The Human Microbiome 101

Jonathan A. Eisen@phylogenomics

University of California, Davis

Talk for #FOGM13

Friday, March 8, 13

The Human Microbiome 101

Jonathan A. Eisen@phylogenomics

University of California, Davis

Talk for #FOGM13

Friday, March 8, 13

Disclosures

• I am an advisor for uBiome.

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Gratuitous Genomics Plot

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Pubmed Hits for Microbiome

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Controls?

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Microbiome Elvis

Pubmed Hits for Microbiome, Elvis

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The Microbiome

• “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”

Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118

Friday, March 8, 13

The Microbiome

• “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”

Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118

Badomics Word?

Friday, March 8, 13

The Microbiome

• “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”

Lora Hooper and Jeff Gordon (Commensal Host-Bacterial Relationships in the Gut Science 11 May 2001: Vol. 292. no. 5519, pp. 1115 - 1118

Badomics Word?

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The Human Microbiome for Dummies

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The Human Microbiome 101

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• We are covered in a cloud of microbes

The Human Microbiome 101

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• We are covered in a cloud of microbes

• This “microbiome” likely is involved in many important human phenotypes

The Human Microbiome 101

Friday, March 8, 13

• We are covered in a cloud of microbes

• This “microbiome” LIKELY is involved in many important human phenotypes

The Human Microbiome 101

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• We are covered in a cloud of microbes

• This “microbiome” LIKELY is INVOLVED in many important human phenotypes

The Human Microbiome 101

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Chapter 1:Think Like and Ecologist

The Human Microbiome 101

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Chapter 2:Incredible Diversity in the Cloud

The Human Microbiome 101

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Studying Microbes

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Microscopy

Studying Microbes

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Culturing Microscopy

Studying Microbes

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Culturing Microscopy

CountCount

Studying Microbes

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<<<<

Culturing Microscopy

CountCount

Studying Microbes

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<<<<

Culturing Microscopy

CountCount

Solution?

Studying Microbes

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<<<<

Culturing Microscopy

CountCount

Solution?

DNA

Studying Microbes

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<<<<

Culturing Microscopy

CountCount

Solution?

DNA

Studying Microbes

rDNA PCR

metagenomics

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Culturing Microscopy

CountCount

Solution?

DNA

Studying Microbes

rDNA PCR

metagenomics

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Biogeography

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Censored

Censored

Human biogeography

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Skin

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Chapter 3:Variation, Variation, Variation

The Human Microbiome 101

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33Friday, March 8, 13

• Microbial community different in many disease states compared to healthy individuals

• Unclear if this is cause or effect in most cases

34Friday, March 8, 13

35Morgan et al. Genome Biology 2012 13:R79 doi:10.1186/gb-2012-13-9-r79

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36Morgan et al. Genome Biology 2012 13:R79 doi:10.1186/gb-2012-13-9-r79

Age Diet Location

Many disease states

ExposurePregant?

Breast fed? Obese

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Chapter 4:Don’t Oversell the Microbiome

The Human Microbiome 101

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Overselling the Microbiome

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Overselling the Microbiome

• Changes in gut bacteria protect against stroke

• Scientists look to mummies for obesity cure

• Good bacteria in the intestine prevent diabetes, study suggests.

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Overselling the Microbiome

• Correlation ≠ Causation• Complexity is astonishing

• 1000s of taxa• Each with intraspecific variation• Viruses, bacteria, archaea,

eukaryotes• Massive risk for false

positive associations

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Turnbaugh et al Nature. 2006 444(7122):1027-31.

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Chapter 5: Ecosystem Dynamics

The Human Microbiome 101

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Colonization

Koenig et al. Proc Natl Acad Sci U S A. 2011 108 Suppl 1:4578-85.

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Milk has Microbes ...

