Originally published in Science Express on 14 April 2005
Science 10 June 2005:
Vol. 308. no. 5728, pp. 1635 - 1638
DOI: 10.1126/science.1110591
Prev | Table of Contents | Next
REPORTS
Diversity of the Human Intestinal Microbial Flora
Paul B. Eckburg,1* Elisabeth M. Bik,2 Charles N. Bernstein,3 Elizabeth
Purdom,4 Les Dethlefsen,2 Michael Sargent,3 Steven R. Gill,5 Karen E.
Nelson,5 David A. Relman1,2,6*
The human endogenous intestinal microflora is an essential "organ" in providing
nourishment, regulating epithelial development, and instructing innate immunity;
yet, surprisingly, basic features remain poorly described. We examined 13,355
prokaryotic ribosomal RNA gene sequences from multiple colonic mucosal sites
and feces of healthy subjects to improve our understanding of gut microbial
diversity. A majority of the bacterial sequences corresponded to uncultivated
species and novel microorganisms. We discovered significant intersubject
variability and differences between stool and mucosa community composition.
Characterization of this immensely diverse ecosystem is the first step in
elucidating its role in health and disease.
1
Division of Infectious Diseases and Geographic Medicine, Stanford University
School of Medicine, Room S-169, 300 Pasteur Drive, Stanford CA 94305–5107,
USA.
2 Department of Microbiology and Immunology, 299 Campus Drive, Room
D300, Fairchild Science Building, Stanford CA 94305–5124, USA.
3 Section of Gastroenterology, Department of Medicine, University of Manitoba,
MS 779-820 Sherbrook Street, Winnipeg, Manitoba R3A 1R9, Canada.
4 Department of Statistics, Sequoia Hall, 390 Serra Mall, Stanford University,
Stanford CA 94305, USA.
5 The Institute for Genomic Research, 9712 Medical Center Drive, Rockville,
MD 20850, USA.
6 Veterans Affairs Palo Alto Health Care System, 3801 Miranda Avenue, Palo
Alto, CA 94304, USA.
*
To whom correspondence should be addressed. E-mail:
eckburg1@stanford.edu (P.B.E.); relman@stanford.edu (D.A.R.)
The endogenous gastrointestinal microbial flora plays a fundamentally important
role in health and disease, yet this ecosystem remains incompletely
characterized and its diversity poorly defined (1). Critical functions of the
commensal flora include protection against epithelial cell injury (2), regulation of
host fat storage (3), and stimulation of intestinal angiogenesis (4). Because of
the insensitivity of cultivation, investigators have begun to explore this
ecosystem using molecular finger-printing methods (5) and sequence analysis
of cloned microbial small-subunit ribosomal RNA genes [16S ribosomal DNA
(rDNA)] (6–9). However, such studies have been limited by the relative paucity
of sequenced gene fragments, the use of fecal biota as a surrogate for the
entire gut microflora, and little attention given to potential differences between
specific anatomical sites. In addition, variation associated with time, diet, and
health status have not been adequately described, nor have the relative
importance and contributions of each source (10).
Surface-adherent and luminal microbial populations may be distinct and may
fulfill different roles within the ecosystem. For example, the biofilm-like
architecture of the mucosal microbiota, in close contact with the underlying gut
epithelium, facilitates beneficial functions including nutrient exchange and
induction of host innate immunity (11). Fecal samples are often used to
investigate the intestinal microflora because they are easily collected. However,
the degree to which composition and function of the fecal microflora differ from
mucosal microflora remains unclear. We undertook a large-scale comparative
analysis of 16S rDNA sequences to characterize better the adherent mucosal
and fecal microbial communities and to examine how these microbial
communities differed between subjects and between mucosal sites.
Mucosal tissue and fecal samples were obtained from three healthy adult
subjects (A, B, and C) who were part of a larger population-based case-control
study (table S1) (12). Mucosal samples were obtained during colonoscopy from
healthy-appearing sites within the six major subdivisions of the human colon:
cecum, ascending colon, transverse colon, descending colon, sigmoid colon,
and rectum. Fecal samples were collected from each subject 1 month following
colonoscopy (12). We focused on 16S rDNA given its universal distribution
among all prokaryotes, the presence of diverse species-specific domains, and
its reliability for inferring phylogenetic relationships (13). The 16S rDNA was
amplified from samples with polymerase chain reaction (PCR) and broad-range
bacterial and archaeal primers (12). The 7 samples from subject B and the fecal
sample from subject C yielded archaeal products; all 21 samples yielded
bacterial products. PCR products were cloned and sequenced bidirectionally,
and numerical ecology approaches were applied.
Initially, a phylotype census was performed on each sample (table S2). A total of
11,831 bacterial and 1524 archaeal near-full-length, nonchimeric 16S rDNA
sequences were subjected to phylogenetic analysis. Using 99% minimum
similarity as the threshold for any pair of sequences in a phylotype (or
operational taxonomic unit) as calculated by dissimilarity matrices and the
DOTUR program (12), we identified a total of 395 bacterial phylotypes (Fig. 1).
In contrast, all 1524 archaeal sequences belonged to a single phylotype
(Methanobrevibacter smithii); these archaeal sequences were excluded from
further analyses. This remarkable apparent difference in diversity of the two
prokaryotic domains in the gut was reminiscent of results from soil and ocean
(14).
Fig. 1. Number of sequences per phylotype for each
sample. The y axis is a neighbor-joining
phylogenetic tree containing one representative of
each of the 395 phylotypes from this study; each
row is a different phylotype. The phyla
(Bacteroidetes, non-Alphaproteobacteria,
unclassified near Cyanobacteria, Actinobacteria,
Firmicutes, Fusobacteria, and
Alphaproteinobacteria, ordered top to bottom) are
color coded as in Fig. 3 and fig. S1. Each column is
labeled by subject (A, B, C) and anatomical site. For
each phylotype, the clone abundance is indicated by
a grayscale value. [View Larger Version of this
Image (48K GIF file)]
Of the 395 bacterial phylotypes, 244 (62%) were novel (table S3), and 80%
represented sequences from species that have not been cultivated (12). Most of
the inferred organisms were members of the Firmicutes and Bacteroidetes phyla
(Fig. 1 and fig. S1), which is concordant with other molecular analyses of the gut
flora (6, 7, 9). The Firmicutes phylum consisted of 301 phylotypes, 191 of which
were novel; most (95%) of the Firmicutes sequences were members of the
Clostridia class. We detected a substantial number of Firmicutes related to
known butyrate-producing bacteria (2454 sequences, 42 phylotypes) (15, 16),
all of which are members of clostridial clusters IV, XIVa, and XVI. We expected
prominent representation of this functional group among our healthy control
subjects, given its role in the maintenance and protection of the normal colonic
epithelium (16). Large variations among the 65 Bacteroidetes phylotypes were
noted between subjects (Fig. 1), as described previously (6, 7). B.
thetaiotaomicron was detected in each subject and is known to be involved in
beneficial functions, including nutrient absorption and epithelial cell maturation
and maintenance (17). Relatively few sequences were associated with the
Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia phyla (fig.
S1). The low abundance of Proteobacteria sequences (including Escherichia
coli) was not surprising, given that facultative species may represent 0.1% of
the bacteria in the strict anaerobic environment of the colon; this is consistent
with previous findings (6, 8, 9). Three sequences from two subjects
(represented by AY916143 [GenBank] ) clustered with unclassified sequences
previously identified from mammalian gut samples. These sequences appear to
represent a novel lineage, deeply branching from the Cyanobacteria phylum and
chloroplast sequences.
No complex microbial community in nature has been sampled to completion. In
addition to its biases and inability to distinguish live from dead organisms, the
limited sensitivity of broad-range PCR may hinder detection of rare phylotypes.
We used several nonparametric methods to explore the diversity and coverage
of our clone libraries. Phylotype richness estimations suggested that at least
500 phylotypes would be detected with continued sequencing from our samples
( 130, 300, and 200 phylotypes in subjects A, B, and C) (Fig. 2 and figs. S2
and S3). These estimates must be considered as lower bounds, because both
the observed and the estimated richness have increased in parallel with
additional sampling effort (Fig. 2 and fig. S3). Coverage was 99.0% over all
bacterial clone libraries combined, meaning that one new unique phylotype
would be expected for every 100 additional sequenced clones (18).
Fig. 2. Collector's curves of observed and estimated
phylotype richness of pooled mucosal samples per
subject. Each curve reflects the series of observed or
estimated richness values obtained as clones are added
to the data set in an arbitrary order. The curves rise less
steeply as an increasing proportion of phylotypes have
been encountered, but novel phylotypes continue to be
identified to the end of sampling. The relatively constant
estimates of the number of unobserved phylotypes in each
subject as observed richness increases (the gap between
observed and estimated richness) indicate that estimated
richness is likely to increase further with additional
sampling. The Chao1 estimator and the abundance-based
coverage estimator (ACE) are similar, but the ACE is less
volatile because it uses more information from the
abundance distribution of observed phylotypes. Individualbased rarefaction curves are depicted in figs. S4 to S6.
[View Larger Version of this Image (22K GIF file)]
The microbial community appeared more diverse in subject B than in A or C,
based on inspection of the richness and evenness of the clone distribution
across the phylogenetic tree (Fig. 1). The Rao diversity coefficient (19), which
accounts for both phylotype abundance and dissimilarity, was indeed higher for
B than for the other subjects (fig. S7). This pattern was not found with
traditional, that is, Shannon and Simpson, diversity indices, which assess only
relative phylotype abundance (20). Within each subject, the mucosal samples
demonstrated similar diversity profiles, regardless of the index used (fig. S7).
Previous investigations have not rigorously addressed possible differences in
the intestinal microflora between subjects, between anatomical sites, or
between stool and mucosal communities. We applied techniques that are based
on the relative abundance of sequences within communities and the extent of
genetic divergence between sequences. We first compared inter- and
intrasubject variability using double principal coordinate analysis (DPCoA) (19).
The greatest amount of variability was explained by intersubject differences;
stool-mucosa differences explained most of the variability remaining in the data
(Fig. 3). The relative lack of variation among mucosal sites was further
examined. The FST statistic of population genetics (21) was used to compare
genetic diversity within each subject; this revealed that the mucosal populations
of subjects A and B were significantly distinct compared with the overall
mucosal diversity (table S5). However, in both of these subjects, a single
mucosal library had a deviant genetic diversity index; exclusion of this library
from the analysis led to an insignificant FST statistic in each case (12). Taken as
a whole, these results confirmed little genetic variation among subject-specific
mucosal libraries.
Fig. 3. DPCoA for (A) colonic mucosa (solid
lines) and stool (dashed lines), (C) colonic
mucosal sites alone, and (D) mucosal sites
excluding Bacteroidetes phylotypes.
Phylotypes are represented as open circles,
colored according to phylum as in Fig. 1.
Phylotype points are positioned in
multidimensional space according to the
square root of the distances between them.
Ellipses indicate the distribution of phylotypes
per sample site, except in (A), where all
mucosal sites are represented by one ellipse.
Percentages shown along the axes represent
the proportion of total Rao dissimilarity
captured by that axis. (A) is the best possible
two-dimensional representation of the Rao
dissimilarities between all samples (12). (B) is
an enlarged view of (A), depicting the centroids
of each site-specific ellipse. Subject ellipse
distributions remain distinct after stool
phylotypes (C) and Bacteroidetes phylotypes
(D) are excluded from the analysis. [View
Larger Version of this Image (43K GIF file)]
We then asked whether nonrandom distributions of phylogenetic lineages
accounted for any variation among all samples. Using a modification of the
phylogenetic (P) test (12, 21), we found that stool and pooled mucosal libraries
harbored distinct lineages (P < 0.001) (table S5); however, distinct lineages
were not found among the individual mucosal libraries. We sought further
anatomic precision in explaining library distinctions using the -LIBSHUFF
program (22). We found that mucosal clone libraries were similar to the other
mucosal libraries from the same subject, with two exceptions (fig. S6). The
library from the ascending colon of subject A was a subset of every other
mucosal population from that subject (P values < 0.0017), and the descending
colon library from subject B was a subset of the ascending colon library in that
subject (P = 0.0005). Such inconsistencies among mucosal subpopulations
suggested a pattern of patchiness in the distribution of mucosal bacteria rather
than a homogenous gradient along the longitudinal axis of the colon. LIBSHUFF also revealed that nearly all mucosal libraries from subjects B and C
were significantly distinct from the corresponding stool library, whereas each
mucosal library from subject A was a subset of the stool library. We postulate
that the fecal microbiota represents a combination of shed mucosal bacteria and
a separate nonadherent luminal population; however, these data must be
interpreted with caution, given the delay between stool and mucosa sampling.
Bacterial diversity within the human colon and feces is greater than previously
described, and most of it is novel. Differences between individuals were
significantly greater than intrasubject differences, with the exception of variation
between stool and adherent mucosal communities. Complicating this picture is
our evidence for patchiness and heterogeneity. This patchiness did not display
an obvious pattern along the course of the colon but may reflect microanatomic
niches. Given that each mucosal sample contained a similar distribution of
organisms within higher order taxa (Fig. 1), the variation we observed at the
genus or species level may be the result of colonization resistance by the more
abundant members within similar functional groups (23). Whether the gut
microbiota undergoes such nonrandom assembly remains unclear.
Ecological statistical approaches reveal previously unrecognized irregularities in
the architecture of complex microbial communities. High-resolution spatial,
temporal, and functional analyses of the adherent human intestinal microbiota
are still needed. In addition, the effects of host genetics and of perturbations
such as immunosuppression, antimicrobials, and change in diet have yet to be
carefully defined. We anticipate that micro-arrays, single-cell analysis, and
metagenomics [e.g., a "Second Human Genome Project" (24)] will complement
the approach we have illustrated and hasten our understanding of humanassociated microbial ecosystems.
References and Notes











1. L. V. Hooper, J. I. Gordon, Science 292, 1115 (2001).[Abstract/Free
Full Text]
2. S. Rakoff-Nahoum, J. Paglino, F. Eslami-Varzaneh, S. Edberg, R.
Medzhitov, Cell 118, 229 (2004). [CrossRef] [ISI] [Medline]
3. F. Backhed et al., Proc. Natl. Acad. Sci. U.S.A. 101, 15718
(2004).[Abstract/Free Full Text]
4. T. S. Stappenbeck, L. V. Hooper, J. I. Gordon, Proc. Natl. Acad. Sci.
U.S.A. 99, 15451 (2002).[Abstract/Free Full Text]
5. E. G. Zoetendal et al., Appl. Environ. Microbiol. 68, 3401
(2002).[Abstract/Free Full Text]
6. H. Hayashi, M. Sakamoto, Y. Benno, Microbiol. Immunol. 46, 535
(2002). [ISI] [Medline]
7. G. L. Hold, S. E. Pryde, V. J. Russell, E. Furrie, H. J. Flint, FEMS
Microbiol. Ecol. 39, 33 (2002). [CrossRef] [ISI]
8. A. Suau et al., Appl. Environ. Microbiol. 65, 4799 (1999).[Abstract/Free
Full Text]
9. X. Wang, S. P. Heazlewood, D. O. Krause, T. H. Florin, J. Appl.
Microbiol. 95, 508 (2003). [CrossRef] [ISI] [Medline]
10. M. C. Horner-Devine, K. M. Carney, B. J. M. Bohannan, Proc. R.
Soc. London 271, 113 (2003). [ISI]
11. J. L. Sonnenburg, L. T. Angenent, J. I. Gordon, Nat. Immunol. 5, 569
(2004). [CrossRef] [ISI] [Medline]














12. Materials and methods are available as supporting material on
Science Online.
13. N. R. Pace, Science 276, 734 (1997).[Abstract/Free Full Text]
14. T. P. Curtis, W. T. Sloan, Curr. Opin. Microbiol. 7, 221 (2004).
[CrossRef] [ISI] [Medline]
15. A. Barcenilla et al., Appl. Environ. Microbiol. 66, 1654
(2000).[Abstract/Free Full Text]
16. S. E. Pryde, S. H. Duncan, G. L. Hold, C. S. Stewart, H. J. Flint,
FEMS Microbiol. Lett. 217, 133 (2002). [CrossRef] [ISI] [Medline]
17. L. V. Hooper et al., Science 291, 881 (2001).[Abstract/Free Full Text]
18. Good's coverage estimates were 99.3%, 97.9%, and 98.3% for
subjects A, B, and C, respectively.
19. S. Pavoine, A. B. Dufour, D. Chessel, J. Theor. Biol. 228, 523 (2004).
[CrossRef] [ISI] [Medline]
20. R. K. Colwell, EstimateS, version 7 (2004)
(http://viceroy.eeb.uconn.edu/estimates).
21. A. P. Martin, Appl. Environ. Microbiol. 68, 3673 (2002).[Free
Full Text]
22. P. D. Schloss, B. R. Larget, J. Handelsman, Appl. Environ. Microbiol.
70, 5485 (2004).[Abstract/Free Full Text]
23. J. Fargione, C. S. Brown, D. Tilman, Proc. Natl. Acad. Sci. U.S.A.
100, 8916 (2003).[Abstract/Free Full Text]
24. D. A. Relman, S. Falkow, Trends Microbiol. 9, 206 (2001). [CrossRef]
[ISI] [Medline]
25. We thank B. Bohannan, M. B. Omary, and S. Holmes (Stanford
University) for helpful comments on the manuscript. This research was
supported by grants from the NIH (no. AI51259) and Ellison Medical Foundation
(D.A.R.), Canadian Institutes of Health Research and Crohn's and Colitis
Foundation of Canada (C.N.B., M.S.), National Science Foundation (E.P.), and
Defense Advanced Research Projects Agency (S.R.G., K.E.N.).
Representatives of novel phylotypes (AY916135 to AY916390) and all other
sequences (AY974810 to AY986384) were deposited in GenBank.
Supporting Online Material
www.sciencemag.org/cgi/content/full/1110591/DC1
Materials and Methods
SOM Text
Figs. S1 to S8
Tables S1 to S6
References
Received for publication 2 February 2005. Accepted for publication 5 April 2005.
The editors suggest the following Related Resources on Science sites:
In Science Magazine
LETTERS
Timing in Collection of Stool Samples
Volker Mai, O. Colin Stine, J. Glenn Morris Jr.;, Paul B. Eckburg, Elisabeth M. Bik, Charles N.
Bernstein, Les Dethlefsen, Elizabeth Purdom, Michael Sargent, Steven R. Gill, Karen E. Nelson,
and David A. Relman (18 November 2005)
Science 310 (5751), 1118. [DOI: 10.1126/science.310.5751.1118]
Full Text » PDF »
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition.
V Mai, B Greenwald, J Glenn Morris Jr, J-P Raufman, and O C Stine (2006)
Gut 55, 1822-1823
Full Text » PDF »
Functional Genomic and Metabolic Studies of the Adaptations of a Prominent Adult Human Gut
Symbiont, Bacteroides thetaiotaomicron, to the Suckling Period.
M. K. Bjursell, E. C. Martens, and J. I. Gordon (2006)
J. Biol. Chem. 281, 36269-36279
Abstract » Full Text » PDF »
Cell-associated {alpha}-amylases of butyrate-producing Firmicute bacteria from the human colon..
A. G. Ramsay, K. P. Scott, J. C. Martin, M. T. Rincon, and H. J. Flint (2006)
Microbiology 152, 3281-3290
Abstract » Full Text » PDF »
Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and
Targeted Bacterial Subgroups in Crohn's Disease.
