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SUPPLEMENTARY INFORMATION
doi:10.1038/nature12447
a
c
b
d
Supplementary Figure 1. a-d,
Sequential colonization profiles reveal that
Bacteroides
species exhibit
saturable niche colonization. Germ-free Swiss Webster (SW) mice were mono-associated with a
chloramphenicol resistant (Cm
r
) bacterial strain containing pFD340-
cat
for 6-9 days and subsequently
challenged orally with ~10
8
CFU of tetracycline resistant (Tet
r
) bacterial strain containing pFD340-
tetQ
(see legend for species). CFU was determined by plating serial dilutions of homogenized feces on BHIS
agar plate with either Cm or Tet selection to distinguish strains. In each panel, initial (dark blue) and
challenge (light blue) strains are shown.
e
, Germ-free SW mice were mono-associated with
B. fragilis
pFD340-
tetQ
for 6 days and subsequently challenged with ~10
8
CFU of
B. fragilis
pFD340-
cat
. This is
the reverse order of colonization compared to Fig. 1c.
f,
Germ-free SW mice were mono-associated with
E. coli
JM109 containing pNJR6 (kanamycin resistant) for 6 days and subsequently challenged with
~10
8
CFU of
E. coli
JM109 containing pFD340 (ampicillin resistant).
In all panels, dashed line indicates
the limit of detection at 100 CFU/g feces. Results are representative of at least 2 independent trials per
experiment (n=1-3 animals/group). Error bars indicate SD.
e
f
a
c
b
d
Supplementary Figure 1. a-d,
Sequential colonization profiles reveal that
Bacteroides
species exhibit
saturable niche colonization. Germ-free Swiss Webster (SW) mice were mono-associated with a
chloramphenicol resistant (Cm
r
) bacterial strain containing pFD340-
cat
for 6-9 days and subsequently
challenged orally with ~10
8
CFU of tetracycline resistant (Tet
r
) bacterial strain containing pFD340-
tetQ
(see legend for species). CFU was determined by plating serial dilutions of homogenized feces on BHIS
agar plate with either Cm or Tet selection to distinguish strains. In each panel, initial (dark blue) and
challenge (light blue) strains are shown.
e
, Germ-free SW mice were mono-associated with
B. fragilis
pFD340-
tetQ
for 6 days and subsequently challenged with ~10
8
CFU of
B. fragilis
pFD340-
cat
. This is
the reverse order of colonization compared to Fig. 1c.
f,
Germ-free SW mice were mono-associated with
E. coli
JM109 containing pNJR6 (kanamycin resistant) for 6 days and subsequently challenged with
~10
8
CFU of
E. coli
JM109 containing pFD340 (ampicillin resistant).
In all panels, dashed line indicates
the limit of detection at 100 CFU/g feces. Results are representative of at least 2 independent trials per
experiment (n=1-3 animals/group). Error bars indicate SD.
e
f
SUPPLEMENTARY INFORMATION
2
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RESEARCH
Supplementary Figure 2. a,
Schematic of functional
in vivo
screen of the
B. fragilis
genome for mouse
gut colonization. 9-10 kb fragments of
B. fragilis
genomic DNA generated by partial digestion with
Sau3
AI were ligated into the
E. coli-Bacteroides
shuttle plasmid pFD340-
catBII
(Cm
r
). Each individual
clone was conjugally transferred into
B. vulgatus
, generating a library of
B. vulgatus
strains carrying a
unique
B. fragilis
genomic DNA fragment. The library was screened for
B. fragilis
-specific niche
colonization phenotype in animals mono-associated with
B. vulgatus
.
b,
Of 2,100 clones screened, only 2
persisted in mice after 30 days. The minimal genetic element common to the two clones (named S16 and
S22) that displayed a colonization phenotype from the
in vivo
screen contains 5 hypothetical open reading
frames: BF3583, BF3582, BF3581, BF3580 and BF3579.
a
b
3583
Supplementary Figure 2. a,
Schematic of functional
in vivo
screen of the
B. fragilis
genome for mouse
gut colonization. 9-10 kb fragments of
B. fragilis
genomic DNA generated by partial digestion with
Sau3
AI were ligated into the
E. coli-Bacteroides
shuttle plasmid pFD340-
catBII
(Cm
r
). Each individual
clone was conjugally transferred into
B. vulgatus
, generating a library of
B. vulgatus
strains carrying a
unique
B. fragilis
genomic DNA fragment. The library was screened for
B. fragilis
-specific niche
colonization phenotype in animals mono-associated with
B. vulgatus
.
b,
Of 2,100 clones screened, only 2
persisted in mice after 30 days. The minimal genetic element common to the two clones (named S16 and
S22) that displayed a colonization phenotype from the
in vivo
screen contains 5 hypothetical open reading
frames: BF3583, BF3582, BF3581, BF3580 and BF3579.
a
b
3583