Intestinal Microbiota Containing Barnesiella Species Cures
Vancomycin-Resistant Enterococcus faecium Colonization
Carles Ubeda,a,e,fVanni Bucci,bSilvia Caballero,a,eAna Djukovic,fNora C. Toussaint,a,eMichele Equinda,a,eLauren Lipuma,a,c,e
Lilan Ling,a,eAsia Gobourne,a,c,eDaniel No,a,c,eYing Taur,a,cRobert R. Jenq,dMarcel R. M. van den Brink,dJoao B. Xavier,b,c
Eric G. Pamera,c,e
Infectious Diseases Service, Department of Medicine,aComputational Biology Center,bLucille Castori Center for Microbes, Inflammation and Cancer,cand Bone Marrow
Transplant Service, Department of Medicine,dMemorial Sloan-Kettering Cancer Center, New York, New York, USA; Immunology Program, Sloan-Kettering Institute, New
York, New York, USAe; Departamento de Genómica y Salud, Centro Superior de Investigación en Salud Pública, Valencia, Spainf
colonizationbythehighlyantibiotic-resistantbacteriumvancomycin-resistant Enterococcus (VRE)canexceed109organisms
thatcontains Barnesiella correlateswithVREelimination.Characterizationofthefecalmicrobiotaofpatientsundergoingallo-
geneichematopoieticstemcelltransplantationdemonstratedthatintestinalcolonizationwith Barnesiella confersresistanceto
numbers of infections caused by organisms such as methicillin-
resistant Staphylococcus aureus, carbapenemase-resistant Entero-
bacteriaceae, vancomycin-resistant Enterococcus (VRE), and Clos-
tridium difficile have increased markedly, and many of these
to-patient transmission of these pathogens is one of the major
challenges confronting hospitals and clinics. Most highly antibi-
otic-resistant bacterial strains belong to genera that colonize mu-
of and domination by bacteria such as Enterobacteriaceae and En-
terococcaceae. Destruction of the normal flora by antibiotic ad-
ministration, however, disinhibits antibiotic-resistant members
of these bacterial families, leading to their expansion to very high
sepsis (3). An additional problem associated with high-density
colonization, however, is the difficulty of preventing transmis-
sion. One microgram of fecal material, representing a volume of
bacteria. Given the density with which resistant bacteria colonize
patients, it is not surprising that hand washing and changing of
transfer of resistant microbes.
Although mechanisms remain to be defined, the recognition
he emergence and spread of highly antibiotic-resistant bacte-
from new. Early studies by Freter, Bohnhoff, and their colleagues
roughly 50 years ago demonstrated that antibiotic administration
enhanced infection with Vibrio cholerae or Salmonella enterica se-
5). Subsequent studies by Thijm et al. demonstrated that antibi-
otic administration resulted in the expansion of oxygen-tolerant
sal bacteria to prevent colonization by exogenous bacteria or
marked expansion of low-frequency commensal bacteria. The as-
of VRE infections was supported by epidemiologic studies dem-
onstrating that administration of antibiotics that kill obligate an-
aerobic bacteria increases the density of VRE colonization in hos-
pitalized patients (7).
prehensive analyses of the commensal microbiota in health and
Received 30 October 2012 Returned for modification 24 November 2012
Accepted 30 December 2012
Published ahead of print 14 January 2013
Editor: A. J. Bäumler
Address correspondence to Carles Ubeda, firstname.lastname@example.org, or Eric G.
Supplemental material for this article may be found at http://dx.doi.org/10.1128
Copyright © 2013, American Society for Microbiology. All Rights Reserved.
March 2013 Volume 81 Number 3Infection and Immunityp. 965–973 iai.asm.org
mice rapidly eliminate VRE from the gut, antibiotic-mediated
disruption of the microbiota enables VRE to expand dramati-
cally in the ileum, cecum, and colon, achieving a state of dom-
inance in which as much as 99% of bacteria are VRE (2). Once
established, VRE persists for months afterwards. Studies in pa-
tients undergoing allogeneic hematopoietic stem cell trans-
plantation (allo-HSCT) also demonstrated intestinal domina-
tion by VRE, an outcome that was associated with the
administration of metronidazole, an antibiotic with potent ac-
tivity against obligate anaerobic bacteria (3). Although it was
evident from these studies that elimination of some members
of the commensal flora promoted expansion and domination
by VRE, it remained unclear which bacterial taxa restrict VRE
colonization and whether the reintroduction of normal prean-
tibiotic flora can eliminate VRE from the gut.
identify bacterial populations that correlate with the clearance of
VRE. We find that elimination of VRE from the gut of mice cor-
relates with intestinal recolonization with bacteria belonging to
the Barnesiella genus. Analysis of the fecal microbiota of allo-
HSCT patients revealed that patients colonized with Barnesiella
are protected from VRE domination.
