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The Use of Defined Microbial Communities To ModelHost-Microbe Interactions in the Human Gut
Janneke Elzinga,a John van der Oost,a Willem M. de Vos,a,b Hauke Smidta
aLaboratory of Microbiology, Wageningen University and Research, Wageningen, The NetherlandsbResearch Programme Unit Human Microbiome, Faculty of Medicine, Helsinki University, Helsinki, Finland
SUMMARY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2DEFINED COMMUNITIES MIMICKING THE NORMAL INTESTINAL MICROBIOTA
IN VIVO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3(Altered) Schaedler Flora . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3Oligo-MM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20SIHUMI(x) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20Toward a Normal Model Gut Microbiota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21Defined Communities in Nonrodents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
OTHER DEFINED COMMUNITIES IN VIVO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Therapeutic Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23Minimal Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
CRITICAL EVALUATION OF DEFINED COMMUNITIES IN VIVO: THE MICROBIOTA . . . . . 24How Representative Are Defined Microbiota Models of a Normal Microbiota? . . . . . . . . . 24Simplified versus Complex Communities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25Bottom-Up versus Top-Down Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27Future Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
CRITICAL EVALUATION OF DEFINED COMMUNITIES IN VIVO: THE HOST . . . . . . . . . . . . . . 28Host Parameters Influencing the Microbiota . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28Validation of In Vivo Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
DEFINED COMMUNITIES IN VITRO . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Modeling the Intestinal Microbiota In Vitro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31Modeling the Host In Vitro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32Validation of In Vitro Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
CONCLUSIONS AND FUTURE OUTLOOK . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33ACKNOWLEDGMENTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34REFERENCES . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34AUTHOR BIOS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
SUMMARY The human intestinal ecosystem is characterized by a complex interplaybetween different microorganisms and the host. The high variation within the hu-man population further complicates the quest toward an adequate understanding ofthis complex system that is so relevant to human health and well-being. To studyhost-microbe interactions, defined synthetic bacterial communities have been intro-duced in gnotobiotic animals or in sophisticated in vitro cell models. This review re-inforces that our limited understanding has often hampered the appropriate designof defined communities that represent the human gut microbiota. On top of this,some communities have been applied to in vivo models that differ appreciably fromthe human host. In this review, the advantages and disadvantages of using definedmicrobial communities are outlined, and suggestions for future improvement ofhost-microbe interaction models are provided. With respect to the host, technologi-cal advances, such as the development of a gut-on-a-chip system and intestinal or-ganoids, may contribute to more-accurate in vitro models of the human host. Withrespect to the microbiota, due to the increasing availability of representative cul-tured isolates and their genomic sequences, our understanding and controllability of
Citation Elzinga J, van der Oost J, de Vos WM,Smidt H. 2019. The use of defined microbialcommunities to model host-microbeinteractions in the human gut. Microbiol MolBiol Rev 83:e00054-18. https://doi.org/10.1128/MMBR.00054-18.
Copyright © 2019 American Society forMicrobiology. All Rights Reserved.
Address correspondence to Janneke Elzinga,[email protected].
Published 13 March 2019
REVIEW
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the human gut “core microbiota” are likely to increase. Taken together, these ad-vancements could further unravel the molecular mechanisms underlying the humangut microbiota superorganism. Such a gain of insight would provide a solid basis forthe improvement of pre-, pro-, and synbiotics as well as the development of newtherapeutic microbes.
KEYWORDS animal model, gut-on-a-chip, in vitro model, intestinal microbiota,minimal microbiota
INTRODUCTION
Given its involvement in metabolic, nutritional, physiological, and immunologicalprocesses, the human intestinal microbiome can be regarded as an essential organof the human body (1). Further strengthening its clinical relevance, the intestinalmicrobiome has been linked to numerous disease conditions, including metabolic andimmune disorders, cancer, and neurodegenerative diseases (2). However, apart from aremarkable increase in the amount of genome sequence data of the human gutmicrobiota, progress in functional insight has been hampered by its complexity: theexistence of more than 1,000 prevalent species (3), combined with the high interper-sonal variation within the human population in terms of genetics, environment, andhabits, results in a complex entity termed the human microbiome superorganism (4).The number of known host-microbe interactions has grown rapidly over the pastdecades, yet many aspects still remain obscure.
To solve this complexity, there is a need for a reductionist approach in which bothhost and microbiome are simplified to the extent that experimental variables can betightly controlled and deliberately manipulated. Regarding the microbiota, synthetic ordefined communities have been proposed as useful models to study microbial ecology(5). In recent years, the number of cultivable gastrointestinal microbial species hasrapidly expanded (3) by the use of sophisticated or brute-force culturomics approaches(6, 7). These strategies have allowed for the design of defined communities that arerepresentative of the normal human intestinal microbiota. With respect to the humanhost, laboratory animals, notably mice, have proven valuable models for developinghuman medicine. The colonization of germfree (GF) animals with defined bacterialcommunities, resulting in gnotobiotic animals, has already been applied for decades.During the 1960s and 1970s, it was recognized that the intestines of GF animals displayaberrant histological, anatomical, and physiological characteristics compared to con-ventional laboratory animals (8). The development of the Schaedler cocktail for colo-nization of the murine gut (9) marked one of the first attempts to normalize GF mice.An altered version has been widely adopted as a standardized gut microbiota by animalbreeders and biomedical researchers ever since. Over time, various other definedcommunities have been designed to generate gnotobiotic animals for purposes be-yond standardization; they have proven to be a valuable in vivo tool to study microbialecology (e.g., microbial invasion, microbe-microbe interactions, and metabolism) andhost-microbe interactions. However, mice and other animal models have variouslimitations that hamper their use as models for the human microbiome, as was recentlyreviewed (10, 11). Interesting alternatives concern the development of sophisticated invitro models, such as organ-on-a-chip systems and organoids.
This review summarizes existing models of host-microbe interactions in whichdefined communities, as models of the (human) gut microbiota, were applied. We aimto present all in vivo studies that used defined microbial communities representing theintestinal microbiota of healthy individuals and in which host parameters were con-sidered. The designs of these model communities, as well as the selection of their host,are compared and critically evaluated. The potential uses of defined communities in invitro (cellular) models, as a surrogate host, are outlined as well. We conclude bydiscussing the increased value, opportunities, and possible obstacles when applyingdefined communities in to-be-developed in vitro host-microbe interaction models.
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DEFINED COMMUNITIES MIMICKING THE NORMAL INTESTINAL MICROBIOTAIN VIVO
A number of recent studies addressed host-microbe interactions in vivo by usingdefined communities representative of the healthy human gut microbiota (Tables 1 to 3).These include various mouse studies with more- or less-defined intestinal microbiota,which are summarized below. Studies in which animals were antibiotic treated beforebacterial colonization are excluded from our analysis, as their reproducibility andgnotobiology cannot be ensured (12). The following section first discusses the specif-ically named defined communities applied in rodents (Table 1) (n � 31), followed bynon-specifically-named communities in rodents (Table 2) (n � 16). Finally, the definedcommunities administered to nonrodent models are discussed (Table 3) (n � 6).