P. D. Scanlan, F. Shanahan, C. O'Mahony, and J. R. Marchesi (2006)
J. Clin. Microbiol. 44, 3980-3988
Abstract » Full Text » PDF »
Differences between Tissue-Associated Intestinal Microfloras of Patients with Crohn's Disease and
Ulcerative Colitis.
U. Gophna, K. Sommerfeld, S. Gophna, W. F. Doolittle, and S. J. O. Veldhuyzen van Zanten
(2006)
J. Clin. Microbiol. 44, 4136-4141
Abstract » Full Text » PDF »
Culture-independent analysis of indomethacin-induced alterations in the rat gastrointestinal
microbiota..
A. B. Dalby, D. N. Frank, A. L. St. Amand, A. M. Bendele, and N. R. Pace (2006)
Appl. Envir. Microbiol. 72, 6707-6715
Abstract » Full Text » PDF »
Introducing SONS, a Tool for Operational Taxonomic Unit-Based Comparisons of Microbial
Community Memberships and Structures..
P. D. Schloss and J. Handelsman (2006)
Appl. Envir. Microbiol. 72, 6773-6779
Abstract » Full Text » PDF »
New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain
Chimeras.
K. E. Ashelford, N. A. Chuzhanova, J. C. Fry, A. J. Jones, and A. J. Weightman (2006)
Appl. Envir. Microbiol. 72, 5734-5741
Abstract » Full Text » PDF »
Molecular Diversity, Cultivation, and Improved Detection by Fluorescent In Situ Hybridization of a
Dominant Group of Human Gut Bacteria Related to Roseburia spp. or Eubacterium rectale.
R. I. Aminov, A. W. Walker, S. H. Duncan, H. J. M. Harmsen, G. W. Welling, and H. J. Flint (2006)
Appl. Envir. Microbiol. 72, 6371-6376
Abstract » Full Text » PDF »
Symbiotic bacteria direct expression of an intestinal bactericidal lectin..
H. L. Cash, C. V. Whitham, C. L. Behrendt, and L. V. Hooper (2006)
Science 313, 1126-1130
Abstract » Full Text » PDF »
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulinresistant mice.
M.-E. Dumas, R. H. Barton, A. Toye, O. Cloarec, C. Blancher, A. Rothwell, J. Fearnside, R.
Tatoud, V. Blanc, J. C. Lindon, S. C. Mitchell, E. Holmes, M. I. McCarthy, J. Scott, D. Gauguier,
and J. K. Nicholson (2006)
PNAS 103, 12511-12516
Abstract » Full Text » PDF »
Short-chain Fatty acids: ready for prime time?.
C. C. Roy, C. L. Kien, L. Bouthillier, and E. Levy (2006)
Nutr Clin Pract 21, 351-366
Abstract » Full Text » PDF »
Molecular Profiling of the Clostridium leptum Subgroup in Human Fecal Microflora by PCRDenaturing Gradient Gel Electrophoresis and Clone Library Analysis.
J. Shen, B. Zhang, G. Wei, X. Pang, H. Wei, M. Li, Y. Zhang, W. Jia, and L. Zhao (2006)
Appl. Envir. Microbiol. 72, 5232-5238
Abstract » Full Text » PDF »
Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions..
L. C. Paulino, C.-H. Tseng, B. E. Strober, and M. J. Blaser (2006)
J. Clin. Microbiol. 44, 2933-2941
Abstract » Full Text » PDF »
Molecular approaches to the role of the microbiota in inflammatory bowel disease..
C. O ELSON, Y. CONG, F. QI, R. M HERSHBERG, and S. R TARGAN (2006)
Ann. N.Y. Acad. Sci. 1072, 39-51
Abstract » Full Text » PDF »
Intestinal bacterial microflora--a potential source of chronic inflammation in patients with chronic
kidney disease.
P. Kotanko, M. Carter, and N. W. Levin (2006)
Nephrol. Dial. Transplant. 21, 2057-2060
Full Text » PDF »
Culture-independent characterization of the digestive-tract microbiota of the medicinal leech
reveals a tripartite symbiosis..
P. L. Worthen, C. J. Gode, and J. Graf (2006)
Appl. Envir. Microbiol. 72, 4775-4781
Abstract » Full Text » PDF »
NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes..
T. Z. DeSantis Jr, P. Hugenholtz, K. Keller, E. L. Brodie, N. Larsen, Y. M. Piceno, R. Phan, and
G. L. Andersen (2006)
Nucleic Acids Res. 34, W394-W399
Abstract » Full Text » PDF »
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.
B. S. Samuel and J. I. Gordon (2006)
PNAS 103, 10011-10016
Abstract » Full Text » PDF »
A hybrid two-component system protein of a prominent human gut symbiont couples glycan
sensing in vivo to carbohydrate metabolism.
E. D. Sonnenburg, J. L. Sonnenburg, J. K. Manchester, E. E. Hansen, H. C. Chiang, and J. I.
Gordon (2006)
PNAS 103, 8834-8839
Abstract » Full Text » PDF »
Metagenomic analysis of the human distal gut microbiome..
S. R. Gill, M. Pop, R. T. DeBoy, P. B. Eckburg, P. J. Turnbaugh, B. S. Samuel, J. I. Gordon, D. A.
Relman, C. M. Fraser-Liggett, and K. E. Nelson (2006)
Science 312, 1355-1359
Abstract » Full Text » PDF »
Rapid Succession within the Veillonella Population of a Developing Human Oral Biofilm In Situ.
R. J. Palmer Jr., P. I. Diaz, and P. E. Kolenbrander (2006)
J. Bacteriol. 188, 4117-4124
Abstract » Full Text » PDF »
Whole-Genome Transcription Profiling Reveals Genes Up-Regulated by Growth on Fucose in the
Human Gut Bacterium "Roseburia inulinivorans"..
K. P. Scott, J. C. Martin, G. Campbell, C.-D. Mayer, and H. J. Flint (2006)
J. Bacteriol. 188, 4340-4349
Abstract » Full Text » PDF »
Unexpected diversity and complexity of the guerrero negro hypersaline microbial mat..
R. E. Ley, J. K. Harris, J. Wilcox, J. R. Spear, S. R. Miller, B. M. Bebout, J. A. Maresca, D. A.
Bryant, M. L. Sogin, and N. R. Pace (2006)
Appl. Envir. Microbiol. 72, 3685-3695
Abstract » Full Text » PDF »
Fecal bacterial diversity in a wild gorilla..
J. C. Frey, J. M. Rothman, A. N. Pell, J. B. Nizeyi, M. R. Cranfield, and E. R. Angert (2006)
Appl. Envir. Microbiol. 72, 3788-3792
Abstract » Full Text » PDF »
Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis..
K. Lucke, S. Miehlke, E. Jacobs, and M. Schuppler (2006)
J. Med. Microbiol. 55, 617-624
Abstract » Full Text » PDF »
Molecular Characterization of Subject-Specific Oral Microflora during Initial Colonization of
Enamel.
P. I. Diaz, N. I. Chalmers, A. H. Rickard, C. Kong, C. L. Milburn, R. J. Palmer Jr., and P. E.
Kolenbrander (2006)
Appl. Envir. Microbiol. 72, 2837-2848
Abstract » Full Text » PDF »
Denitrifier Community Composition along a Nitrate and Salinity Gradient in a Coastal Aquifer..
A. E. Santoro, A. B. Boehm, and C. A. Francis (2006)
Appl. Envir. Microbiol. 72, 2102-2109
Abstract » Full Text » PDF »
Application of sequence-based methods in human microbial ecology.
L. Weng, E. M. Rubin, and J. Bristow (2006)
Genome Res. 16, 316-322
Abstract » Full Text » PDF »
A molecular revolution in the study of intestinal microflora.
E Furrie (2006)
Gut 55, 141-143
Abstract » Full Text » PDF »
Bile salt biotransformations by human intestinal bacteria.
J. M. Ridlon, D.-J. Kang, and P. B. Hylemon (2006)
J. Lipid Res. 47, 241-259
Abstract » Full Text » PDF »
Molecular analysis of the bacterial microbiota in the human stomach.
E. M. Bik, P. B. Eckburg, S. R. Gill, K. E. Nelson, E. A. Purdom, F. Francois, G. Perez-Perez, M.
J. Blaser, and D. A. Relman (2006)
PNAS 103, 732-737
Abstract » Full Text » PDF »
Rapid quantitative profiling of complex microbial populations.
C. Palmer, E. M. Bik, M. B. Eisen, P. B. Eckburg, T. R. Sana, P. K. Wolber, D. A. Relman, and P.
O. Brown (2006)
Nucleic Acids Res. 34, e5
Abstract » Full Text » PDF »
Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid
bacteria.
J. Boekhorst, Q. Helmer, M. Kleerebezem, and R. J. Siezen (2006)
Microbiology 152, 273-280
Abstract » Full Text » PDF »
Reciprocal epithelial-mesenchymal FGF signaling is required for cecal development.
X. Zhang, T. S. Stappenbeck, A. C. White, K. J. Lavine, J. I. Gordon, and D. M. Ornitz (2006)
Development 133, 173-180
Abstract » Full Text » PDF »
Colonization of the Cecal Mucosa by Helicobacter hepaticus Impacts the Diversity of the
Indigenous Microbiota.
C. J. Kuehl, H. D. Wood, T. L. Marsh, T. M. Schmidt, and V. B. Young (2005)
Infect. Immun. 73, 6952-6961
Abstract » Full Text » PDF »
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the
microbial "pan-genome".
H. Tettelin, V. Masignani, M. J. Cieslewicz, C. Donati, D. Medini, N. L. Ward, S. V. Angiuoli, J.
Crabtree, A. L. Jones, A. S. Durkin, R. T. DeBoy, T. M. Davidsen, M. Mora, M. Scarselli, I.
Margarit y Ros, J. D. Peterson, C. R. Hauser, J. P. Sundaram, W. C. Nelson, R. Madupu, L. M.
Brinkac, R. J. Dodson, M. J. Rosovitz, S. A. Sullivan, S. C. Daugherty, D. H. Haft, J. Selengut, M.
L. Gwinn, L. Zhou, N. Zafar, H. Khouri, D. Radune, G. Dimitrov, K. Watkins, K. J. B. O'Connor, S.
Smith, T. R. Utterback, O. White, C. E. Rubens, G. Grandi, L. C. Madoff, D. L. Kasper, J. L.
Telford, M. R. Wessels, R. Rappuoli, and C. M. Fraser (2005)
PNAS 102, 13950-13955
Abstract » Full Text » PDF »
From The Cover: Microbial regulation of intestinal radiosensitivity.
P. A. Crawford and J. I. Gordon (2005)
PNAS 102, 13254-13259
Abstract » Full Text » PDF »
Lipotechoic acid in lactobacilli: D-Alanine makes the difference.
W. M. de Vos (2005)
PNAS 102, 10763-10764
Full Text » PDF »
Obesity alters gut microbial ecology.
R. E. Ley, F. Backhed, P. Turnbaugh, C. A. Lozupone, R. D. Knight, and J. I. Gordon (2005)
PNAS 102, 11070-11075
Abstract » Full Text » PDF »
Science 11 May 2001:
Vol. 292. no. 5519, pp. 1115 - 1118
DOI: 10.1126/science.1058709
Prev | Table of Contents | Next
VIEWPOINT
Commensal Host-Bacterial Relationships in the Gut
Lora V. Hooper and Jeffrey I. Gordon*
One potential outcome of the adaptive coevolution of humans and bacteria is
the development of commensal relationships, where neither partner is harmed,
or symbiotic relationships, where unique metabolic traits or other benefits are
provided. Our gastrointestinal tract is colonized by a vast community of
symbionts and commensals that have important effects on immune function,
nutrient processing, and a broad range of other host activities. The current
genomic revolution offers an unprecedented opportunity to identify the molecular
foundations of these relationships so that we can understand how they
contribute to our normal physiology and how they can be exploited to develop
new therapeutic strategies.
Department of Molecular Biology and Pharmacology, Washington University
School of Medicine, St. Louis, MO 63110, USA.
* To whom correspondence should be addressed. E-mail:
jgordon@molecool.wustl.edu
The first draft of our complete DNA sequence represents a historic event in our
quest for self-knowledge (1, 2). Knowing our genotype highlights the need to
understand how environmental factors interact with our genetic traits to
influence health and predispose us to illness. In the midst of the current
revolution in comparative and functional genomics, it is therefore appropriate to
consider another form of self-knowledge: the contributions of our microbial
partners to our biology. From birth to death, we are colonized by a vast,
complex, and dynamic consortium of microorganisms that may outnumber our
somatic and germ cells (3). The Nobel laureate Joshua Lederberg has
suggested using the term "microbiome" to describe the collective genome of our
indigenous microbes (microflora), the idea being that a comprehensive genetic
view of Homo sapiens as a life-form should include the genes in our microbiome
(4).
Bacteria have inhabited Earth for at least 2.5 billion years (5). As a result, our
predecessors have had to adapt to a biosphere dominated by microbes.
However, we have minimal knowledge of how coevolution with indigenous
microorganisms has shaped our genome and microbiome, as well as our
physiology and postnatal development. For example, the human genome
encodes 223 proteins with significant homology to bacterial but not eukaryotic
proteins, suggesting that they were acquired through horizontal transfer of
bacterial genes (1). Unfortunately, the components of our microbiome remain
poorly defined. Like most complex ecosystems, enumerating membership in the
various microbial societies that reside on our body surfaces has been hindered
by the fact that most societal members cannot be cultured ex vivo.
Moreover, most microbial genome-sequencing projects have focused on
pathogens. Those that have embraced nonpathogens have turned to Archaea to
understand the evolutionary diversification of protocytes and eukaryotes or to
extremophiles to examine their adaptations to harsh environments and their
potential for performing commercially applicable chemistry (6).
Interactions between bacteria and their hosts can be viewed in terms of a
continuum between symbiosis, commensalism, and pathogenicity, with
symbiosis and commensalism grouped under the general heading of mutualism
(Fig. 1). "Symbiosis" refers to a relationship between two different species
where at least one partner benefits without harming the other and is typically
centered on metabolic capabilities that allow either or both partners to exploit an
otherwise unavailable or poorly utilizable nutrient foundation (7, 8). The term
"commensal" comes from the medieval Latin "commensalis," meaning "at table
together," and generally refers to partners that coexist without detriment but
without obvious benefit. A pathogenic relationship results in damage to the host.
Symbiosis and commensalism have been viewed as potential outcomes of a
dynamic "arms race" (9) initiated when a pathogen encounters a vulnerable
host. In this race, a change in one combatant is matched by an adaptive
response in the other. In some settings, the arms race evolves toward
attenuation of virulence and peaceful coexistence, with or without frank
codependence (symbiosis). In other circumstances, the pathogenic relationship
is sustained by the development of effective countermeasures that bypass the
host's innate or adaptive defenses (Fig. 1). Ewald has coined the term
"evolutionary epidemiology" to underscore how a comprehensive analysis of
disease prevalence and spread must include the set of adaptive responses of
host and pathogen to one another and their outside environment over time (10).
He and others have emphasized that the concept of obligate evolution of
parasites (pathogens) to benignness should be rejected on the basis of empiric
as well as theoretical considerations (11).
Fig. 1. Mutualism. Commensalism and symbiosis are presented as part of a
continuum, distinguished by the identification of specific benefits derived by one
or both members of a host-bacterial partnership. Commensalism or symbiosis is
a potential but not inevitable outcome of the dynamic coevolution of hostbacterial relationships. Genetic diversity reflects the balance of factors that
promote variation (point mutation, recombination, and gene transfer) versus
factors that act to stabilize the genome (DNA repair enzymes, restriction
modification systems, and barriers to horizontal transfer of genes) (6). [View
Larger Version of this Image (19K GIF file)]
THE INTESTINE AS AN ARENA FOR STUDYING MUTUALISTIC
RELATIONSHIPS
Because most of our bacterial symbionts and commensals reside in our
intestine (3), it should be an arena where their interplay with us should have
great, if not the greatest, significance to our biology. The species composition of
symbionts and commensals varies along the length of the gut, changes as we
develop and age, and is influenced by our environment. Molecular approaches,
such as broad-range sequencing of 16S ribosomal RNA (rRNA) genes (12), are
just now being used to define shifts in the composition of the gut flora during an
individual's life or to assess its biodiversity in geographically defined healthy
populations and in different disease states (13). The benefits provided by most
identified members of this microflora have yet to be deciphered. Therefore,
pending further information, we will use commensal as a generic label as we
discuss current information, hypotheses, and questions about the foundations of
mutualism in the intestine.
IMMUNE TOLERANCE TO GUT COMMENSALS
Although the mammalian gut must be sufficiently permeable to support efficient
absorption of nutrients, it must avoid potentially damaging immune responses to
dietary proteins and commensals. Innate defenses, such as epithelial production
of -defensins and mucins, help prevent bacteria from crossing the mucosal
barrier (14-16). Additional protection is afforded by secretory immunoglobulin A
(sIgA). sIgA against commensal antigens is specifically induced in the intestinal
mucosa (17). In contrast to the sIgA response to pathogen-derived epitopes,
which requires costimulation by antigen-specific T cells, induction of sIgA
against commensal antigens is T cell independent in mice (17). Such
independence presumably allows the host to respond to shifts in the commensal
flora without eliciting a deleterious immune response. This pathway may be part
of an evolutionarily primitive form of adaptive immunity (17).
Nonpathogenic bacteria may directly influence the intestinal epithelium to limit
immune activation. Neish et al. (18) demonstrated that an avirulent Salmonella
strain abrogates production of inflammatory cytokines in cultured human
intestinal epithelial cells. The mechanism involves I B, which blocks nuclear
factor B (NF- B) nuclear localization. The Salmonella strain was able to inhibit
ubiquitination and degradation of I B, thus blocking NF- B-directed
transactivation of genes encoding inflammatory mediators (18). In addition,
commensals can help fortify the epithelial barrier. Bacteroides thetaiotaomicron
is a prominent, genetically manipulatable member of the normal mouse and
human distal intestinal microflora (19-21). B. thetaiotaomicron colonization of
germ-free mouse intestine induces expression of decay-accelerating factor,
which inhibits cytotoxic damage from microbial activation of secreted
complement components; complement-reactive protein (CRP)-ductin, a putative
receptor for intestinal trefoil factors that facilitate repair of damaged epithelium;
and Sprr2a, a member of the family of small proline-rich proteins known to
participate in cutaneous barrier functions (22).
There is mounting evidence that commensals acquired during the early
postnatal period are required for the development of tolerance not only to
themselves but also to other luminal antigens (23, 24). For example, Sudo et al.
reported that T helper 2-mediated immune responses to ovalbumin were not
susceptible to oral tolerance induction in germ-free mice, but susceptibility was
restored after the introduction of a single component of the preweaning
microflora into neonates (23). The increasing prevalence of atopy (tendency to
allergy) in Western industrialized societies has led to the hypothesis that an
overly hygienic life-style has altered the normal pattern of intestinal colonization
during infancy and produced a lack of tolerance to otherwise harmless food
proteins and inhaled antigens (25, 26).
CONTRIBUTIONS OF THE COMMENSAL FLORA TO PATHOLOGIC
STATES
The relationship between indigenous gut microbes and their hosts can shift from
commensalism toward pathogenicity in certain diseases. Inflammatory bowel
disease (IBD), which includes ulcerative colitis and Crohn's disease, affects
0.1% of the population in Western societies. The pathogenesis of IBD appears
to involve an "inappropriate" activation of the mucosal immune system. This
activation has been linked to a loss of tolerance to gut commensals (27, 28).
