nihms314237.pdf

Has the microbiota played a critical role in the evolution of the

adaptive immune system?

Yun Kyung Lee

and

Sarkis K. Mazmanian

Division of Biology, California Institute of Technology, Pasadena, California, 91125, USA

Abstract

Although microbes have been classically viewed as pathogens, it is now well established that the

majority of host-bacterial interactions are symbiotic. During development and into adulthood, gut

bacteria shape the tissues, cells and molecular profile of our gastrointestinal immune system. This

partnership, forged over many millennia of co-evolution, is based on a molecular exchange

involving bacterial signals that are recognized by host receptors to mediate beneficial outcomes

for both microbe and man. We explore herein how specific aspects of the adaptive immune system

are influenced by intestinal commensal bacteria. Understanding the molecular mechanisms which

mediate symbiosis between commensal bacteria and humans may redefine how we view the

evolution of adaptive immunity, and as a result, the way we approach treating numerous

immunologic disorders.

We are (fortunately) not alone- humans provide residence to numerous microbial

communities comprised of hundreds of individual bacterial species. Although teleological

design may predict that the immune system evolved to eliminate infectious microbes, we

now know that almost every environmentally exposed surface of our bodies is teeming with

symbiotic microbes (Fig. 1). These polymicrobial communities contribute profoundly to the

architecture and function of the tissues they inhabit, and thus play an important role in the

balance between health and disease. The notion that commensal microbes critically affect

tissue and cell development in humans can be rationalized when this process is viewed from

an evolutionary perspective. Bacteria populated the Earth 2 billion years before the first

signs of eukaryotic life, and occupy almost every terrestrial and aquatic niche on our planet.

Mitochondria and chloroplasts of eukaryotic cells are descended from bacteria, suggesting

that bacteria may have had an active role in the evolution of higher organisms. As

multicellular metazoans evolved more complex body plans, bacteria acquired the ability to

inhabit new anatomical niches. Animals represent a stable, nutrient rich ecosystem for

microbes to thrive; hence host health is paramount to the microbiota. In turn, the host

benefits from a diverse commensal microbiota which help digest complex carbohydrates and

provide essential nutrients to mammals. Symbionts are not the only microbes the host

encounters, however. An important challenge faced by the host immune system is

distinguishing between beneficial and pathogenic microbes, because both share similar

molecular patterns that are recognized by the innate immune system (such as

lipopolysaccharide, peptidogycan, lipoproteins, flagellin). Discrimination between specific

microbes may be a feature of the adaptive immune system, which can recognize discrete

molecular sequences and mount both pro- and anti-inflammatory responses depending on

the nature of the antigen. In particular, CD4

T cells are quite plastic and differentiate into

numerous subsets after development in the thymus, and thus are capable of sensing

environmental cues from the microbiota. As adaptive immunity evolved in higher

To whom correspondence should be addressed. sarkis@caltech.edu.

NIH Public Access

Author Manuscript

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Published in final edited form as:

Science

. 2010 December 24; 330(6012): 1768–1773. doi:10.1126/science.1195568.

NIH-PA Author Manuscript

vertebrates, the ability of this system to recognize and respond to specific microorganisms

may have been driven by evolutionary forces provided by the microbiota itself, resulting in

immune functions beyond simply clearing microbial pathogens (which in theory also helps

the microbiota by improving host health). Recent evidence shows that the commensal

microbiota ‘programs’ many aspects of T cell differentiation, thus augmenting the

developmental instructions of the host genome to engender the full function of the adaptive

immune system.

This article will review concepts derived from gnotobiology (Greek for ‘known life’;

‘gnosis’ meaning knowledge and ‘bios’ meaning life) to unravel how commensal bacteria

promote the development and function of adaptive immunity. In particular, we will explore

how CD4

T-helper cell subsets within the gastrointestinal and systemic immune system are

shaped (perhaps even controlled) by our microbiota, and theorize how and why gut bacteria

evolved to so profoundly influence immunologic wellbeing. Understanding human co-

evolution with our microbiota may lead to a philosophical and conceptual redefinition of the

microbial world, and provide clinical advances toward the treatment of autoimmunity and

inflammatory diseases by harnessing the immunomodulatory properties of human

commensal bacteria.

