fastidiosus

Paludibacter propionicigenesDysgonomonas capnocytophagoidesProteiniphilum acetatigenes

DSM 29508Enterorhabdus caecimuris

Enterorhabdus mucosicola

Asaccharobacter celatusAdlercreutzia equolifaciens

Clostridium ramosumClostridium spiroforme

Clostridium cocleatum

Catenibacterium mitsuokai

Sharpea azabuensisEggerthia catenaformis

Kandleria vitulina

DSM 29487

DSM 29481Clostridium innocuum

Eubacterium dolichum

Eubacterium limosumPseudoramibacter alactolyticus

Anaerofustis stercorihominisDSM 28593Clostridium butyricum

Ruminococcus bromiiClostridium sporosphaeroidesDSM 26090

Clostridium leptumAnaerotruncus colihominis

Ethanoligenens harbinenseClostridium cellulosi

Pseudoflavonifractor capillosusFlavonifractor plautii

Intestinimonas butyriciproducensDSM 27579Clostridium virideOscillibacter ruminantum

Subdoligranulum variabileFaecalibacterium prausnitzii

Eubacterium ventriosumRoseburia hominis

Clostridium clostridioformeClostridium symbiosum

DSM 29486DSM 28559

Blautia wexleraeDSM 29492

Blautia schinkii

Blautia productaBlautia hydrogenotrophicaBlautia hansenii

Clostridium oroticumEubacterium contortumEubacterium fissicatena

DSM 29489Ruminococcus gnavus

Dorea longicatenaClostridium scindensClostridium hylemonaeDSM 28560

100

100

100100

100

10096

100100

100

100

100100

90100

100

76

64100

100

10092

100

100100

100

100

100

100

100

10094

67100

10098

100100

100

10084

100

100

100

96

10061

9961

100

100

100100

82100

100

100

100

100

6496

100

93

100

10091

94100

100

100100

100100

100100

100

LachnospiraceaeRum

inococcaceaeErysipelotrichaceae

Proposed family clusters

Supplementary Figure 1. Whole proteome-based phylogenomic tree of novel taxa within miBCand closely related species. Affiliation to phyla and families is as in the List of Prokaryotic names withStanding in Nomenclature1. Analysis was based on the latest GBDP algorithm2 and inferred as describedpreviously3 and visualized using iTOL4. Details are given in the Methods section. Type strains are printedin bold face. Label colors represent family affiliation, whereas the outer column denotes the respectivephylum.

Supplementary Figure 2. Distribution of all pairwise 16S rRNA gene sequence similarities.The histograms show the number of comparisons that matched the given percentage identitydisplayed on the x-axis. Analysis included the 15 novel taxa isolated from the mouse gut and62 reference strains. Bars are colored according to the phyla involved in each respective comparison.The figure was visualized using the ggplot package6 for the R statistical framework..

Phyla of reference strainsto which mouse isolateswere compared to:

Actinobacteria

Bacteroidetes

Firmicutes

Proteobacteria

within-mouse comp.

% sequence similarity (16S rRNA gene)

Freq

uenc

y

2 µm2 µm

Frisingicoccus murisDSM 28559

Extibacter murisDSM 28560

Irregularibacter murisDSM 28593

Pasteurella caecimurisDSM 28627

Longicatena caecimuris DSM 29481

10 µm

Cuneatibacter caecimuris DSM 29486

5 µm

2 µm

2 µm

5 µm

Longibaculum muris DSM 29487

5 µm

‘Blautia caecimuris’DSM 29492

2 µm

Enterorhabdus muris DSM 29508

Flintibacter butyricusDSM 27579

Acutalibacter murisDSM 26090

2 µm

2 µm

5 µm

Muricomes intestini DSM 29489

Supplementary Figure 3. Light

microscopic images of novel bacteria

within miBC. The images are

representatives of approximately 20 observed

microscopic fields and three to five recorded

images per strain. Microscopic pictures of

‘Bacteroides caecimuris’ DSM 26085,

‘Turicimonas muris’ DSM 26109, and

‘Muribaculum intestinale’ DSM 28989 will be

published elsewhere (Brugiroux et al.)

0%

40%

80%

0%

40%

80%

Tot. prevalenceD

ietM

ouse geneticsH

ousing lab

‘Acutalibactermuris’

DSM26090T

‘Muribaculumintestinale’DSM28989T

‘Bacteroidescaecimuris’DSM26085T

‘Enterorhabdusmuris’

DSM29508T

‘Flintibacterbutyricus’

DSM27579T

>60 % <60 %

high-fat control

swiss websterSV129SJL-C57BL/6SJLNODC57BL/6BALB/c129S

UGOTUCPHPfizerNIFESDTUBGI (as in Xiao et al., Nat Biotech, 2015)

Supplementary Figure 4. Occurrence of the 5 novel bacteria in miBC that matchedmetagenomic species. Technical details are given in the text. The metagenomic dataset wasobtained from 184 mouse fecal samples originating from 6 housing laboratories and 5 differentproviders5. Original data are provided Supplementary Table 5.

pvalue:0.00106 corrected:0.0046re

lativ

e se

quen

ce a

bund

ance

(%)

F8

F5

F7F6

F2

F3

F1

F4

Number ofpositive samples

1

5

4

6

5

23

37

5

Total

5

5

4

8

5

23

38

5

F8F5 F7F6F2 F3F1 F4

0

5

10

15

20

family S24−7 (’Muribaculaceae’)

Supplementary Figure 5. Relative sequence abundance of family S24-7. Caecal samples collected from 93 mice housed in eight animal facilities (F1-8) were analyzed by high-throughput 16S rRNA genesequencing. The total number of mice per facility and those which were positive for family S24-7(number of positive samples) are indicated below the boxplots, which show median values andinter-quartile ranges. The p-value was obtained using ANOVA and corrected following theBenjamini-Hochberg method.