Several observations illustrate this point. Both Crohn's disease and ulcerative
colitis respond to treatment with broad-spectrum antibiotics (29, 30). The
spontaneous colitis that develops in human leukocyte antigen-B27/ 2microgloblin transgenic rats and in knockout mice that lack interleukin-2 or T cell
receptors is abrogated when animals are raised under germ-free conditions (3133). Conventionally raised mice deficient in interleukin-10 (IL-10) develop patchy
chronic colitis similar to that encountered in humans with Crohn's disease,
whereas germ-free mice do not (34, 35).
What is not clear is whether the inflammatory responses in IBD, both within the
gut and at extraintestinal sites, are elicited in response to a specific subset of
intestinal microbes or whether tolerance to commensals is affected generally.
An interesting question is whether barrier function is first compromised by
"intrinsic" defects in epithelial integrity, by infection with enteropathogens, or by
loss of commensal-dependent signals necessary to maintain the physical
integrity of the epithelium and hypo-responsiveness of the mucosal immune
system. Part of this question may be answered when human IBD susceptibility
genes, such as IBD-1 (36), are identified. Other clues are coming from
comparisons of conventionally raised and germ-free animals. For example,
conventionally raised IL-10-deficient mice exhibit increased ileal and colonic
permeability by 2 weeks of age, well before the appearance of histopathologic
changes in the gut. This change in permeability, which is accompanied by
increased production of interferon- and tumor necrosis factor- , does not occur
in germ-free IL-10-/- mice (37).
ASSESSING THE IMPACT OF COMMENSALS ON OTHER ASPECTS OF
GUT PHYSIOLOGY AND DEVELOPMENT
Because the intestinal ecosystem is characterized by dynamic and reciprocal
interactions among its microflora, epithelium, and immune system, cultured cells
may not accurately portray in vivo responses to commensals. An alternative
approach is to use germ-free inbred strains of mice as genetically defined
simplified in vivo assay systems for studying the impact of colonization, with
single or multiple members of the microflora, on intestinal gene expression.
DNA microarrays provide a powerful tool for comprehensively profiling
transcriptional responses to colonization in these gnotobiotic systems and
thereby defining the breadth of potential functions modulated by commensals.
In addition to fortifying barrier functions, DNA microarray analyses have shown
that colonization of germ-free mice with B. thetaiotaomicron affects expression
of host genes that regulate postnatal maturation, nutrient uptake and
metabolism, processing of xenobiotics, and angiogenesis (22). The increased
expression of genes involved in absorption of carbohydrates, as well as
breakdown and absorption of complex lipids (19), provides a potential molecular
explanation for the observation that germ-free rodents must consume ~30%
more calories to sustain their body weight than do conventionally raised animals
(38). These findings suggest a testable hypothesis: namely, that compositional
differences may exist in the microflora of lean and obese individuals and that
such differences could affect their nutrient-processing capabilities.
ESTABLISHING MICROBIAL COMMUNITIES IN DIFFERENT REGIONS OF
THE GASTROINTESTINAL TRACT
The host and microbial factors that direct establishment and maintenance of a
spatially diversified gut microflora in mice and humans remain largely unknown.
Community formation likely proceeds through a complex regulatory network of
host-microbial and microbial-microbial interactions predicated on exploiting and
developing suitable nutrient foundations and dependent on intra- and
interspecies communications systems. Nutrient exchange in the constantly
perfused gut could occur through biofilms (39), although biofilm formation in the
intestine has not been reported to date. Given the importance of quorum
sensing in regulating microbial-microbial communications and biofilm formation,
it seems likely that it would be used by some or many components of an
emerging bacterial community to establish residence in intestinal habitats.
Development of dental plaque provides the one well-studied example of
community formation that employs some of these proposed mechanisms. The
complex biofilm plaque community is assembled through an orderly process
involving initial adhesion of early colonizers (e.g., Streptococcus spp.) to a hostderived structure (an acquired pellicle on the tooth surface), followed by
secondary colonization through interbacterial adhesion and intergeneric
communications. Ultimately, a structure is created that is predominated by
Gram-negative anaerobes (40-42).
Studies with germ-free mice have revealed that positioning of
B. thetaiotaomicron in the postnatal distal small intestine (ileum) may be
achieved, at least in part, through an active collaboration between host and
microbe centered on glycan synthesis and utilization. Production of a subset of
epithelial fucosylated glycans is normally induced in the ileum at the sucklingweaning transition in conventionally raised but not in germ-free mice (43). This
induction occurs at the same time that B. thetaiotaomicron and other
commensal anaerobes are first gaining a foothold. Synthesis of these epithelial
glycans is elicited by a B. thetaiotaomicron signal whose expression is regulated
by a fucose-binding bacterial transcription factor. This factor senses
environmental levels of fucose and coordinates the decision to generate a signal
for production of host fucosylated glycans when environmental fucose is limited
or to induce expression of the bacteria's fucose utilization operon when fucose
is abundant (44).
These considerations suggest a potential explanation for the striking structural
diversity of oligosaccharide outer chain segments in mammalian glycans. This
diversity, which arises principally from the nontemplate combinatorial nature of
carbohydrate synthesis and modification, has generally not been associated
with clearly delineated functions. By matching host carbohydrate structures with
the capacity of bacterial species to produce glycosidases and to use the
resulting enzymatic products, these glycans may serve as a nutrient foundation
that helps organize initial colonization of the developing intestine. An elaborate
series of combinatorial bacterial-host and bacterial-bacterial interactions may
subsequently shape the metabolic milieu in a manner permissive for
establishing a more diversified collection of bacterial species (Fig. 2). Species
diversification, in turn, could benefit the developing host by providing new
metabolic capabilities at critical times during postnatal development, by
supplying microbial factors that influence other aspects of host postnatal
development (22), and/or by affording resistance to colonization by potential
pathogens that cannot compete with entrenched residents of the microbial
community for nutrients.
Fig. 2. Establishing a microbial community in the intestine. One postulated
component of the nutrient foundation is the diverse collection of outer chain
segments in epithelial glycans. Some microorganisms may function as "covert
symbionts," whose contribution is to help to create a metabolic milieu that favors
incorporation of other species into an emerging community that provides direct
benefit to the host. [View Larger Version of this Image (16K GIF file)]
There are a number of carefully studied examples of symbionts influencing the
development of host tissues, including Vibrio fischeri-induced development of a
light organ in the squid Euprymna scolopes (8) or the formation of root or stem
nodules in plants by various genera of soil bacteria (7). The idea that a
bacterium such as B. thetaiotaomicron can collaborate with its host to regulate
postnatal intestinal development is logical, considering their mutual reliance.
The impact of commensals on postnatal developmental processes needs to be
examined in other colonized mammalian tissues and in other eukaryotes that
support a microflora.
COMMENSALS AS THERAPEUTIC AGENTS
The adaptations of symbionts and commensals to life in nutritionally
advantageous host niches provide a rationale for using these organisms as
therapeutic agents. In its simplest expression, components of the normal flora
are given as live biological supplements (probiotics) that confer some host
benefit. For example, giving Lactobacillus spp. to IL-10-deficient mice
attenuates their colitis (45). Probiotic preparations containing Bifidobacterium,
Lactobacillum, and Streptococcus spp. are beneficial in treating chronic
"pouchitis," a complication following surgical intervention for ulcerative colitis
(46). In addition, nonpathogenic Escherichia coli provided effective probiotic
therapy in a randomized double-blind trial of patients with active ulcerative colitis
(30).
Unfortunately, molecular tools are not yet available to define the effects of such
probiotic interventions on the composition of a host's microflora. The
development of microarrays containing rRNA gene sequences from different
members of the gut microflora represents a potential starting point
for determining whether identifiable changes in species composition can be
associated with particular disease states and, subsequently, for designing
hypothesis-based therapeutic trials of probiotic supplements (Fig. 3).
Fig. 3. Questions and suggested approaches for the future. The term
"microbiome" (3) refers to the collective genomes of members of a microflora.
The human intestinal microflora is estimated to contain 500 to 1000 species, at
least 50% of which cannot be cultivated ex vivo. Assuming an average microbial
genome size of 5 million base pairs (bp) and 4000 genes per genome, the 2.5billion- to 5-billion-bp intestinal microbiome may contain 2 million to 4 million
genes (i.e., ~50 to 100 times as many as our "own" genome). "Gnotobiotic"
comes from the Greek "known life" and refers to animals with defined
microbiological status [germ free (having no detectable microorganisms) or
colonized with one or more known species]. [View Larger Version of this Image
(22K GIF file)]
Recent experiments have expanded the definition of probiotics by
demonstrating that genetically engineered commensals can be used as
platforms for delivering drugs, antimicrobial agents, and vaccines to defined
host niches. For example, a strain of Lactococcus lactis programmed to produce
IL-10 provided therapeutic benefit in two mouse models of IBD (47). The human
commensal Streptococcus gordonii, engineered to produce an antibody
fragment with antimicrobial properties, resolved vaginal Candida albicans
infections in rats (48). Finally, oral inoculation of Lactobacilli expressing tetanus
toxin fragment C induced local and systemic immune responses to the
expressed antigen (49).
The ultimate therapeutic reduction of the symbiont-host or commensal-host
relationship will be the identification of microbial products, produced in host
niches, that affect processes disordered in a given disease state. For example,
microbial signals that fortify the epithelial barrier or attenuate the activity of the
mucosal immune system may be useful in treating IBD. Identifying such
microbial signals will be challenging and may require simultaneous monitoring of
microbial and host gene expression during the course of colonization of defined
gnotobiotic models (Fig. 3).
ANTIBIOTICS
If probiotics offer benefit to the host, what are the dangers of drugs that
significantly disrupt the microflora? Although the development of antibiotics has
been one of the great triumphs of modern medicine, indiscriminate use
predisposes humans to opportunistic infections and will certainly exacerbate the
present crisis of antibiotic resistance (50). For example, the human colon, with a
microbial density approaching 1012 organisms per gram, is well suited for
horizontal gene transfer of antibiotic resistance genes via conjugal elements
(plasmids or conjugative transposons) (51). Shoemaker et al. found such
transfer between members of the genus Bacteroides, as well as between Gram-
negative Bacteroides spp. and Gram-positive bacteria (51). Once transfer
occurs, antibiotic resistance is maintained in the absence of antibiotic selection
(51). Given the impact of commensals on immune and other physiologic
functions, we also need to consider the possibility that disruption of our
commensal relationships by indiscriminate use of antibiotics during or even after
completion of postnatal development may be an environmental risk factor that
contributes to disease predilection in certain hosts.
THE FUTURE
Future efforts to define the molecular foundations of mutualism in the human
gut will be challenging and will require multidisciplinary approaches (Fig. 3). The
rewards for attacking this complex problem in interspecies relationships should
include new insights about the genetic and biochemical strategies that we and
our microbial partners use to adapt to one another, new understanding of what
constitutes a pathogen, and new approaches for preventing and treating
infectious diseases.
REFERENCES
1. International Human Genome Sequencing Consortium, Nature 409,
860 (2001).
2. J. C. Venter, et al., Science 291, 1304 (2001) [Abstract/Free Full Text] .
3. D. C. Savage, Annu. Rev. Microbiol. 31, 107 (1977) [CrossRef] [ISI]
[Medline] .
4. J. Lederberg, personal communication.
5. J. J. Brocks, G. A. Logan, R. Buick, R. E. Summons, Science 285, 1033
(1999) [Abstract/Free Full Text] .
6. K. E. Nelson, I. T. Paulsen, J. F. Heidelberg, C. M. Fraser, Nature
Biotechnol. 18, 1049 (2000) [CrossRef] [ISI] [Medline].
7. X. Perret, C. Staehelin, W. J. Broughton, Microbiol. Mol. Biol. Rev. 64, 180
(2000) [Abstract/Free Full Text].
8. K. L. Visick and M. J. McFall-Ngai, J. Bacteriol. 182, 1779 (2000) [Free
Full Text] .
9. M. Steinert, U. Hentschel, J. Hacker, Naturwissenschaften 87, 1 (2000)
[CrossRef] [ISI] [Medline] .
10. P. W. Ewald, Oxf. Surv. Evol. Biol. 5, 215 (1988) .
11. ___, Evolution of Infectious Disease (Oxford Univ. Press, New York, 1984).
12. I. Kroes, P. W. Lepp, D. A. Relman, Proc. Natl. Acad. Sci. U.S.A. 96, 14547
(1999) [Abstract/Free Full Text] .
13. A. Suau, et al., Appl. Environ. Microbiol. 65, 4799 (1999) [Abstract/Free
Full Text] .
14. C. L. Wilson, et al., Science 286, 113 (1999) [Abstract/Free Full Text] .
15. H. Ogawa, K. Fukushima, I. Sasaki, S. Matsuno, Am. J. Physiol.
Gastrointest. Liver Physiol. 279, G492 (2000) [Abstract/Free Full Text].
16. T. Ayabe, et al., Nature Immunol. 1, 113 (2000) [CrossRef] [ISI] [Medline].
17. A. J. Macpherson, et al., Science 288, 2222 (2000) [Abstract/Free Full Text]
.
18. A. S. Neish, et al., Science 289, 1560 (2000) [Abstract/Free Full Text] .
19. W. E. C. Moore and L. V. Holdeman, Appl. Microbiol. 27, 961 (1974) [ISI]
[Medline] .
20. T. Ushijima, M. Takahashi, K. Tatewaki, Y. Ozaki, Microbiol. Immunol. 27,
985 (1983) [ISI] [Medline] .
21. A. A. Salyers, G. Bonheyo, N. B. Shoemaker, Methods 20, 35 (2000)
[CrossRef] [ISI] [Medline].
22. L. V. Hooper, et al., Science 291, 881 (2001) [Abstract/Free Full Text] .
23. N. Sudo, et al., J. Immunol. 159, 1739 (1997) [Abstract] .
24. M. C. Moreau and G. Corthier, Infect. Immun. 56, 2766 (1988)
[Abstract/Free Full Text] .
25. D. P. Strachan, Br. Med. J. 299, 1259 (1989) [ISI] [Medline] .
26. A. E. Wold, Allergy 53, 20 (1998) [ISI] [Medline] .
27. R. Duchmann, Clin. Exp. Immunol. 102, 448 (1995) [ISI] [Medline] .
28. A. MacPherson, U. Y. Khoo, I. Forgacs, J. Philpott-Howard, I. Bjarnason,
Gut 38, 365 (1996).
29. L. Sutherland, et al., Gut 32, 1071 (1991) [Abstract] .
30. B. J. Rembacken, A. M. Snelling, P. M. Hawkey, D. M. Chalmers, A. T. R.
Axon, Lancet 354, 635 (1999) [CrossRef] [ISI] [Medline] .
31. H. C. Rath, et al., J. Clin. Invest. 98, 945 (1996) [Abstract/Free Full Text] .
32. N. V. Contractor, et al., J. Immunol. 160, 385 (1998) [Abstract/Free
Full Text] .
33. L. Dianda, et al., Am. J. Pathol. 150, 91 (1997) [Abstract] .
34. R. Kuhn, J. Lohler, D. Rennick, K. Rajewsky, W. Muller, Cell 75, 263 (1993)
[CrossRef] [ISI] [Medline] .
35. R. K. Sellon, et al., Infect. Immun. 66, 5224 (1998) [Abstract/Free Full Text] .
36. S. R. Brant, et al., Gastroenterology 119, 1483 (2000) [CrossRef] [ISI]
[Medline] .
37. K. L. Madsen, et al., Inflammatory Bowel Dis. 5, 262 (1999) [ISI] [Medline].
38. B. S. Wostmann, C. Larkin, A. Moriarty, E. Bruckner-Kardoss, Lab. Anim.
Sci. 33, 46 (1983) [ISI] [Medline] .
39. M. E. Davey, G. A. O'Toole, Microbiol. Mol. Biol. Rev. 64, 847 (2000).
40. B. Rosan and R. J. Lamont, Microbes Infect. 12, 1599 (2000) [CrossRef].
41. P. E. Kolenbrander, Annu. Rev. Microbiol. 54, 413 (2000) [CrossRef] [ISI]
[Medline] .
42. H. Xie, et al., J. Bacteriol. 182, 7067 (2000) [Abstract/Free Full Text] .
43. L. Bry, P. G. Falk, T. Midtvedt, J. I. Gordon, Science 273, 1380 (1996)
[Abstract] .
44. L. V. Hooper, J. Xu, P. G. Falk, T. Midtvedt, J. I. Gordon, Proc. Natl. Acad.
Sci. U.S.A. 96, 9833 (1999) [Abstract/Free Full Text] .
45. K. L. Madsen, J. S. Doyle, L. D. Jewell, M. M. Tavernini, R. N. Fedorak,
Gastroenterology 116, 1107 (1999) [CrossRef] [ISI] [Medline] .
46. P. Gionchetti, et al., Gastroenterology 119, 305 (2000) [CrossRef] [ISI]
[Medline] .
47. L. Steidler, et al., Science 289, 1352 (2000) [Abstract/Free Full Text] .
48. C. Beninati, et al., Nature Biotechnol. 18, 1060 (2000) [CrossRef] [ISI]
[Medline].
49. D. M. Shaw, et al., Immunology 100, 510 (2000) [CrossRef] [ISI] [Medline] .
50. S. B. Levy, B. Marshall, S. Schluederberg, D. Rowse, J. Davis, Antimicrob.
Agents Chemother. 32, 1801 (1988) [Abstract/Free Full Text] .
51. N. B. Shoemaker, H. Vlamakis, K. Hayes, A. A. Salyers, Appl. Environ.
Microbiol. 67, 561 (2001) [Abstract/Free Full Text] .
10.1126/science.1058709
Include this information when citing this paper.
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease.
M P Conte, S Schippa, I Zamboni, M Penta, F Chiarini, L Seganti, J Osborn, P Falconieri, O
Borrelli, and S Cucchiara (2006)
Gut 55, 1760-1767
Abstract » Full Text » PDF »
On the definition of a criterion of immunogenicity.
T. Pradeu and E. D. Carosella (2006)
PNAS 103, 17858-17861
Abstract » Full Text » PDF »
Short-chain Fatty acids: ready for prime time?.
C. C. Roy, C. L. Kien, L. Bouthillier, and E. Levy (2006)
Nutr Clin Pract 21, 351-366
Abstract » Full Text » PDF »
Immunology of Crohn's disease..
H. BRAAT, M. P PEPPELENBOSCH, and D. W HOMMES (2006)
Ann. N.Y. Acad. Sci. 1072, 135-154
Abstract » Full Text » PDF »
Toll-like receptor signaling and its relevance to intestinal inflammation..
E. CARIO and D. K PODOLSKY (2006)
Ann. N.Y. Acad. Sci. 1072, 332-338
Abstract » Full Text » PDF »
Homeostatic Effects of TLR9 Signaling in Experimental Colitis..
J. LEE, D. RACHMILEWITZ, and E. RAZ (2006)
Ann. N.Y. Acad. Sci. 1072, 351-355
Abstract » Full Text » PDF »
The QseC sensor kinase: A bacterial adrenergic receptor.
M. B. Clarke, D. T. Hughes, C. Zhu, E. C. Boedeker, and V. Sperandio (2006)
PNAS 103, 10420-10425
Abstract » Full Text » PDF »
Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis..
K. Lucke, S. Miehlke, E. Jacobs, and M. Schuppler (2006)
J. Med. Microbiol. 55, 617-624
Abstract » Full Text » PDF »
The Front Line of Enteric Host Defense against Unwelcome Intrusion of Harmful Microorganisms:
Mucins, Antimicrobial Peptides, and Microbiota.