Friday, March 8, 13

The Built Environment

ORIGINAL ARTICLE

Architectural design influences the diversity andstructure of the built environment microbiome

Steven W Kembel1, Evan Jones1, Jeff Kline1,2, Dale Northcutt1,2, Jason Stenson1,2,Ann M Womack1, Brendan JM Bohannan1, G Z Brown1,2 and Jessica L Green1,3

1Biology and the Built Environment Center, Institute of Ecology and Evolution, Department ofBiology, University of Oregon, Eugene, OR, USA; 2Energy Studies in Buildings Laboratory,Department of Architecture, University of Oregon, Eugene, OR, USA and 3Santa Fe Institute,Santa Fe, NM, USA

Buildings are complex ecosystems that house trillions of microorganisms interacting with eachother, with humans and with their environment. Understanding the ecological and evolutionaryprocesses that determine the diversity and composition of the built environment microbiome—thecommunity of microorganisms that live indoors—is important for understanding the relationshipbetween building design, biodiversity and human health. In this study, we used high-throughputsequencing of the bacterial 16S rRNA gene to quantify relationships between building attributes andairborne bacterial communities at a health-care facility. We quantified airborne bacterial communitystructure and environmental conditions in patient rooms exposed to mechanical or windowventilation and in outdoor air. The phylogenetic diversity of airborne bacterial communities waslower indoors than outdoors, and mechanically ventilated rooms contained less diverse microbialcommunities than did window-ventilated rooms. Bacterial communities in indoor environmentscontained many taxa that are absent or rare outdoors, including taxa closely related to potentialhuman pathogens. Building attributes, specifically the source of ventilation air, airflow rates, relativehumidity and temperature, were correlated with the diversity and composition of indoor bacterialcommunities. The relative abundance of bacteria closely related to human pathogens was higherindoors than outdoors, and higher in rooms with lower airflow rates and lower relative humidity.The observed relationship between building design and airborne bacterial diversity suggests thatwe can manage indoor environments, altering through building design and operation the communityof microbial species that potentially colonize the human microbiome during our time indoors.The ISME Journal advance online publication, 26 January 2012; doi:10.1038/ismej.2011.211Subject Category: microbial population and community ecologyKeywords: aeromicrobiology; bacteria; built environment microbiome; community ecology; dispersal;environmental filtering

Introduction

Humans spend up to 90% of their lives indoors(Klepeis et al., 2001). Consequently, the way wedesign and operate the indoor environment has aprofound impact on our health (Guenther andVittori, 2008). One step toward better understandingof how building design impacts human healthis to study buildings as ecosystems. Built envi-ronments are complex ecosystems that containnumerous organisms including trillions of micro-organisms (Rintala et al., 2008; Tringe et al., 2008;Amend et al., 2010). The collection of microbiallife that exists indoors—the built environment

microbiome—includes human pathogens and com-mensals interacting with each other and with theirenvironment (Eames et al., 2009). There have beenfew attempts to comprehensively survey the builtenvironment microbiome (Rintala et al., 2008;Tringe et al., 2008; Amend et al., 2010), with moststudies focused on measures of total bioaerosolconcentrations or the abundance of culturable orpathogenic strains (Berglund et al., 1992; Toivolaet al., 2002; Mentese et al., 2009), rather than a morecomprehensive measure of microbial diversity inindoor spaces. For this reason, the factors thatdetermine the diversity and composition of the builtenvironment microbiome are poorly understood.However, the situation is changing. The develop-ment of culture-independent, high-throughputmolecular sequencing approaches has transformedthe study of microbial diversity in a variety ofenvironments, as demonstrated by the recent explo-sion of research on the microbial ecology of aquaticand terrestrial ecosystems (Nemergut et al., 2011)

Received 23 October 2011; revised 13 December 2011; accepted13 December 2011

Correspondence: SW Kembel, Biology and the Built EnvironmentCenter, Institute of Ecology and Evolution, Department of Biology,University of Oregon, Eugene, OR 97405, USA.E-mail: skembel@uoregon.edu

