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Jeffrey I. Gordon, MD. Director of the center for Genome Sciences and Systems Biology at Washington University, St. Louis. Presenter: rui zhang. Resume. In 1969, he got his bachelor’s degree in Biology at Oberlin College in Ohio.

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Jeffrey I. Gordon, MD

  • Director of the center for Genome Sciences and Systems Biology at Washington University, St. Louis

Presenter: ruizhang



  • In 1969, he got his bachelor’s degree in Biology at Oberlin College in Ohio.
  • Over the next four years, he received his medical training at the University of Chicago and graduated with honors in 1973.
  • After two years as intern and junior assistant resident in Medicine at Barnes Hospital, St Louis
  • In 1975, Gordon joined the Laboratory of Biochemistry at the National Cancer Institute as a Research Associate.
  • In1978, he returned to Barnes Hospital to become Senior Assistant Resident and then Chief Medical Resident at Washington University Medical Service.
  •  In 1981 he completed a fellowship in medicine (Gastroenterology) at Washington University School of Medicine.
  • Asst. Prof. (1981–1984), Assoc. Prof. (1985–1987), Prof. (1987–1991) Medicine and Biological Chemistry at Washington University
  •  In 1991, he became head of the Dept. Molecular Biology & Pharmacology (1991–2004).
  •  2004-present: Gordon is currently the Director of the Center for Genome Sciences at Washington University.

Present Research

  • The mutualistic interactions between humans and 10-100 trillion microbes that colonize each person’s gastrointestinal tract.
  • They employ germ-free and gnotobiotic mice as model hosts, which may be colonized with defined, simplified microbial communities. These model intestinal microbiotas are more amenable to well-controlled experimentation.
  • Jeffrey Gordon has become an international pioneer in studying gut microbial ecology and evolution, using innovative methods to interpret metagenomic and gut microbial genomic sequencing data.
  • The gut microbiota plays a role in host fat storage and obesity. 
  • Gordon and co-workers have used DNA pyrosequencing technology to perform metagenomics on the intestinal contents of obese mice, demonstrating that the gut microbiota of fat mice possess an increased capacity for helping the host in harvesting energy from the diet.A study of the microbial ecology of obese human subjects on two different weight loss diets indicate that the same principles may be operating in humans.
  • His group has applied the sequencing of bacterial and archaeal genomes to describe the microbial functional genomic and metabolomic underpinnings of microbial adaptation to the gastrointestinal habitat.This approach has been extended to describe the role of the adaptive immune system in maintaining the host-microbial relationship.

Dr. Gordon is the lead author of an influential 2005 National Human Genome Research Institute white-paper entitled “Extending Our View of Self: the Human Gut Microbiome Initiative (HGMI)”. In 2007 the Human Microbiome Project was listed on the NIH Roadmap for Medical Research as one of the New Pathways to Discovery.

  • His noticeable remark is: "We think that there are 10 times more microbial cells on and in our bodies than there are human cells. That means that we're 90 percent microbial and 10 percent human. There's also an estimated 100 times more microbial genes than the genes in our human genome. So we're really a compendium [and] an amalgamation of human and microbial parts.", though Scientific American points out that this refers only to the number of cells, not to the absolute weight or space occupied.

Selected Honors Received

  • Alpha Omega Alpha (1973)
  • John A. and George L. Hartford Foundation Fellowship (1981-1984)
  • Established Investigator, American Heart Association (1985-1990)
  • Young Investigator Award, American Federation for Clinical Research (1990)
  • Young Scientist Award, National Institute of Diabetes and Digestive and Kidney Diseases (1990)
  • Distinguished Achievement Award, American Gastroenterological Association (AGA) (1992)
  • Fellow, American Association for the Advancement of Science (1992)
  • MERIT Award, NIDDK (DK30292, Regulation of Gene Expression in the Intestine) (1993)
  • Marion Merrell Dow Distinguished Prize in Gastrointestinal Physiology, American Physiological Society (1994)
  • Fellow, American Academy of Microbiology (2001)
  • Elected, National Academy of Sciences (2001)
  • Janssen/AGA Sustained Achievement Award in Digestive Sciences (2003)
  • Senior Scholar Award in Global Infectious Diseases, Ellison Medical Foundation (2003)
  • Elected, American Academy of Arts & Sciences (2004)
  • ASM Lecturer, 105th Annual Meeting, American Society of Microbiology (2005)
  • MERIT Award, NIDDK (DK30292 – Genomic and Metabolic Foundations of Human-Microbial Symbiosis in the Gut, 2006; second MERIT award for grant)
  • Distinguished Service Award, The University of Chicago (2008)
  • Harvey Society Lecturer (2008)
  • Elected, Institute of Medicine of the National Academies (2008)
  • Chair, Section 42 (Medical Physiology and Metabolism), National Academy of Sciences (2010-2013)
  • Distinguished Scientist Award, NIDDK, NIH (2010)
  • Danone International Prize for Nutrition (2011)
  • Honorary Doctorate, University of Gothenburg (2011)
  • Association of American Medical Colleges (AAMC) Award for Distinguished Research in the Biomedical Sciences (2012)
  • Selman A. Waksman Award in Microbiology, National Academy of Sciences (2013)
  • Robert Koch Award (2013).