How Does the Microbiota Shape Host Immune Development and Function?

Although microbes reside in several anatomical locations including the skin, vagina and

mouth, the lower gastrointestinal tract of mammals harbors the greatest density and diversity

of commensal microorganisms. These include bacteria, archaea, fungi, viruses, protozoans

and in some cases, multicellular helminthes; however, bacteria predominate and reach 100

trillion microbial cells in the colon. Recent efforts to sequence the bacterial genomes of the

microbiota (known as the microbiome), have begun to reveal its genetic identity (1) and

suggest our microbiome contains over 150 times the number of non-redundant genes than in

the human genome (2). For decades, microbiological techniques to culture bacteria in the

laboratory have only identified cultivatable organisms, which represent a minority of the

microbial species of the gut. The aggregate human microbiota likely contains between

1,000–1,150 bacterial species (spread among all people sampled), with each person

harboring approximately 160 bacterial species (2). This suggests an individual’s microbiome

is relatively distinct in composition and adaptable to environmental changes and/or host

genetics.

Germ-free animals (born and raised in the absence of all microbes) provide important

insights into how the microbiota affects the host immune system. The development of gut-

associated lymphoid tissues (GALT), the first line of defense for the intestinal mucosa, is

defective in germ-free mice. Germ-free mice display fewer and smaller Peyer’s patches,

smaller and less cellular mesenteric lymph nodes (MLNs) and less cellular lamina propria of

the small intestine compared to animals with a microbiota (3–7). Besides developmental

defects in tissue formation, the cellular and molecular profile of the intestinal immune

system is also compromised in germ-free mice. In germ-free mice, intestinal epithelial cells

(IECs), which line the gut and form a physical barrier between luminal contents and the

immune system, exhibit reduced expression of toll-like receptors (TLRs) and major

histocompatibility molecule II (MHC II) (8–9), which are involved in pathogen sensing and

antigen presentation, respectively. Interspersed between epithelial cells is a specialized

population of T cells known as intra-epithelial lymphocytes (IELs). IELs from germ-free

mice are reduced in number, and their cytotoxicity is compromised (10–11). Microbial

colonization expands specific subsets of intestinal

γδ

T cells (12). Germ-free mice also have

reduced numbers of CD4

T cells in the lamina propria (13). The development of isolated

lymphoid follicles (ILFs), specialized intestinal structures made of mostly dendritic cells

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(DC) and B cell aggregates, is also dependent on the microbiota (14). Therefore, multiple

populations of intestinal immune cells require the microbiota for their development and their

function.

The absence of a microbiota also leads to several extra-intestinal defects, including reduced

numbers of CD4

T cells in the spleen, fewer and smaller germinal centers within the spleen

and reduced systemic antibody levels, which suggests that the microbiota are capable of

shaping systemic immunity (15–17). Beyond development, the microbiota also influences

functional aspects of intestinal and systemic immunity, including pathogen clearance. Germ-

free mice are more susceptible to infectious agents such as

Shigella flexneri

Bacillus

anthracis and Leishmania

(18). Peptidoglycan from the microbiota enhances neutrophil

cytotoxicity following systemic infections by

Streptococcus pneumoniae

and

Staphylococcus aureus

(19). During systemic challenge of mice with

Listeria

monocytogenes

, germ-free mice harbored an increased bacterial burden in the liver, spleen

and peritoneal cavity (20). Moreover, trafficking of T lymphocytes to the peritoneal cavity

in response to

Listeria

infection is impaired in germ-free mice.

The contributions of the microbiota to the development and function of the immune system

appear to be fundamental. A more robust immune system, equipped with a diverse arsenal of

cells and molecules, is better able to combat microbial pathogens and ultimately provides a

healthier residence for commensal bacteria. This view implies that host mechanisms and the

microbiota may have evolved to collaborate against infectious agents. Indeed, several

reports now show an antagonistic relationship between overt pathogens and the microbiota.