V. Lievin-Le Moal and A. L. Servin (2006)
Clin. Microbiol. Rev. 19, 315-337
Abstract » Full Text » PDF »
Differential cytokine response from dendritic cells to commensal and pathogenic bacteria in
different lymphoid compartments in humans.
L. O'Mahony, L. O'Callaghan, J. McCarthy, D. Shilling, P. Scully, S. Sibartie, E. Kavanagh, W. O.
Kirwan, H. P. Redmond, J. K. Collins, and F. Shanahan (2006)
Am J Physiol Gastrointest Liver Physiol 290, G839-G845
Abstract » Full Text » PDF »
Modulation of Neonatal Microbial Recognition: TLR-Mediated Innate Immune Responses Are
Specifically and Differentially Modulated by Human Milk.
E. LeBouder, J. E. Rey-Nores, A.-C. Raby, M. Affolter, K. Vidal, C. A. Thornton, and M. O. Labeta
(2006)
J. Immunol. 176, 3742-3752
Abstract » Full Text » PDF »
Transepithelial Pathogen Uptake into the Small Intestinal Lamina Propria.
A. Vallon-Eberhard, L. Landsman, N. Yogev, B. Verrier, and S. Jung (2006)
J. Immunol. 176, 2465-2469
Abstract » Full Text » PDF »
Layers of mutualism with commensal bacteria protect us from intestinal inflammation.
C Mueller and A J Macpherson (2006)
Gut 55, 276-284
Full Text » PDF »
Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach.
C Manichanh, L Rigottier-Gois, E Bonnaud, K Gloux, E Pelletier, L Frangeul, R Nalin, C Jarrin, P
Chardon, P Marteau, J Roca, and J Dore (2006)
Gut 55, 205-211
Abstract » Full Text » PDF »
Comparative analysis of proteins with a mucus-binding domain found exclusively in lactic acid
bacteria.
J. Boekhorst, Q. Helmer, M. Kleerebezem, and R. J. Siezen (2006)
Microbiology 152, 273-280
Abstract » Full Text » PDF »
To DGC or not to DGC: oxygen guarding in the termite Zootermopsis nevadensis (Isoptera:
Termopsidae).
J. R. B. Lighton and E. A. Ottesen (2005)
J. Exp. Biol. 208, 4671-4678
Abstract » Full Text » PDF »
Identification and Molecular Cloning of a Novel Glycoside Hydrolase Family of Core 1 Type OGlycan-specific Endo-{alpha}-N-acetylgalactosaminidase from Bifidobacterium longum.
K. Fujita, F. Oura, N. Nagamine, T. Katayama, J. Hiratake, K. Sakata, H. Kumagai, and K.
Yamamoto (2005)
J. Biol. Chem. 280, 37415-37422
Abstract » Full Text » PDF »
Effect of Lactobacillus GG on intestinal integrity in Malawian children at risk of tropical
enteropathy.
L. Galpin, M. J Manary, K. Fleming, C.-N. Ou, P. Ashorn, and R. J Shulman (2005)
Am. J. Clinical Nutrition 82, 1040-1045
Abstract » Full Text » PDF »
Cutting Edge: Bacterial Modulation of Epithelial Signaling via Changes in Neddylation of Cullin-1.
L. S. Collier-Hyams, V. Sloane, B. C. Batten, and A. S. Neish (2005)
J. Immunol. 175, 4194-4198
Abstract » Full Text » PDF »
Metabonomic Identification of Two Distinct Phenotypes in Sprague-Dawley (Crl:CD(SD)) Rats.
L. C. Robosky, D. F. Wells, L. A. Egnash, M. L. Manning, M. D. Reily, and D. G. Robertson (2005)
Toxicol. Sci. 87, 277-284
Abstract » Full Text » PDF »
From The Cover: Enhanced antiinflammatory capacity of a Lactobacillus plantarum mutant
synthesizing modified teichoic acids.
C. Grangette, S. Nutten, E. Palumbo, S. Morath, C. Hermann, J. Dewulf, B. Pot, T. Hartung, P.
Hols, and A. Mercenier (2005)
PNAS 102, 10321-10326
Abstract » Full Text » PDF »
Monitoring Age-Related Susceptibility of Young Mice To Oral Salmonella enterica Serovar
Typhimurium Infection Using an In Vivo Murine Model.
S. M. BURNS-GUYDISH, I. N. OLOMU, H. ZHAO, R. J. WONG, D. K. STEVENSON, and C. H.
CONTAG (2005)
Pediatr. Res. 58, 153-158
Abstract » Full Text » PDF »
Diversity of the Human Intestinal Microbial Flora.
P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E.
Nelson, and D. A. Relman (2005)
Science 308, 1635-1638
Abstract » Full Text » PDF »
Host Distributions of Uncultivated Fecal Bacteroidales Bacteria Reveal Genetic Markers for Fecal
Source Identification.
L. K. Dick, A. E. Bernhard, T. J. Brodeur, J. W. Santo Domingo, J. M. Simpson, S. P. Walters, and
K. G. Field (2005)
Appl. Envir. Microbiol. 71, 3184-3191
Abstract » Full Text » PDF »
Strain-Specific Effects of Probiotics on Gut Barrier Integrity following Hemorrhagic Shock.
M. D. Luyer, W. A. Buurman, M. Hadfoune, G. Speelmans, J. Knol, J. A. Jacobs, C. H. C. Dejong,
A. J. M. Vriesema, and J. W. M. Greve (2005)
Infect. Immun. 73, 3686-3692
Abstract » Full Text » PDF »
Events at the Host-Microbial Interface of the Gastrointestinal Tract III. Cell-to-cell signaling among
microbial flora, host, and pathogens: there is a whole lot of talking going on.
M. B. Clarke and V. Sperandio (2005)
Am J Physiol Gastrointest Liver Physiol 288, G1105-G1109
Abstract » Full Text » PDF »
Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn.
L. Fenner, V. Roux, M.-N. Mallet, and D. Raoult (2005)
Int J Syst Evol Microbiol 55, 1335-1337
Abstract » Full Text » PDF »
Green medicine.
O. Epstein (2005)
J. R. Soc. Med. 98, 203-205
Full Text » PDF »
Mouse Paneth Cell Secretory Responses to Cell Surface Glycolipids of Virulent and Attenuated
Pathogenic Bacteria.
H. Tanabe, T. Ayabe, B. Bainbridge, T. Guina, R. K. Ernst, R. P. Darveau, S. I. Miller, and A. J.
Ouellette (2005)
Infect. Immun. 73, 2312-2320
Abstract » Full Text » PDF »
Compartmentalization of the Mucosal Immune Responses to Commensal Intestinal Bacteria.
A. J. MACPHERSON and T. UHR (2004)
Ann. N.Y. Acad. Sci. 1029, 36-43
Abstract » Full Text » PDF »
Immune Regulation in the Intestine: A Balancing Act between Effector and Regulatory T Cell
Responses.
F. POWRIE (2004)
Ann. N.Y. Acad. Sci. 1029, 132-141
Abstract » Full Text » PDF »
Immune Response to Mycoplasma pulmonis in Nasal Mucosa Is Modulated by the Normal
Microbiota.
G. Henriksson, L. Helgeland, T. Midtvedt, P. Stierna, and P. Brandtzaeg (2004)
Am. J. Respir. Cell Mol. Biol. 31, 657-662
Abstract » Full Text » PDF »
Building an Intestine -- Architectural Contributions of Commensal Bacteria.
J. Madara (2004)
N. Engl. J. Med. 351, 1685-1686
Full Text » PDF »
Impact of commensal microbiota on murine gastrointestinal tract gene ontologies.
D. M. Mutch, R. Simmering, D. Donnicola, G. Fotopoulos, J. A. Holzwarth, G. Williamson, and I.
Corthesy-Theulaz (2004)
Physiol Genomics 19, 22-31
Abstract » Full Text » PDF »
Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium.
M. Derrien, E. E. Vaughan, C. M. Plugge, and W. M. de Vos (2004)
Int J Syst Evol Microbiol 54, 1469-1476
Abstract » Full Text » PDF »
Biodiversity of Vibrios.
F. L. Thompson, T. Iida, and J. Swings (2004)
Microbiol. Mol. Biol. Rev. 68, 403-431
Abstract » Full Text » PDF »
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic
Conversion.
H. Brussow, C. Canchaya, and W.-D. Hardt (2004)
Microbiol. Mol. Biol. Rev. 68, 560-602
Abstract » Full Text » PDF »
Probiotics and human health: a clinical perspective.
H S Gill and F Guarner (2004)
Postgrad. Med. J. 80, 516-526
Abstract » Full Text » PDF »
Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress
response in mice.
N. Sudo, Y. Chida, Y. Aiba, J. Sonoda, N. Oyama, X.-N. Yu, C. Kubo, and Y. Koga (2004)
J. Physiol. 558, 263-275
Abstract » Full Text » PDF »
Spatial Distribution and Stability of the Eight Microbial Species of the Altered Schaedler Flora in
the Mouse Gastrointestinal Tract.
R. B. Sarma-Rupavtarm, Z. Ge, D. B. Schauer, J. G. Fox, and M. F. Polz (2004)
Appl. Envir. Microbiol. 70, 2791-2800
Abstract » Full Text » PDF »
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active
inflammatory bowel disease.
S J Ott, M Musfeldt, D F Wenderoth, J Hampe, O Brant, U R Folsch, K N Timmis, and S
Schreiber (2004)
Gut 53, 685-693
Abstract » Full Text » PDF »
Functional modulation of enterocytes by gram-positive and gram-negative microorganisms.
J.-M. Otte and D. K. Podolsky (2004)
Am J Physiol Gastrointest Liver Physiol 286, G613-G626
Abstract » Full Text » PDF »
Ablation of the Tamm-Horsfall protein gene increases susceptibility of mice to bladder colonization
by type 1-fimbriated Escherichia coli.
L. Mo, X.-H. Zhu, H.-Y. Huang, E. Shapiro, D. L. Hasty, and X.-R. Wu (2004)
Am J Physiol Renal Physiol 286, F795-F802
Abstract » Full Text » PDF »
Symbiont-Induced Changes in Host Actin during the Onset of a Beneficial Animal-Bacterial
Association.
J. R. Kimbell and M. J. McFall-Ngai (2004)
Appl. Envir. Microbiol. 70, 1434-1441
Abstract » Full Text » PDF »
The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533.
R. D. Pridmore, B. Berger, F. Desiere, D. Vilanova, C. Barretto, A.-C. Pittet, M.-C. Zwahlen, M.
Rouvet, E. Altermann, R. Barrangou, B. Mollet, A. Mercenier, T. Klaenhammer, F. Arigoni, and M.
A. Schell (2004)
PNAS 101, 2512-2517
Abstract » Full Text » PDF »
Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut.
K. Suzuki, B. Meek, Y. Doi, M. Muramatsu, T. Chiba, T. Honjo, and S. Fagarasan (2004)
PNAS 101, 1981-1986
Abstract » Full Text » PDF »
Diversity of Bacteria Associated with Natural Aphid Populations.
S. Haynes, A. C. Darby, T. J. Daniell, G. Webster, F. J. F. van Veen, H.C.J. Godfray, J. I.
Prosser, and A. E. Douglas (2003)
Appl. Envir. Microbiol. 69, 7216-7223
Abstract » Full Text » PDF »
Evidence of Regio-specific Glycosylation in Human Intestinal Mucins: PRESENCE OF AN ACIDIC
GRADIENT ALONG THE INTESTINAL TRACT.
C. Robbe, C. Capon, E. Maes, M. Rousset, A. Zweibaum, J.-P. Zanetta, and J.-C. Michalski
(2003)
J. Biol. Chem. 278, 46337-46348
Abstract » Full Text » PDF »
Plasticity of Repetitive DNA Sequences within a Bacterial (Type IV) Secretion System Component.
R. A. Aras, W. Fischer, G. I. Perez-Perez, M. Crosatti, T. Ando, R. Haas, and M. J. Blaser (2003)
J. Exp. Med. 198, 1349-1360
Abstract » Full Text » PDF »
Comparative Genomics of Insect-Symbiotic Bacteria: Influence of Host Environment on Microbial
Genome Composition.
R. V. M. Rio, C. Lefevre, A. Heddi, and S. Aksoy (2003)
Appl. Envir. Microbiol. 69, 6825-6832
Abstract » Full Text » PDF »
The intestine and its microflora are partners for the protection of the host: report on the Danone
Symposium "The Intelligent Intestine," held in Paris, June 14, 2002.
P. Bourlioux, B. Koletzko, F. Guarner, and V. Braesco (2003)
Am. J. Clinical Nutrition 78, 675-683
Abstract » Full Text » PDF »
Role of passive and adaptive immunity in influencing enterocyte-specific gene expression.
S. L. Jenkins, J. Wang, M. Vazir, J. Vela, O. Sahagun, P. Gabbay, L. Hoang, R. L. Diaz, R.
Aranda, and M. G. Martin (2003)
Am J Physiol Gastrointest Liver Physiol 285, G714-G725
Abstract » Full Text » PDF »
Dendritic cells and the intestinal bacterial flora: a role for localized mucosal immune responses.
H. H. Uhlig and F. Powrie (2003)
J. Clin. Invest. 112, 648-651
Abstract » Full Text » PDF »
Elucidation of the Transmission Patterns of an Insect-Borne Bacterium.
A. C. Darby and A. E. Douglas (2003)
Appl. Envir. Microbiol. 69, 4403-4407
Abstract » Full Text » PDF »
Bacteria-host communication: The language of hormones.
V. Sperandio, A. G. Torres, B. Jarvis, J. P. Nataro, and J. B. Kaper (2003)
PNAS 100, 8951-8956
Abstract » Full Text » PDF »
Prophage Genomics.
C. Canchaya, C. Proux, G. Fournous, A. Bruttin, and H. Brussow (2003)
Microbiol. Mol. Biol. Rev. 67, 238-276
Abstract » Full Text » PDF »
A Genomic View of the Human-Bacteroides thetaiotaomicron Symbiosis.
J. Xu, M. K. Bjursell, J. Himrod, S. Deng, L. K. Carmichael, H. C. Chiang, L. V. Hooper, and J. I.
Gordon (2003)
Science 299, 2074-2076
Abstract » Full Text » PDF »
Culture-Independent Molecular Analysis of Microbial Constituents of the Healthy Human Outer Ear.
D. N. Frank, G. B. Spiegelman, W. Davis, E. Wagner, E. Lyons, and N. R. Pace (2003)
J. Clin. Microbiol. 41, 295-303
Abstract » Full Text » PDF »
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells.
T. S. Stappenbeck, L. V. Hooper, and J. I. Gordon (2002)
PNAS 99, 15451-15455
Abstract » Full Text » PDF »
Critical Roles of Activation-Induced Cytidine Deaminase in the Homeostasis of Gut Flora.
S. Fagarasan, M. Muramatsu, K. Suzuki, H. Nagaoka, H. Hiai, and T. Honjo (2002)
Science 298, 1424-1427
Abstract » Full Text » PDF »
The genome sequence of Bifidobacterium longum reflects its adaptation to the human
gastrointestinal tract.
M. A. Schell, M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M.-C. Zwahlen, F.
Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni (2002)
PNAS 99, 14422-14427
Abstract » Full Text » PDF »
Public Health Considerations in Human Consumption of Wild Game.
A. S. AHL, D. NGANWA, and S. WILSON (2002)
Ann. N.Y. Acad. Sci. 969, 48-50
Abstract » Full Text » PDF »
A Gnotobiotic Transgenic Mouse Model for Studying Interactions between Small Intestinal
Enterocytes and Intraepithelial Lymphocytes.
I. U. Mysorekar, R. G. Lorenz, and J. I. Gordon (2002)
J. Biol. Chem. 277, 37811-37819
Abstract » Full Text » PDF »
Fluorescent Amplified Fragment Length Polymorphism and Repetitive Extragenic Palindrome-PCR
Fingerprinting Reveal Host-Specific Genetic Diversity of Vibrio halioticoli-Like Strains Isolated from
the Gut of Japanese Abalone.
T. Sawabe, F. L. Thompson, J. Heyrman, M. Cnockaert, K. Hayashi, R. Tanaka, M. Yoshimizu, B.
Hoste, J. Swings, and Y. Ezura (2002)
Appl. Envir. Microbiol. 68, 4140-4144
Abstract » Full Text » PDF »
Extensive Profiling of a Complex Microbial Community by High-Throughput Sequencing.
J. E. Hill, R. P. Seipp, M. Betts, L. Hawkins, A. G. Van Kessel, W. L. Crosby, and S. M.
Hemmingsen (2002)
Appl. Envir. Microbiol. 68, 3055-3066
Abstract » Full Text » PDF »
Science 2 February 2001:
Vol. 291. no. 5505, pp. 881 - 884
DOI: 10.1126/science.291.5505.881
Prev | Table of Contents | Next
REPORTS
Molecular Analysis of Commensal Host-Microbial Relationships in
the Intestine
Lora V. Hooper,1 Melissa H. Wong,1 Anders Thelin,2 Lennart Hansson,2 Per
G. Falk,12 Jeffrey I. Gordon1*
Human beings contain complex societies of indigenous microbes, yet little is
known about how resident bacteria shape our physiology. We colonized germfree mice with Bacteroides thetaiotaomicron, a prominent component of the
normal mouse and human intestinal microflora. Global intestinal transcriptional
responses to colonization were observed with DNA microarrays, and the cellular
origins of selected responses were established by laser-capture
microdissection. The results reveal that this commensal bacterium modulates
expression of genes involved in several important intestinal functions, including
nutrient absorption, mucosal barrier fortification, xenobiotic metabolism,
angiogenesis, and postnatal intestinal maturation. These findings provide
perspectives about the essential nature of the interactions between resident
microorganisms and their hosts.
1
Department of Molecular Biology and Pharmacology, Washington University
School of Medicine, St. Louis, MO 63110, USA.
2 AstraZeneca R&D Mölndal, SE-431 83 Mölndal, Sweden.
* To whom correspondence should be addressed: E-mail:
jgordon@molecool.wustl.edu
Human beings harbor an incredibly complex and abundant ensemble of
microbes. We are in contact with components of this microflora from birth, yet
little is known about their influence on normal development and physiology. The
human intestine is more densely populated with microorganisms than any other
organ and is a site where the microflora may have a pronounced impact on our
biology. We tested this idea at a molecular level using a simplified mouse model
of the interactions between gut commensals and their host. In this model, adult
germ-free animals are colonized with Bacteroides thetaiotaomicron. This
anaerobe was chosen because it can be genetically manipulated and is a
prominent member of the adult mouse and human gut microflora. Moreover,
B. thetaiotaomicron normally colonizes the distal small intestine (ileum) during
the suckling-weaning transition, a time of rapid and pronounced functional
maturation of the gut (1, 2). We previously used this model to show how
B. thetaiotaomicron regulates production of ileal epithelial fucosylated glycans
for its own nutritional benefit (3).
As so little is known about the range of intestinal functions that are shaped by
components of the microflora, we used high-density oligonucleotide arrays for
analysis of the host transcriptional responses evoked by B. thetaiotaomicron
colonization. In addition, we defined the cellular origins of a subset of these
responses using laser-capture microdissection and real-time quantitative
reverse transcriptase polymerase chain reaction (qRT-PCR) and examined the
specificity of selected B. thetaiotaomicron-elicited responses using other
members of the normal flora.