MATERIALS AND METHODS
Mouse models, housing conditions, and VRE infection. Experiments
were done with 7-week-old C57BL/6J female mice purchased from Jack-
son Laboratory, housed with irradiated food, and provided with acidified
water. Mice were individually housed to avoid contamination between
mice due to coprophagia. When knockout mice were infected with VRE,
each knockout mouse was cohoused with a wild-type mouse for at least 1
month before infection to minimize differences between their intestinal
microbiotas. To generate mice defective in Toll-like receptor (TLR) sig-
lps2 mice were provided by B. Beutler (The Scripps Research Institute,
University of California, San Diego, CA), and MyD88?/?mice were ob-
tained from S. Akira (University of Osaka, Osaka, Japan). Rag1?/?mice,
which cannot develop T cells or B cells, were obtained from Jackson Lab-
oratory. Rip2?/?mice, which are defective in NOD-like receptor signal-
ing, were provided by R. Flavell (Yale University, New Haven, CT). All
mice were backcrossed at least nine times onto the C57BL/6 background.
For experimental infections with VRE, mice were treated with ampicillin
1 week of treatment, mice were infected by means of oral gavage with 108
CFU of the vancomycin-resistant Enterococcus faecium strain purchased
from ATCC (stock number 700221). One day after infection, antibiotic
treatment was stopped and VRE levels were determined at different time
points by plating serial dilutions of fecal pellets on Enterococcosel agar
plates (Difco) with vancomycin (8 ?g/ml; Sigma). VRE colonies were
previously described (2), PCR of the vanA gene, which confers resistance
to vancomycin, confirmed the presence of VRE in infected mice. In the
experiment shown in Fig. 5, mice were infected 2 weeks after antibiotic
treatment was stopped. All animal studies were performed in compliance
with Memorial Sloan-Kettering institutional guidelines and approved by
the institution’s institutional animal care and use committee (IACUC).
Fecal transplantation and bacterial culture administration. Fecal
pellets from untreated mice were resuspended in phosphate-buffered sa-
line (PBS) (1 fecal pellet/1 ml of PBS). For each experiment, several fecal
total of 200 ?l of the resuspended pool fecal material was given by oral
gavage to VRE-infected mice over 3 consecutive days, starting 1 day after
antibiotic treatment was stopped. For bacterial cultures, a 100-fold dilu-
tion of resuspended fecal material was grown on CDC anaerobe blood
from the bacterial cultures were administered, by oral gavage, to VRE-
infected mice over 3 consecutive days, beginning 1 day after antibiotic
treatment was stopped.
Sample collection and DNA extraction. Fresh stool pellets were ob-
tained before mice were euthanized. The samples were immediately fro-
zen and stored at ?80°C. DNA was extracted using a phenol-chloroform
ously described (2).
16S rRNA gene amplification and 454 pyrosequencing. For each
sample, 3 replicate 25-?l PCRs were performed, with each containing 50
buffer, and 0.2 ?M concentrations of the following primers, designed to
amplify the V1-V3 region as previously described (8): a modified primer
CCTGGCTCAG-3=), composed of 454 Lib-L primer B (underlined) and
the universal bacterial primer 8F (italics), and the modified primer 534R
534R (italics). Cycling conditions were 94°C for 3 min and 23 cycles of
94°C for 30 s, 56°C for 30 s, and 72°C for 1 min. Replicate PCRs were
pooled, and amplicons were purified using the QIAquick PCR purifica-
tion kit (Qiagen). PCR products were sequenced on a 454 GS FLX Tita-
nium platform by following the 454 Roche recommended procedures.
lished study (3).
mothur (9). Sequences were converted to standard FASTA format. Se-
lymer stretches longer than 8 bp, with no exact match to the forward
primer or a barcode, or that did not align with the appropriate 16S rRNA
variable region were not included in the analysis. Using the 454 base
quality scores, which range from 0 to 40 (0 being an ambiguous base),
sequences were trimmed using a sliding-window technique such that the
met. Sequences were aligned to the 16S rRNA gene using as the template
the SILVA reference alignment (10) and the Needleman-Wunsch algo-
rithm with the default scoring options. Potentially chimeric sequences
were removed using the ChimeraSlayer program (11). To minimize the
rare-abundance sequences that differ in 1 or 2 nucleotides from a high-
abundance sequence were merged to the high-abundance sequence using
the pre.cluster option in mothur. Sequences were grouped into opera-
tional taxonomic units (OTUs) using the average-neighbor algorithm.