The ISME Journal (2012), 1–11& 2012 International Society for Microbial Ecology All rights reserved 1751-7362/12

www.nature.com/ismej

Microbial Biogeography of Public Restroom SurfacesGilberto E. Flores1, Scott T. Bates1, Dan Knights2, Christian L. Lauber1, Jesse Stombaugh3, Rob Knight3,4,

Noah Fierer1,5*

1 Cooperative Institute for Research in Environmental Science, University of Colorado, Boulder, Colorado, United States of America, 2 Department of Computer Science,

University of Colorado, Boulder, Colorado, United States of America, 3 Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, United

States of America, 4 Howard Hughes Medical Institute, University of Colorado, Boulder, Colorado, United States of America, 5 Department of Ecology and Evolutionary

Biology, University of Colorado, Boulder, Colorado, United States of America

Abstract

We spend the majority of our lives indoors where we are constantly exposed to bacteria residing on surfaces. However, thediversity of these surface-associated communities is largely unknown. We explored the biogeographical patterns exhibitedby bacteria across ten surfaces within each of twelve public restrooms. Using high-throughput barcoded pyrosequencing ofthe 16 S rRNA gene, we identified 19 bacterial phyla across all surfaces. Most sequences belonged to four phyla:Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria. The communities clustered into three general categories: thosefound on surfaces associated with toilets, those on the restroom floor, and those found on surfaces routinely touched withhands. On toilet surfaces, gut-associated taxa were more prevalent, suggesting fecal contamination of these surfaces. Floorsurfaces were the most diverse of all communities and contained several taxa commonly found in soils. Skin-associatedbacteria, especially the Propionibacteriaceae, dominated surfaces routinely touched with our hands. Certain taxa were morecommon in female than in male restrooms as vagina-associated Lactobacillaceae were widely distributed in femalerestrooms, likely from urine contamination. Use of the SourceTracker algorithm confirmed many of our taxonomicobservations as human skin was the primary source of bacteria on restroom surfaces. Overall, these results demonstrate thatrestroom surfaces host relatively diverse microbial communities dominated by human-associated bacteria with clearlinkages between communities on or in different body sites and those communities found on restroom surfaces. Moregenerally, this work is relevant to the public health field as we show that human-associated microbes are commonly foundon restroom surfaces suggesting that bacterial pathogens could readily be transmitted between individuals by the touchingof surfaces. Furthermore, we demonstrate that we can use high-throughput analyses of bacterial communities to determinesources of bacteria on indoor surfaces, an approach which could be used to track pathogen transmission and test theefficacy of hygiene practices.

Citation: Flores GE, Bates ST, Knights D, Lauber CL, Stombaugh J, et al. (2011) Microbial Biogeography of Public Restroom Surfaces. PLoS ONE 6(11): e28132.doi:10.1371/journal.pone.0028132

Editor: Mark R. Liles, Auburn University, United States of America

Received September 12, 2011; Accepted November 1, 2011; Published November 23, 2011

Copyright: ! 2011 Flores et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permitsunrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: This work was supported with funding from the Alfred P. Sloan Foundation and their Indoor Environment program, and in part by the NationalInstitutes of Health and the Howard Hughes Medical Institute. The funders had no role in study design, data collection and analysis, decision to publish, orpreparation of the manuscript.

Competing Interests: The authors have declared that no competing interests exist.