For example,

Salmonella

trigger intestinal inflammation, which reduces the numbers and

diversity of the microbiota, a process which promotes bacterial infection (21). Depletion of

the microbiota diminishes intestinal immune responses that help control enteric infections by

Citrobacter rodentium

and

Campylobacter jejuni

(22). Given the role of the microbiota in

immune system function, harnessing the immunomodulatory capabilities of the microbiota

may offer novel avenues for development of anti-microbial therapies for infectious disease.

How does the Microbiota Provide Signals to Instruct Peripheral Regulatory

T cell Differentiation?

Although many cell types are influenced by the microbiota, we will focus here on the

emerging role of the microbiota on effector CD4

T cell differentiation. After lineage

commitment in the thymus, naïve CD4

T cells enter the periphery where they sense

environmental signals that further instruct their maturation and function. During an

infection, microbial and host signals provide cues to naïve CD4

T cells to induce their

differentiation into various pro- and anti-inflammatory subsets. For instance, infection by

intracellular pathogens drives the development of T-helper 1 (Th1) cells, whereas

extracellular pathogens induce the differentiation of Th2 and Th17 subsets (23). These pro-

inflammatory cells coordinate many aspects of the innate and adaptive immune response to

clear microbial invaders. CD4

T cells can also adopt an anti-inflammatory phenotype.

Regulatory T cells (Tregs) control unwanted immune system activation and dampen

inflammation after microbial infection. Expression of the Treg cell-specific transcription

factor Foxp3 (forkhead box P3) induces regulatory phenotypes and functions by CD4

cells (24). Foxp3

T cells develop in the thymus shortly after birth, and deletion or depletion

of Foxp3

T cells leads to severe multi-organ lymphoproliferative disease and autoimmunity

(25). Besides the thymus-derived CD4

Foxp3

T cells (‘natural’ Tregs), various subsets of

Tregs can be generated in the gut from naïve T cells (‘inducible’ Tregs), some of which

produce the anti-inflammatory cytokine interleukin-10 (26). Moreover, intestinal bacteria

may be critically involved in the differentiation of some gut Treg subsets (29–31).

Accordingly, several commensal bacteria (e.g.,

Bifidobacteria infantis

Faecalibacterium

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prausnitzii

) have been shown to induce Foxp3+ Tregs and IL-10 production in the gut (32–

33).

Members of the genus

Bacteroides

are prominent in the mammalian gastrointestinal tract,

and are also potent stimulators of the mucosal immune system of mammals (34). The gut

microorganism

Bacteroides fragilis

has emerged as a model system for the study of

immune-bacterial symbiosis. During colonization of mice with

B. fragilis

, the bacterial

molecule Polysaccharide A (PSA) directs the cellular and physical development of the

immune system (16). Moreover,

B. fragilis

is able to prevent intestinal pathology in two

independent models of experimental colitis in a PSA-dependent manner (35). Furthermore,

in mouse models of experimental colitis, oral treatment of mice with purified PSA protects

against weight loss, decreases pro-inflammatory cytokine expression in the gut, and inhibits

lymphocyte infiltration that is associated with disease. The protective effects of PSA were

likely mediated by CD4

T cell production of IL-10 because CD4

T lymphocytes from

mesenteric lymph nodes of PSA treated mice produced elevated amounts of IL-10. IL-10-

deficient CD4

T cells abolished the protective effects of PSA in both colitis models. These

studies identify PSA as a beneficial microbial molecule, which suppresses inflammation-

driven host pathology.

No consensus has been reached about whether Foxp3

Treg cells in the intestinal tissues of

germ-free mice are defective (36–40); however, production of IL-10 is reduced within the

GALT of germ-free animals (13, 36, 41). Foxp3

Treg cells in the colon of germ-free mice

exhibit reduced IL-10 expression, and colonization of germ-free mice with PSA-producing

bacteria (but not PSA-deficient

B. fragilis

) restores IL-10 expression (42). PSA increases the

Foxp3 expression by Treg cells, and colonization of germ-free animals with

B. fragilis

augments the

in vitro

suppressive activity of Tregs in a PSA-dependent manner (42). PSA

protects and cures animals from experimental colitis by inducing Foxp3

Treg cells and

IL-10 production. These findings imply that optimal Foxp3

Treg cell differentiation in the

colon requires signals from the microbiota and the host genome. They also suggest specific

commensal bacteria may have evolved to promote Treg cell differentiation in the gut to

actively engender mucosal tolerance to the host. If validated in human disease, these

findings may lead to probiotic therapies for colitis based on microbial-driven Treg induction.