Sequences with distance-based similarity of 97% or greater were assigned
to the same OTU. OTU-based microbial diversity was estimated by cal-
performed for each sequence using the Bayesian classifier algorithm de-
scribed by Wang and colleagues with the bootstrap cutoff 60% (14). In
most cases, classification was able to be assigned to the genus level. Hier-
archical clustering shown in Fig. 1 was performed using the option hclust
of the statistical computing program R, version 2.14.0, with the default
Statistical analysis. An unpaired Student t test was used within the
GraphPad Prism program to determine if VRE levels were statistically
significantly different (P ? 0.05) between groups of VRE-infected mice.
or Barnesiella levels and bacterial taxon recovery, the Spearman correla-
Spearman correlation test calculates a coefficient value ranging from ?1
Ubeda et al.
iai.asm.org Infection and Immunity
to ?1, with positive values indicating positive correlation between bacte-
order to test if a detected association was statistically significant.
in patients that develop VRE domination (VRE represents ?30% of their
fecal microbiota) than in patients that do not, we made use of a set of 16S
rRNA sequences from a previous study in which the fecal microbiota
course (3). In order to calculate the relative abundance of Barnesiella in
each stool sample, sequences were classified using mothur as described
siella were divided by the total number of sequences in that specific
sample. The Kruskal-Wallis test was applied to analyze if the relative
dominated patients prior to domination (67 samples from 34 patients)
than in all samples from patients that never developed VRE domination
(251 samples from 55 patients). In a second step, we performed 10,000
iterations of first randomly selecting 34 negative patients and then com-
paring their samples to the predomination samples of all 34 VRE-domi-
nated patients, again using the Kruskal-Wallis test on Barnesiella abun-
calculated (see Results).
ous studies from our laboratory demonstrated that untreated
mice rapidly and completely eliminate orally administered VRE
lin become dominated by VRE (2). Once dominated, mice con-
by quantitative cultures (Fig. 1A). To determine whether admin-
istration of normal intestinal flora to dominated mice can elimi-
with PBS under anaerobic conditions for administration to VRE-
dominated mice by oral gavage. Quantitative culturing of “trans-
days, starting 1 day after antibiotic cessation. (A) Numbers of VRE CFU in the fecal pellets of infected mice were quantified every other day for two consecutive
weeks (n ? 6). Black dots represent PBS-treated mice and red dots represent fecal transplant-treated mice. (B) Composition of the microbiotas of four PBS and
four fecal transplant (FE) mice was analyzed 15 days following infection and compared with that of the microbiotas of three untreated mice (NT). Hierarchical
clustering was used to cluster samples by their microbiota composition at the genus level. Each column represents one mouse. Each row represents one genus.
The most predominant phyla (left) and genera (right) are indicated.
Gut Microbiota Containing Barnesiella Suppresses VRE
March 2013 Volume 81 Number 3iai.asm.org 967
planted” mice demonstrated that VRE colonization was reduced
of VRE within 7 days of fecal transfer (Fig. 1A).
To determine the breadth of microbial reconstitution, we am-
plified bacterial 16S rRNA genes from fecal pellets isolated from
colonized with VRE and that either received PBS or were recon-
stituted with normal fecal microbiota. Hierarchical clustering of
mice on the basis of microbiota composition demonstrated that
untreated and reconstituted mice were similar while VRE-domi-
nated mice were distinct (Fig. 1B).