Supplementary Figure 6. Dendrogram analysis of PFAM profiles. The dendrogram was

calulcated in the R programming environment using the Jaccard method. The heatmap shows

PFAM in a binary presence/absence fashion (blue/white) ranked according to decreasing PFAM

prevalence (from left to right) across all samples (metagenomes and cultivable genome collections).

Core (present in all samples) and isolate-specific PFAM are indicated by the black line and green

arrows, respectively. Corresponding PFAM lists are provided in Supplementary Table 12.

SIHUMI (8 strains)

MIBAC-1 (18 strains)

ASF (8 strains)

Metagenomes (n = 17)

miBC (76 species)

PFAMs

Supplementary Table 1. List of strains included in the mouse intestinal bacterial

collection. This file contains (A) the list of 100 strains in miBC with corresponding

information, including: species name, original strain designation, DSMZ number,

Genbank accession number of 16S rRNA gene sequences, most closely related

species, taxonomy, genome accession number, atmosphere requirement, and origin; (B)

information on the minimal bacterial consortia analyzed in the present study.

Supplementary Table 2. Genome-derived pairwise similarities between all 16S

rRNA gene sequences.

Supplementary Table 3. All pairwise digital DNA:DNA hybridization (dDDH)

estimates with confidence intervals. See the Methods section for details on the

calculation procedure.

Supplementary Table 4. Enzymatic profiles of novel bacterial taxa as assessed

with the suitable API test strips.

Supplementary Table 5. Metagenomic species analysis. The 15 novel bacterial taxa

obtained in the present study were analyzed against the mouse gene catalog5 and

searched for similarity with metagenomic species (MGS). This file contains information

on (A) the number of hits to the gene catalog for each new species; (B) MGS

characteristics for the 5 new taxa with significant hits; and (C) number of fecal samples

positive for each of these 5 taxa across the different mouse categories

Supplementary Table 6. High-throughput 16S rRNA gene sequence analysis:

Metadata and OTU table with normalized relative sequence abundances. A total of

93 mouse caecal samples were analyzed by sequencing V5/6 regions of the 16S rRNA

gene as described in detail in the text. Data were analyzed using IMNGS

(www.imngs.org) with a pipeline developed in-house based on UPARSE7. OTUs

occurring at a relative abundance >0.1 % total reads in at least one sample were kept

for analysis.

Supplementary Table 7. High-throughput 16S rRNA gene sequence analysis: raw

sequence counts.

Supplementary Table 8. Animal facility-specific indicator species as derived by

high-throughput 16S rRNA gene sequence analysis.

Supplementary Table 9. Raw output of the integrated 16S rRNA-based studies

based on IMNGS. The tool is available at www.imngs.org. The nearly full-length 16S

rRNA gene sequences of all 76 species in miBC were used as queries to assess their

occurrence and prevalence in the pool of 51,073 high-throughput 16S rRNA datasets

stored in the Sequence Read Archive (SRA). The present file contains the raw output of

the analysis as delivered by IMNGS, including sequence counts for each miBC species

and SRA samples at the level of 97% sequence identity.

Supplementary Table 10. List of mouse and human fecal metagenomes used in

the present study to assess coverage by the collection of cultured strains and by

minimal bacteriomes.

Supplementary Table 11. Composition of the random sets of miBC-derived strains

used to test the relevance of the data-driven selection MIBAC-1.

Supplementary Table 12. Core and miBC-specific PFAM features.

Supplementary Sequence File. This file contains the partial nucleotide sequences of

all operational taxonomic units from the high-throughput 16S rRNA gene dataset

generated in the present study.

Supplementary references

1. Euzeby JP. List of Bacterial Names with Standing in Nomenclature: a folder

available on the Internet. International journal of systematic bacteriology 47, 590-

592 (1997).

2. Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. Genome sequence-based

species delimitation with confidence intervals and improved distance functions.

BMC bioinformatics 14, 60 (2013).

3. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Highly parallelized inference of

large genome-based phylogenies. In: Concurrency Computation Practice and

Experience (ed^(eds) (2014).

4. Letunic I, Bork P. Interactive Tree Of Life v2: online annotation and display of

phylogenetic trees made easy. Nucleic acids research 39, W475-478 (2011).

5. Xiao L, et al. A catalog of the mouse gut metagenome. Nature biotechnology 33,

1103-1108 (2015).

6. Wickham H. Ggplot2: Elegant Graphics for Data Analysis. Springer (2009).

7. Edgar RC. UPARSE: highly accurate OTU sequences from microbial amplicon

reads. Nature methods 10, 996-998 (2013).