* E-mail: noah.fierer@colorado.edu

Introduction

More than ever, individuals across the globe spend a largeportion of their lives indoors, yet relatively little is known about themicrobial diversity of indoor environments. Of the studies thathave examined microorganisms associated with indoor environ-ments, most have relied upon cultivation-based techniques todetect organisms residing on a variety of household surfaces [1–5].Not surprisingly, these studies have identified surfaces in kitchensand restrooms as being hot spots of bacterial contamination.Because several pathogenic bacteria are known to survive onsurfaces for extended periods of time [6–8], these studies are ofobvious importance in preventing the spread of human disease.However, it is now widely recognized that the majority ofmicroorganisms cannot be readily cultivated [9] and thus, theoverall diversity of microorganisms associated with indoorenvironments remains largely unknown. Recent use of cultiva-tion-independent techniques based on cloning and sequencing ofthe 16 S rRNA gene have helped to better describe these

communities and revealed a greater diversity of bacteria onindoor surfaces than captured using cultivation-based techniques[10–13]. Most of the organisms identified in these studies arerelated to human commensals suggesting that the organisms arenot actively growing on the surfaces but rather were depositeddirectly (i.e. touching) or indirectly (e.g. shedding of skin cells) byhumans. Despite these efforts, we still have an incompleteunderstanding of bacterial communities associated with indoorenvironments because limitations of traditional 16 S rRNA genecloning and sequencing techniques have made replicate samplingand in-depth characterizations of the communities prohibitive.With the advent of high-throughput sequencing techniques, wecan now investigate indoor microbial communities at anunprecedented depth and begin to understand the relationshipbetween humans, microbes and the built environment.

In order to begin to comprehensively describe the microbialdiversity of indoor environments, we characterized the bacterialcommunities found on ten surfaces in twelve public restrooms(six male and six female) in Colorado, USA using barcoded

PLoS ONE | www.plosone.org 1 November 2011 | Volume 6 | Issue 11 | e28132

the stall in), they were likely dispersed manually after women usedthe toilet. Coupling these observations with those of thedistribution of gut-associated bacteria indicate that routine use oftoilets results in the dispersal of urine- and fecal-associated bacteriathroughout the restroom. While these results are not unexpected,they do highlight the importance of hand-hygiene when usingpublic restrooms since these surfaces could also be potentialvehicles for the transmission of human pathogens. Unfortunately,previous studies have documented that college students (who arelikely the most frequent users of the studied restrooms) are notalways the most diligent of hand-washers [42,43].

Results of SourceTracker analysis support the taxonomicpatterns highlighted above, indicating that human skin was theprimary source of bacteria on all public restroom surfacesexamined, while the human gut was an important source on oraround the toilet, and urine was an important source in women’srestrooms (Figure 4, Table S4). Contrary to expectations (seeabove), soil was not identified by the SourceTracker algorithm asbeing a major source of bacteria on any of the surfaces, includingfloors (Figure 4). Although the floor samples contained family-leveltaxa that are common in soil, the SourceTracker algorithmprobably underestimates the relative importance of sources, like

Figure 3. Cartoon illustrations of the relative abundance of discriminating taxa on public restroom surfaces. Light blue indicates lowabundance while dark blue indicates high abundance of taxa. (A) Although skin-associated taxa (Propionibacteriaceae, Corynebacteriaceae,Staphylococcaceae and Streptococcaceae) were abundant on all surfaces, they were relatively more abundant on surfaces routinely touched withhands. (B) Gut-associated taxa (Clostridiales, Clostridiales group XI, Ruminococcaceae, Lachnospiraceae, Prevotellaceae and Bacteroidaceae) were mostabundant on toilet surfaces. (C) Although soil-associated taxa (Rhodobacteraceae, Rhizobiales, Microbacteriaceae and Nocardioidaceae) were in lowabundance on all restroom surfaces, they were relatively more abundant on the floor of the restrooms we surveyed. Figure not drawn to scale.doi:10.1371/journal.pone.0028132.g003

Figure 4. Results of SourceTracker analysis showing the average contributions of different sources to the surface-associatedbacterial communities in twelve public restrooms. The ‘‘unknown’’ source is not shown but would bring the total of each sample up to 100%.doi:10.1371/journal.pone.0028132.g004

Bacteria of Public Restrooms

PLoS ONE | www.plosone.org 5 November 2011 | Volume 6 | Issue 11 | e28132

10 FEBRUARY 2012 VOL 335 SCIENCE www.sciencemag.org 650

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In just that short time, the microbes had begun to take on a “signature” of outside air (more types from plants and soil), and 2 hours after the windows were shut again, the proportion of microbes from the human body increased back to pre-vious levels.