Adult male germ-free mice were inoculated with B. thetaiotaomicron and killed
10 days later (4). Ileal RNA was isolated from mice with >107 colony-forming
units (CFU) of bacteria per milliliter of ileal contents. Earlier studies had shown
that 10 days was sufficient to produce robust colonization of the ileum and that
107 CFU/ml were necessary for full induction of fucosylated glycan expression
in the ileal epithelium (3, 5). Affymetrix Mu11K and Mu19K GeneChips,
representing ~25,000 mouse genes, were used to compare ileal gene
expression in age-matched germ-free and colonized animals.
mRNAs represented by 118 probe sets changed twofold with colonization as
defined by duplicate microarray hybridizations (6). Transcripts represented by
95 probe sets increased, whereas those represented by 23 probe sets
decreased. Seventy-one genes, represented by 84 probe sets, were assigned to
functional groups, whereas 34 transcripts were from uncharacterized genes or
expressed sequence tag clusters (7). The microarray data reveal the
unanticipated breadth of this commensal's impact on expression of genes
involved in modulating fundamental intestinal functions.
Germ-free rodents require a higher caloric intake to maintain their weight than
those with a microflora (8). Microarray analysis provided molecular insights into
how B. thetaiotaomicron improves host nutrient absorption and processing.
Colonization led to increased ileal levels of Na+/glucose cotransporter (SGLT-1)
mRNA (Table 1) (7, 9). Concerted increases were seen in several components
of the host's lipid absorption machinery, including pancreatic lipase-related
protein-2 (PLRP-2), colipase, a fatty acid-binding protein (L-FABP), and
apolipoprotein A-IV (7) (Table 1). The prominent decrease in expression of
fasting-induced adipose factor, a PPAR target that is repressed with fat feeding
(10), provided further evidence for augmented lipid uptake in colonized mice.
Micronutrient absorption also appears to be augmented by colonization, as
evidenced by a threefold increase in expression of the high-affinity epithelial
copper transporter (CRT1) and five- to sixfold decreases in expression of
metallothioneins I and II and ferritin heavy chain, which sequester heavy metals
within cells (7) (Table 1).
Table 1. Real-time qRT-PCR verification of selected colonization-associated
changes in gene expression. Assays were performed with the pooled ileal RNA
samples used for the microarray studies. Mean values for triplicate
determinations ±1 SD are shown. See (7) for a comprehensive list of 71 genes
that change with colonization.
Gene
Fold
(relative to germ-free)
Na+/glucose cotransporter (SGLT-1)
2.6 ± 0.9
Colipase
6.6 ± 1.9
Liver fatty acid-binding protein (L-FABP)
4.4 ± 1.4
Metallothionein I (MT-I)
5.4 ± 0.7
Polymeric immunoglobulin receptor (pIgR)
2.6 ± 0.7
Decay-accelerating factor (DAF)
5.7 ± 1.5
Small proline-rich protein 2a (sprr2a)
205 ± 64
Glutathione S-transferase (GST)
2.1 ± 0.1
Multidrug resistance protein (Mdr1a)
3.8 ± 1.0
Lactase-phlorizin hydrolase
4.1 ± 0.6
Adenosine deaminase (ADA)
2.6 ± 0.5
Angiogenin-3
9.1 ± 1.8
The DNA microarray and confirmatory qRT-PCR analyses measure host
responses in a complex tissue composed of multiple cell types. An in vivo model
will, unlike cell culture-based models, preserve the contributions of other cell
lineages and environmental factors in shaping the response. The challenge is to
recover the responding cell population, without perturbing its expressed
mRNAs, so that its reaction to the microorganism can be characterized
quantitatively. To define the cellular responses in our in vivo model, we
combined laser-capture microdissection (LCM) with qRT-PCR. LCM was used
to recover three cell populations from frozen sections of ileum (11), including
epithelium from crypts (containing proliferating undifferentiated cells plus
differentiated members of the Paneth cell lineage), epithelium overlying villi
(containing postmitotic, differentiated members of the other three intestinal
epithelial lineages), and mesenchyme underlying crypt-villus units [see (7) for
LCM images]. Specific mRNAs in the LCM populations were quantified by RTPCR.
Colipase is produced by pancreatic exocrine acinar cells, but we discovered
that colipase is also expressed in ileal crypt epithelium, where it increased 10fold upon B. thetaiotaomicron colonization (Fig. 1 and Table 1). Colipase plays a
critical role in lipid metabolism by stimulating the activity of both pancreatic
triglyceride lipase and pancreatic lipase-related protein-2 (12). Localization of
colipase in the crypt epithelium and its regulation by a gut commensal reveal a
previously unappreciated mechanism for lipid processing in the intestinal
epithelium.
Fig. 1. Real-time qRT-PCR analysis of colonization-associated changes in gene
expression in laser-capture microdissected ileal cell populations. Values are
expressed relative to levels in germ-free mesenchyme (9). Each mRNA was
assayed in triplicate in three to four independent experiments. Representative
results (mean ± 1 SD) from pairs of germ-free (gf) and colonized (col) mice are
plotted. [View Larger Version of this Image (15K GIF file)]
An intact mucosal barrier is critical for constraining resident intestinal microbes.
Barrier disruption can provoke immune responses that cause pathology such as
inflammatory bowel disease (13). Bacteroides thetaiotaomicron colonization
produces no detectable inflammatory response, as judged by histologic surveys
(5) and by the absence of a discernible induction or repression of immune
response genes represented on the microarrays. An influx of immunoglobulin A
(IgA)-producing B cells does occur in the ileal mucosa 10 days after introduction
of B. thetaiotaomicron (5), but similar commensal-induced IgA responses have
been shown to be T cell-independent and to enforce barrier integrity (14).
The influx of IgA-producing B cells was accompanied by increased expression
of the polymeric immunoglobulin receptor (pIgR) that transports IgA across the
epithelium (Table 1). There was augmented expression of the CRP-ductin gene
encoding both a mucus layer component (MUCLIN) and a putative receptor for
trefoil peptides (15, 16). Decay-accelerating factor (DAF), an apical epithelial
inhibitor of complement-mediated cytolysis, increased sixfold (7) (Table 1).
Coincident enhancement of expression of these three genes should help
prevent bacteria from crossing the epithelial barrier and avoid mucosal damage
from activation of complement components in intestinal secretions.
The most pronounced response to B. thetaiotaomicron was an increase in small
proline-rich protein-2 (sprr2a) mRNA (Table 1). sprr family members contribute
to the barrier functions of squamous epithelia, both as a component of the
cornified cell envelope and as cross-bridging proteins linked to desmosomal
desmoplakin (17). LCM/qRT-PCR revealed that sprr2a mRNA is present in the
epithelium, primarily on the villus rather than crypt, and that B. thetaiotaomicron
elicits a 280-fold increase in its villus epithelial expression (Fig. 1). The epithelial
sprr2a response suggests that this protein participates in fortifying the intestinal
epithelial barrier in response to bacterial colonization.
Environmental and dietary constituents, as well as drugs, are detoxified in the
intestine by oxidation or conjugation. Colonization produced a twofold decrease
in expression of glutathione S-transferase, which conjugates glutathione to a
variety of electrophiles, and a fourfold decrease in multidrug resistance protein1a (Mdr1a), which exports glutathione-conjugated compounds from the
epithelium (18) (Table 1). Debrisoquine hydroxylase (CYP2D2), which is
involved in oxidative drug metabolism in humans (19), also declined threefold.
These results indicate that colonization with B. thetaiotaomicron affects the
host's capacity to metabolize xenobiotics and endogenous toxins.
Previous electrophysiological studies of germ-free and conventionally raised
animals indicate that the microflora influences gut motility (20). Colonization led
to two- to fivefold increases in mRNAs encoding L-glutamate transporter, Lglutamate decarboxylase (converts glutamate to -aminobutyric acid), vesicleassociated protein-33 (a synaptobrevin-binding protein involved in
neurotransmitter release) (21), and enteric -actin and cysteine-rich protein-2
(muscle-specific proteins). These results suggest that B. thetaiotaomicron may
affect components of the enteric nervous system (22) and motility.
Bacteroides thetaiotaomicron colonizes the mouse (and human) gut during the
weaning period (1, 2). This stage in postnatal gut development is marked by
several maturational changes, including reductions in ileal epithelial lactase,
which hydrolyzes milk sugar (23). Ileal epithelial lactase levels also fall as adult
germ-free mice are colonized with B. thetaiotaomicron (Table 1). Adenosine
deaminase (ADA) and polyamines are effectors of postnatal intestinal
maturation (24, 25). Colonization increased expression of both ADA and
ornithine decarboxylase (ODC) antizyme, a regulator of polyamine synthesis
(26), suggesting that commensals may perform an instructive role in postnatal
intestinal maturation (7) (Table 1).
Colonization increased expression of angiogenin-3, a secreted protein with
known angiogenic activity (27, 28), and angiogenin-related protein, which does
not have any apparent angiogenic activity (29). Angiogenin-3 was originally
identified in NIH 3T3 fibroblasts (27), but little is known about its cellular origins
in tissues. LCM/qRT-PCR revealed that angiogenin-3 mRNA is largely confined
to the crypt epithelium and that colonization results in a sevenfold increase in its
crypt expression (Fig. 1). This increase accounts for the change in expression
defined by microarray and qRT-PCR analyses of total ileal RNA (Table 1).
Localization of a secreted angiogenesis factor in the crypt epithelium puts it in a
strategic position to function as an effector of several host responses to
microbial colonization (e.g., enhanced absorption and distribution of nutrients).
Our findings raise two questions. Are similar host responses elicited by other
components of the gut microflora, and do changes in the metabolic capacity of
B. thetaiotaomicron affect ileal gene expression? To examine the first question,
age-matched adult male mice (n = 4 to 8 mice per group) were colonized for
10 days with B. thetaiotaomicron, Bifidobacterium infantis (a prominent
component of the preweaning human and mouse ileal flora and a commonly
used probiotic), Escherichia coli K12 (a normal component of human intestinal
flora), or a "complete" ileal/cecal microflora harvested from conventionally raised
mice (5). qRT-PCR was used to compare mRNA levels in each group (all
animals had 107 CFU/ml ileal contents). Ileal expression of colipase and
angiogenin-3 was induced after colonization with each of the three organisms
and by the complete ileal/cecal flora (Fig. 2). Moreover, the ileal levels of
colipase and angiogenin-3 mRNAs in these ex-germ-free mice were comparable
to those of age-matched mice conventionally raised since birth (Fig. 2). In
contrast, the response of sprr2a to colonization depended on the colonizing
species: B. infantis and E. coli produced only small increases (Fig. 2). Mdr1a
and glutathione S-transferase also exhibited species-specific responses.
Bacteroides thetaiotaomicron suppressed and E. coli and B. infantis stimulated
expression of both genes, whereas the multicomponent ileal/cecal flora
produced no significant (i.e., twofold) change in levels of either mRNA
compared with germ-free controls. The differing Mdr1a/GST responses suggest
that variations in xenobiotic metabolism between individuals may arise, in part,
from differences in their resident gut flora.
Fig. 2. Specificity of host responses to colonization with different members of
the microflora. Germ-free mice were inoculated with one of the indicated
organisms or with a complete ileal/cecal flora from conventionally raised mice
(Conv. µflora) (4). Ileal RNAs, prepared from animals colonized at 107 CFU/ml
ileal contents 10 days after inoculation, were pooled, and levels of each mRNA
shown were analyzed by real-time qRT-PCR. Mean values (±1 SD) for triplicate
determinations are plotted. [View Larger Version of this Image (18K GIF file)]
The only B. thetaiotaomicron genes currently known to link changes in bacterial
metabolism with host responses are those involved in fucose utilization (3).
Transposon-mediated mutagenesis of fucI (encoding fucose isomerase) blocks
the organism's ability to use fucose as a carbon source and to signal
fucosylated glycan production in the ileal epithelium (3). Microarray analysis of
the host response to colonization revealed no appreciable differences between
isogenic mutant and wild-type strains. This similarity extends to all genes in
Table 1. Future identification of microbial factors that interlink microbial and host
physiology will require characterization of changes in B. thetaiotaomicron gene
expression as a function of colonization.
In summary, the studies described above provide a broad-based in vivo
characterization of transcriptional responses to colonization with a prototypic gut
commensal. Our results reveal that commensals are able to modulate
expression of host genes that participate in diverse and fundamental
physiological functions. The species selectivity of some of the colonizationassociated changes in gene expression emphasizes how our physiology can be
affected by changes in the composition of our indigenous microflora. The fusion
of germ-free technology, functional genomics, and LCM/qRT-PCR makes it
possible to use in vivo systems to quantify the impact of a microbial population
on host cell gene expression.
REFERENCES AND NOTES
1.
W. E. C. Moore and L. V. Holdeman, Appl. Microbiol. 27, 961 (1974) [ISI]
[Medline] .
2.
T. Ushijima, M. Takahashi, K. Tatewaki, Y. Ozaki, Microbiol. Immunol.
27, 985 (1983) [ISI] [Medline] .
3.
L. V. Hooper, J. Xu, P. G. Falk, T. Midtvedt, J. I. Gordon, Proc. Natl.
Acad. Sci. U.S.A. 96, 9833 (1999) [Abstract/Free Full Text] .
4.
Age-matched groups of 7- to 15-week-old germ-free NMRI/KI mice were
maintained in plastic gnotobiotic isolators on a 12-hour light cycle and given
free access to an autoclaved chow diet (B&K Universal). Males were
inoculated with B. thetaiotaomicron strain VPI-5482 (3), the isogenic Fu-4
strain lacking a functional fucI gene (3), E. coli K12, or Bifidobacterium
infantis (ATCC15697). Mice were killed 10 days later, 2 hours after lights
were turned on. The distal 1 cm of the small intestine was used to define
CFU/ml ileal contents. The 3 cm of intestine just proximal to this segment was
used to isolate total ileal RNA (Qiagen RNeasy kit).
5.
L. Bry, P. G. Falk, T. Midtvedt, J. I. Gordon, Science 273, 1380 (1996)
[Abstract] .
6.
Total ileal RNA samples, prepared from four mice from three
independent colonizations and from age-matched male germ-free controls
(n = 8), were each pooled in equal amounts for generation of biotinylated
cRNA targets. Two targets were prepared, independently, from 30 µg of each
total cellular RNA pool (30). Each cRNA was hybridized to Mu11K and
Mu19K chip sets according to Affymetrix protocols. The overall fluorescence
intensity across each chip was scaled to a target intensity of 150. Pairwise
comparisons of "germ-free" versus "colonized" expression levels were
performed. A twofold difference was considered significant if three criteria
were met: The GeneChip software returned a difference call of Increased or
Decreased, the mRNA was called Present by GeneChip software in either
germ-free or colonized RNA, and the difference was observed in duplicate
microarray hybridizations.
7.
See supplemental material at http://gordonlab.wustl.edu.
8.
B. S. Wostmann, C. Larkin, A. Moriarty, E. Bruckner-Kardoss, Lab. Anim.
Sci. 33, 46 (1983) [ISI] [Medline] .
9.
SYBR Green-based qRT-PCR (31) used gene-specific primers (7) and
deoxyribonuclease-treated RNAs. Control experiments established that
amplicons were derived from cDNA and not from primer-dimers or genomic
DNA. Signals were normalized to glyceraldehyde 3-phosphate
dehydrogenase mRNA. Normalized data were used to quantitate relative
levels of a given mRNA in germ-free and colonized ileums (
CT analysis;
User Bulletin #2, ABI Prism 7700 Sequence Detection System).
10.
S. Kersten, et al., J. Biol. Chem. 275, 28488 (2000) [Abstract/Free
Full Text] .
11.
Seven-micrometer-thick sections were cut from ileums harvested
immediately after the death of three sets of germ-free and colonized mice that
were independent of those used for microarray profiling. LCM was conducted
with the PixCell II system (Arcturus, 7.5-µm-diameter laser spot) and RNA
was prepared (Stratagene RNA Micro-Isolation Kit; protocols in
http://dir.nichd.nih.gov/lcm/protocol.htm).
12.
M. E. Lowe, M. H. Kaplan, L. Jackson-Grusby, D. D'Agostino, M. J.
Grusby, J. Biol. Chem. 273, 31215 (1998) [Abstract/Free Full Text] .
13.
P. G. Falk, L. V. Hooper, T. Midtvedt, J. I. Gordon, Microbiol. Mol. Biol.
Rev. 62, 1157 (1998) [Abstract/Free Full Text].
14.
A. J. Macpherson, et al., Science 288, 2222 (2000) [Abstract/Free
Full Text] .
15.
R. C. DeLisle, M. Petitt, K. S. Isom, D. Ziemer, Am. J. Physiol. 275, G219
(1998) [Abstract/Free Full Text] .
16.
L. Thim and E. Mørtz, Regul. Pept. 90, 61 (2000) [CrossRef] [ISI]
[Medline] .
17.
P. M. Steinert and L. N. Marekov, Mol. Biol. Cell 10, 4247 (1999)
[Abstract/Free Full Text] .
18.
R. W. Johnstone, A. A. Ruefli, M. J. Smyth, Trends Biochem. Sci. 25, 1
(2000) [CrossRef] [ISI] [Medline] .
19.
M. Ingelman-Sundberg, M. Oscarson, R. A. McLellan, Trends
Pharmacol. Sci. 20, 342 (1999) [CrossRef] [ISI] [Medline] .
20.
E. Husebye, P. M. Hellstrom, T. Midtvedt, Dig. Dis. Sci. 39, 946 (1994)
[CrossRef] [ISI] [Medline] .
21.
P. A. Skehel, R. Fabian-Fine, E. R. Kandel, Proc. Natl. Acad. Sci. U.S.A.
97, 1101 (2000) [Abstract/Free Full Text] .
22.
M. T. Liu, J. D. Rothstein, M. D. Gershon, A. L. Kirchgessner, J.
Neurosci. 17, 4764 (1997) [Abstract/Free Full Text] .
23.
S. D. Krasinski, et al., Am. J. Physiol. 267, G584 (1994) [Abstract/Free
Full Text] .
24.
G. D. Lux, L. J. Marton, S. B. Baylin, Science 210, 195 (1980)
[Abstract/Free Full Text] .
25.
J. M. Chinsky, et al., Differentiation 42, 172 (1990) [CrossRef] [ISI]
[Medline] .
26.
J. Nilsson, S. Koskiniemi, K. Persson, B. Grahn, I. Holm, Eur.
J. Biochem. 250, 223 (1997) [Abstract] .
27.
X. Fu and M. P. Kamps, Mol. Cell Biol. 17, 1503 (1997) [Abstract] .
28.
X. Fu, W. G. Roberts, V. Nobile, R. Shapiro, M. P. Kamps, Growth
Factors 17, 125 (1999) [ISI] [Medline] .
29.
V. Nobile, B. L. Vallee, R. Shapiro, Proc. Natl. Acad. Sci. U.S.A. 93, 4331
(1996) [Abstract/Free Full Text] .
30.
C. K. Lee, R. G. Klopp, R. Weindruch, T. A. Prolla, Science 285, 1390
(1999) [Abstract/Free Full Text] .
31.
N. Steuerwald, J. Cohen, R. J. Herrera, C. A. Brenner, Mol. Hum.
Reprod. 5, 1034 (1999) [Abstract/Free Full Text] .
32.
We thank C. Hong, E. Skogman, and B. Basta for technical assistance.
This work was funded by NIH grant DK30292 and AstraZeneca.
16 October 2000; accepted 4 January 2001
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Effects of Commensal Bacteria on Intestinal Morphology and Expression of Proinflammatory
Cytokines in the Gnotobiotic Pig.