Awards from Washington University

and St. Louis area institutions

  • Outstanding Faculty Mentor Award, Graduate Student Council, Washington University (2000, first recipient of this annual award)
  • Second Century Award, Washington University School of Medicine (2005)
  • Carl and Gerty Cori Faculty Achievement Award Washington University (2009)
  • Founder’s Day Distinguished Faculty Award, Washington University (2011)
  • Peter H. Raven Lifetime Achievement Award, Academy of Science, St. Louis (2012)
  • Danforth Science Award, Donald Danforth Plant Science Center (2012)


  • Hooper, L.V., Wong, M.H., Thelin, A., Hansson, L., Falk, P.G, and Gordon, J.I. Molecular analysis of commensal host-microbial relationships in the intestine.Science 291: 881-884 (2001).
  • Xu, J., Bjursell, M.K., Himrod, J., Deng, S. Carmichael, L.K., Chiang, H.C., Hooper, L.V., and Gordon, J.I.  A genomic view of the human-Bacteroidesthetaiotaomicronsymbiosis. Science,299:2074-2076 (2003).
  • Hooper, L.V., Stappenbeck, T.S., Hong, C.V., Gordon, J.I. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nature Immunol.4: 269-273 (2003).
  • Bäckhed, F., Ding, H., Wang, T., Hooper, L.V., Koh, G. Y., Nagy, A., Semenkovich, C.F. Gordon, J. I.  The gut microbiota as an environmental factor that regulates fat storage. Proc NatlAcadSci USA101:15718-15723 (2004).
  • Sonnenburg, J.L., Xu, J., Leip, D.D., Chen, C.H., Westover, B. P., Weatherford, J., Buhler, J.D., Gordon, J.I.  Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science307:1955-1959 (2005).
  • Rawls, J.F., Mahowald, M.A., Ley, R.E., Gordon, J.I. Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127:423-33 (2006).
  • Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. Microbial ecology: human gut microbes associated with obesity. Nature444: 1022-1023 (2006). 
  • Turnbaugh, P.J., Ley, R.E., Mahowald, M.A., Magrini, V., Mardis, E.R. and Gordon, J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006; 444:1027-1031 (2006).
  • Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., and Gordon, J.I. Evolution of mammals and their gut microbes. Science320:1647-1651 (2008). 


  • Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B., Duncan, A., Ley, R.E., Sogin, M.L., Jones, J., Roe, B.A., Affourtit, J.P., Egholm, M., Henrissat, B., Heath, A.C., Knight, R. and Gordon J.I. A core gut microbiome in obese and lean twins.Nature457:480-484 (2009).
  • Reyes, A., Haynes, M., Hanson, N., Angly, F., Heath, A., Rohwer, F., and Gordon, J.I. Viruses in the fecal microbiota of monozygotic twins and their mothers.  Nature466: 334-338(2010).
  • McNulty, N, Yatsunenko, T, Hsiao, A., Faith, J., Muegge, B., Goodman, A., Henrissat, B., Oozeer, R., Cools, Portier, S., Gobert, G., Chervaux, C., Knights, D., Lozupone, C., Knight, R., Duncan, A.E., Bain, J.R., Muehlbauer, M.J., Newgard, C.B., Heath, A.C., and Gordon, J.I. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Science Translational Medicine3: 106ra106, (2011).
  • Muegge, B., Kuczynski, J., Knights, D., Clemente, J.C., Gonzalez, A., Fontana, L., Henrissat, L., Knight, R., and Gordon, J.I., Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science332: 970-974 (2011).
  • Faith, J.J., McNulty, N.P., Rey, F.E., and Gordon, J.I. Predicting a human gut microbiota’s response to diet in gnotobiotic mice. Science333: 101-104 (2011).
  • Goodman, A.L., Kallstrom, G., Faith, J.J., Reyes, A., Moore, A., Dantas, G., and Gordon, J.I. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic miceProc. Natl. Acad. Sci USA108: 6252-625 (2011).
  • Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., Heath, A.C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J.G., Lozupone, C.A., Lauber, C., Clemente, J.C., Knights, D., Knight, R., and Gordon, J.I. Human gut microbiome viewed across age and geography.  Nature486: 222-227 (2012).
  • Smith, M.I., Yatsunenko, T., Manary, M.J., Trehan, I., Mkakosya, R., Cheng, J., Kau, A., Rich, S.S., Concannon, P., Mychaleckyj, J.C., Liu, J., Houpt, E., Li, J.V., Holmes, E., Nicholson, J., Knights, D., Ursell, L.K., Knight, R., and Gordon, J.I. Gut microbiomes of Malawian twin pairs discordant for kwashiorkor. Science,339: 548-554 (2013).