(Altered) Schaedler Flora
In 1965, Russel W. Schaedler colonized GF mice with a defined microbial communitycomposed of strains isolated from normal mice, to study the fate of the bacteria in thegastrointestinal tract (GIT) and their effect on cecum size. With respect to theseparameters, it turned out that the Schaedler flora (SF) was able to, at least partially,normalize the cecum size of GF mice in comparison with animals raised under con-ventional conditions (9). The defined microbial population was supplied to animalvendors to serve as a community that could limit infection of ex-GF rodents withopportunistic pathogens. Schaedler developed several different bacterial cocktails overtime. In 1978, Roger P. Orcutt set out to standardize and improve the SF flora, but inview of the monitoring costs, the total number of bacterial species was limited to eight.Orcutt made a selection of bacterial species (altered Schaedler flora [ASF]) based ontheir representation and stable colonization in the murine gut, their ease of identifi-cation (morphologically), and their presence in or interference with isolator contami-nants. For instance, the cocci and spore-forming, blunt-ended rods were eliminated,which represented the majority of isolator contaminants. Also, the amount of faculta-tive anaerobes was limited, as they outgrew aerobic isolator contaminants and thusimpeded the ability to detect the latter (13). The ASF consists of six Firmicutes (Clos-tridium species [ASF356], Lactobacillus intestinalis or Lactobacillus acidophilus [ASF360],Lactobacillus murinus or Lactobacillus salivarius [ASF361], Eubacterium plexicaudatum[ASF492], Pseudoflavonifractor sp. [ASF500], and Clostridium sp. [ASF502]), one Bacte-roidetes species (Parabacteroides distasonis [ASF519]), and one Deferribacteres species(Mucispirillum schaedleri [ASF457]).
The ASF has been used multiple times as a reference or minimal defined microbiota,and its applications were extensively reviewed elsewhere (14). Several studies involvingASF in mice (or other animals) reported its effect on host parameters (Tables 1 to 3). Thelist is probably not exhaustive, given the wide application of ASF mice as a control orminor population in studies, which makes these studies harder to identify.
The applications of ASF in rodents varied from wild-type strains (mostly C57BL/6 butalso C3H/HeN and Swiss Webster mice) to models prone to diseases, including irritablebowel disease (IBD) (15–17), type I diabetes (18), or colorectal cancer (19). The ASF lacksProteobacteria, a phylum shared by mice and humans, whereas some researchersintroduced Proteobacteria to ASF mice, such as Oxalobacter formigenes (20) and Esch-erichia coli (21). Other studies included only selected members of the ASF, because notall members were found to successfully colonize the murine cecum (18) or to test thelevels of colonization resistance of different combinations of ASF members (22). Overall,the application of ASF for the study host-microbe interactions has been quite diverse,regarding host strain, gut region of interest, and host parameters studied.
Although the ASF has been used multiple times as a reference microbiota and hasaided in the establishment of other defined microbiota, such as Oligo-MM and theBristol microbiota, its representability of the normal gut microbiota has been criticized(23), as discussed below.
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TAB
LE1
Stud
ies
usin
gsp
ecifi
cally
nam
edde
fined
com
mun
ities
tost
udy
host
-mic
rob
ein
tera
ctio
nsin
vivo
(n�
31)a
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
Scha
edle
rflo
ra(5
spec
ies)
2La
ctob
acill
ussp
p.,
anae
rob
icSt
rept
ococ
cus
sp.(
grou
pN
),Ba
cter
oide
sst
rain
,En
tero
cocc
ussp
.,co
lifor
mst
rain
Mou
seM
ouse
(NR)
20N
RN
R4
wk
(3w
k–4
mo)
Col
oniz
atio
np
atte
rn;c
ecal
size
9
ASF
(8sp
ecie
s)A
SF35
6:Cl
ostr
idiu
msp
ecie
sA
SF36
0:La
ctob
acill
usin
test
inal
isor
Lact
obac
illus
acid
ophi
lus
ASF
361:
Lact
obac
illus
mur
inus
orLa
ctob
acill
ussa
livar
ius
ASF
457:
Muc
ispi
rillu
msc
haed
leri
ASF
492:
Euba
cter
ium
plex
icau
datu
mA
SF50
0:Ps
eudo
flavo
nifr
acto
rsp
.A
SF50
2:Cl
ostr
idiu
msp
.A
SF51
9:Pa
raba
cter
oide
sdi
stas
onis
Mou
seM
ouse
(HA
/IC
R)30
NR
Both
Adu
lt(1
4–56
days
)D
eath
afte
rC.
botu
linum
infe
ctio
n;fe
cal
C.bo
tulin
umto
xin
excr
etio
n;co
loni
zatio
np
atte
rnof
C.bo
tulin
um
36
Mou
seRa
t(F
344)
1–5
Ster
ilefo
od(C
harle
sRi
ver)
adlib
itum
MN
R(2
wk)
Hep
atic
geno
toxi
city
ofm
onon
itrot
olue
neis
omer
s;m
etab
olic
activ
atio
nof
2NT
by
inte
stin
alb
acte
ria;c
ecal
bac
teria
lco
nten
t
169
Mou
seM
ouse
(sci
dC
.B-1
7)4–
6A
utoc
lave
dp
elle
ted
diet
adlib
itum
NR
NR
(8–1
2w
kp
ostr
econ
stitu
tion
CD
4�T
cells
)
Aft
erH
elic
obac
ter
hepa
ticus
infe
ctio
n,re
ctal
pro
lap
se;
clin
ical
lyse
vere
dise
ase;
gros
sly
thic
kene
dco
lon,
cecu
m,a
ndre
ctum
onne
crop
sy;c
olon
icin
flam
mat
ion
scor
e;co
loni
cep
ithel
ial
cell
pro
lifer
atio
n;hi
stop
atho
logy
16
Mou
seRa
t(H
LA-B
27on
33-3
/F34
4)7–
11N
RA
tle
ast
M2
mo
(1m
o)G
ross
gut
scor
e,le
vels
ofM
POan
dIL
-1B
ince
cal
tissu
e;hi
stol
ogic
alin
flam
mat
ory
scor
eof
cecu
man
dan
trum
15
Mou
seM
ouse
(C3H
/HeN
)4–
8Ir
radi
ated
diet
(Har
lan
Tekl
ad)
NR
6–8
wk
(9–1
4w
k)A
fter
colo
niza
tion
with
Hel
icob
acte
rbi
lisor
Brac
hysp
irahy
odys
ente
riae,
ceca
lp
atho
logi
cal
gros
san
dhi
stol
ogic
alsc
ores
;ser
umIg
G1
�Ig
G2a
Ab
resp
onse
170
Mou
seM
ouse
(C3H
/HeN
)7–
10Ir
radi
ated
diet
(Har
lan
Tekl
ad)
NR
6–8
wk
(10
wk)
Feca
lb
acte
rial
cont
ents
(aft
erH
.bili
sin
fect
ion)
;cec
alp
atho
logi
cal
scor
es;c
ecal
hist
olog
ical
chan
ges;
seru
mim
mun
oglo
bul
in
171
Mou
seM
ouse
(SW
)2–
5N
RN
R6–
9w
k(N
R)Pr
esen
ceof
Th17
cells
and
Foxp
3�re
gula
tory
cells
inLP
ofsm
all
inte
stin
e
172
Mou
seM
ouse
(C57
BL/6
)N
RN
RN
RN
RTo
tal
inte
stin
alIg
Aan
din
test
inal
IgA
,ant
i-CBi
r1;
pro
lifer
atio
nof
sple
nic
CBi
r1Tg
Tce
llsaf
ter
CBi
r1ga
vage
173
(Con
tinue
don
next
pag
e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
Mou
seM
ouse
(B6.