T. W. Shirkey, R. H. Siggers, B. G. Goldade, J. K. Marshall, M. D. Drew, B. Laarveld, and A. G.
Van Kessel (2006)
Experimental Biology and Medicine 231, 1333-1345
Abstract » Full Text » PDF »
The Roles of Bacteria and TLR4 in Rat and Murine Models of Necrotizing Enterocolitis..
T. Jilling, D. Simon, J. Lu, F. J. Meng, D. Li, R. Schy, R. B. Thomson, A. Soliman, M. Arditi, and
M. S. Caplan (2006)
J. Immunol. 177, 3273-3282
Abstract » Full Text » PDF »
Immunology of Crohn's disease..
H. BRAAT, M. P PEPPELENBOSCH, and D. W HOMMES (2006)
Ann. N.Y. Acad. Sci. 1072, 135-154
Abstract » Full Text » PDF »
Mortality and Growth Performance of Broilers Given Drinking Water Supplemented with ChickenSpecific Probiotics.
H. M. Timmerman, A. Veldman, E. van den Elsen, F. M. Rombouts, and A. C. Beynen (2006)
Poult. Sci. 85, 1383-1388
Abstract » Full Text » PDF »
Role of MyD88 in Phosphatidylinositol 3-Kinase Activation by Flagellin/Toll-like Receptor 5
Engagement in Colonic Epithelial Cells.
S. H. Rhee, H. Kim, M. P. Moyer, and C. Pothoulakis (2006)
J. Biol. Chem. 281, 18560-18568
Abstract » Full Text » PDF »
The systems biology of infection in animal models bears fruit.
L. R. Hoffman and S. I. Miller (2006)
PNAS 103, 9377-9378
Full Text » PDF »
Probiotic use in clinical practice: what are the risks?.
R. J Boyle, R. M Robins-Browne, and M. L. Tang (2006)
Am. J. Clinical Nutrition 83, 1256-1264
Abstract » Full Text » PDF »
Probiotics and inflammatory bowel diseases..
A-P Bai and Q Ouyang (2006)
Postgrad. Med. J. 82, 376-382
Abstract » Full Text » PDF »
Expression and Regulation of Cornified Envelope Proteins in Human Corneal Epithelium.
L. Tong, R. M. Corrales, Z. Chen, A. L. Villarreal, C. S. De Paiva, R. Beuerman, D.-Q. Li, and S.
C. Pflugfelder (2006)
Invest. Ophthalmol. Vis. Sci. 47, 1938-1946
Abstract » Full Text » PDF »
Epidermal barrier formation and recovery in skin disorders..
J. A. Segre (2006)
J. Clin. Invest. 116, 1150-1158
Abstract » Full Text » PDF »
Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis..
K. Lucke, S. Miehlke, E. Jacobs, and M. Schuppler (2006)
J. Med. Microbiol. 55, 617-624
Abstract » Full Text » PDF »
The Front Line of Enteric Host Defense against Unwelcome Intrusion of Harmful Microorganisms:
Mucins, Antimicrobial Peptides, and Microbiota.
V. Lievin-Le Moal and A. L. Servin (2006)
Clin. Microbiol. Rev. 19, 315-337
Abstract » Full Text » PDF »
Differential cytokine response from dendritic cells to commensal and pathogenic bacteria in
different lymphoid compartments in humans.
L. O'Mahony, L. O'Callaghan, J. McCarthy, D. Shilling, P. Scully, S. Sibartie, E. Kavanagh, W. O.
Kirwan, H. P. Redmond, J. K. Collins, and F. Shanahan (2006)
Am J Physiol Gastrointest Liver Physiol 290, G839-G845
Abstract » Full Text » PDF »
Supplementation of the diet with high-viscosity Beta-glucan results in enrichment for lactobacilli in
the rat cecum..
J. Snart, R. Bibiloni, T. Grayson, C. Lay, H. Zhang, G. E. Allison, J. K. Laverdiere, F. Temelli, T.
Vasanthan, R. Bell, and G. W. Tannock (2006)
Appl. Envir. Microbiol. 72, 1925-1931
Abstract » Full Text » PDF »
Layers of mutualism with commensal bacteria protect us from intestinal inflammation.
C Mueller and A J Macpherson (2006)
Gut 55, 276-284
Full Text » PDF »
Specific probiotic therapy attenuates antibiotic induced visceral hypersensitivity in mice.
E F Verdu, P Bercik, M Verma-Gandhu, X-X Huang, P Blennerhassett, W Jackson, Y Mao, L
Wang, F Rochat, and S M Collins (2006)
Gut 55, 182-190
Abstract » Full Text » PDF »
Anti-Inflammatory Effect of Lactobacillus casei on Shigella-Infected Human Intestinal Epithelial
Cells.
M.-T. Tien, S. E. Girardin, B. Regnault, L. Le Bourhis, M.-A. Dillies, J.-Y. Coppee, R. BourdetSicard, P. J. Sansonetti, and T. Pedron (2006)
J. Immunol. 176, 1228-1237
Abstract » Full Text » PDF »
Rapid quantitative profiling of complex microbial populations.
C. Palmer, E. M. Bik, M. B. Eisen, P. B. Eckburg, T. R. Sana, P. K. Wolber, D. A. Relman, and P.
O. Brown (2006)
Nucleic Acids Res. 34, e5
Abstract » Full Text » PDF »
How Stress Induces Intestinal Hypersensitivity.
A. G. Buret (2006)
Am. J. Pathol. 168, 3-5
Full Text » PDF »
Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and
intestinal barrier transcriptome.
A. Schumann, S. Nutten, D. Donnicola, E. M. Comelli, R. Mansourian, C. Cherbut, I. CorthesyTheulaz, and C. Garcia-Rodenas (2005)
Physiol Genomics 23, 235-245
Abstract » Full Text » PDF »
Pathophysiological role of Toll-like receptor 5 engagement by bacterial flagellin in colonic
inflammation.
S. H. Rhee, E. Im, M. Riegler, E. Kokkotou, M. O'Brien, and C. Pothoulakis (2005)
PNAS 102, 13610-13615
Abstract » Full Text » PDF »
Probiotics as mainstream allergy therapy?.
S H Murch (2005)
Arch. Dis. Child. 90, 881-882
Full Text » PDF »
Genetic Diversity of Viable, Injured, and Dead Fecal Bacteria Assessed by Fluorescence-Activated
Cell Sorting and 16S rRNA Gene Analysis.
K. Ben-Amor, H. Heilig, H. Smidt, E. E. Vaughan, T. Abee, and W. M. de Vos (2005)
Appl. Envir. Microbiol. 71, 4679-4689
Abstract » Full Text » PDF »
Regulation of polymeric immunoglobulin receptor expression by reovirus.
K. Pal, C. S. Kaetzel, K. Brundage, C. A. Cunningham, and C. F. Cuff (2005)
J. Gen. Virol. 86, 2347-2357
Abstract » Full Text » PDF »
The mucosal immune system: from control of inflammation to protection against infections.
D. Kaiserlian, N. Cerf-Bensussan, and A. Hosmalin (2005)
J. Leukoc. Biol. 78, 311-318
Abstract » Full Text » PDF »
BACTERIAL INTERACTIONS WITH CELLS OF THE INTESTINAL MUCOSA: TOLL-LIKE RECEPTORS
AND NOD2.
E Cario (2005)
Gut 54, 1182-1193
Full Text » PDF »
Regulation of the Polymeric Ig Receptor by Signaling through TLRs 3 and 4: Linking Innate and
Adaptive Immune Responses.
T. A. Schneeman, M. E. C. Bruno, H. Schjerven, F.-E. Johansen, L. Chady, and C. S. Kaetzel
(2005)
J. Immunol. 175, 376-384
Abstract » Full Text » PDF »
Monitoring Age-Related Susceptibility of Young Mice To Oral Salmonella enterica Serovar
Typhimurium Infection Using an In Vivo Murine Model.
S. M. BURNS-GUYDISH, I. N. OLOMU, H. ZHAO, R. J. WONG, D. K. STEVENSON, and C. H.
CONTAG (2005)
Pediatr. Res. 58, 153-158
Abstract » Full Text » PDF »
Diversity of the Human Intestinal Microbial Flora.
P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E.
Nelson, and D. A. Relman (2005)
Science 308, 1635-1638
Abstract » Full Text » PDF »
Involvement of Innate Immunity in the Development of Inflammatory and Autoimmune Diseases.
H. TLASKALOVA-HOGENOVA, L. TUCKOVA, R. STEPANKOVA, T. HUDCOVIC, L. PALOVAJELINKOVA, H. KOZAKOVA, P. ROSSMANN, D. SANCHEZ, J. CINOVA, T. HRNCIR, M.
KVERKA, L. FROLOVA, H. UHLIG, F. POWRIE, and P. BLAND (2005)
Ann. N.Y. Acad. Sci. 1051, 787-798
Abstract » Full Text » PDF »
Construction, Analysis, and {beta}-Glucanase Screening of a Bacterial Artificial Chromosome
Library from the Large-Bowel Microbiota of Mice.
J. Walter, M. Mangold, and G. W. Tannock (2005)
Appl. Envir. Microbiol. 71, 2347-2354
Abstract » Full Text » PDF »
Toll-like receptor-4 is required for intestinal response to epithelial injury and limiting bacterial
translocation in a murine model of acute colitis.
M. Fukata, K. S. Michelsen, R. Eri, L. S. Thomas, B. Hu, K. Lukasek, C. C. Nast, J. Lechago, R.
Xu, Y. Naiki, A. Soliman, M. Arditi, and M. T. Abreu (2005)
Am J Physiol Gastrointest Liver Physiol 288, G1055-G1065
Abstract » Full Text » PDF »
TLR Signaling in the Gut in Health and Disease.
M. T. Abreu, M. Fukata, and M. Arditi (2005)
J. Immunol. 174, 4453-4460
Abstract » Full Text » PDF »
Glycan Foraging in Vivo by an Intestine-Adapted Bacterial Symbiont.
J. L. Sonnenburg, J. Xu, D. D. Leip, C.-H. Chen, B. P. Westover, J. Weatherford, J. D. Buhler,
and J. I. Gordon (2005)
Science 307, 1955-1959
Abstract » Full Text » PDF »
Physiological Basis for Novel Drug Therapies Used to Treat the Inflammatory Bowel Diseases I.
Pathophysiological basis and prospects for probiotic therapy in inflammatory bowel disease.
F. Shanahan (2005)
Am J Physiol Gastrointest Liver Physiol 288, G417-G421
Abstract » Full Text » PDF »
Developmental Diethylstilbestrol Exposure Alters Genetic Pathways of Uterine Cytodifferentiation.
W.-W. Huang, Y. Yin, Q. Bi, T.-C. Chiang, N. Garner, J. Vuoristo, J. A. McLachlan, and L. Ma
(2005)
Mol. Endocrinol. 19, 669-682
Abstract » Full Text » PDF »
Regulation of intestinal ontogeny: effect of glucocorticoids and luminal microbes on
galactosyltransferase and trehalase induction in mice.
N. N. Nanthakumar, D. Dai, D. Meng, N. Chaudry, D. S. Newburg, and W. A. Walker (2005)
Glycobiology 15, 221-232
Abstract » Full Text » PDF »
Probiotic Lactobacillus spp. Diminish Helicobacter hepaticus-Induced Inflammatory Bowel Disease
in Interleukin-10-Deficient Mice.
J. A. Pena, A. B. Rogers, Z. Ge, V. Ng, S. Y. Li, J. G. Fox, and J. Versalovic (2005)
Infect. Immun. 73, 912-920
Abstract » Full Text » PDF »
Commentary: Remembrance of microbes past.
G. W Tannock (2005)
Int. J. Epidemiol. 34, 13-15
Full Text » PDF »
Compartmentalization of the Mucosal Immune Responses to Commensal Intestinal Bacteria.
A. J. MACPHERSON and T. UHR (2004)
Ann. N.Y. Acad. Sci. 1029, 36-43
Abstract » Full Text » PDF »
Immune Response to Mycoplasma pulmonis in Nasal Mucosa Is Modulated by the Normal
Microbiota.
G. Henriksson, L. Helgeland, T. Midtvedt, P. Stierna, and P. Brandtzaeg (2004)
Am. J. Respir. Cell Mol. Biol. 31, 657-662
Abstract » Full Text » PDF »
The gut microbiota as an environmental factor that regulates fat storage.
F. Backhed, H. Ding, T. Wang, L. V. Hooper, G. Y. Koh, A. Nagy, C. F. Semenkovich, and J. I.
Gordon (2004)
PNAS 101, 15718-15723
Abstract » Full Text » PDF »
Prebiotic carbohydrates modify the mucosa associated microflora of the human large bowel.
S J Langlands, M J Hopkins, N Coleman, and J H Cummings (2004)
Gut 53, 1610-1616
Abstract » Full Text » PDF »
Expression Profiling Reveals Novel Innate and Inflammatory Responses in the Jejunal Epithelial
Compartment during Infection with Trichinella spiralis.
P. A. Knight, A. D. Pemberton, K. A. Robertson, D. J. Roy, S. H. Wright, and H. R. P. Miller
(2004)
Infect. Immun. 72, 6076-6086
Abstract » Full Text » PDF »
Impact of commensal microbiota on murine gastrointestinal tract gene ontologies.
D. M. Mutch, R. Simmering, D. Donnicola, G. Fotopoulos, J. A. Holzwarth, G. Williamson, and I.
Corthesy-Theulaz (2004)
Physiol Genomics 19, 22-31
Abstract » Full Text » PDF »
MEK Is a Key Modulator for TLR5-induced Interleukin-8 and MIP3{alpha} Gene Expression in Nontransformed Human Colonic Epithelial Cells.
S. H. Rhee, A. C. Keates, M. P. Moyer, and C. Pothoulakis (2004)
J. Biol. Chem. 279, 25179-25188
Abstract » Full Text » PDF »
A Special Fondness for Lactobacilli.
G. W. Tannock (2004)
Appl. Envir. Microbiol. 70, 3189-3194
Full Text » PDF »
Inflammation of the cystic fibrosis mouse small intestine.
O. Norkina, S. Kaur, D. Ziemer, and R. C. De Lisle (2004)
Am J Physiol Gastrointest Liver Physiol 286, G1032-G1041
Abstract » Full Text » PDF »
Spatial Distribution and Stability of the Eight Microbial Species of the Altered Schaedler Flora in
the Mouse Gastrointestinal Tract.
R. B. Sarma-Rupavtarm, Z. Ge, D. B. Schauer, J. G. Fox, and M. F. Polz (2004)
Appl. Envir. Microbiol. 70, 2791-2800
Abstract » Full Text » PDF »
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active
inflammatory bowel disease.
S J Ott, M Musfeldt, D F Wenderoth, J Hampe, O Brant, U R Folsch, K N Timmis, and S
Schreiber (2004)
Gut 53, 685-693
Abstract » Full Text » PDF »
Is the mucosal route of administration essential for probiotic function? Subcutaneous
administration is associated with attenuation of murine colitis and arthritis.
B Sheil, J McCarthy, L O'Mahony, M W Bennett, P Ryan, J J Fitzgibbon, B Kiely, J K Collins, and
F Shanahan (2004)
Gut 53, 694-700
Abstract » Full Text » PDF »
Case of aortic endocarditis caused by Lactobacillus casei.
L. Ze-Ze, R. Tenreiro, A. Duarte, M. J. Salgado, J. Melo-Cristino, L. Lito, M. M. Carmo, S.
Felisberto, and G. Carmo (2004)
J. Med. Microbiol. 53, 451-453
Abstract » Full Text » PDF »
Escherichia coli LPS induces heat shock protein 25 in intestinal epithelial cells through MAP
kinase activation.
K. Kojima, M. W. Musch, M. J. Ropeleski, D. L. Boone, A. Ma, and E. B. Chang (2004)
Am J Physiol Gastrointest Liver Physiol 286, G645-G652
Abstract » Full Text » PDF »
From The Cover: Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut
microbiota.
J. F. Rawls, B. S. Samuel, and J. I. Gordon (2004)
PNAS 101, 4596-4601
Abstract » Full Text » PDF »
Induction of Protective IgA by Intestinal Dendritic Cells Carrying Commensal Bacteria.
A. J. Macpherson and T. Uhr (2004)
Science 303, 1662-1665
Abstract » Full Text » PDF »
Symbiont-Induced Changes in Host Actin during the Onset of a Beneficial Animal-Bacterial
Association.
J. R. Kimbell and M. J. McFall-Ngai (2004)
Appl. Envir. Microbiol. 70, 1434-1441
Abstract » Full Text » PDF »
Bacteria-Induced Intestinal Cancer in Mice with Disrupted Gpx1 and Gpx2 Genes.
F.-F. Chu, R. S. Esworthy, P. G. Chu, J. A. Longmate, M. M. Huycke, S. Wilczynski, and J. H.
Doroshow (2004)
Cancer Res. 64, 962-968
Abstract » Full Text » PDF »
Colonic Bacterial Flora: Changing Understandings in the Molecular Age.
V. Mai and J. G. Morris Jr. (2004)
J. Nutr. 134, 459-464
Abstract » Full Text » PDF »
A Multicomponent System Is Required for Tetracycline-Induced Excision of Tn4555.
A. C. Parker and C. J. Smith (2004)
J. Bacteriol. 186, 438-444
Abstract » Full Text » PDF »
Role of Commensal Bacteria in Development of Gut-Associated Lymphoid Tissues and Preimmune
Antibody Repertoire.
K.-J. Rhee, P. Sethupathi, A. Driks, D. K. Lanning, and K. L. Knight (2004)
J. Immunol. 172, 1118-1124
Abstract » Full Text » PDF »
Expression of mitochondrial HMGCoA synthase and glutaminase in the colonic mucosa is
modulated by bacterial species.
C. Cherbuy, C. Andrieux, E. Honvo-Houeto, M. Thomas, C. Ide, N. Druesne, C. Chaumontet, B.
Darcy-Vrillon, and P.-H. Duee (2004)
FEBS J. 271, 87-95
Abstract » Full Text » PDF »
Some Dietary Fibers Increase Elimination of Orally Administered Polychlorinated Biphenyls but
Not That of Retinol in Mice.
Y. Kimura, Y. Nagata, and R. K. Buddington (2004)
J. Nutr. 134, 135-142
Abstract » Full Text » PDF »
Evidence of Regio-specific Glycosylation in Human Intestinal Mucins: PRESENCE OF AN ACIDIC
GRADIENT ALONG THE INTESTINAL TRACT.
C. Robbe, C. Capon, E. Maes, M. Rousset, A. Zweibaum, J.-P. Zanetta, and J.-C. Michalski
(2003)
J. Biol. Chem. 278, 46337-46348
Abstract » Full Text » PDF »
Diversity and Succession of the Intestinal Bacterial Community of the Maturing Broiler Chicken.
J. Lu, U. Idris, B. Harmon, C. Hofacre, J. J. Maurer, and M. D. Lee (2003)
Appl. Envir. Microbiol. 69, 6816-6824
Abstract » Full Text » PDF »
Colonization of Gnotobiotic Mice with Human Gut Microflora at Birth Protects Against Escherichia
coli Heat-Labile Enterotoxin-Mediated Abrogation of Oral Tolerance.
V. GABORIAU-ROUTHIAU, P. RAIBAUD, C. DUBUQUOY, and M.-C. MOREAU (2003)
Pediatr. Res. 54, 739-746
Abstract » Full Text » PDF »
Role of passive and adaptive immunity in influencing enterocyte-specific gene expression.