Annu Rev Nutr. 2002 Apr 4.

How host-microbial interactions shape the nutrient environment of the mammalian intestine.

Humans and other mammals are colonized by a vast, complex, and dynamic consortium of microorganisms. One evolutionary driving force for maintaining this metabolically active microbial society is to salvage energy from nutrients, particularly carbohydrates, that are otherwise nondigestible by the host. Much of our understanding of the molecular mechanisms by which members of the intestinal microbiota degrade complex polysaccharides comes from studies of Bacteroidesthetaiotaomicron, a prominent and genetically manipulatable component of the normal human and mouse gut. Colonization of germ-free mice with B. thetaiotaomicron has shown how this anaerobe modifies many aspects of intestinal cellular differentiation/gene expression to benefit both host and microbe. These and other studies underscore the importance of understanding precisely how nutrient metabolism serves to establish and sustain symbiotic relationships between mammals and their bacterial partners.


Mammals absorb simple sugars, such as glucose and galactose, via active transport in the proximal regions of their small intestine. However, they have limited intrinsic capacity to digest dietary polysaccharides.

  • Undigested polysaccharides such as cellulose, xylan, and undigested starch, as well as host-derived glycans (mucins and glycosphingolipids) pass into the distal regions of the small intestine (ileum) and colon where they are degraded by resident microbes.
  • Bacteria ferment the resulting monosaccharides, and the byproducts of this fermentation (short chain fatty acids) are absorbed and utilized by the host.

Overview of host and bacterial contributions to carbohydrate utilization in the intestine.


Monosaccharides released from carbohydrate polymers are converted in the bacterial cytoplasm to pyruvate via glycolysis, which results in net production of ATP.

  • In the highly anaerobic environment of the distal intestine, additional carbon and energy is extracted from pyruvate by microbial fermentation. The predominant end-products of fermentation are acetate, propionate, and butyrate.
  • To recover some of the nutritional value of polysaccharides degraded by gut microbes, mammalian hosts absorb and utilize these short chain fatty acid species.

Overview of bacterial fermentation in the intestine.


Proc NatlAcadSci U S A 2002 Nov 13.

Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells.

The adult mouse intestine contains an intricate vascular network. The factors that control development of this network are poorly understood. Quantitative three-dimensional imaging studies revealed that a plexus of branched interconnected vessels developed in small intestinal villi during the period of postnatal development that coincides with assembly of a complex society of indigenous gut microorganisms (microbiota). To investigate the impact of this environmental transition on vascular development, we compared the capillary networks of germ-free mice with those of ex-germ-free animals colonized during or after completion of postnatal gut development. Adult germ-free mice had arrested capillary network formation. The developmental program can be restarted and completed within 10 days after colonization with a complete microbiota harvested from conventionally raised mice, or with Bacteroidesthetaiotaomicron, a prominent inhabitant of the normal mouse/human gut. Paneth cells in the intestinal epithelium secrete antibacterial peptides that affect luminal microbial ecology. Comparisons of germ-free and B. thetaiotaomicron-colonized transgenic mice lacking Paneth cells established that microbial regulation of angiogenesis depends on this lineage. These findings reveal a previously unappreciated mechanism of postnatal animal development, where microbes colonizing a mucosal surface are assigned responsibility for regulating elaboration of the underlying microvasculature by signaling through a bacteria-sensing epithelial cell.


Rapid microbial induction of angiogenesis in small intestinal villi of adult ex-germ-free mice.(A) Germ-free (GF) mouse. (B) Age-matched ex-germ-free conventionalized (CONV) mouse killed 10 days after colonization with an unfractionatedmicrobiota harvested from a conventionally raised “donor.” (C) Ex-germ-free mouse 10 days after colonization with B. thetaiotaomicron (B. theta) alone. 