Rag�
/�)
NR
NR
F8–
10w
k(1
0da
ys)
Hom
eost
atic
and
spon
tane
ous
pro
lifer
atio
nof
TCR
TgT
cells
inLP
174
Mou
seM
ouse
(C57
BL/6
)5–
8A
utoc
lave
dch
owN
R8
wk
(at
leas
t3
dpi)
Aft
erin
fect
ion,
S.Ty
phi
mur
ium
leve
lsin
mes
ente
ricly
mp
hno
des,
sple
en,c
ecum
,and
fece
s;ce
cal
pat
holo
gysc
ore;
ceca
lm
icro
bio
tade
nsity
;b
acte
rial
cont
ent
and
mic
rob
iota
com
ple
xity
infe
ces
97
ASF
(8an
d9
spec
ies)
8sp
ecie
s:A
SF9
spec
ies:
ASF
�Es
cher
ichi
aco
liH
A10
8or
HA
107
9sp
ecie
s:M
ouse
Mou
se(C
57BL
/6)
3N
RN
RN
R(1
19da
ys)
No.
ofIg
Ap
lasm
ace
llsp
erin
test
inal
villu
sin
duod
enum
,jej
unum
,ile
um,
and
colo
n;Ig
A-b
acte
rium
bin
ding
inin
test
ine;
anti-
E.co
liIg
Atit
er
21
ASF
(8sp
ecie
s)M
ouse
Mou
se(N
MRI
,C
57BL
/6,B
ALB
/c,
NIH
Swis
s,SW
,NM
RI,
MyD
88�
/�
Tica
m1�
/�,
SMA
RTA
,C
57BL
/6.C
D45
.1�
)
3–10
NR
NR
NR
(up
to28
days
)C
ecal
bac
teria
lco
nten
ts;
colo
nic
Treg
cell
resp
onse
and
rela
tive
IL-1
0ex
pre
ssio
nin
sple
en,M
LN,P
eyer
’sp
atch
es,c
olon
ican
dsm
all
inte
stin
alLP
,tho
raci
cdu
ctly
mp
h;IL
-17
pro
duct
ion;
rela
tive
abun
danc
eof
stra
ins;
mic
rosc
opic
loca
lizat
ion
inco
lon
and
smal
lin
test
ine
175
Mou
seM
ouse
(Nod
1�/�
and
Nod
2�/�
onC
57BL
/6b
ackg
roun
d)
NR
NR
NR
6–9
wk
(NR)
Cec
alb
acte
rial
cont
ents
;in
test
inal
tissu
eco
nduc
tanc
ean
dC
r-ED
TAflu
x;E-
cadh
erin
pro
tein
exp
ress
ion
and
RegI
II-ga
mm
am
RNA
exp
ress
ion
inco
lon;
surv
ival
,col
itis
dise
ase
seve
rity,
hist
olog
ysc
ore,
and
mye
lop
erox
idas
eac
tivity
afte
rD
SSin
duct
ion;
colo
nic
IL-6
,IL-
10,M
CP-
1,IF
N-c
,TN
F-�
,IL-
12p
70le
vels
17
Mou
seM
ouse
(C57
BL/6
)N
RA
utoc
lave
dfo
odBo
th8–
12w
k(8
–12
wk)
RegI
II-ga
mm
aRN
Aan
dp
rote
inex
pre
ssio
nin
ileum
and
colo
n
176
(Con
tinue
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pag
e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
Mou
seM
ouse
(C57
BL/6
and
C57
BL/6
TSLP
R�/�
)
3–5
NR
NR
NR
(28
days
)Ex
pre
ssio
nof
thym
icst
rom
ally
mp
hop
oiet
inm
RNA
inin
test
inal
epith
elia
lce
llor
colo
nic
LP(L
P);%
ofC
D4�
Tce
llsse
cret
ing
IL-1
7Aan
dIF
Nga
mm
ain
the
colo
nic
LPan
dM
LN;e
xpan
sion
ofco
loni
cTr
egce
llsin
colo
nic
LPan
dM
LN;e
xpre
ssio
nof
rece
pto
rfo
rTS
LPb
yC
D4�
and
regu
lato
ryT
cells
177
Mou
seM
ouse
(NIH
Swis
s)4
NR
NR
3da
ys(3
days
)St
ruct
ure
ofm
yent
eric
ple
xus,
nerv
ede
nsity
,ave
rage
no.
ofH
uC/D
-pos
itive
mye
nter
icne
uron
sp
erga
nglio
n,ce
llb
ody
size
,and
aver
age
no.
ofnN
OS-
pos
itive
neur
ons
per
mye
nter
icga
nglio
nin
duod
enum
,jej
unum
,and
ileum
;sm
all
inte
stin
alm
otili
ty(f
requ
ency
and
amp
litud
eof
mus
cle
cont
ract
ions
)in
duod
enum
,je
junu
m,a
ndile
umb
efor
ean
daf
ter
gene
ral
neur
alor
spec
ific
nitr
ergi
cb
lock
ade
178
Mou
seM
ouse
(C57
BL/6
)5–
14A
utoc
lave
dm
ouse
bre
eder
’sdi
et(H
arla
n),
unlim
ited
acce
ss
Both
6–12
wk
(3w
k)C
olon
ichi
stol
ogy,
infla
mm
ator
y(M
PO)
activ
ity,
ente
rop
athy
(pre
senc
eof
feca
lal
bum
in),
and
cyto
kine
exp
ress
ion;
feca
lm
icro
bio
tap
rofil
es;c
olon
icge
neex
pre
ssio
n;p
rop
ortio
nof
T-ce
llsu
bty
pes
inco
loni
cLP
and
othe
rm
ucos
alan
dsy
stem
icim
mun
eco
mp
artm
ents
81
ASF
(8sp
ecie
s)(O
ligo-
MM
12
was
also
used
,but
noho
stp
aram
eter
sw
ere
asse
ssed
)
Mou
seM
ouse
(C57
BL/6
)3
(ASF
),5–
23(O
ligo-
MM
)N
RBo
thN
RTh
ickn
esse
sof
tota
lco
lon
and
colo
nin
ner
muc
us(A
SF);
muc
ustu
rnov
ertim
e(A
SF);
alp
hadi
vers
ityin
colo
nan
dce
cum
(Olig
o-M
M)
26
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tinue
don
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e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
ASF
(8an
d9
spec
ies)
8sp
ecie
s:A
SF9
spec
ies:
ASF
�O
xalo
bact
erfo
rmig
enes
9sp
ecie
s:M
ouse
Mou
se(S
W)
4–7
LM-4
85au
tocl
avab
lero
dent
diet
,fre
eac
cess
M(n
oge
nder
effe
ctob
serv
ed)
3–9
mo
(3–9
mo
�6
wk)
Bact
eria
lle
vels
inst
omac
h,ce
cum
,pro
xim
alco
lon,
and
ceca
lm
ucos
a;b
ody
wt;
diet
ary
oxal
ate
inta
ke;c
ecal
and
feca
lox
alat
ele
vels
;ur
ine
vol;
urin
ary
met
abol
itele
vels
;cec
alw
etw
t;ce
cal
wat
erm
etab
olite
s
20
Part
ial
ASF
(6sp
ecie
s)A
SF35
6,-3
61,-
492,
-502
,-5
19,a
nd-5
00(A
SF36
0an
d-4
57di
dno
tco
loni
ze)
Mou
seM
ouse
(NO
D.M
yD88
KO)
Non
e9–
23N
RBo
thN
R(u
pto
30w
k)In
cide
nce
ofdi
abet
es;
hist
olog
ical
scor
esof
pan
crea
ticis
let
dest
ruct
ion
18
Part
ial
ASF
(4an
d5
spec
ies)
4sp
ecie
s:A
SF36
0,A
SF36
1,A
SF45
7,A
SF51
95
spec
ies:
4sp
ecie
s�
Buty
rivib
riofib
risol
vens
(typ
eI,
ATC
C19
171;
typ
eII,
ATC
C51
255)
4sp
ecie
s:
5sp
ecie
s:
Mou
sean
db
ovin
e
Mou
se(B
ALB
/c)
4–5
Aut
ocla
ved
low
-fib
erdi
et(5
SRZ,
cata
log
no.