S. L. Jenkins, J. Wang, M. Vazir, J. Vela, O. Sahagun, P. Gabbay, L. Hoang, R. L. Diaz, R.
Aranda, and M. G. Martin (2003)
Am J Physiol Gastrointest Liver Physiol 285, G714-G725
Abstract » Full Text » PDF »
Inaugural Article: Honor thy symbionts.
J. Xu and J. I. Gordon (2003)
PNAS 100, 10452-10459
Abstract » Full Text » PDF »
Double blind, placebo controlled trial of two probiotic strains in interleukin 10 knockout mice and
mechanistic link with cytokine balance.
J McCarthy, L O'Mahony, L O'Callaghan, B Sheil, E E Vaughan, N Fitzsimons, J Fitzgibbon, G C
O'Sullivan, B Kiely, J K Collins, and F Shanahan (2003)
Gut 52, 975-980
Abstract » Full Text »
Live probiotics protect intestinal epithelial cells from the effects of infection with enteroinvasive
Escherichia coli (EIEC).
S Resta-Lenert and K E Barrett (2003)
Gut 52, 988-997
Abstract » Full Text »
The Squid-Vibrio Symbioses: From Demes to Genes.
J. R. Kimbell and M. J. McFall-Ngai (2003)
Integr. Comp. Biol. 43, 254-260
Abstract » Full Text » PDF »
Tumor necrosis factor regulates intestinal epithelial cell migration by receptor-dependent
mechanisms.
J. Corredor, F. Yan, C. C. Shen, W. Tong, S. K. John, G. Wilson, R. Whitehead, and D. B. Polk
(2003)
Am J Physiol Cell Physiol 284, C953-C961
Abstract » Full Text » PDF »
Molecular features of adult mouse small intestinal epithelial progenitors.
T. S. Stappenbeck, J. C. Mills, and J. I. Gordon (2003)
PNAS 100, 1004-1009
Abstract » Full Text » PDF »
Distinct gene expression profiles characterize the histopathological stages of disease in
Helicobacter-induced mucosa-associated lymphoid tissue lymphoma.
A. Mueller, J. O'Rourke, J. Grimm, K. Guillemin, M. F. Dixon, A. Lee, and S. Falkow (2003)
PNAS 100, 1292-1297
Abstract » Full Text » PDF »
NotI passporting to identify species composition of complex microbial systems.
V. Zabarovska, A. S. Kutsenko, L. Petrenko, G. Kilosanidze, O. Ljungqvist, E. Norin, T. Midtvedt,
G. Winberg, R. Mollby, V. I. Kashuba, I. Ernberg, and E. R. Zabarovsky (2003)
Nucleic Acids Res. 31, e5
Abstract » Full Text » PDF »
Victivallis vadensis gen. nov., sp. nov., a sugar-fermenting anaerobe from human faeces.
E. G. Zoetendal, C. M. Plugge, A. D. L. Akkermans, and W. M. de Vos (2003)
Int J Syst Evol Microbiol 53, 211-215
Abstract » Full Text » PDF »
Probiotic Bacterium Prevents Cytokine-induced Apoptosis in Intestinal Epithelial Cells.
F. Yan and D. B. Polk (2002)
J. Biol. Chem. 277, 50959-50965
Abstract » Full Text » PDF »
The Genome in Its Ecological Context: Philosophical Perspectives on Interspecies Epigenesis.
S. F. Gilbert (2002)
Ann. N.Y. Acad. Sci. 981, 202-218
Abstract » Full Text » PDF »
Commensal ocular bacteria degrade mucins.
M Berry, A Harris, R Lumb, and K Powell (2002)
Br. J. Ophthalmol. 86, 1412-1416
Abstract » Full Text » PDF »
Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells.
T. S. Stappenbeck, L. V. Hooper, and J. I. Gordon (2002)
PNAS 99, 15451-15455
Abstract » Full Text » PDF »
Elimination of Colon Cancer in Germ-free Transforming Growth Factor Beta 1-deficient Mice.
S. J. Engle, I. Ormsby, S. Pawlowski, G. P. Boivin, J. Croft, E. Balish, and T. Doetschman (2002)
Cancer Res. 62, 6362-6366
Abstract » Full Text » PDF »
PCR detection of Mycobacterium paratuberculosis in Crohn's disease granulomas isolated by laser
capture microdissection.
P Ryan, M W Bennett, S Aarons, G Lee, J K Collins, G C O'Sullivan, J O'Connell, and F
Shanahan (2002)
Gut 51, 665-670
Abstract » Full Text » PDF »
Expression Profiling of Periodontal Ligament Cells Stimulated with Enamel Matrix Proteins in vitro:
A Model for Tissue Regeneration.
P.M. Brett, M. Parkar, I. Olsen, and M. Tonetti (2002)
J. Dent. Res. 81, 776-783
Abstract » Full Text » PDF »
Molecular Cloning and Characterization of a Novel alpha 1,2-Fucosyltransferase (CE2FT-1) from
Caenorhabditis elegans.
Q. Zheng, I. Van Die, and R. D. Cummings (2002)
J. Biol. Chem. 277, 39823-39832
Abstract » Full Text » PDF »
A Gnotobiotic Transgenic Mouse Model for Studying Interactions between Small Intestinal
Enterocytes and Intraepithelial Lymphocytes.
I. U. Mysorekar, R. G. Lorenz, and J. I. Gordon (2002)
J. Biol. Chem. 277, 37811-37819
Abstract » Full Text » PDF »
Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by
Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes.
E. G. Zoetendal, K. Ben-Amor, H. J. M. Harmsen, F. Schut, A. D. L. Akkermans, and W. M. de
Vos (2002)
Appl. Envir. Microbiol. 68, 4225-4232
Abstract » Full Text » PDF »
Mucosa-Associated Bacteria in the Human Gastrointestinal Tract Are Uniformly Distributed along
the Colon and Differ from the Community Recovered from Feces.
E. G. Zoetendal, A. von Wright, T. Vilpponen-Salmela, K. Ben-Amor, A. D. L. Akkermans, and W.
M. de Vos (2002)
Appl. Envir. Microbiol. 68, 3401-3407
Abstract » Full Text » PDF »
Lactobacillus acidophilus (strain LB) from the resident adult human gastrointestinal microflora
exerts activity against brush border damage promoted by a diarrhoeagenic Escherichia coli in
human enterocyte-like cells.
V Lievin-Le Moal, R Amsellem, A L Servin, and M-H Coconnier (2002)
Gut 50, 803-811
Abstract » Full Text » PDF »
Overexpression of CRIP in transgenic mice alters cytokine patterns and the immune response.
L. Lanningham-Foster, C. L. Green, B. Langkamp-Henken, B. A. Davis, K. T. Nguyen, B. S.
Bender, and R. J. Cousins (2002)
Am J Physiol Endocrinol Metab 282, E1197-E1203
Abstract » Full Text » PDF »
Selection of Multipotent Stem Cells during Morphogenesis of Small Intestinal Crypts of Lieberkuhn
Is Perturbed by Stimulation of Lef-1/beta -Catenin Signaling.
M. H. Wong, J. Huelsken, W. Birchmeier, and J. I. Gordon (2002)
J. Biol. Chem. 277, 15843-15850
Abstract » Full Text » PDF »
Current Understanding of Gastrointestinal Immunoregulation and Its Relation to Food Allergy.
P. BRANDTZAEG (2002)
Ann. N.Y. Acad. Sci. 964, 13-45
Abstract » Full Text » PDF »
Probiotics: a role in the treatment of intestinal infection and inflammation?.
E Isolauri, P V Kirjavainen, and S Salminen (2002)
Gut 50, iii54-59
Abstract » Full Text » PDF »
Decreased Postnatal Survival and Altered Body Weight Regulation in Procolipase-deficient Mice.
D. D'Agostino, R. A. Cordle, J. Kullman, C. Erlanson-Albertsson, L. J. Muglia, and M. E. Lowe
(2002)
J. Biol. Chem. 277, 7170-7177
Abstract » Full Text » PDF »
Molecular Diversity of Lactobacillus spp. and Other Lactic Acid Bacteria in the Human Intestine as
Determined by Specific Amplification of 16S Ribosomal DNA.
H. G.H.J. Heilig, E. G. Zoetendal, E. E. Vaughan, P. Marteau, A. D.L. Akkermans, and W. M. de
Vos (2002)
Appl. Envir. Microbiol. 68, 114-123
Abstract » Full Text » PDF »
Molecular Monitoring of Succession of Bacterial Communities in Human Neonates.
C. F. Favier, E. E. Vaughan, W. M. De Vos, and A. D. L. Akkermans (2002)
Appl. Envir. Microbiol. 68, 219-226
Abstract » Full Text » PDF »
A Novel NF-{kappa}B/Rel Site in Intron 1 Cooperates with Proximal Promoter Elements to Mediate
TNF-{alpha}-Induced Transcription of the Human Polymeric Ig Receptor.
H. Schjerven, P. Brandtzaeg, and F.-E. Johansen (2001)
J. Immunol. 167, 6412-6420
Abstract » Full Text » PDF »
Inaugural Article: Modulation of intestinal gene expression by dietary zinc status: Effectiveness of
cDNA arrays for expression profiling of a single nutrient deficiency.
R. K. Blanchard, J. B. Moore, C. L. Green, and R. J. Cousins (2001)
PNAS 98, 13507-13513
Abstract » Full Text » PDF »
The intestinal stem cell niche: There grows the neighborhood.
J. C. Mills and J. I. Gordon (2001)
PNAS 98, 12334-12336
Full Text » PDF »
Bacteriotherapy: the time has come.
P. Huovinen (2001)
BMJ 323, 353-354
Full Text » PDF »
Extranuclear sequestration of phospho-Jun N-terminal kinase and distorted villi produced by
activated Rac1 in the intestinal epithelium of chimeric mice.
T. S. Stappenbeck and J. I. Gordon (2001)
Development 128, 2603-2614
Abstract » Full Text » PDF »
Microarrays for microbiologists.
S. Lucchini, A. Thompson, and J. C. D. Hinton (2001)
Microbiology 147, 1403-1414
Full Text » PDF »
Science 2 June 2006:
Vol. 312. no. 5778, pp. 1355 - 1359
DOI: 10.1126/science.1124234
Prev | Table of Contents | Next
RESEARCH ARTICLES
Metagenomic Analysis of the Human Distal Gut Microbiome
Steven R. Gill,1* Mihai Pop,1 Robert T. DeBoy,1 Paul B. Eckburg,2,3,4 Peter
J. Turnbaugh,5 Buck S. Samuel,5 Jeffrey I. Gordon,5 David A. Relman,2,3,4
Claire M. Fraser-Liggett,1,6 Karen E. Nelson1
The human intestinal microbiota is composed of 1013 to 1014 microorganisms
whose collective genome ("microbiome") contains at least 100 times as many
genes as our own genome. We analyzed 78 million base pairs of unique DNA
sequence and 2062 polymerase chain reaction–amplified 16S ribosomal DNA
sequences obtained from the fecal DNAs of two healthy adults. Using metabolic
function analyses of identified genes, we compared our human genome with the
average content of previously sequenced microbial genomes. Our microbiome
has significantly enriched metabolism of glycans, amino acids, and xenobiotics;
methanogenesis; and 2-methyl-D-erythritol 4-phosphate pathway–mediated
biosynthesis of vitamins and isoprenoids. Thus, humans are superorganisms
whose metabolism represents an amalgamation of microbial and human
attributes.
1
The Institute for Genomic Research, 9712 Medical Center Drive, Rockville,
MD 20850, USA.
2 Department of Medicine, Stanford University School of Medicine, Stanford, CA
94305, USA.
3 Department of Microbiology and Immunology, 299 Campus Drive, Stanford
University, Stanford, CA 94305, USA.
4 Veterans Affairs Palo Alto Health Care System, Palo Alto, CA 94304, USA.
5 Center for Genome Sciences, Washington University School of Medicine, St.
Louis, MO 63108, USA.
6 Departments of Pharmacology and Physiology and Microbiology and Tropical
Diseases, George Washington University School of Medicine, Washington, DC
20037, USA.
*
Present address: Department of Oral Biology, The State University of New
York at Buffalo, Buffalo, NY 14214, USA.
Present address: Center for Bioinformatics and Computational Biology,
University of Maryland, College Park, MD 20742, USA.
To whom correspondence should be addressed. E-mail: srgill@buffalo.edu
Our body surfaces are home to microbial communities whose aggregate
membership outnumbers our human somatic and germ cells by at least an order
of magnitude. The vast majority of these microbes (10 to 100 trillion) inhabit our
gastrointestinal tract, with the greatest number residing in the distal gut, where
they synthesize essential amino acids and vitamins and process components of
otherwise indigestible contributions to our diet such as plant polysaccharides
(1). The most comprehensive 16S ribosomal DNA (rDNA) sequence-based
enumeration of the distal gut and fecal microbiota published to date underscores
its highly selected nature. Among the 70 divisions (deep evolutionary lineages)
of Bacteria and 13 divisions of Archaea described to date, the distal gut and
fecal microbiota of the three healthy adults surveyed was dominated by just two
bacterial divisions, the Bacteroidetes and the Firmicutes, which made up >99%
of the identified phylogenetic types (phylotypes), and by one prominent
methanogenic archaeon, Methanobrevibacter smithii (2). The human distal gut
microbiome is estimated to contain 100 times as many genes as our 2.85–
billion base pair (bp) human genome (1). Therefore, a superorganismal view of
our genetic landscape should include genes embedded in our human genome
and the genes in our affiliated microbiome, whereas a comprehensive view of
our metabolome would encompass the metabolic networks based in our
microbial communities.
Progress made with 16S rDNA-based enumerations has disclosed significant
differences in community membership between healthy adults (2, 3), differences
that may contribute to variations in normal physiology between individuals or
that may predispose to disease. For example, studies of humans and
gnotobiotic mouse models indicate that our mutualistic relations with the gut
microbiota influence maturation of the immune system (4), modulate responses
to epithelial cell injury (5), affect energy balance (6), and support
biotransformations that we are ill-equipped to perform on our own, including
processing of xenobiotics (7). However, we are limited by our continued inability
to cultivate the majority of our indigenous microbial community members, biases
introduced by preferential polymerase chain reaction (PCR) amplification of 16S
rDNA genes and by our limited ability to infer organismal function from these
gene sequences.
As with soil (8) and ocean (9), metagenomic analysis of complex communities
offers an opportunity to examine in a comprehensive manner how ecosystems
respond to environmental perturbations, and in the case of humans, how our
microbial ecosystems contribute to health and disease. In the current study, we
use a metagenomics approach to reveal microbial genomic and genetic diversity
and to identify some of the distinctive functional attributes encoded in our distal
gut microbiome.
Sequencing the microbiome. Although whole-genome shotgun sequencing
and assembly have historically been applied to the study of single organisms,
recent reports from Venter et al. (9) and Baker et al. (10) have demonstrated the
utility of this approach for studying mixed microbial communities. Variations in
the relative abundance of each member of the microbial community and their
respective genome sizes determine the final depth of sequence coverage for
any organism at a particular level of sequencing. This means that the genome
sequences of abundant species will be well represented in a set of random
shotgun reads, whereas lower abundance species may be represented by a
small number of sequences. In fact, the size and depth of coverage (computed
as the ratio between the total length of the reads placed into contigs and the
total size of the contigs) of genome assemblies generated from a metagenomics
project can provide information on relative species abundance.
A total of 65,059 and 74,462 high-quality sequence reads were generated from
random DNA libraries created with fecal specimens of two healthy humans
(subjects 7 and 8). These two subjects, ages 28 and 37, female and male,
respectively, had not used antibiotics or any other medications during the year
before specimen collection (11). The combined sequenced distal gut
"microbiome" of subjects 7 and 8 consisted of 17,668 contigs that assembled
into 14,572 scaffolds, totaling 33,753,108 bp. The scaffolds ranged in size from
1000 to 57,894 bp and the contigs from 92 to 44,747 bp. The average depth of
sequence coverage in contigs was 2.13-fold. Forty percent of the reads (56,292
total) could not be assembled into contigs, most likely because of a combination
of low depth of coverage and low abundance of some organisms within the
specimens. Together, these singletons accounted for an additional 45,078,063
bp of DNA.
A total of 50,164 open reading frames (ORFs) were predicted from the data set
(25,077 for subject 7 and 25,087 for subject 8). These ORFs correspond to
19,866 unique database matches (13,293 for subject 7; 12,273 for subject 8;
5700 that were present in both). ORF-based alignments against public
databases identified 259 contigs in subject 7 and 330 in subject 8 that could be
assigned to members of Archaea, plus 5992 contigs from subject 7 and 7138
from subject 8 assignable to members of Bacteria (table S1). The remaining
contigs either did not match any known ORFs or were ambiguously assigned.
Insight into the diversity within our samples was obtained by comparison of a
subset of the shotgun reads to the completed sequence of Bifidobacterium
longum, a member of the lactic acid bacteria present in the distal gut of healthy
humans (12). A total of 1965 reads from the combined data set from subjects 7
and 8 could be aligned to the genome sequence of B. longum. These reads
represented a total of 1,617,706 bp of DNA sequence, which corresponds to
0.7-fold coverage of the B. longum genome. There was a great deal of
heterogeneity in nucleotide sequence in the 1965 reads that aligned with the B.
longum genome sequence (80 to 100% identity) with 52% of the reads aligned
at less than 95% identity (Fig. 1A). These data suggest that these reads are not
derived from a single discrete strain of B. longum in subjects 7 and 8, but
instead, reflect the presence of multiple strains, as well as other Bifidobacterium
phylotypes in the distal gut microbiota.
Fig. 1. Comparison of random metagenome reads with
completed genome of Bifidobacterium longum and
Methanobrevibacter smithii. (A) Percent identity plot
(PIP) of alignments of shotgun reads along the genome
of B. longum strain NCC2705. The x axis represents the
coordinate along the genome, and the y axis represents
the percent identity of the match. (B) Percent identity
plot (PIP) of the alignment of shotgun reads along the
draft genome of M. smithii. The x axis represents the
coordinate along a pseudomolecule formed by
concatenating all contigs in the M. smithii draft
assembly. The y axis represents the percent identity of
the match. The variation in the percent identity of the
matches between the shotgun reads from subjects 7
and 8 as compared with the genome sequences of B.
longum NCC2705 suggests considerable diversity
among Bifidobacterium-like organisms within our
samples. Alignments of the reads to the draft genome of
M. smithii exhibit a much narrower range of percent
identity (89% of alignments were at 95% or better
identity as compared with 48% for B. longum),
consistent with lower levels of diversity among archaeal
members of the gastrointestinal tract. [View Larger
Version of this Image (23K GIF file)]
Previous work (2) has shown that archaeal species, in particular M. smithii, are
also major players in the human distal gut ecosystem. M. smithii was
represented in our data set at 3.5-fold coverage, as indicated by the 7955
shotgun reads that matched this draft assembly (Fig. 1B). The presence of M.
smithii is also supported by the identification of eight partial-length 16S rDNA
sequences with 99.65 to 100% identity to M. smithii. Unlike B. longum, the
majority (89%) of alignments to M. smithii had 95% or better sequence identity
to the draft assembly, indicating low divergence between Methanobrevibacter
strains present in our samples. More than half of the archaeal contigs in our
data set had significant similarity to M. smithii: 145 of 259 archaeal contigs in
subject 7 and 174 of 330 archaeal contigs from subject 8 had matches 100
bases, and 80% identity to a deep draft assembly of this genome (13),
consistent with previous reports on the abundance of this species in the human
gut.