Paneth cell and microbial regulation of angiogenesis. (A–D) Confocal scans of 120-μm-thick cryosections showing the upper thirds of villi. (A) Germ-free, Paneth cell-deficient P28 male CR2-tox176 mouse. (B) Age- and gender-matched, germ-free, Paneth-cell-containing normal littermate. (C) Ex-germ-free P28 CR2-tox176 mouse examined 7 days after colonization with B. thetaiotaomicron. (D) P28 nontransgenic mouse killed 7 days after mono-association with B. thetaiotaomicron.


Science.2003 Mar 28

A genomic view of the human-Bacteroidesthetaiotaomicron symbiosis.

The human gut is colonized with a vast community of indigenous microorganisms that help shape our biology. Here, we present the complete genome sequence of the Gram-negative anaerobe Bacteroidesthetaiotaomicron, a dominant member of our normal distal intestinal microbiota. Its 4779-member proteome includes an elaborate apparatus for acquiring and hydrolyzing otherwise indigestible dietary polysaccharides and an associated environment-sensing system consisting of a large repertoire of extracytoplasmic function sigma factors and one- and two-component signal transduction systems. These and other expanded paralogous groups shed light on the molecular mechanisms underlying symbiotic host-bacterial relationships in our intestine.


Trends Microbiol. 2003 Apr

Commensal bacteria make a difference.

The importance of the gut microbiota has been recognized since the days of Pasteur. What makes today different from yesterday, and tomorrow so exciting, is that we now have the tools to identify the molecular mechanisms that regulate assembly of the microbiota and determine how its components affect postnatal mammalian development and adult physiology.


Proc NatlAcadSci U S A. 2004 Mar 30

Gnotobioticzebrafish reveal evolutionarily conserved responses to the gut microbiota.

Animals have developed the means for supporting complex and dynamic consortia of microorganisms during their life cycle. A transcendent view of vertebrate biology therefore requires an understanding of the contributions of these indigenous microbial communities to host development and adult physiology. These contributions are most obvious in the gut, where studies of gnotobiotic mice have disclosed that the microbiota affects a wide range of biological processes, including nutrient processing and absorption, development of the mucosal immune system, angiogenesis, and epithelial renewal. The zebrafish(Daniorerio) provides an opportunity to investigate the molecular mechanisms underlying these interactions through genetic and chemical screens that take advantage of its transparency during larval and juvenile stages. Therefore, we developed methods for producing and rearing germ-free zebrafish through late juvenile stages. DNA microarray comparisons of gene expression in the digestive tracts of 6 days post fertilization germ-free, conventionalized, and conventionally raised zebrafish revealed 212 genes regulated by the microbiota, and 59 responses that are conserved in the mouse intestine, including those involved in stimulation of epithelial proliferation, promotion of nutrient metabolism, and innate immune responses. The microbial ecology of the digestive tracts of conventionally raised and conventionalized zebrafish was characterized by sequencing libraries of bacterial 16S rDNAamplicons. Colonization of germ-free zebrafish with individual members of its microbiota revealed the bacterial species specificity of selected host responses. Together, these studies establish gnotobioticzebrafish as a useful model for dissecting the molecular foundations of host-microbial interactions in the vertebrate digestive tract.


Nat Immunol. 2004 Jun

Getting a grip on things: how do communities of bacterial symbionts become established in our intestine?

The gut contains our largest collection of resident microorganisms. One obvious question is how microbial communities establish and maintain themselves within a perfused intestine. The answers, which may come in part from observations made by environmental engineers and glycobiologists, have important implications for immunologists who wish to understand how indigenous microbial communities are accommodated. Here we propose that the mucus gel layer overlying the intestinal epithelium is a key contributor to the structural and functional stability of this microbiota and its tolerance by the host.


The fingerlike projections are villi. Most of the mucus gel layer that normally overlies the villus epithelium has been lost during sample processing; arrows indicate remnants. Scale bar, 100 μm.

By analogy to anaerobic upflow bioreactors that lack static carrier material, biofilm formation and retention of autochthonous components of the microbiota is made possible in part by use of mucus as a key element in the selfimmobilization process.

(i) Poorly settling materials (undigested food particles, planktonic bacteria) are rapidly washed out.

(ii) Dense aggregates are formed by microbes themselves, undigested food, shed elements of the mucus gel and/or exfoliated epithelial cells. Aggregates serve as a scaffold for assembling microbial consortia, may be further transformed through microbial or mechanical processing and may have dynamic interactions with other granules and/or with the mucus gel layer.