1813
680)
,hig
h-fib
erdi
et(5
SVL,
cata
log
no.
1813
901)
,or
trib
utyr
indi
et(5
AVC
,cat
alog
no.1
8149
61)
NR
NR
(2.5
–5m
oaf
ter
colo
rect
alca
ncer
indu
ctio
n)
Col
orec
tal
tum
orm
ultip
licity
,tu
mor
size
,and
tum
orgr
ade;
leve
lsof
LDH
A,
lact
ate,
but
yrat
e,H
3ac,
and
tota
lH
3in
colo
nic
tissu
ean
dtu
mor
s;lu
min
alSC
FAle
vels
;H3a
can
dex
pre
ssio
nle
vels
ofFa
s,p
21,a
ndp
27ge
nes
inco
loni
ctis
sue
and
tum
ors;
apop
tosi
san
dce
llp
rolif
erat
ion
leve
lsin
colo
nic
tissu
ean
dtu
mor
s
19
Part
ial
ASF
(4,5
,7,a
nd7
spec
ies)
4sp
ecie
s:A
SF35
6,A
SF36
0,A
SF36
1,an
dA
SF51
95
spec
ies:
ASF
360,
ASF
361,
ASF
457,
SB2
(ASF
502)
,an
dA
SF51
97
spec
ies:
ASF
356,
ASF
360,
ASF
361,
ASF
457,
ASF
500,
SB2
(ASF
502)
,an
dA
SF51
97
spec
ies:
4sp
ecie
s�
E.co
liM
t1B1
,St
rept
ococ
cus
dani
elia
eER
D01
G,S
taph
yloc
occu
sxy
losu
s33
-ERD
13C
(mor
ew
ithO
ligo-
MM
[see
bel
ow])
4sp
ecie
s:
5sp
ecie
s:
7sp
ecie
s:
7sp
ecie
s:
Mou
seM
ouse
(C57
BL/6
)4–
6N
RBo
th0
or8–
12w
k(8
–12
wk
or40
days
)Fe
cal
bac
teria
lco
nten
t;b
acte
rial
load
ofS.
Typ
him
uriu
min
fece
s,ce
cum
,and
MLN
;rel
ativ
ece
cal
wt;
func
tiona
lge
nom
ican
alys
isof
bac
teria
22
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tinue
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e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
Olig
o-M
M(1
2,15
,and
17sp
ecie
s)12
spec
ies,
Olig
o-M
M:
Acu
talib
acte
rm
uris
KB18
,Fla
voni
frac
tor
plau
tiiYL
31,C
lost
ridiu
mcl
ostr
idio
form
eYL
32,
Blau
tiaco
ccoi
des
YL58
,Cl
ostr
idiu
min
nocu
umI4
6,La
ctob
acill
usre
uter
iI4
9,En
tero
cocc
usfa
ecal
isKB
1,Ba
cter
oide
sca
ecim
uris
I48,
Mur
ibac
ulum
inte
stin
ale
YL27
,Bifi
doba
cter
ium
long
umsu
bsp
.ani
mal
isYL
2,Tu
ricim
onas
mur
isYL
45,A
kker
man
sia
muc
inip
hila
YL44
15sp
ecie
s:12
spec
ies
�3
facu
ltat
ive
anae
rob
es(E
.co
liM
t1B1
,St
rept
ococ
cus
dani
elia
eER
D01
G,S
taph
yloc
occu
sxy
losu
s33
-ERD
13C
)17
spec
ies:
12sp
ecie
s�
5A
SFm
emb
ers
(ASF
360,
ASF
361,
ASF
457,
SB2
[ASF
502]
,ASF
519)
12sp
ecie
s:
15sp
ecie
s:
17sp
ecie
s:
Mou
seM
ouse
(C57
BL/6
)4–
6N
RBo
th0
(8–1
2w
k)Fe
cal
bac
teria
lco
nten
t;b
acte
rial
load
ofS.
Typ
him
uriu
min
fece
s,ce
cum
,and
MLN
;rel
ativ
ece
cal
wt;
func
tiona
lge
nom
ican
alys
isof
bac
teria
22
Olig
o-M
M(1
2an
d13
spec
ies)
12sp
ecie
s:O
ligo-
MM
13sp
ecie
s:12
spec
ies
�Cl
ostr
idiu
msc
inde
nsA
TCC
3570
4
12sp
ecie
s:
13sp
ecie
s:
Mou
seM
ouse
(C57
BL/6
)5–
8N
RN
R0
(6–1
2w
k)Fe
cal
and
ceca
lb
acte
rial
cont
ents
;cec
alle
vels
oflip
ocal
in-2
;cal
pro
tect
inex
pre
ssio
nin
ceca
ltis
sue;
hist
opat
holo
gyof
cecu
m;
ceca
lb
ileac
idm
etab
olom
e
SIH
UM
I(x)
(7an
d8
spec
ies)
:SI
HU
MI:
Ana
eros
tipes
cacc
aeD
SM14
662
orD
SM14
667,
Bact
eroi
des
thet
aiot
aom
icro
nD
SM20
79,B
.lon
gum
NC
C27
05,B
laut
iapr
oduc
taD
SM29
50,C
lost
ridiu
mra
mos
umD
SM14
02,E
.co
liK-
12M
G16
55,
Lact
obac
illus
plan
taru
mD
SM20
174
SIH
UM
I(x)
Clos
trid
ium
buty
ricum
DSM
1070
2
7sp
ecie
s:
8sp
ecie
s:
Hum
anRa
t(S
pra
gue-
Daw
ley)
3–21
Ster
ilize
dst
anda
rdch
ow(2
25g/
kgof
bod
yw
tp
rote
in,5
0g/
kgcr
ude
fat,
65g/
kgas
h,13
5g/
kgm
oist
ure,
480
g/kg
N-f
ree
extr
act)
,fe
rmen
tab
le-
fiber
-fre
edi
et,
inul
indi
et,p
ectin
diet
,and
high
-fat
and
low
-fat
diet
s
Both
0–3
mo
(2–3
8w
k)St
abili
tyof
mic
rob
iota
inof
fsp
ring;
SCFA
conc
nan
dp
Hin
cecu
m,c
olon
,and
fece
s;b
acte
rial
coun
tsin
cecu
m,c
olon
,and
fece
s;M
idtv
edt
crite
ria
27
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tinue
don
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pag
e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
SIH
UM
I(x)
(8an
d9
spec
ies)
8sp
ecie
s:SI
HU
MI(x
)9
spec
ies:
8sp
ecie
s�
A.
muc
inip
hila
ATC
CBA
A-8
35
9sp
ecie
s:H
uman
Mou
se(C
3H)
5–10
NR
NR
12w
k(5
–15
days
)Ba
cter
ial
cell
no.a
ndp
rop
ortio
nsin
cecu
man
dco
lon;
ceca
lan
dco
loni
chi
stop
atho
logy
scor
es;
exp
ress
ion
ofp
roin
flam
mat
ory
cyto
kine
sin
ceca
lan
dco
loni
cm
ucos
a;se
rum
pro
tein
leve
lsof
pro
infla
mm
ator
ycy
toki
nes;
no.o
fS.
Typ
him
uriu
mce
llsin
MLN
and
sple
en;s
ize;
mac
rop
hage
infil
trat
ion
ince
cal
tissu
e;lo
caliz
atio
nof
A.m
ucin
iphi
laan
dS.