Obligate anaerobic bacteria clear VRE. The large intestine
microbiota consists of many different bacterial taxa that can be
grouped into obligate anaerobes, i.e., oxygen-intolerant bacte-
ria, and oxygen-tolerant bacteria. To determine whether VRE
-intolerant bacteria, we cultured murine feces under strictly
anaerobic conditions or under normal atmospheric conditions
and reconstituted mice with bacteria harvested from these cul-
tures. While aerobically cultured fecal pellets did not eliminate
VRE, anaerobically cultured bacteria were as effective as un-
fractionated feces at reducing the density of VRE colonization
The mechanism by which anaerobic bacteria prevent the ex-
pansion of oxygen-tolerant bacteria, such as Enterococcus, in the
commensal bacteria and their products. For example, intestinal
lipopolysaccharide (LPS) or systemic flagellin can stimulate TLRs
and induce epithelial cell expression of Reg3?, a bactericidal C-
of TLRs, Nod1 or Nod2, or T cell- or antibody-mediated mecha-
nisms in VRE elimination by fecal transfer, we used MyD88/Trif,
Rip2, and Rag1 knockout mice for colonization by VRE, followed
by reconstitution with normal fecal flora (see Fig. S1 in the sup-
plemental material). Fecal reconstitution resulted in equivalent
reductions of VRE colonization in wild-type and knockout mice,
transplantation. Although reconstitution with fecal flora mark-
edly reduced VRE density in the colon, the magnitude of reduc-
same experiment. We reasoned that variability in VRE elimi-
nation reflected differences in reconstitution with distinct bac-
terial taxa following transfer and that comparing the microbi-
ota of mice that eliminated VRE with that of mice that only
partially cleared VRE might enable us to correlate the presence
of specific anaerobic bacteria with VRE clearance. Figure 3
shows the relative abundance of different bacterial taxa and
described in Fig. 2 (Fig. 3A and B). These results demonstrate
that reconstitution of mice varies and that the magnitude of
VRE elimination also varies within specific groups by a factor
of up to 1,000 (Fig. 3B, PBS group).
Other studies have suggested that the recovery of microbial
for elimination of antibiotic-resistant pathogens (17). Analysis of
the overall microbial diversity using the Shannon diversity index
bial diversity but were able to suppress VRE colonization
is important for VRE elimination.
Reconstitution with Barnesiella correlates with VRE clear-
ance. In order to identify key members of the microbiota that
suppress VRE colonization and to facilitate the analysis of these
complex data, we stratified experimental mice according to VRE
taxa on a heat map (Fig. 4A). While reconstitution of mice with
bacterial taxa varied from mouse to mouse irrespective of VRE
density, clearance of VRE was markedly enhanced in mice recol-
onized with bacteria belonging to the Barnesiella genus (Fig. 4A).
The Spearman rank correlation test demonstrates that recoloni-
zation with Barnesiella negatively correlates with VRE coloniza-
tion (Fig. 4B) (P ? 1.32?7). These results suggest that the Barne-
siella genus contributes to the clearance of VRE colonization. It is
possible, however, that additional bacterial genera corecover with
that positively correlate with recovery of Barnesiella, we used the
Spearman correlation test (see Fig. S2 in the supplemental mate-
rial) to compare the abundance of Barnesiella with the relative
abundance of other bacterial genera. The Barnesiella genus be-
longs to the family Porphyromonadaceae, within the phylum Bac-
teroidetes. While unclassified sequences belonging to the Porphy-
romonadaceae family correlated positively with the prevalence of
Barnesiella, we also found a positive correlation with the genera
Coprobacillus and Adlercreutzia. To determine if these two genera
presence of Barnesiella in mice with reduced prevalence of VRE
(?100 VRE CFU/10 mg feces). While 16 out of 17 mice with low
were colonized with Coprobacillus or Adlercreutzia, demonstrat-
FIG2 Commensal anaerobic bacteria suppress VRE colonization in antibiot-
ic-treated mice. Mice were infected with 108VRE CFU after 1 week of ampi-
cillin treatment. One day after infection, ampicillin treatment was stopped.
Mice were orally gavaged for three consecutive days, starting 1 day after anti-
biotic cessation, with PBS, a suspension of fecal pellets from untreated mice
(feces), or an aerobic (aero) or anaerobic (anaero) culture of fecal microbiota
were analyzed 5 weeks after infection (n ? 8 to 10). Limit of detection, 10
CFU/10 mg. ***, significantly different (P ? 0.001) from the PBS group; ns,
Ubeda et al.
iai.asm.orgInfection and Immunity
ing a greater correlation between Barnesiella colonization and
suppression of VRE colonization.
To determine whether Barnesiella can prevent intestinal colo-
nization with VRE, mice that had been treated with ampicillin
were reconstituted with commensal bacterial cultures prior to
VRE infection. As shown in Fig. 5, mice that were gavaged with
PBS or the aerobically cultured fecal microbiota became densely
VRE colonized. However, most mice that received anaerobically
cultured fecal microbiota became resistant to VRE colonization.