The s tudy, which appeared online 26 Janu-ary in The ISME Journal, found that mechanically ventilated rooms had lower microbial diversity than ones with open win-dows. The availability of fresh air translated into lower proportions of microbes associ-ated with the human body, and consequently, fewer potential pathogens. Although this result suggests that having natural airfl ow may be healthier, Green says answering that question requires clinical data; she’s hoping to convince a hospital to participate in a study to see if the incidence of hospital-acquired infections is associated with a room’s micro-bial community.

For his part, Peccia, who is also a Sloan grantee, is merging microbiology and the

physics of aerosols to look more closely at how the movement of air affects microbes. Peccia says his group is building on work by air-quality engineers and scientists, but “we want to add biology to the equation.”

Bacteria in air behave like other particles; their size dictates how they disperse or settle. Humans in a room not only shed microbes from their skin and mouths, but they also drum up microbial material from the fl oor as

they move around. But to quantify those con-tributions, Peccia’s team has had to develop new methods to collect airborne bacteria and extract their DNA, as the microbes are much less abundant in air than on surfaces.

In one recent study, they used air fi lters to sample airborne particles and microbes in a classroom during 4 days during which students were present and 4 days during which the room was vacant. They measured the abundance and type of fungal and bac-terial genomes present and estimated the microbes’ concentrations in the entire room. By accounting for bacteria entering and leav-

ing the room through ventilation, they calculated that people shed or resuspended about 35 million bacterial cells per person per hour. That number is much higher than the several-hundred-thousand maximum previously estimated to be present in indoor air, Peccia reported last fall at the American Association for Aerosol Research Conference in Orlando, Florida.

His group’s data also suggest that rooms have “memories” of past human inhabitants. By kick-ing into the air settled microbes from the fl oor, occupants expose themselves not just to the microbes of a person coughing next to them, but also possibly to those from a person who coughed in the room a few hours or even days ago.

Peccia hopes to come up with ways to describe the distribution of bacteria indoors that can be used in conjunction with exist-ing knowledge about particulate matter and chemicals in designing healthier buildings. “My hope is that we can bring this enough to the forefront that people who do aerosol sci-ence will fi nd it as important to know biology as to know physics and chemistry,” he says.

Still, even though he’s a willing partici-

pant in indoor microbial ecology research, Peccia thinks that the field has yet to gel. And the Sloan Foundation’s Olsiewski shares some of his con-cern. “Everybody’s gen-erating vast amounts of

data,” she says, but looking across data sets can be diffi cult because groups choose dif-ferent analytical tools. With Sloan support, though, a data archive and integrated analyt-ical tools are in the works.

To foster collaborations between micro-biologists, architects, and building scientists, the foundation also sponsored a symposium on the microbiome of the built environment at the 2011 Indoor Air conference in Austin, Texas, and launched a Web site, MicroBE.net, that’s a clearinghouse of information on the fi eld. Although Olsiewski won’t say how long the foundation will fund its indoor microbial ecology program, she says Sloan is committed to supporting all of the current projects for the next few years. The program’s ultimate goal, she says, is to create a new fi eld of scientifi c inquiry that eventually will be funded by tradi-tional government funding agencies focused on basic biology and environmental policy.

Matthew Kane, a microbial ecologist and program director at the U.S. National Sci-ence Foundation (NSF), says that although there was interest in these questions prior to the Sloan program, the Sloan Foundation has taken a directed approach to funding the research, and “I have no doubt that their investment is going to reap great returns.” So far, though, NSF has funded only one study on indoor microbes: a study of Pseudomonas bacteria in human households.