Typ
him
uriu
m;m
ucin
form
atio
n,m
ucus
thic
knes
s,m
ucus
com
pos
ition
,and
no.
ofm
ucin
-fille
dce
lls
28
SIH
UM
I(x)
(8an
d9
spec
ies)
8sp
ecie
s:SI
HU
MI(x
)9
spec
ies:
8sp
ecie
s�
Fuso
bact
eriu
mva
rium
ATC
C85
01
9sp
ecie
s:H
uman
Mou
se(C
3H/H
eOuJ
)12
Irra
diat
edst
anda
rdch
owR0
3-40
F0
(8w
k)Bo
dyw
t;dr
ym
ass
ofce
cum
and
colo
n;b
acte
rial
cont
ent
ince
cum
and
colo
n;p
olya
min
eco
ncn
ince
cum
and
colo
n;SC
FAco
ncn
ince
cum
and
colo
n;hi
stol
ogy
ofce
cum
and
dist
alco
lon
(thi
ckne
sses
ofcr
ypt,
epith
elia
lla
yer,
muc
osa,
sub
muc
osa,
mus
cula
risex
tern
a);m
itosi
san
dap
opto
sis
ofce
cal
and
dist
alco
loni
ctis
sue
30
Hum
anM
ouse
(Prm
/Alf,
C3H
/He)
12–1
3St
erili
zed
pel
lete
dst
anda
rdch
owR0
3-40
F0
(56
�1
days
)Le
ngth
sof
smal
l,la
rge,
and
who
lein
test
ines
;th
ickn
esse
sof
mus
cle,
cryp
t,an
dvi
lliin
pro
xim
alan
dsm
all
inte
stin
ean
dco
lon;
feca
lan
dce
cal
mic
rob
ial
cont
ents
;cec
alco
ncn
ofSC
FAs
and
pol
yam
ines
31
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tinue
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e)
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TAB
LE1
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylae
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
df
No.
ofan
imal
s/g
roup
Ch
owSe
xA
ge
(col
lect
ion
tim
e[s]
c )St
udy
outc
ome(
s)d
Refe
ren
ce
SIH
UM
I(x)
(7an
d8
spec
ies)
7sp
ecie
s:SI
HU
MI(x
)w
ithou
tC.
ram
osum
8sp
ecie
s:SI
HU
MI(x
)
7sp
ecie
s:
8sp
ecie
s:
Hum
anM
ouse
(C3H
/HeO
uJ)
3–9
Irra
diat
edlo
w-f
ator
high
-fat
diet
adlib
itum
M0
(16
wk)
Body
wt;
%bo
dyfa
t;ad
ipos
etis
sue
wt
(epi
didy
mal
,m
esen
teric
,and
subc
utan
eous
);en
ergy
inta
ke;
food
effic
ienc
y;di
gest
ibili
tyof
high
-fat
diet
;dig
estib
leen
ergy
;ce
cala
ndco
loni
cba
cter
ial
cont
ents
per
spec
ies;
bloo
dgl
ucos
e;le
ptin
gene
expr
essio
nin
epid
idym
altis
sue;
liver
wt;
liver
trig
lyce
ride
leve
ls;liv
ergl
ycog
enco
nten
ts;
expr
essio
nof
gene
sin
volv
edin
lipid
tran
spor
t,lip
idsy
nthe
sis,c
hole
ster
olsy
nthe
sis,
and
lipid
cata
bolis
m;g
ene
expr
essio
nof
prot
eins
invo
lved
insm
alli
ntes
tinal
gluc
ose
upta
ke;S
CFA
form
atio
nin
cecu
m,c
olon
,and
port
alve
inpl
asm
a;ge
neex
pres
sion
ofSC
FA-re
late
dpr
otei
nsin
colo
nic
muc
osa;
gene
expr
essio
nof
lipid
tran
spor
tan
dst
orag
epr
otei
nsin
ileum
;pa
ram
eter
sof
inte
stin
alpe
rmea
bilit
yan
dlo
w-g
rade
infla
mm
atio
n
32
SIH
UM
I(x)
(8an
d9
spec
ies)
8sp
ecie
s:SI
HU
MI(x
)9
spec
ies:
8sp
ecie
s�
A.
muc
inip
hila
ATC
CBA
A-8
35
9sp
ecie
s:H
uman
Mou
se(C
57BL
/6.
129P
2-Il1
0tm
1Cgn
)
5–6
Irra
diat
edst
anda
rdch
ow(f
ortifi
edty
pe
1310
;A
ltro
min
,Lag
e,G
erm
any)
adlib
itum
M0
or8
wk
(3w
k)Bo
dyw
t;hi
stop
atho
logy
scor
esin
subm
ucos
a,LP
,sur
face
epith
eliu
m,a
ndlu
men
;col
onle
ngth
;rel
ativ
em
RNA
leve
lsof
Tnfa
,Ifn
g,an
dRe
g3g;
feca
llip
ocal
in-2
conc
n;fe
cala
ndce
calb
acte
riall
evel
s;ce
cal
hist
olog
y;no
.ofg
oble
tce
llspe
r10
0ep
ithel
ialc
ells
ince
cum
and
colo
n;m
ucus
laye
rth
ickn
ess
inco
lon;
rela
tive
Muc
2m
RNA
leve
lsin
dist
alsm
alli
ntes
tine,
cecu
m,a
ndco
lon
29
aA
bb
revi
atio
ns:M
,mal
e;F,
fem
ale;
SW,S
wis
sW
ebst
er;L
P,la
min
ap
rop
ria;M
LN,m
esen
teric
lym
ph
node
s;M
PO,m
yelo
per
oxid
ase;
NR,
not
rep
orte
d;SC
FA,s
hort
-cha
infa
tty
acid
;Tre
gce
ll,re
gula
tory
Tce
ll;IL
-1B,
inte
rleuk
in-
1B;A
b,a
ntib
ody;
TCR,
T-ce
llre
cep
tor;
dpi,
days
pos
tinfe
ctio
n;D
SS,d
extr
anso
dium
sulfa
te;I
FN,i
nter
fero
n;TN
F-�
,tum
orne
cros
isfa
ctor
alp
ha;2
NT,
2-ni
trot
olue
ne;H
3ac,
pan
-his
tone
3ac
etyl
atio
n;LD
HA
,lac
tate
dehy
drog
enas
eA
;nN
OS,
neur
onal
nitr
icox
ide
synt
hase
;TgT
cells
,tra
nsge
nic
Tce
lls;M
CP-
1,m
onoc
yte
chem
oatt
ract
ant
pro
tein
1.bTw
odi
ffer
ent
stra
ins
test
edar
eco
unte
das
one
spec
ies.
Stra
ins
wer
eno
tal
way
sre
por
ted.
Path
ogen
icsp
ecie
s,in
the
case
ofan
infe
ctio
nm
odel
,are
not
incl
uded
.c T
heco
loni
zatio
ntim
ein
clud
esth
etim
efr
omco
loni
zatio
n(t
ime
zero
inth
eca
seof
tran
sfer
ofm
icro
bio
tato
offs
prin
g)un
tilan
din
clud
ing
the
time
ofsa
crifi
ceor
the
end
ofex
per
imen
tal
(e.g
.,di
etar
y)m
anip
ulat
ions
,in
case
sw
here
this
iscl
early
stat
edin
the
pap
er.I
fag
eis
give
nan
dan
imal
sar
eco
loni
zed
atb
irth,
the
age
isin
clud
edin
the
colo
niza
tion
time.
dSt
udy
outc
omes
are
rep
orte
don
lyfo
ran
imal
sco
loni
zed
with
the
defin
edco
mm
unity
ofin
tere
st.
e,F
irmic
utes
;,B
acte
roid
etes
;,A
ctin
obac
teria
;,P
rote
obac
teria
;,V
erru
com
icro
bia;
,oth
er.
f The
colo
rco
des
from
left
torig
htin
the
illus
trat
ion
are
asfo
llow
s:,s
tom
ach;
,duo
denu
m;
,jej
unum
;,i
leum
;,c
ecum
;,c
olon
;,r
ectu
m;
,fec
es.