One mouse that received anaerobically cultured microbiota
lacked Barnesiella and was densely colonized with VRE.
The Barnesiella genus is associated with protection against
VRE domination in transplant patients. Patients undergoing
allo-HSCT have a high incidence of intestinal domination and
associated bacteremia with VRE (3). In general, patients have a
domination with different oxygen-tolerant bacterial species, with
fecal samples before transplantation and throughout hospitaliza-
tion from 94 patients undergoing allo-HSCT and determined the
microbiota composition. Thus, when patients developed VRE
domination (VRE relative abundance, ?30% of the microbiota),
we were able to characterize the microbiota that preceded the
development of VRE domination (Fig. 6A). This analysis demon-
strated that most patients had a diverse flora prior to VRE domi-
nation (Fig. 6B), similar to that of patients who did not develop
VRE domination (3). The majority of allo-HSCT patients do not
develop VRE domination, a finding which may be explained by
Barnesiella may play a role in protecting patients from VRE dom-
ination. Figure 6C shows the relative abundance of Barnesiella in
compared to that in samples from patients who went on to de-
velop VRE domination. Samples from patients who did not de-
velop VRE domination contained higher levels of Barnesiella (av-
erage, 2.5 ? 10?3parts per unit) than samples from patients who
progressed to VRE domination (average, 4.5 ? 10?5parts per
unit). Results obtained using the Kruskal-Wallis test indicate that
the difference observed in Barnesiella abundance between the
groups of samples was statistically significant (P ? 0.02). In order
to ensure that the difference between these two sample sets is not
attributable to a small number of outliers, we performed 10,000
iterations of randomly selecting 34 negative patients and com-
inated patients. This step confirmed the results (Kruskal-Wallis
P ? 0.04; standard error [SE], 0.0004). These results suggest that
tected from VRE domination while the absence of this genus ren-
ders patients more vulnerable to VRE domination.
anaerobic bacteria result in dense colonization of the intestine
with VRE (3, 7), it has remained unclear whether a specific subset
of anaerobic bacteria inhibits VRE colonization. Our studies in
mice and humans demonstrate that a microbiota containing bac-
teria that belong to the Barnesiella genus restricts colonization of
the intestinal tract by VRE. Further studies will be required to
determine which species and strains within the Barnesiella genus
suppress VRE, the density of Barnesiella spp. required for VRE
(B) VRE CFU numbers. (C) Shannon diversity index of murine fecal samples obtained 5 weeks after infection. Each column represents one mouse. For the
microbiota composition, the most abundant bacterial taxa are indicated with different colors.
Gut Microbiota Containing Barnesiella Suppresses VRE
March 2013 Volume 81 Number 3iai.asm.org 969
Ubeda et al.
iai.asm.orgInfection and Immunity
bacterial taxa are required to eliminate VRE.
The majority of intestinal obligate anaerobes belong to the
Firmicutes and Bacteroidetes phyla. Our analyses of murine mi-
crobiotas of reconstituted mice did not identify taxa belonging
other hand, our studies demonstrate that when species of
Barnesiella, a genus within the Porphyromonadaceae family of
the Bacteroidetes phylum, are part of the intestinal microbiota,
the density of VRE decreases until it is ultimately cleared. In
addition to the family Porphyromonadaceae, the Bacteroidetes
Bacteria belonging to the Bacteroidaceae family include Bacte-
roides fragilis, which produces polysaccharides that stimulate
innate and adaptive immune development in the gut (18). Re-
cent studies have implicated bacteria belonging to the Prevotel-
laceae family with bowel inflammation in mice treated with
dextran sulfate sodium (DSS) and with the development of
steatohepatitis in mice treated with a methionine-choline-de-
ficient diet (19, 20). In contrast, the Porphyromonadaceae fam-
ily, including the genus Barnesiella, has not been associated
with immune development or inflammatory diseases in the
intestine. Consistent with our findings, studies with antibiotic-
treated mice correlated colonization withPorphyromonadaceae
with resistance to infection by Salmonella enterica serovar Ty-
phimurium and Citrobacter rodentium; however, in those stud-
ies, the protective bacterial genera were not identified (21, 22).