How does the Microbiota Instruct T-helper Cell Differentiation?

Although the microbiota has been shown to affect the Th1/Th2 balance in systemic immune

compartments (43), studies have not yet observed symbiotic microbial effects on Th1 or Th2

cells at mucosal surfaces. In contrast, Th17 cell development in the gut is specifically

impacted by commensal bacteria. Germ-free mice are deficient in the production of IL-17

from CD4

T cells (the hallmark cytokine of Th17 cells) of the small intestinal lamina

propria (39). Only a minor defect was noted for

γδ

T cells, which suggests that the lack of

Th17 cells was not due to an overall deficiency in immune activation, and that specific

features of the immune response are sensitive to the microbiota. One mechanism of

intestinal Th17 cell differentiation may be production of Adenosine 5

′

-triphosphate (ATP) in

the lamina propria by commensal bacteria, which drives the production of Th17-inducing

cytokines by resident lamina propria cells (45). Germ-free animals display a reduction in

fecal ATP amounts and treatment of mice with a non-hydrolysable ATP analogue increased

the number of gut Th17 cells (45).

Not all bacterial species of the microbiota are similar in their ability to promote non-

pathogenic T cell responses during normal colonization of animals. Of the numerous

bacterial phylotypes that comprise the normal microbiota of mice, only segmented

filamentous bacteria (SFBs) have been shown to direct intestinal T-helper cell development.

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A role for SFBs was identified by reconstituting germ-free mice with various subsets of

bacterial consortia and measuring cytokine production in gut mucosal tissues (41). SFBs,

which are known to tightly adhere to the intestinal mucosa (and to Peyer’s patches of the

ileum), induced the development of T-helper cells in the lamina propria and in cell

aggregates of Peyer’s patches. This activity was not found in even very complex groups of

bacteria tested if they were missing SFBs. In a contemporary report, a comparison of the

microbiota of mice that contained Th17 cells with mice deficient in these cell types

identified SFBs as being sufficient to restore Th17 cells to germ-free mice and

conventionally raised mice that lack Th17 cells (46). Gene expression analysis showed that

SFBs induce a spectrum of intestinal immune responses including production of cytokines

and chemokines, antimicrobial peptides, and serum amyloid A (SAA), which was shown

vitro

to support Th17 cell differentiation. SFB colonization protected animals from intestinal

infection with

Citrobacter rodentium

, a bacterial pathogen of animals that causes acute

intestinal inflammation similar to enteropathogenic

Escherichia coli

(EPEC) in humans.

Thus, commensal SFBs induce a tonic (or controlled) inflammatory response in the gut

through Th17 cell development that does not cause pathology and is protective against

infection with pathogenic bacteria. These new studies build on research done several

decades ago that SFBs promote germinal center development, mucosal IgA responses and

recruitment of intraepithelial lymphocytes (47–49). Collectively, it appears that only a

particular subset of bacteria from the gut microbiota directly influences Th17 immune

responses.

Are Non-infectious Human Diseases Influenced by the Microbiota?

Numerous autoimmune diseases result from dysregulation of the adaptive immune system.