Elzinga et al. Microbiology and Molecular Biology Reviews
June 2019 Volume 83 Issue 2 e00054-18 mmbr.asm.org 10
on April 5, 2021 by guest
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nloaded from
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TAB
LE2
Stud
ies
usin
gno
n-sp
ecifi
cally
-nam
edde
fined
com
mun
ities
inro
dent
sto
stud
yho
st-m
icro
be
inte
ract
ions
invi
vo(n
�16
)a
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
,F-s
trai
ns,a
ndN
-str
ains
(2,9
,11,
41,a
nd13
0sp
ecie
s)2
spec
ies:
E.co
liC
25�
Lact
obac
illus
9sp
ecie
s:2
spec
ies
�En
tero
cocc
us�
Lact
obac
illus
�Ca
ndid
a�
4m
orp
holo
gica
llydi
ffer
ent
stra
ins
ofG
ram
-neg
ativ
ean
aero
bes
11sp
ecie
s:9
spec
ies
�2
stra
ins
ofG
ram
-ne
gativ
ean
aero
bes
with
fusi
form
mor
pho
logy
41sp
ecie
s:11
spec
ies
�30
addi
tiona
lst
rain
sof
Gra
m-n
egat
ive
anae
rob
es13
0sp
ecie
s:50
stra
ins
ofG
ram
-neg
ativ
est
rict
anae
rob
es(N
)�
80fa
cult
ativ
ean
aero
bes
(F)
2sp
ecie
s:
Oth
ers
not
spec
ified
Mou
seM
ouse
(CD
-1)
4–57
Aut
ocla
ved
Lob
und
diet
L-35
6or
pel
lete
dst
erile
diet
from
Cha
rles
Rive
rM
ouse
Farm
s
NR
NR
(1–6
0da
ys)
Cec
alnu
mb
erof
E.co
liC
25b
acte
ria;c
ecal
size
;hi
stop
atho
logy
ofst
omac
h,sm
all
inte
stin
e,ce
cum
,and
colo
n
33
N-
and
F-st
rain
s(6
0,96
,and
97sp
ecie
s)60
spec
ies:
N-s
trai
ns�
14fa
cult
ativ
ean
aero
bes
�E.
coli
C25
96st
rain
s:F-
stra
ins
�E.
coli
C25
,E.c
oli
40T,
orSh
igel
la97
stra
ins:
F-st
rain
s�
E.co
liC
25�
Shig
ella
orE.
coli
40T
Not
spec
ified
Mou
seM
ouse
(CD
-1)
5–75
Ster
ilize
dLo
bun
ddi
etL-
356,
Cha
rles
Rive
rfo
rmul
a7R
F,Lo
bun
ddi
etL-
485,
orPu
rina
bre
eder
chow
NR
NR
(4w
k)C
ecal
size
;cec
alle
vels
offa
tty
acid
s;ce
cal
leve
lsof
E.co
li;p
Hof
ceca
lco
nten
ts
34
NA
(4sp
ecie
s)La
ctob
acill
ussp
ecie
s1
and
2,Ba
cter
oide
ssp
.,St
rept
ococ
cus
grou
pN
Rat?
Rat
(Sp
ragu
e-D
awle
y)N
one
2A
utoc
lave
dst
anda
rddi
ete
sup
ple
men
ted
with
caff
eic
acid
NR
NR
Urin
ary
met
abol
ites
ofca
ffei
cac
ids
179
(Con
tinue
don
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pag
e)
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(2,2
,2,2
,3,3
,4,5
,6,6
,6,
8,8,
9,13
,15,
and
17sp
ecie
s)2
spec
ies:
Act
inob
acill
uss3
�St
rept
ococ
cus
s12
spec
ies:
Bact
eroi
des
s8�
Act
inob
acill
uss3
2sp
ecie
s:Eu
bact
eriu
ms1
0�
Mic
roco
ccus
s62
spec
ies:
Clos
trid
ium
C1
�C
23
spec
ies:
Bact
eroi
des
s8�
Act
inob
acill
uss3
�E.
coli
s73
spec
ies:
Shig
ella
flexn
eri
�C
5�
C6
4sp
ecie
s:C
1–C
44
spec
ies:
S.fle
xner
i�
C3–
C5
6sp
ecie
s:C
1–C
66
spec
ies:
Act
inob
acill
uss3
�St
rept
ococ
cus
s1�
Lact
obac
illus
s4�
Cory
neba
cter
ium
s5�
Mic
roco
ccus
s6�
Stre
ptoc
occu
ss2
6sp
ecie
s:S.
flexn
eri
�C
5–C
98
spec
ies:
6sp
ecie
s(A
ctin
obac
illus
,etc
.)�
Bact
eroi
des
s8�
E.co
lis7
8sp
ecie
s:S.
flexn
eri
�C
3–C
99
spec
ies:
C1–
C9
13sp
ecie
s:C
1–C
1315
spec
ies:
C1–
1517
spec
ies:
8sp
ecie
s(A
ctin
obac
illus
,etc
.)�
C1–
C9
2sp
ecie
s(2
�):
2sp
ecie
s:
3sp
ecie
s:
6sp
ecie
s:
8sp
ecie
s:
4,9,
13,a
nd15
spec
ies:
17sp
ecie
s:
Hum
anan
dm
ouse
Mou
se(C
D-1
)�
2St
erili
zed
com
mer
cial
diet
(Usi
ned’
Alim
enta
tion
Ratio
nnel
le)
adlib
itum
Both
2–5
mo
(4w
kaf
ter
last
inoc
ulat
ion)
No.
ofIg
Ap
lasm
ocyt
esin
duod
enum
38
(Con
tinue
don
next
pag
e)
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(2,2
,2,2
,2,2
,2,2
,and
3sp
ecie
s)2
and
2sp
ecie
s:Cl
ostr
idiu
mE
orP
with
E.co
liK-
122
spec
ies
(�6)
:Clo
strid
ium
E�
E.co
liS,
Prot
eus
mira
bilis
,Kle
bsie
llapn
eum
onia
e,Ba
cter
oide
s(A
listip
es)
putr
edin
is,
Veill
onel
laal
cale
scen
s,or
Clos
trid
ium
perf
ringe
ns3
spec
ies:
Clos
trid
ium
Ean
dP
�E.
coli
K-12
2sp
ecie
s(5
�):
2sp
ecie
s:
2sp
ecie
s(2
�):
3sp
ecie
s:
Mou
se,
rat,
hum
an
Mou
se(C
3H)
2–6
Aut
ocla
ved
com
mer
cial
diet
NR
Adu
lt(u
pto
51da
ys)
Feca
lb
acte
rial
coun
ts;
(muc
osal
)hi
stol
ogy
ofst
omac
h,je
junu
m,i
leum
,ce
cum
,and
colo
n
180
UW
-GL
(9sp
ecie
s)G
ener
aLa
ctob
acill
us,
Baci
llus,
Clos
trid
ium
and
Cory
neba
cter
ium
Spec
ies
not
defin
ed?