Factors influencing the density of Porphyromonadaceae in the
colon include dietary fat intake (23), exposure to stress (24),
and possibly major histocompatibility complex (MHC) haplo-
Previous studies demonstrated that intestinal colonization by
VRE can be suppressed by MyD88-dependent and microbiota-
mediated induction of RegIII? expression by epithelial cells (15).
cells, or T cells. Thus, commensal flora-mediated inhibition of
dense intestinal VRE colonization can be indirect, by innate im-
tion by the anaerobic flora remain undefined.
surface, and the metazoan colon represents an essential, and for
many anaerobic species, sole, sanctuary. Despite their density in
the colon and their proximity to the bloodstream, obligate anaer-
obes rarely cause human disease and their survival depends on
their host’s survival. Obligate anaerobes of the gut promote their
host’s survival by limiting the expansion of oxygen-tolerant bac-
teria, which, by and large, are the subset containing most of the
intestinal pathogens. Our results suggest that Barnesiella spp., by
restricting the growth of VRE, regulate the composition of the
FIG 4 Colonization with the Barnesiella genus correlates with VRE elimination. (A) Genus level composition of the fecal microbiota (red heat map) and VRE
CFU levels (blue heat map) for the different mice described in Fig. 2 5 weeks after VRE infection. Only the microbial taxa representing at least 1% of the
values range from ?1 (maximum positive correlation value) to ?1 (maximum inverse correlation value). Each point represents one genus. To analyze the
statistical significance of a given coefficient Spearman value, P values were computed using the asymptotic t approximation. Spearman coefficient values with a
P value of ?0.05 are indicated.
FIG5 Commensal anaerobic bacteria prevent VRE intestinal colonization. Mice were treated with ampicillin and, after antibiotic treatment was stopped, were
represents one mouse.
Gut Microbiota Containing Barnesiella Suppresses VRE
March 2013 Volume 81 Number 3 iai.asm.org 971
microbiota and optimize host survival. Although some studies
demonstrate that obligate anaerobes of the gut can trigger and/or
promote inflammatory diseases, the ability of other anaerobes to
This work was supported by grants from the National Institutes of Health
Foundation (to E.G.P.), from the Spanish MICINN (SAF2011-29458 to
C.U.), and from the Marie-Curie Career Integration Grant (PCIG09-GA-
1. Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Comparative Sequencing
Program NISC, Henderson DK, Palmore TN, Segre JA. 2012. Tracking
a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with
whole-genome sequencing. Sci. Transl. Med. 4:148ra116. doi:10.1126
2. Ubeda C, Taur Y, Jenq RR, Equinda MJ, Son T, Samstein M, Viale A,
Socci ND, Van Den Brink MR, Kamboj M, Pamer EG. 2010. Vanco-
mycin-resistant Enterococcus domination of intestinal microbiota is en-
abled by antibiotic treatment in mice and precedes bloodstream invasion
in humans. J. Clin. Invest. 120:4332–4341.
3. Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, Lee
YJ, Dubin KA, Socci ND, Viale A, Perales M-A, Jenq RR, van den Brink
MRM, Pamer EG. 2012. Intestinal domination and the risk of bacteremia
in patients undergoing allogeneic hematopoietic stem cell transplanta-
tion. Clin. Infect. Dis. 55(7):905–914.
4. Freter R. 1955. The fatal enteric cholera infection in the guinea pig,
achieved by inhibition of normal enteric flora. J. Infect. Dis. 97:57–65.
5. Bohnhoff M, Miller C. 1964. Resistance of the mouse’s intestinal tract to
experimental Salmonella infection. J. Exp. Med. 120:817–828.
6. Thijm HA, van der Waaij D. 1979. The effect of three frequently applied
antibiotics on the colonization resistance of the digestive tract of mice. J.
Hyg. (Lond.) 82:397–405.
7. Donskey CJ, Chowdhry TK, Hecker MT, Hoyen CK, Hanrahan JA,
Hujer AM, Hutton-Thomas RA, Whalen CC, Bonomo RA, Rice LB.
2000. Effect of antibiotic therapy on the density of vancomycin-resistant
enterococci in the stool of colonized patients. N. Engl. J. Med. 343:1925–
8. Buffie CG, Jarchum I, Equinda M, Lipuma L, Gobourne A, Viale A, Ubeda
C, Xavier J, Pamer EG. 2012. Profound alterations of intestinal microbiota
following a single dose of clindamycin results in sustained susceptibility to
9. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB,
Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B,
Thallinger GG, Van Horn DJ, Weber CF. 2009. Introducing mothur:
open-source, platform-independent, community-supported software for
10. Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, Glöck-
ner FO. 2007. SILVA: a comprehensive online resource for quality
Nucleic Acids Res. 35:7188–7196.
11. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G,
Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, Desantis TZ,
Human Microbiome Consortium, Petrosino JF, Knight R, Birren BW.
2011. Chimeric 16S rRNA sequence formation and detection in Sanger and
12. Huse SM, Welch DM, Morrison HG, Sogin ML. 2010. Ironing out the
wrinkles in the rare biosphere through improved OTU clustering. Envi-
ron. Microbiol. 12:1889–1898.
13. Magurran AE. 2004. Measuring biological diversity. Afr. J. Aquat. Sci.
14. Wang Q, Garrity GM, Tiedje JM, Cole JR. 2007. Naive Bayesian classifier
Appl. Environ. Microbiol. 73:5261–5267.
15. Brandl K, Plitas G, Mihu CN, Ubeda C, Jia T, Fleisher M, Schnabl
B, DeMatteo RP, Pamer EG. 2008. Vancomycin-resistant enterococci
exploit antibiotic-induced innate immune deficits. Nature 455:804–
16. Kinnebrew MA, Ubeda C, Zenewicz LA, Smith N, Flavell RA, Pamer
EG. 2010. Bacterial flagellin stimulates Toll-like receptor 5-dependent
defense against vancomycin-resistant Enterococcus infection. J. Infect.
17. Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, Schmidt
TM, Young VB. 2008. Decreased diversity of the fecal microbiome in
during VRE domination. (B) Shannon diversity index of samples from patients during VRE domination and prior to VRE domination and from patients that
never developed VRE domination. (C) Relative abundance (parts per unit; total microbiota ? 1) of the Barnesiella genus in samples from patients that did not
two sections (from 0 to 0.005 and from 0.01 to 0.11 parts per unit). Blue dashed lines indicate the means in each group of samples.
Ubeda et al.
iai.asm.orgInfection and Immunity
18. Mazmanian S, Liu C, Tzianabos A, Kasper D. 2005. An immunomodu- Download full-text
latory molecule of symbiotic bacteria directs maturation of the host im-
mune system. Cell 122:107–118.
19. Henao-Mejia J, Elinav E, Jin C, Hao L, Mehal WZ, Strowig T, Thaiss
CA, Kau AL, Eisenbarth SC, Jurczak MJ, Camporez J-P, Shulman GI,
Gordon JI, Hoffman HM, Flavell RA. 2012. Inflammasome-mediated
dysbiosis regulates progression of NAFLD and obesity. Nature 482:179–
20. Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ,
Peaper DR, Bertin J, Eisenbarth SC, Gordon JI, Flavell RA. 2011.
NLRP6 inflammasome regulates colonic microbial ecology and risk for
colitis. Cell 145:745–757.
21. Ferreira RBR, Gill N, Willing BP, Antunes LCM, Russell SL, Croxen
MA, Finlay BB. 2011. The intestinal microbiota plays a role in Salmonel-
la-induced colitis independent of pathogen colonization. PLoS One
22. Wlodarska M, Willing B, Keeney KM, Menendez A, Bergstrom KS, Gill
N, Russell SL, Vallance BA, Finlay BB. 2011. Antibiotic treatment alters
ter rodentium-induced colitis. Infect. Immun. 79:1536–1545.
23. Liu T, Hougen H, Vollmer AC, Hiebert SM. 2012. Gut bacteria profiles
of Mus musculus at the phylum and family levels are influenced by satu-
ration of dietary fatty acids. Anaerobe 18:331–337.
24. Bailey MT, Dowd SE, Galley JD, Hufnagle AR, Allen RG, Lyte M. 2011.
Exposure to a social stressor alters the structure of the intestinal microbi-
ota: implications for stressor-induced immunomodulation. Brain Behav.
25. Gomez A, Luckey D, Yeoman CJ, Marietta EV, Berg Miller ME, Murray
JA, White BA, Taneja V. 2012. Loss of sex and age driven differences in
the gut microbiome characterize arthritis-susceptible 0401 mice but not
arthritis-resistant 0402 mice. PLoS One 7:e36095. doi:10.1371/journal
Gut Microbiota Containing Barnesiella Suppresses VRE
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