(iii) Aggregates and mucus promote nutrient harvest and metabolic exchange. Outer membrane polysaccharide-binding proteins may facilitate attachment of some species, such as members of Bacteroides, to mucus glycans. These interactions can be regulated by ‘scaffolding factors’, such as host or microbial lectins, and host IgA. Regional variation in the glycan composition and thickness of the mucus biofilm could serve as a ‘molecular zip code’ that helps promote niche-specific interactions and nutrient harvest.

View of the distal small intestine of a mouse

by scanning electron microscopy.

Proposed mechanism for microbial retention in the gut.


Proc NatlAcadSci U S A. 2004 Nov 2

The gut microbiota as an environmental factor that regulates fat storage.

New therapeutic targets for noncognitive reductions in energy intake, absorption, or storage are crucial given the worldwide epidemic of obesity. The gut microbial community (microbiota) is essential for processing dietary polysaccharides. We found that conventionalization of adult germ-free (GF) C57BL/6 mice with a normal microbiota harvested from the distal intestine (cecum) of conventionally raised animals produces a 60% increase in body fat content and insulin resistance within 14 days despite reduced food intake. Studies of GF and conventionalized mice revealed that the microbiota promotes absorption of monosaccharides from the gut lumen, with resulting induction of de novo hepatic lipogenesis. Fasting-induced adipocyte factor (Fiaf), a member of the angiopoietin-like family of proteins, is selectively suppressed in the intestinal epithelium of normal mice by conventionalization. Analysis of GF and conventionalized, normal and Fiaf knockout mice established that Fiaf is a circulating lipoprotein lipase inhibitor and that its suppression is essential for the microbiota-induced deposition of triglycerides in adipocytes. Studies of Rag1-/- animals indicate that these host responses do not require mature lymphocytes. Our findings suggest that the gut microbiota is an important environmental factor that affects energy harvest from the diet and energy storage in the host.


Schematic view of how the gut microbiota effects host fat storage. The microbiota acts through Fiaf(Fasting-induced adipocyte factor) to coordinate increased hepatic lipogenesis with increased LPL (Lipoprotein lipase) activity in adipocytes, thereby promoting storage of calories harvested from the diet into fat.


Science. 2005 Mar 25

Host-bacterial mutualism in the human intestine.

The distal human intestine represents an anaerobic bioreactor programmed with an enormous population of bacteria, dominated by relatively few divisions that are highly diverse at the strain/subspecies level. This microbiota and its collective genomes (microbiome) provide us with genetic and metabolic attributes we have not been required to evolve on our own, including the ability to harvest otherwise inaccessible nutrients. New studies are revealing how the gut microbiota has coevolved with us and how it manipulates and complements our biology in ways that are mutually beneficial. We are also starting to understand how certain keystone members of the microbiota operate to maintain the stability and functional adaptability of this microbial organ.


Representation of the diversity of bacteria in the human intestine.

Phylogenetic tree of the domain bacteria based on 8903 representative 16S rRNA gene sequences. Wedges represent divisions: Those numerically abundant in the human gut are red, rare divisions are green, and undetected are black. Wedge length is a measure of evolutionary distance from the common ancestor.


Science. 2005 Mar 25

Glycan foraging in vivo by an intestine-adapted bacterial symbiont.

Germ-free mice were maintained on polysaccharide-rich or simple-sugar diets and colonized for 10 days with an organism also found in human guts, Bacteroidesthetaiotaomicron, followed by whole-genome transcriptional profiling of bacteria and mass spectrometry of cecalglycans. We found that these bacteria assembled on food particles and mucus, selectively induced outer-membrane polysaccharide-binding proteins and glycoside hydrolases, prioritized the consumption of liberated hexose sugars, and revealed a capacity to turn to host mucus glycans when polysaccharides were absent from the diet. This flexible foraging behavior should contribute to ecosystem stability and functional diversity.


Proc NatlAcadSci U S A. 2005 Aug 2

Obesity alters gut microbial ecology.

We have analyzed 5,088 bacterial 16S rRNA gene sequences from the distal intestinal (cecal) microbiota of genetically obese ob/ob mice, lean ob/+ and wild-type siblings, and their ob/+ mothers, all fed the same polysaccharide-rich diet. Although the majority of mouse gut species are unique, the mouse and human microbiota(s) are similar at the division (superkingdom) level, with Firmicutes and Bacteroidetes dominating. Microbial-community composition is inherited from mothers. However, compared with lean mice and regardless of kinship, ob/ob animals have a 50% reduction in the abundance of Bacteroidetes and a proportional increase in Firmicutes. These changes, which are division-wide, indicate that, in this model, obesity affects the diversity of the gut microbiotaand suggest that intentional manipulation of community structure may be useful for regulating energy balance in obese individuals.