The incidences of autoimmune diseases such as multiple sclerosis (MS), type 1 diabetes

(T1D) and rheumatoid arthritis (RA) are rapidly increasing in Western societies, suggesting

alterations in environment factors that regulate the adaptive immune system. As appreciation

for the immunomodulatory potentials of commensal bacteria have increased, we and others

have proposed that lifestyle changes have caused a fundamental alteration in our association

with the microbial world (50–51). Altered diets, widespread antibiotic use and other societal

factors in developed countries may result in an unnatural shift in the community

composition of a ‘healthy’ microbiota, leading to altered microbial colonization known as

dysbiosis. Whether dysbiosis causes any human disease is yet unproven (insights may come

from microbiome sequencing projects); however, evidence in mice suggests dysbiosis may

affect autoimmunity by altering the balance between toleragenic and inflammatory members

of the microbiota (Fig. 2). PSA from

B. fragilis

, previously shown to treat experimental

colitis in the gut, is also able to prevent and cure experimental autoimmune

encephalomyelitis (EAE; an animal model for multiple sclerosis) (52). Oral treatment of

animals with PSA reduced Th17 cell development and increased Treg numbers in the central

nervous system (CNS). Furthermore, germ-free animals display reduced Th17 cell numbers

in the spleen and spinal cords, and do not develop RA or EAE (inflammation in joints and

the CNS, respectively) (53–54). The inflammatory responses in both RA and EAE are

promoted by Th17 cells and prevented by Tregs, which suggests that the effects of gut

bacteria on the adaptive immune system likely extend beyond the gastrointestinal tract to

influence autoimmune diseases that are seemingly unrelated to microbial infections.

Why only specific commensal bacteria induce Th17 cell differentiation remains unclear.

Th17 responses are critical at mucosal surfaces to control infections by extracellular

pathogens. IL-17 production recruits neutrophils to the site of infection and induces

antimicrobial peptide expression and other mediators of immunity. If there is an

evolutionary rationale for the ability of SFBs to induce Th17 cell differentiation, one

interpretation is that they mediate a state of ‘controlled inflammation’, which prepares the

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gastrointestinal tract for an invading pathogen. SFBs are not overt pathogens and colonize

animals as symbionts, and thus Th17 induction may lead to more enhanced immune

responses that protect against acute infectious agents (such as

C. rodentium

). Besides this

beneficial outcome, it appears that SFB colonization also leads to adverse host effects. Th1

and Th17 cells of the adaptive immune system promote autoimmunity. As a result, microbes

which stimulate T-helper cell development may (inadvertently) also increase the inherent

immune reactivity of the host, potentially leading to host-destructive pathologies mediated

by the adaptive immune system. This notion is supported by a role for SFBs in promoting

RA and EAE during induced animal models, both of which involve Th17 cell inflammation

(53–54). The enhancement of RA and EAE by SFBs establishes that the microbiota can

adversely influence autoimmune disease outside the gut. Therefore, SFBs can colonize

healthy animals without causing illness; but when the host is immunocompromised or under

inflammatory conditions, SFBs can be detrimental. We propose that certain microbes, such

as SFBs, which can peacefully co-exist with a healthy host but still retain pathogenic

potential be termed ‘pathobionts’, to distinguish them from opportunistic pathogens which

are acquired from the environment and cause acute infections (55). Pathobionts may

represent organisms on the evolutionary continuum between an acute pathogen and

commensal, whose sustained relationships with the host induces the development of

additional layers of mucosal defense while promoting the unwanted side effect of

autoimmune disease. The significance of Th17 cell-inducing organisms such as SFBs to

animal models of autoimmunity remains to be further established, as caveats exist such as

the fact that animals from colonies devoid of SFBs can develop autoimmune disease. Also,

how the microbiota may contribute to human autoimmunity needs to be determined. SFB

colonization of animals, however, does provide a model system for testing concepts linking

specific gut bacteria to non-intestinal immune disorders. The identification of bacterial

molecules required for SFBs to induce Th17 cell responses may reveal why this particular

organism is capable of promoting the development of pro-inflammatory T cells.

Furthermore, studies that delineate the gene regulatory networks induced by SFB

colonization may enhance our understanding of the evolutionary forces that resulted in Th17

lineage development.