�p
hyla
know
n,b
utex
act
com
pos
ition
not
defin
ed
NR
Mou
se(B
ALB
/c)
Tota
lof
3St
erili
zed
Rals
ton
Purin
adi
et50
10C
Both
0(6
0–90
days
)C
ecal
leve
lsof
bac
teria
and
Cand
ida
albi
cans
;hi
stol
ogy
ofto
ngue
and
stom
ach
37
NA
(6sp
ecie
s)St
rept
ococ
cus
(Ent
eroc
occu
s)fa
ecal
is,
Lact
obac
illus
brev
is,
Aer
obac
ter
aero
gene
s,St
aphy
loco
ccus
epid
erm
idis
,Bac
tero
ides
spur
ius
(?),
aye
ast
fung
us
?�
phy
lum
coul
dno
tb
ere
trie
ved
NR
Mou
se(B
ALB
/c/A
BOM
f)N
one
3–6
Ster
ilize
dfo
od(2
diff
eren
tp
roce
dure
s)N
R0
(14
wk)
Seru
mle
vels
ofIg
G1,
IgG
2,Ig
M,a
ndIg
A10
8
Part
ial
orco
mp
lete
UW
-GL
(2,3
,and
9sp
ecie
s)2
spec
ies:
Lact
obac
illus
�Cl
ostr
idiu
m3
spec
ies:
2sp
ecie
s�
Baci
llus
9sp
ecie
s:U
W-G
L
2,3
spec
ies:
NR
and
mou
seM
ouse
(HA
/IC
R)10
–48
NR
Both
Adu
lt(1
4–56
days
)
Dea
thaf
ter
C.bo
tulin
umin
fect
ion;
feca
lC.
botu
linum
toxi
nex
cret
ion;
colo
niza
tion
pat
tern
ofC.
botu
linum
36
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tinue
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e)
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(2sp
ecie
s)B.
thet
aiot
aom
icro
nVP
I-54
82�
Des
ulfo
vibr
iopi
ger
ATC
C29
098
Hum
anM
ouse
(NM
RI/K
I)4–
5A
utoc
lave
dp
olys
acch
arid
e-ric
hdi
et(B
&K)
adlib
itum
M(s
ubse
t)A
dult
or12
wk
(14–
28da
ys)
Bact
eria
lco
nten
tsin
cecu
man
ddi
stal
colo
n;b
acte
rial
gene
exp
ress
ion;
glyc
anle
vels
ince
cum
;SC
FAp
rodu
ctio
nin
cecu
m;
seru
mac
etat
e;liv
ertr
igly
cerid
es;e
pid
idym
alfa
tp
ad
109
NA
(2,6
,and
10sp
ecie
s)2
spec
ies:
Stap
hylo
cocc
usep
ider
mid
is�
Veill
onel
lapa
rvul
a6
and
10sp
ecie
s:an
aero
bic
stra
ins
isol
ated
from
aco
nven
tiona
lm
ale
mou
se(n
otsp
ecifi
ed)
2sp
ecie
s:M
ouse
Mou
se(B
10.B
R)45
–73
Ster
ilize
dST
1(In
stitu
teof
Phys
iolo
gyA
SC
R)M
21da
ys(1
2m
o)O
ccur
renc
eof
anky
losi
ngen
thes
opat
hyof
the
ankl
e;co
lon
hist
olog
y;b
acte
rial
cont
ents
inile
uman
dco
lon
181
NA
(2sp
ecie
s)B.
thet
aiot
aom
icro
n�
Euba
cter
ium
rect
ale
Hum
anM
ouse
(NM
RI/K
I)4–
5Ir
radi
ated
stan
dard
low
-fa
t,p
lant
pol
ysac
char
ide-
rich
diet
(die
t20
18fr
omH
arla
ndTe
klad
);hi
gh-f
at,“
high
-sug
ar”
Wes
tern
-typ
edi
et(c
atal
ogno
.961
32;
Har
lan
Tekl
ad);
orlo
w-f
at,h
igh-
suga
rdi
et(c
atal
ogno
.03
317;
Har
lan
Tekl
ad)
M11
wk
(14
days
)Ba
cter
ial
gene
exp
ress
ion;
ceca
lco
loni
zatio
nle
vels
;fe
rmen
tatio
nef
ficie
ncy
ince
cum
;col
onic
gene
exp
ress
ion;
pro
tein
exp
ress
ion
ince
cum
85
NA
(3,8
,9,a
nd10
spec
ies)
3sp
ecie
s:E.
coli
HS,
Bact
eroi
des
vulg
atus
DSM
1447
,B.
thet
aiot
aom
icro
nD
SM20
798
spec
ies:
3sp
ecie
s�
B.lo
ngum
NC
C27
05,
Blau
tiaha
nsen
iiD
SM20
583,
C.sc
inde
nsD
SM56
76,E
ubac
teriu
mve
ntrio
sum
DSM
3988
,La
ctob
acill
usrh
amno
sus
NC
C40
079
spec
ies:
8sp
ecie
s�
Colli
nsel
laae
rofa
cien
sD
SM39
79(c
olon
ized
mos
tm
ice)
10sp
ecie
s:9
spec
ies
�Fa
ecal
ibac
teriu
mpr
ausn
itzii
DSM
1767
7(d
idno
tco
loni
zem
ice)
3sp
ecie
s:
8sp
ecie
s:
9sp
ecie
s:
10sp
ecie
s:
Hum
anM
ouse
(C3H
/HeN
)15
in tota
lSt
erile
stan
dard
chow
diet
orsw
itch
tohi
gh-f
atdi
etad
libitu
m
Both
7w
k(7
0da
ysaf
ter
1st
inoc
ulat
ion)
Feca
lan
dce
cal
bac
teria
lce
llco
unts
;bod
yw
t;m
etab
olite
sin
urin
ean
dp
lasm
a
39
(Con
tinue
don
next
pag
e)
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nloaded from
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(15
and
19sp
ecie
s)15
spec
ies:
Bact
eroi
des
cacc
ae,B
acte
roid
esov
atus
,B.
thet
aiot
aom
icro
n,Ba
cter
oide
sun
iform
is,B
.vu
lgat
us,B
acte
roid
esst
rain
WH
2,C.
scin
dens
,Cl
ostr
idiu
msp
irofo
rme,
C.ae
rofa
cien
s,D
orea
long
icat
ena,
E.re
ctal
e,F.
prau
snitz
ii,Pa
raba
cter
oide
sdi
stas
onis
,Rum
inoc
occu
sob
eum
,Rum
inoc
occu
sto
rque
s(s
trai
nin
form
atio
nno
tac
cess
ible
)19
spec
ies:
15sp
ecie
s�
Bifid
obac
teriu
man
imal
issu
bsp
.lac
tisC
NC
MI-2
494,
Lact
obac
illus
delb
ruec
kii
sub
sp.b
ulga
ricus
CN
CM
I-163
2�
CN
CM
I-151
9,La
ctoc
occu
sla
ctis
sub
sp.
crem
oris
CN
CM
I-163
1,an
dSt
rept
ococ
cus
ther
mop
hilu
sC
NC
MI-1
630
15sp
ecie
s:
19sp
ecie
s:
Hum
anM
ouse
(C57
BL/6
J)5
Aut
ocla
ved
low
-fat
,p
lant
pol
ysac
char
ide-
rich
diet
(B&
Kra
tan
dm
ouse
auto
clav
able
chow
,cat
alog
no.