Cell. 2006 Feb 24

Ecological and evolutionary forces shaping microbial diversity in the human intestine.

The human gut is populated with as many as 100 trillion cells, whose collective genome, the microbiome, is a reflection of evolutionary selection pressures acting at the level of the host and at the level of the microbial cell. The ecological rules that govern the shape of microbial diversity in the gut apply to mutualists and pathogens alike.


Selection pressure on host results in group selection of a microbial community



Operating at Different Levels in the Human-Microbial Hierarchy Brown arrows indicate selection pressures and point to the unit under selection (red). Black arrows indicate emergent properties of one level that affect higher levels in the hierarchy.

According to hierarchy theory, higher levels place constraints on possible organizational solutions at lower levels. Ecologic principles predict that host-driven (‘‘topdown’’) selection for functional redundancy would result in a community composed of widely divergent microbial lineages (divisions) whose genomes contain functionally similar suites of genes. Another prediction is the widespread occurrence of, and abundant mechanisms for, lateral gene transfer. In contrast, competition between members of the microbiota would exert ‘‘bottom-up’’ selection pressure that results in specialized genomes with functionally distinct suites of genes (metabolic traits). Once established, these lineage-specific traits can be maintained by barriers to homologous recombination.

Host immune system

and inter-microbial dynamics select for specific microbes

Emergent properties of community influence host fitness

Phenotypes of cells influences emergent properties of community

Selection of cell phenotype results in selection of specific genomes

Whole genome interactions, such as regulation of gene expression, influence phenotype of cells

Selection of genome results in fixation or loss of individual genes

Gene content influences genome-level functions

Schematic Diagram of the Selection Pressures


Percent representation of divisions in each environment.

Variation in Bacterial Diversity within the Colonic Microbiotas of Three Healthy Humans.

These phylogenetic trees are based on the 16S rRNA bacterial sequence data set (n = 11,831) and alignmen.


Science. 2006 Jun 2

Metagenomic analysis of the human distal gut microbiome.

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 approximately 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.


Proc NatlAcadSci U S A. 2006 Jun 27

A humanized gnotobiotic mouse model of host-archaeal-bacterial mutualism.

Our colons harbor trillions of microbes including a prominent archaeon, Methanobrevibactersmithii. To examine the contributions of Archaea to digestive health, we colonized germ-free mice with Bacteroidesthetaiotaomicron, an adaptive bacterial forager of the polysaccharides that we consume, with or without M. smithii or the sulfate-reducing bacterium Desulfovibriopiger. Whole-genome transcriptional profiling of B. thetaiotaomicron, combined with mass spectrometry, revealed that, unlike D. piger, M. smithii directs B. thetaiotaomicron to focus on fermentation of dietary fructans to acetate, whereas B. thetaiotaomicron-derived formate is used by M. smithii for methanogenesis. B. thetaiotaomicron-M. smithiicocolonization produces a significant increase in host adiposity compared with monoassociated, or B. thetaiotaomicron-D. pigerbiassociated, animals. These findings demonstrate a link between this archaeon, prioritized bacterial utilization of polysaccharides commonly encountered in our modern diets, and host energy balance.


Cell. 2006 Oct 20

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection.

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.


Summary of shared and distinct bacterial divisions in the zebrafish, mouse, and human gut microbiota.

Comparison of Input and Output Communities following Reciprocal Transplantation of Gut Microbiotas in GnotobioticZebrafish and Mice

Bacterial divisions and their lineages detected in the zebrafish digestive tract, mouse cecum, and human colon.


Nature. 2006 Dec 21

Microbial ecology: human gut microbes associated with obesity.

Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.


Nature. 2006 Dec 21

An obesity-associated gut microbiome with increased capacity for energy harvest.

The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity.


Proc NatlAcadSci U S A. 2007 May 1

In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut.

Complex microbial communities reside within the intestines of humans and other vertebrates. Remarkably little is known about how these microbial consortia are established in various locations within the gut, how members of these consortia behave within their dynamic ecosystems, or what microbial factors mediate mutually beneficial host-microbial interactions. Using a gnotobioticzebrafish-Pseudomonas aeruginosa model, we show that the transparency of this vertebrate species, coupled with methods for raising these animals under germ-free conditions can be used to monitor microbial movement and localization within the intestine in vivo and in real time. Germ-free zebrafish colonized with isogenic P. aeruginosa strains containing deletions of genes related to motility and pathogenesis revealed that loss of flagellar function results in attenuation of evolutionarily conserved host innate immune responses but not conserved nutrient responses. These results demonstrate the utility of gnotobioticzebrafish in defining the behavior and localization of bacteria within the living vertebrate gut, identifying bacterial genes that affect these processes, and assessing the impact of these genes on host-microbial interactions.