Autoimmune diseases such as MS, T1D and RA are associated with a spectrum of genetic

polymorphisms as shown by recent genome wide association studies. Given that

concordance rates for disease among monozygotic twins averages between 20–40%,

environmental factors are crucial for the manifestations of symptoms (56). We predict that

autoimmunity can result from the combination of an altered human genome

and

an altered

microbiome (Fig. 2). Patients with autoimmunity likely have a genetic landscape that

predisposes them to self-reactivity, and in some cases, certain gut bacteria may promote

disease by activating the adaptive immune system. Potential future treatments for

autoimmunity may include treatment of dysbiosis, because whereas the human genome is

static and intransigent to manipulation, the microbiome is conceivably more amenable to

therapeutic alterations. Understanding the molecular mechanisms of how symbiotic

microbes affect immune reactions to self antigens may provide insight into the causes, and

potential cures, for autoimmune diseases.

Did the Microbiota Influence the Evolution of Adaptive Immunity?

The adaptive immune system distinguishes between self and foreign antigens, and mounts

an appropriate response to clear invading pathogens by recognizing non-self molecules. The

microbiota presents a challenge to the adaptive immune system, because it contains an

enormous foreign antigenic burden, which must be either ignored or tolerated to maintain

health. One hypothesis for how this occurs is ‘immunologic ignorance’, whereby spatial

separation of bacteria from the immune system or down-modulation of innate immunity

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prevents overt inflammation (57). This notion is feasible, because the innate immune system

cannot distinguish pathogens from symbionts because both share similar molecular patterns

(such as TLR ligands). Rather than ignorance, tolerance could also be induced by the

microbiota, given the capacity of gut bacteria to induce Treg lineage differentiation.

Molecules produced by our microbiome may be considered ‘self’, because inflammatory

bowel disease (IBD) is thought to, in part, involve a loss of tolerance to antigens of the

microbiota. Therefore it appears that rather than ignore them, we may tolerate the microbiota

similar to antigens encoded by our own genome. This then raises the question of whether

symbiotic bacteria evolved mechanisms to suppress unwanted inflammation toward the

microbiota by actively inducing mucosal tolerance. Several studies now suggest this to be

the case (32–33, 42). The necessity for the microbiota to induce tolerance as a requirement

for colonization, if true, provides a rationale for why symbiotic bacteria may have

influenced critical aspects of the adaptive immune system throughout mammalian evolution.

Although T cells can adopt numerous effector cell fates (such as Th1, Th2, Th3, Th9, etc),

there are common mechanistic foundations to Th17 and Treg cell development.

Differentiation of both lineages are promoted by transforming growth factor

(TGF

);

Tregs require TGF

(and retinoic acid), whereas TGF

and IL-6 promote Th17 development

(23). The central transcription factors for Treg cells and Th17 cells (Foxp3 and ROR

respectively) are co-expressed in naïve CD4

T cells, physically interact with each other,

and differentially respond to cytokine stimulation to help determine lineage commitment

between Foxp3

Treg and Th17 differentiation (58). Furthermore, Th17 cells can develop

from Foxp3

Treg cell precursors (59). As mentioned above, germ-free animals show

decreased Th17 cell development in several anatomic locations (39, 45, 53–54) and re-

colonization with a microbiota (containing SFBs) promotes Th17 cells (46, 53–54). On the

basis of this knowledge, we propose a hypothetical model for how specific commensal

bacteria network with an evolving adaptive immune system (Fig. 3). Thymically-derived

Foxp3

Treg cells developed under the control of the evolutionary ancient molecule TGF

It is tempting to speculate that commensal microbes (for example

B. fragilis

) may have

‘learned’ to augment this process by further promoting differentiation of existing Treg cells

into expanded subsets, such as those producing IL-10 at mucosal surfaces. This expanded

Treg cell repertoire could have provided the host with a mechanism to tolerate foreign

antigens of the microbiota. Pathobionts such as SFBs may have further modified the

development of adaptive immunity by promoting the differentiation of Th17 cells, in part

from Foxp3

precursors. In support of this notion, IL-17 family members have only been

found in vertebrates (60). Other pro-inflammatory cytokines (IL-6, IL-21 and IL-1) along

with TGF

are required to induce IL-17 production, perhaps suggesting Th17 cells might be

a more recent invention than Treg cells. Perhaps the evolution of specific immune responses

was not mainly driven by pathogens (as is popular assumption), but instead by organisms

that developed more sustained relationships with the host such as commensals and

pathobionts. As these new symbiotic relationships were forged through host-microbial co-

evolution, novel additions to the immune system were introduced over millennia. Although

this hypothesis requires validation, Treg and Th17 cells provide a powerful means by which

mucosal surfaces can be protected from unwanted inflammatory responses to the microbiota

(by Treg cells) while still being capable of potently responding to microbial infections (with

Th17 cells).