As studies like Green’s building ecology analysis progress, they should shed light on how indoor environments differ from those traditionally studied by microbial ecologists. “It’s important to have a quantitative under-standing of how building design impacts microbial communities indoors, and how these communities impact human health,” Green says. But it remains to be seen whether we’ll someday design and maintain our build-ings with microbes in mind.

–COURTNEY HUMPHRIES

Courtney Humphries is a freelance writer in Boston and author of Superdove.

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Bathroom biogeography. By swabbing different surfaces in public restrooms, researchers determined that microbes vary in where they come from depend-ing on the surface (chart).

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Colonization gone wrong

Necrotizing enterocolitis

C-sections

Friday, March 8, 13

Disturbing our microbiome

Friday, March 8, 13

Restoring the Microbiome?

Friday, March 8, 13

Restoring the Microbiome

Friday, March 8, 13

Fecal transplants

Friday, March 8, 13

Chapter 6: We May Not Be In Charge

The Human Microbiome 101

Friday, March 8, 13

Vertebrate Microbiomes

Diverse microorganisms and microbial communities are a feature of modern life on the Earth, and have probably been necessary for the evolution of life as we know it1.

Microorganisms formed spatially organized communi-ties as early as 3.25 billion years ago, when some left their mark in the fossil record2. Today, microbial life is found in diverse communities all over the biosphere. The high level of novelty that is necessary for microorganisms to develop a diversity of cell lineages and inhabit a vast range of habitats probably required that whole com-munities exchange innovations1. Comparative studies of microbial communities are starting to reveal which environmental features, such as biogeography, salinity or redox potential, have important effects on the organiza-tion of microbial diversity3–6. These types of analyses are now being extended to the microbial communities that populate a globally ubiquitous but ephemeral habitat: the body surfaces of animals, including those of humans.

Multicellular eukaryotes have existed for at least one-quarter of the Earth’s history, or 1.2 billion years7. Thus, an already long history of interaction between multicel-lular life-forms and microbial communities preceded, and probably shaped, the evolution of vertebrates. The legacy of ancient associations between hosts and their epibiotic microbial communities is evident in the present-day effects that the gut microbiota exerts on host biology, which range from the structure and functions of the gut and the innate and adaptive immune systems, to

host energy metabolism8–11. Host responses to microbial colonization are evolutionarily conserved among diverse vertebrates, including zebrafish, mice and humans12. The underlying factors that dictate our interactions with our microbial partners therefore provide some of the foundations of our Homo sapiens genome.

If microbial communities are, and have always been, so intricately associated with their vertebrate hosts, then how specialized are body-associated microbial lineages to vertebrates and how distinct are they from those that populate the non-living environments of the biosphere? In this Analysis, we place our human gut microbiota in the context of many other diverse microbiotas, from our close relatives the primates, to more distantly related mammals, other metazoans and ‘free-living’ microbial communities. This evolutionary ecology perspective helps put the recently initiated international Human Microbiome Project (see Further information)13 in the context of the biosphere within which humans and their microorganisms have evolved.

Diet and the evolution of modern humansFood is central to the evolution of H. sapiens. During the first half of the evolution of our lineage, Australopithecus species split from prehistoric apes and persisted from ~4.4 Mya (million years ago) until ~2.5 Mya14. This early split has been associated with a dietary shift to seeds and soft fruits, based on comparisons of australopithecine

*Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA. ‡Department of Microbiology, Cornell University, Ithaca, New York 14850, USA. §Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA. ||Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA. ¶These authors contributed equally to this work. Correspondence to J.I.G. e-mail: jgordon@wustl.edu

MicrobiotaThe complete set of microbial lineages that live in a particular environment.

Worlds within worlds: evolution of the vertebrate gut microbiotaRuth E. Ley*‡¶, Catherine A. Lozupone*§¶, Micah Hamady||, Rob Knight§ and Jeffrey I. Gordon*

Abstract | 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.