Proc NatlAcadSci U S A. 2007 Jun 19

Genomic and metabolic adaptations of Methanobrevibactersmithii to the human gut.

The human gut is home to trillions of microbes, thousands of bacterial phylotypes, as well as hydrogen-consuming methanogenicarchaea. Studies in gnotobiotic mice indicate that Methanobrevibactersmithii, the dominant archaeon in the human gut ecosystem, affects the specificity and efficiency of bacterial digestion of dietary polysaccharides, thereby influencing host calorie harvest and adiposity. Metagenomic studies of the gut microbial communities of genetically obese mice and their lean littermates have shown that the former contain an enhanced representation of genes involved in polysaccharide degradation, possess more archaea, and exhibit a greater capacity to promote adiposity when transplanted into germ-free recipients. These findings have led to the hypothesis that M. smithii may be a therapeutic target for reducing energy harvest in obese humans. To explore this possibility, we have sequenced its 1,853,160-bp genome and compared it to other human gut-associated M. smithii strains and other Archaea. We have also examined M. smithii'stranscriptome and metabolome in gnotobiotic mice that do or do not harbor Bacteroidesthetaiotaomicron, a prominent saccharolytic bacterial member of our gut microbiota. Our results indicate that M. smithii is well equipped to persist in the distal intestine through (i) production of surface glycans resembling those found in the gut mucosa, (ii) regulated expression of adhesin-like proteins, (iii) consumption of a variety of fermentation products produced by saccharolytic bacteria, and (iv) effective competition for nitrogenous nutrient pools. These findings provide a framework for designing strategies to change the representation and/or properties of M. smithii in the human gut microbiota.


Nature. 2007 Oct 18

The human microbiome project.

A strategy to understand the microbial components of the human genetic and metabolic landscape and how they contribute to normal physiology and predisposition to disease.

The core is viewed as a set of shared genes found in a given habitat (e.g. gut, mouth, skin) in all humans. The core is surrounded by a set of variably represented genes: this variation could be influenced by a combination of factors.

The hazy line surrounding the core indicates the possibility that over the course of human ‘micro-evolution’ new genes may be added to the core microbiome while others may be lost.

The concept of a core human microbiome


Cell Host Microbe. 2008 Apr 17

Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome.

We have investigated the interrelationship between diet, gut microbial ecology, and energy balance using a mouse model of obesity produced by consumption of a prototypic Western diet. Diet-induced obesity (DIO) produced a bloom in a single uncultured clade within the Mollicutes class of the Firmicutes, which was diminished by subsequent dietary manipulations that limit weight gain. Microbiota transplantation from mice with DIO to lean germ-free recipients promoted greater fat deposition than transplants from lean donors. Metagenomic and biochemical analysis of the gut microbiome together with sequencing and metabolic reconstructions of a related human gut-associated Mollicute (Eubacteriumdolichum) revealed features that may provide a competitive advantage to members of the bloom in the Western diet nutrient milieu, including import and processing of simple sugars. Our study illustrates how combining comparative metagenomics with gnotobiotic mouse models and specific dietary manipulations can disclose the niches of previously uncharacterized members of the gut microbiota.


Science. 2008 Jun 20

Evolution of mammals and their gut microbes.

Mammals are metagenomic in that they are composed of not only their own gene complements but also those of all of their associated microbes. To understand the coevolution of the mammals and their indigenous microbial communities, we conducted a network-based analysis of bacterial 16S ribosomal RNA gene sequences from the fecal microbiota of humans and 59 other mammalian species living in two zoos and in the wild. The results indicate that host diet and phylogeny both influence bacterial diversity, which increases from carnivory to omnivory to herbivory; that bacterial communities codiversified with their hosts; and that the gut microbiota of humans living a modern life-style is typical of omnivorous primates.


Nat Rev Microbiol. 2008 Oct

Worlds within worlds: evolution of the vertebrate gut microbiota.

In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.


Proc NatlAcadSci U S A. 2008 Sep 30

The convergence of carbohydrate active gene repertoires in human gut microbes.