Identifying phylotypes. We explored bacterial diversity in both stool samples
with analysis of 16S rDNA sequences from the random shotgun assemblies and
from libraries of cloned, PCR-amplified 16S rDNA. Phylogenetic assessments of
the local microbial community census provide a benchmark for interpreting the
functional predictions from metagenomic data. Of the 237 partial bacterial-length
16S rDNA sequences identified in the shotgun assemblies, we selected 132
bacterial sequences for further analysis (2, 11). Using a 97% minimum pair-wise
similarity definition, 72 bacterial phylotypes were identified. Only one archaeal
phylotype was identified (i.e., M. smithii). Sixteen bacterial phylotypes (22.2%)
were novel, and 60 (83.3%) represented uncultivated species. The bacterial
phylotypes were assigned to only two divisions, the Firmicutes (62 phylotypes,
105 sequences) and the Actinobacteria (10 phylotypes, 27 sequences). Sixty of
the Firmicute phylotypes belonged to the class Clostridia, including Clostridia
cluster XIV and Faecalibacteria. Analysis of 2062 near–full-length PCRamplified 16S rDNA sequences (1024 from subject 7 and 1038 from subject 8)
revealed a similar phylogenetic distribution among higher-order taxa, but a more
diverse population at the species level. Using a 97% similarity phylotype
threshold, 151 phylotypes were identified (23% novel; 150 Firmicutes; 1
Actinobacteria) (fig. S1A). Similar analyses based on a 99% similarity threshold
are provided (11).
Although there were no Bacteroidetes 16S rDNA sequences identified in the
random assemblies and clone libraries, amplification with species-specific 16S
rDNA primers yielded sequences from Bacteroides fragilis and Bacteroides
uniformis. This relative paucity of Bacteroidetes sequences is in conflict with
data from other studies (2, 3). This discrepancy may have been caused by the
known biases associated with the fecal lysis and DNA extraction methods used
in the current study with respect to Bacteroides spp. (14); although less likely, it
is also possible that members of the Bacteroidetes division are less abundant in
the feces of subjects 7 and 8. In addition, with respect to the PCR-amplified 16S
rDNA sequence data, there may be biases associated with the primers or PCR
reaction conditions. Similar arguments may apply to other underrepresented
taxa as well, such as the Actinobacteria and Proteobacteria phyla. Estimates of
diversity indicated that at least 300 unique bacterial phylotypes would be
detected with continued sequencing from these stool samples (fig. S1, B to D).
Comparative functional analysis of the distal gut microbiome. To delineate
how the human distal gut microbiome endows us with physiological properties
that we have not had to evolve on our own, we explored the metabolic potential
of the microbiota in subjects 7 and 8 using KEGG (Kyoto Encyclopedia of
Genes and Genomes, version 37) pathways and COGs (Clusters of
Orthologous Groups) (15, 16). Both annotation schemes contain categories of
metabolic functions organized in multiple hierarchical levels: KEGG analysis
maps enzymes onto known metabolic pathways; COG analysis uses
evolutionary relations (orthologs) to group functionally related genes. Odds
ratios were used to rank the relative enrichment or underrepresentation of COG
and KEGG categories. An odds ratio of one indicates that the community DNA
has the same proportion of hits to a given category as the comparison data set;
an odds ratio greater than one indicates enrichment (more hits to a given
category than expected), whereas an odds ratio less than one indicates
underrepresentation (fewer hits to a given category than expected). Odds ratios
for the KEGG pathway involved in biosynthesis of peptidoglycan (table S3), a
major component of the bacterial cell wall, are consistent with expectations: The
human gut microbiome is highly enriched relative to the human genome (77.88),
similar to all sequenced bacteria (1.83), and moderately enriched relative to all
sequenced Archaea (7.06).
Because we have not obtained saturation (see below), we cannot be confident
that a given COG or KEGG pathway component is not present in the human
distal gut microbiome. Therefore, we have focused our analysis on identified
functional categories that are enriched relative to previously sequenced
genomes.
BLAST comparisons of all sequences yielded 62,036 hits to the COG database,
corresponding to 2407 unique COGs. ACE and Chao1 estimates of community
richness were 2558 and 2553 COGs, respectively. This observed degree of
community COG diversity is greater than that described for an acid mine
drainage (1824 COGs), but less than that described for whale fall (3332), soil
(3394), and Sargasso Sea samples (3714) (17). The number of KEGG
pathways and COG terms enriched in the human distal gut microbiomes of
subjects 7 and 8 is listed in table S2. KEGG maps and COG assignments can
be found at (11, 18, 19).
The metabolome of the human distal gut microbiota. Both human subjects
showed similar patterns of enrichment for each COG (Fig. 2) and KEGG (Fig. 3)
category involved in metabolism. However, compared with subject 7, subject 8
was enriched for energy production and conversion; carbohydrate transport and
metabolism; amino acid transport and metabolism; coenzyme transport and
metabolism; and secondary metabolites biosynthesis, transport, and catabolism
(Fig. 2). At this time, it is not clear whether these differences reflect limited
coverage of their microbiomes or other factors such as host diet, genotype, and
life-style. The analysis presented below combines the genes identified in the
fecal microbiotas of both subjects to create an aggregate "human distal gut
microbiome."
Fig. 2. COG analysis reveals metabolic
functions that are enriched or
underrepresented in the human distal gut
microbiome (relative to all sequenced
microbes). Color code: black, subject 7; gray,
subject 8. Bars above both dashed lines
indicate enrichment, and bars below both
lines indicate underrepresentation (P < 0.05).
Asterisks indicate categories that are
significantly different between the two
subjects (P < 0.05). Secondary metabolites
biosynthesis includes antibiotics, pigments,
and nonribosomal peptides. Inorganic ion
transport and metabolism includes
phosphate, sulfate, and various cation
transporters. [View Larger Version of this
Image (24K GIF file)]
Fig. 3. KEGG pathway reconstructions reveal
metabolic functions that are enriched or
underrepresented in the human distal gut
microbiome as follows: both samples
compared with all sequenced bacterial
genomes in KEGG (blue), the human
genome (red), and all sequenced archaeal
genomes in KEGG (yellow). Asterisks
indicate enrichment (odds ratio > 1, P < 0.05)
or underrepresentation (odds ratio < 1, P <
0.05). The KEGG category, "metabolism of
other amino acids," includes amino acids that
are not incorporated into proteins, such as ßalanine, taurine, and glutathione. Odds ratios
are a measure of relative gene content based
on the number of independent hits to
enzymes present in a given KEGG category.
[View Larger Version of this Image (21K GIF
file)]
The plant polysaccharides that we commonly consume are rich in xylan-, pectin, and arabinose-containing carbohydrate structures. The human genome lacks
most of the enzymes required for degrading these glycans (20). However, the
distal gut microbiome provides us with this capacity (1) (Fig. 3 and tables S3
and S4). The human gut microbiome is enriched for genes involved in starch
and sucrose metabolism (fig. S2) plus the metabolism of glucose, galactose,
fructose, arabinose, mannose, and xylose (table S4). At least 81 different
glycoside hydrolase families are represented in the microbiome, many of which
are not present in the human "glycobiome" (table S5).
Host mucus provides a consistent reservoir of glycans for the microbiota and
thus, in principle, can serve to mitigate the effects of marked changes in the
availability of dietary polysaccharides (1). Gnotobiotic mouse models of the
human gut microbiota have indicated that -linked terminal fucose in host
glycans is an attractive and accessible source of energy for members of the
microbiota such as the Bacteroidetes (1, 6). Several COGs responsible for
fucose utilization are enriched in the human gut microbiome relative to all
microbial genomes (table S4).
Fermentation of dietary fiber or host-derived glycans requires cooperation of
groups of microorganisms linked in a trophic chain. Primary fermenters process
glycans to short-chain fatty acids (SCFAs), mainly acetate, propionate, and
butyrate, plus gases (i.e., H2 and CO2). The bulk of SCFAs are absorbed by the
host: Together, they account for 10% of calories extracted from a Western diet
each day (21). COG analyses demonstrated enrichment of key genes involved
in generating acetate, butyrate, lactate, and succinate in the gut microbiome
compared with all microbial genomes in the COG database (table S6). The most
enriched COG was related to butyrate kinase (odds ratio of 9.30), an enzyme
that facilitates formation of butyrylcoenzyme A by phosphorylating butyrate. This
enrichment underscores the important commitment of the distal gut microbiota
to generating this biologically significant SCFA, which serves as the principal
energy source for colonocytes and may fortify the intestinal mucosal barrier by
stimulating their growth (22).
Accumulation of H2, an end product of bacterial fermentation, reduces the
efficiency of processing of dietary polysaccharides (23). Production of methane
by mesophilic methanogenic archaeons is a major pathway for removing H2
from the human distal gut (23), although sulfate reduction and
homoacetogenesis serve as alternate pathways. Enhancement of bacterial
growth rates, fermentation of polysaccharides, and SCFA production have been
observed when bacteria (e.g., Fibrobacter succinogenes and Ruminococcus
flavefaciens) are cocultured with a Methanobrevibacter species (24). The distal
gut microbiome is enriched for many COGs representing key genes in the
methanogenic pathway (Fig. 4, C and D), consistent with the importance of H2
removal from the distal gut ecosystem via methanogenesis.
Fig. 4. Isoprenoid biosynthesis via the MEP
pathway and methanogenesis are highly
enriched in the distal gut microbiome. (A)
MEP pathway for isoprenoid biosynthesis. (B)
Odds ratio for each COG in the MEP
pathway. All enzymes necessary to convert
DXP to IPP and thiamine are enriched (P <
0.0001 relative to all sequenced microbes).
(C) Location and role of key enzymes in
methanogenesis. (D) Odds ratio for each
COG highlighted in (C). [View Larger Version
of this Image (27K GIF file)]
The distal gut microbiome is enriched for a variety of COGs involved in
synthesis of essential amino acids and vitamins (tables S7 and S8). COGs
representing enzymes in the MEP (2-methyl-D-erythritol 4-phosphate) pathway,
used for biosynthesis of deoxyxylulose 5-phosphate (DXP) and isopenteryl
pyrophosphate (IPP), are notably enriched (P < 0.0001; relative to all
sequenced microbes) (Fig. 4, A and B). DXP is a precursor in the biosynthesis
of vitamins essential for human health, including B1 (thiamine) and B6 (pyridoxal
form) (25). IPP is found in all known prokaryotic and eukaryotic cells and can
give rise to at least 25,000 known derivatives, including archaeal membrane
lipids (26), carotenoids (27), and cholesterol (28). Together, these results
indicate that the MEP pathway is much better represented in the distal human
gut microbiome than was previously known. The MEP pathway has been
proposed as a target for developing new antibiotics, because some pathogenic
bacteria use the MEP pathway instead of the mevanolate pathway for IPP
biosynthesis (29). However, our metagenomic study indicates that this approach
may be detrimental to the microbiota and, in turn, the host.
Detoxification of xenobiotics could impact the host in a variety of ways, ranging
from susceptibility to cancer to the efficiency of drug metabolism. Dietary plant–
derived phenolics, such as flavonoids and cinnamates, have pronounced effects
on mammalian cells (30–32). Hydrolysis of phenolic glycosidic or ester linkages
occurs in the distal gut by microbial ß-glucosidases, ß-rhamnosidases, and
esterases (33). The human distal gut microbiome is enriched for ß-glucosidase
(COG1472, COG2723 in table S4; P < 0.0005; glycosidase families GH3 and
GH9 in table S5). Glucuronide conjugates of xenobiotics and bile salts induce
microbial ß-glucuronidase activity (34). The microbiome is enriched in this
enzyme activity (i.e., COG3250; table S4). KEGG analysis also indicates
enrichment for pathways involved in degradation of tetrachloroethene,
dichloroethane, caprolactam, and benzoate (table S3).
Conclusion. This metagenomics analysis begins to define the gene content
and encoded functional attributes of the gut microbiome in healthy humans.
Future studies are needed to provide deeper coverage of the microbiome and to
assess the effects of age, diet, and pathologic states (e.g., inflammatory bowel
diseases, obesity, and cancer) on the distal gut microbiome of humans living in
different environments. Periodic sampling of the distal gut microbiome (and of
our other microbial communities) may provide insights into the effects of
environmental change on our "microevolution." The results should provide a
broader view of human biology, including new biomarkers for defining our
health; new ways for optimizing our personal nutrition; new ways for predicting
the bioavailability of orally administered drugs; and new ways to forecast our
individual and societal predispositions to disorders such as infections with
pathogens, obesity, and misdirected or maladapted host immune responses of
the gut.
References and Notes









1. F. Backhed, R. E. Ley, J. L. Sonnenburg, D. A. Peterson, J. I. Gordon,
Science 307, 1915 (2005).[Abstract/Free Full Text]
2. P. B. Eckburg et al., Science 308, 1635 (2005).[Abstract/Free
Full Text]
3. R. E. Ley et al., Proc. Natl. Acad. Sci. U.S.A. 102, 11070
(2005).[Abstract/Free Full Text]
4. S. K. Mazmanian, C. H. Liu, A. O. Tzianabos, D. L. Kasper, Cell 122,
107 (2005). [CrossRef] [ISI] [Medline]
5. S. Rakoff-Nahoum, J. Paglino, F. Eslami-Varzaneh, S. Edberg, R.
Medzhitov, Cell 118, 229 (2004). [CrossRef] [ISI] [Medline]
6. F. Backhed et al., Proc. Natl. Acad. Sci. U.S.A. 101, 15718
(2004).[Abstract/Free Full Text]
7. J. K. Nicholson, E. Holmes, I. D. Wilson, Nat. Rev. Microbiol. 3, 431
(2005). [CrossRef] [ISI] [Medline]
8. M. R. Rondon et al., Appl. Environ. Microbiol. 66, 2541
(2000).[Abstract/Free Full Text]
9. J. C. Venter et al., Science 304, 66 (2004).[Abstract/Free Full Text]

























10. G. W. Tyson et al., Nature 428, 25 (2004). [CrossRef] [ISI] [Medline]
11. Materials and methods are available as supporting material on
Science Online.
12. M. A. Schell et al., Proc. Natl. Acad. Sci. U.S.A. 99, 14422
(2002).[Abstract/Free Full Text]
13. (http://gordonlab.wustl.edu/supplemental/Gill/Msmithii/draftgenome/).
14. A. L. McOrist, M. Jackson, A. R. Bird, J. Microbiol. Methods 50, 131
(2002). [CrossRef] [ISI] [Medline]
15. M. Kanehisa, S. Goto, S. Kawashima, Y. Okuno, M. Hattori, Nucleic
Acids Res. 32, D277 (2004).[Abstract/Free Full Text]
16. R. L. Tatusov et al., BMC Bioinformatics 4, 41 (2003). [CrossRef]
[Medline]
17. S. G. Tringe et al., Science 308, 554 (2005).[Abstract/Free Full Text]
18. (http://gordonlab.wustl.edu/supplemental/Gill).
19. Database available as supporting material on Science Online.
20. URL (http://afmb.cnrs-mrs.fr/CAZY/).
21. N. I. McNeil, Am. J. Clin. Nutr. 39, 338 (1984).[Abstract/Free
Full Text]
22. D. L. Topping, P. M. Clifton, Physiol. Rev. 81, 1031
(2001).[Abstract/Free Full Text]
23. A. J. Stams, Antonie Van Leeuwenhoek 66, 271 (1994). [CrossRef]
[ISI] [Medline]
24. J. L. Rychlik, T. May, Curr. Microbiol. 40, 176 (2000). [CrossRef] [ISI]
[Medline]
25. M. Rodriguez-Concepcion, A. Boronat, Plant Physiol. 130, 1079
(2002).[Free Full Text]
26. J. Pereto, P. Lopez-Garcia, D. Moreira, Trends Biochem. Sci. 29, 469
(2004). [CrossRef] [ISI] [Medline]
27. D. Umeno, A. V. Tobias, F. H. Arnold, Microbiol. Mol. Biol. Rev. 69,
51 (2005).[Abstract/Free Full Text]
28. K. C. Wang, S. Ohnuma, Biochim. Biophys. Acta 1529, 33 (2000).
[ISI] [Medline]
29. M. Begley et al., FEBS Lett. 561, 99 (2004). [CrossRef] [ISI] [Medline]
30. J. J. Reiners Jr., R. Clift, P. Mathieu, Carcinogenesis 20, 1561
(1999).[Abstract/Free Full Text]
31. C. A. Rice-Evans, N. J. Miller, G. Paganga, Free Radic. Biol. Med.
20, 933 (1996). [CrossRef] [ISI] [Medline]
32. G. Williamson, G. W. Plumb, Y. Uda, K. R. Price, M. J. Rhodes,
Carcinogenesis 17, 2385 (1996).[Abstract/Free Full Text]
33. H. Schneider, A. Schwiertz, M. D. Collins, M. Blaut, Arch. Microbiol.
171, 81 (1999). [CrossRef] [ISI] [Medline]
34. A. K. Mallett, C. A. Bearne, I. R. Rowland, Appl. Environ. Microbiol.
46, 591 (1983).[Abstract/Free Full Text]

35. We thank W. Nelson and I. Hance (The Institute for Genomic
Research), L. Dethlefsen and E. Bik (Stanford), and D. Leip (Washington
University) for their valuable assistance. This work was supported by Defense
Advanced Research Projects Agency (DARPA) and the Office of Naval
Research grant no. ONR-N00014-02-1-1002 (S.R.G., K.E.N.), the W. M. Keck
Foundation (J.I.G.), the Ellison Medical Foundation (D.A.R., J.I.G.), and NIH
grants AI51259 (D.A.R.) and DK70977 (J.I.G.). B.S.S. is a recipient of a
graduate research fellowship from the NSF (DGE-0202737). This wholegenome shotgun project has been deposited at the DNA Data Bank of Japan
(DDBJ), European Molecular Biology Laboratory (EMBL), and GenBank under
the project accession AAQK00000000 (subject 7) and AAQL00000000 (subject
8). The version described in this paper is the first version, AAQK01000000 and
AAQL01000000. All near–full-length 16S rDNA sequences were deposited at
DDBJ/EMBL/GenBank under the accessions DQ325545 to DQ327606.
Supporting Online Material
www.sciencemag.org/cgi/content/full/312/5778/1355/DC1
Materials and Methods
Figs. S1 and S2
Tables S1 to S8
References
Received for publication 22 December 2005. Accepted for publication 5 May
2006.
THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Effect of bowel preparation and colonoscopy on post-procedure intestinal microbiota composition.
V Mai, B Greenwald, J Glenn Morris Jr, J-P Raufman, and O C Stine (2006)
Gut 55, 1822-1823
Full Text » PDF »
Functional Genomic and Metabolic Studies of the Adaptations of a Prominent Adult Human Gut
Symbiont, Bacteroides thetaiotaomicron, to the Suckling Period.
M. K. Bjursell, E. C. Martens, and J. I. Gordon (2006)
J. Biol. Chem. 281, 36269-36279
Abstract » Full Text » PDF »
Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulinresistant mice.
M.-E. Dumas, R. H. Barton, A. Toye, O. Cloarec, C. Blancher, A. Rothwell, J. Fearnside, R.
Tatoud, V. Blanc, J. C. Lindon, S. C. Mitchell, E. Holmes, M. I. McCarthy, J. Scott, D. Gauguier,
and J. K. Nicholson (2006)
PNAS 103, 12511-12516
Abstract » Full Text » PDF »
A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.
B. S. Samuel and J. I. Gordon (2006)
PNAS 103, 10011-10016
Abstract » Full Text » PDF »