776 | OCTOBER 2008 | VOLUME 6 www.nature.com/reviews/micro

ANALYSIS

Genera that cross the divide. Another way to visualize the vertebrate gut–environment dichotomy is by using a network diagram that displays, in addition to the clus-tering of hosts with similar microbiotas, the bacterial genera they share. In this representation of the data, the vertebrate gut samples are more connected to one another than to the environmental samples (FIG. 4a,b). As in the UniFrac-based analysis, the non-gut human samples also occupy an intermediate position between the free-living and the gut communities. FIGURE 5 shows the phylogenetic classification of operational taxonomic units (OTUs) that are shared between samples: among humans, an over-whelming number of these are from the Firmicutes, with a smaller number from the Bacteroidetes. By contrast, the free-living communities share OTUs from a wider range of phyla. Samples from the guts of obese humans cluster away from the samples of healthy subjects, and most of their shared OTUs are found in the Firmicutes. This obser-vation is consistent with the finding that samples from obese individuals have a higher number of OTUs from Firmicutes than samples from lean subjects31.

Bacterial genera that inhabit both the vertebrate gut-associated microbiotas and the free-living com-munities can be considered to be cosmopolitan. As the analyses discussed above mainly determine the dominant members of a microbiota, these genera are presumed to grow and subsist in the gut environment (autochthonous members) rather than simply passing through as transient members of the gut microbial community (allochthonous members). Among these cosmopolitan groups was the Pseudomonadaceae

family of the gammaproteobacteria class. This fam-ily contained OTUs from both the vertebrate gut and free-living communities in saline and non-saline habitats. Members of the Enterobacteriales order (also from the gammaproteobacteria) were detected in the vertebrate gut, termite gut and other invertebrates, as well as in a surface soil sample and anoxic saline water. Staphylococcaceae family members (from the phylum Firmicutes and class Bacilli) were common in the ver-tebrate gut samples, but were also detected in soil and cultures derived from freshwater and saline habitats. Finally, members of the Fusobacterium genus were detected in salt-water sediments, in addition to the vertebrate gut. The cosmopolitan distribution of these organisms might have made them particularly impor-tant for introducing novel functions during evolution of the gut microbiota, as they could bring new useful genes from the global microbiome into the gut microbiome through horizontal gene transfer. However, it should be noted that some OTUs that are common in humans

Nature Reviews | Microbiology

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Figure 3 | Relative abundance of phyla in samples. Bar graph showing the proportion of sequences from each sample that could be classified at the phylum level. The colour codes for the dominant Firmicutes and Bacteroidetes phyla are shown. For a complete description of the colour codes see Supplementary information S2 (figure). ‘Other humans’ refers to body habitats other than the gut; for example, the mouth, ear, skin, vagina and vulva (see Supplementary information S1 (table)).

Figure 4 | Network analysis of bacterial communities from animal-associated and free-living communities. The panel on the left includes a schematic key that illustrates features of the network analysis and genera keys for panels a and b. Labels are sample nodes. Rounded squares represent operational taxonomic units (OTUs) shared by two or more samples (shown in grey in panels a and b), whereas diamonds represent the set of OTUs that are unique to a sample. Network diagrams are colour coded according to habitat.

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ANALYSIS

782 | OCTOBER 2008 | VOLUME 6 www.nature.com/reviews/micro

ANALYSIS

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Human superorganism

• Human-microbe associations are very old• Microbial genes on a person >> human

genes• Your microbes are coadapted to each

other• Microbes known to manipulate

EVERYTHING imaginable in hosts

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Chapter 8: What Next

The Human Microbiome 101

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Quantified Self

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American Gut

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uBiome

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Personal Microbiomes

Personal Genomes

Personal Microbiomes

Family history ++ --

Disease risk ++ --

Treatment ++ --

Research ++ ++

Data returned ++ ++

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Last thoughts

• Microbiome counselors?• Who owns the microbiome?• Need 1000s of small studies• Conservation of the microbiome?• Openness is critical

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