The extreme variation in gene content among phylogenetically related microorganisms suggests that gene acquisition, expansion, and loss are important evolutionary forces for adaptation to new environments. Accordingly, phylogenetically disparate organisms that share a habitat may converge in gene content as they adapt to confront shared challenges. This response should be especially pronounced for functional genes that are important for survival in a particular habitat. We illustrate this principle by showing that the repertoires of two different types of carbohydrate-active enzymes, glycoside hydrolases and glycosyltransferases, have converged in bacteria and archaea that live in the human gut and that this convergence is largely due to horizontal gene transfer rather than gene family expansion. We also identify gut microbes that may have more similar dietary niches in the human gut than would be expected based on phylogeny. The techniques used to obtain these results should be broadly applicable to understanding the functional genes and evolutionary processes important for adaptation in many environments and useful for interpreting the large number of reference microbial genome sequences being generated for the International Human Microbiome Project.


Nature. 2008 Oct 23

Innate immunity and intestinal microbiota in the development of Type 1 diabetes.

Type 1 diabetes (T1D) is a debilitating autoimmune disease that results from T-cell-mediated destruction of insulin-producing beta-cells. Its incidence has increased during the past several decades in developed countries, suggesting that changes in the environment (including the human microbial environment) may influence disease pathogenesis. The incidence of spontaneous T1D in non-obese diabetic (NOD) mice can be affected by the microbial environment in the animal housing facility or by exposure to microbial stimuli, such as injection with mycobacteria or various microbial products. Here we show that specific pathogen-free NOD mice lacking MyD88 protein (an adaptor for multiple innate immune receptors that recognize microbial stimuli) do not develop T1D. The effect is dependent on commensal microbes because germ-free MyD88-negative NOD mice develop robust diabetes, whereas colonization of these germ-free MyD88-negative NOD mice with a defined microbial consortium (representing bacterial phyla normally present in human gut) attenuates T1D. We also find that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD88-negative NOD donors attenuates T1D in germ-free NOD recipients. Together, these findings indicate that interaction of the intestinal microbes with the innate immune system is a critical epigenetic factor modifying T1D predisposition.


Proc NatlAcadSci U S A. 2008 Oct 28

Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41.

The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. The products of polysaccharide fermentation include short-chain fatty acids that are ligands for Gpr41, a G protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. To examine the contribution of Gpr41 to energy balance, we compared Gpr41-/- and Gpr41+/+ mice that were either conventionally-raised with a complete gut microbiota or were reared germ-free and then cocolonized as young adults with two prominent members of the human distal gut microbial community: the saccharolytic bacterium, Bacteroidesthetaiotaomicron and the methanogenicarchaeon, Methanobrevibactersmithii. Both conventionally-raised and gnotobiotic Gpr41-/- mice colonized with the model fermentative community are significantly leaner and weigh less than their WT (+/+) littermates, despite similar levels of chow consumption. These differences are not evident when germ-free WT and germ-free Gpr41 knockout animals are compared. Functional genomic, biochemical, and physiologic studies of germ-free and cocolonized Gpr41-/- and +/+ littermates disclosed that Gpr41-deficiency is associated with reduced expression of PYY, an enteroendocrine cell-derived hormone that normally inhibits gut motility, increased intestinal transit rate, and reduced harvest of energy (short-chain fatty acids) from the diet. These results reveal that Gpr41 is a regulator of host energy balance through effects that are dependent upon the gut microbiota.


Genome Biol. 2010

Direct sequencing of the human microbiome readily reveals community differences.

Culture-independent studies of human microbiotaby direct genomic sequencing reveal quite distinct differences among communities, indicating that improved sequencing capacity can be most wisely utilized to study more samples, rather than more sequences per sample.


Nature. 2012 May 9

Human gut microbiome viewed across age and geography.

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.


Differences in the fecal microbial communities of Malawians, Amerindians and residents of the USA at different ages(a)UniFrac distances (it is a method to calculate a distance measure between organismal communities using phylogenetic information, and is widely used in metagenomics.) between children and adults decrease with increasing age of children in each population. Each point shows an average distance between a child and all adults unrelated to that child but from the same country. Results are derived from bacterial V4-16S rRNA datasets.


Nature. 2012 Sep 13

Diversity, stability and resilience of the human gut microbiota.

Trillions of microbes inhabit the human intestine, forming a complex ecological community that influences normal physiology and susceptibility to disease through its collective metabolic activities and host interactions. Understanding the factors that underlie changes in the composition and function of the gut microbiota will aid in the design of therapies that target it. This goal is formidable. The gut microbiota is immensely diverse, varies between individuals and can fluctuate over time - especially during disease and early development. Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.


Genome Res. 2013 Oct

Meta-analyses of studies of the human microbiota.

Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ilealCrohn's disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.