7378
000)
M6–
8 wk
(42
days
)
Feca
lan
dce
cal
bac
teria
lco
nten
t;b
acte
rial
gene
exp
ress
ion;
urin
ary
met
abol
ites
40
NA
(2sp
ecie
s)B.
thet
aiot
aom
icro
nVP
I-54
82(A
TCC
2914
8)�
F.pr
ausn
itzii
A2-
165
(DSM
1767
7)
Hum
anRa
t(F
344)
6–16
Irra
diat
edp
olys
acch
arid
e-ric
hdi
et(R
03,S
AFE
)
M�
3m
o(3
0da
ysaf
ter
inoc
ulat
ion
ofF.
prau
snitz
ii)
Hos
tge
neex
pre
ssio
nin
colo
nic
epith
eliu
m;c
ecal
SCFA
conc
n;ox
idor
educ
tion
pot
entia
lin
ceca
lco
nten
ts;
colo
nic
cryp
tde
pth
;to
tal
cells
/cry
pt
inco
lon;
exp
ress
ion
ofdi
ffer
entia
tion
pro
tein
sof
secr
etor
ylin
eage
(KLF
-4,C
hgA
);M
uc2
pro
duct
ion
inco
loni
cep
ithel
ium
;col
onic
muc
ingl
ycos
ylat
ion
182
(Con
tinue
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e)
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(2sp
ecie
s)B.
thet
aiot
aom
icro
nVP
I-54
82�
B.lo
ngum
NC
C27
05
Hum
anM
ouse
(SW
)3
Stan
dard
diet
(Pur
ina
Lab
Die
t5K
67)
NR
NR
(10
days
)Fe
cal
bac
teria
lco
nten
t;m
etab
olite
sin
fece
san
dur
ine
86
NA
(2,8
,and
9sp
ecie
s)2
spec
ies:
B.th
etai
otao
mic
ron
�D
.pi
ger
8sp
ecie
s:B.
thet
aiot
aom
icro
n,B.
cacc
ae,B
.ova
tus,
E.re
ctal
e,M
arvi
nbry
antia
form
atex
igen
s,C.
aero
faci
ens,
E.co
li,Cl
ostr
idiu
msy
mbi
osum
9sp
ecie
s:8
spec
ies
�D
.pi
ger
2sp
ecie
s:
8sp
ecie
s:
9sp
ecie
s:
Hum
anM
ouse
(NM
RI)
4–20
Irra
diat
edlo
w-f
at/h
igh-
pla
nt-p
olys
acch
arid
eor
high
-fat
/hig
h-si
mp
le-s
ugar
diet
adlib
itum
,HF/
HS
diet
with
mod
ified
sulfa
teco
ncn
(600
-fol
dra
nge)
,or
HF/
HS
diet
sup
ple
men
ted
with
chon
droi
tinsu
lfate
M7–
8w
k(2
wk)
Feca
lb
acte
rial
rela
tive
abun
danc
e;fe
cal
met
atra
nscr
ipto
me;
gene
exp
ress
ion
ofD
.pig
er;
gene
exp
ress
ion
ofm
ouse
pro
xim
alco
lon;
ceca
lm
etab
olite
s
42
NA
(14
spec
ies)
�vi
rusl
ike
par
ticle
sC.
aero
faci
ens
ATC
C25
986,
B.ca
ccae
ATC
C43
185,
B.ov
atus
ATC
C84
83,B
.th
etai
otao
mic
ron
VPI-
5482
�73
30,
Bact
eroi
des
unifo
rmis
ATC
C84
92,B
acte
roid
esvu
lgat
usA
TCC
8482
,Ba
cter
oide
sce
llulo
sily
ticus
WH
2,Pa
raba
cter
oide
sdi
stas
onis
ATC
C85
03,C
.sc
inde
nsA
TCC
3570
4,C.
sym
bios
umA
TCC
1494
0,C.
spiro
form
eD
SM15
52,
D.l
ongi
cate
naD
SM13
814,
E.re
ctal
eA
TCC
3365
6,R.
obeu
mA
TCC
2917
4
Hum
anM
ouse
(C57
BL/6
J)5
Aut
ocla
ved
low
-fat
/hi
gh-p
lant
-p
olys
acch
arid
edi
et(B
&K)
adlib
itum
NR
8w
k(4
6da
ys)
Gut
bar
rier
and
imm
une
func
tion;
over
all
heal
thst
atus
;bod
yw
tan
dad
ipos
ity;n
o.of
CD
4�
and
CD
8�T
cells
insp
leen
san
dM
LN;f
ecal
bac
teria
lco
nten
tan
dvi
ral
abun
danc
e;ge
netic
chan
ges
upon
vira
lat
tack
(pha
gere
sist
ance
);b
acte
rial
cont
ents
ofp
roxi
mal
and
dist
alsm
all
inte
stin
es,c
ecum
,and
colo
n;p
rop
hage
activ
atio
n
45
(Con
tinue
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June 2019 Volume 83 Issue 2 e00054-18 mmbr.asm.org 16
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br.asm.org/
Dow
nloaded from
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TAB
LE2
(Con
tinue
d)
Con
sort
ium
(no.
ofsp
ecie
sb)
Div
isio
nof
ph
ylaf
Stra
inso
urce
(s)
Hos
tsp
ecie
s(s
trai
n)
Part
ofth
eg
utst
udie
dg
No.
ofan
imal
s/g
roup
Ch
owSe
x
Ag
e(c
olle
ctio
nti
me[
s]c )
Stud
you
tcom
e(s)
dRe
fere
nce
NA
(14
spec
ies)
B.ov
atus
DSM
1896
,Ba
cter
oide
sun
iform
isD
SM84
92,B
.th
etai
otao
mic
ron
DSM
2079
,B.c
acca
eD
SM19
024,
Barn
esie
llain
test
inih
omin
isYI
T118
60,R
oseb
uria
inte
stin
alis
1461
0(L
1-82
),E.
rect
ale
DSM
1762
9(A
1-86
),F.
prau
snitz
iiD
SM17
677
(A2-
165)
,Mar
vinb
ryan
tiafo
rmat
exig
ens
DSM
1446
9(I-
52),
C.sy
mbi
osum
DSM
934,
C.ae
rofa
cien
sD
SM39
79,
E.co
liH
S,A
.muc
inip
hila
DSM
2295
9M
uc,D
.pi
ger
ATC
C29
098
Hum
anM
ouse
(SW
)To
tal
of51
Aut
ocla
ved
stan
dard
fiber
-ric
h(1
5%di
etar
yfib
er),
fiber
-fr
ee,o
rp
reb
iotic
(add
ition
ofp
urifi
edso
lub
legl
ycan
s)di
etad
libitu
m
Both
8–9
wk
(54
days
)
Mic
rob
ial
com
pos
ition
infe
ces,
cecu
m,c
olon
iclu
men
,and
muc
usla
yer;
bac
teria
lC
AZy
me
exp
ress
ion
ince
cum
;m
ucin
-sp
ecifi
ctr
ansc
ripts
inB.
cacc
ae,A
.m
ucin
iphi
la,a
ndB.
thet
aiot
aom
icro
n;ce
cal
mic
rob
ial
enzy
me
activ
ities
;lev
els
ofSC
FAs
and
orga
nic
acid
s;co
loni
cm
ucus
laye
rth
ickn
ess;
colo
nic
exp
ress
ion
ofm
ucus
-p
rodu
ctio
n-re
late
dge
nes;
no.o
fgo
ble
tce
llsin
colo
n;hi
stop
atho
logy
;b
ody
wt;
feca
llip
ocal
in;
colo
nle
ngth
;cec
altr
ansc
ripto
me;
afte
rin
fect
ion
with
C.ro
dent
ium
,his
tolo
gica
lsc
ores
ofce
cum
and
colo
n,ar
eaof
infla
med
tissu
ein
cecu
m,s
urvi
val,
asce
ndin
gan
dde
scen
ding
colo
nan
dre
ctum
,adh
eren
tC.
rode
ntiu
mb
acte
riain
colo
n
43
aA
bb
revi
atio
ns:N
A,c
onso
rtiu
mna
me
not
avai
lab
le/a
pp
licab
le;A
SC
R,A
cade
my
ofSc
ienc
esof
the
Cze
chRe
pub
lic;C
hgA
,chr
omog
rani
nA
;KLF