B. fragilis

and SFBs represent model organisms that have been experimentally

validated to provide these functions; other microbes may possess similar activities.

Together, the coordination of Treg and Th17 responses appears ideally suited to benefit both

the microbiota and the host, and may represent an important evolutionary partnership for

human health.

Co-opting an antigen-specific adaptive immune system by the microbiota may extend

beyond simply a host-derived process for controlling microbial infections. During co-

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habitation with the microbiota, evolution of the vertebrate genome occurred under the

influence of signals from symbiotic bacteria. In fact, the evolutionary forces that contributed

to immune system development during lifelong microbial associations may be dominant

compared to those of transient encounters by microbial pathogens (which are rare and

opportunistic). Thus, symbiotic microbes may have influenced features of adaptive immune

system evolution and function more profoundly than pathogens, possibly to protect both host

and microbiota from invading infections. As an increasing body of knowledge links the

microbiota to Treg and Th17 phenotypes that mediate autoimmunity, it is imperative to

determine how signals from the microbiota shape gene regulatory networks by CD4

T cells

following their thymic development. If these co-evolutionary interactions are relatively

recent inventions, is autoimmunity an unwanted side effect from fine-tuning of the

peripheral adaptive immune system by the microbiota? As the influences of the microbiota

on autoimmune diseases are unraveled, it can be envisioned that harnessing the ability of the

microbiota to induce tolerance through Treg cells may provide novel treatments for

autoimmunity by correcting immunologic imbalances found in an evolving adaptive

immune system. Finally, as we harbor 10-fold more bacterial cells than human cells,

explorations into how the microbiota may have influenced the evolution of adaptive

immunity might redefine how we view our ‘microbial selves’.

Acknowledgments

We thank members of the Mazmanian laboratory for their critical review of the manuscript. Work in the laboratory

of the authors is supported by funding from the National Institutes of Health (DK078938, DK083633, AI088626),

Damon Runyon Cancer Research Foundation and the Crohn’s and Colitis Foundation of America to S.K.M.

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Fig. 1.

The microbiome of various anatomical location of the human body. Numerous bacterial

species colonize the mouth, upper airways, skin, vagina and intestinal tract of humans. The

phylogenic trees show the speciation of bacterial clades from common ancestors at each

anatomical site. Although the communities in different regions of the body share

similarities, they each have a unique site-specific ‘fingerprint’ made of many distinct

microbes. Each site has a very high level of diversity, as shown by the individual lines on

the dendograms. Data is from the NIH funded Human Microbiome Project, and circles

represent bacterial species whose sequences are known.

NOTE TO SCIENCE EDITORS: the

figure of the body was taken from GOOGLE images and the phylogenic trees were taken

from the Human Microbiome Project. Please address any copyright issues and/or redraw

figures.

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Fig. 2.

How the microbiome and the human genome contribute to inflammatory disease. In a

simplified model, the community composition of the human microbiome helps to shape the

balance between immuneregulatory (Treg) and pro-inflammatory (Th17) T cells. The

molecules produced by a given microbiome network work with the molecules produced by

the human genome to determine this equilibrium. (

) In a healthy microbiome, there is an

optimal proportion of both pro- and anti-inflammatory organisms (represented here by SFBs

and

B. fragilis

), which provide signals to the developing immune system (controlled by the

host genome) that leads to a balance of Treg and Th17 cell activities. In this scenario, the

host genome can contain ‘autoimmune specific’ mutations (represented by the stars), but

disease does not develop. (

B, C

) The genome of patients with multiple sclerosis, type I

diabetes, rheumatoid arthritis and Crohn’s disease contain a spectrum of variants that are

linked to disease by genome wide association studies (reviewed in (61)). Environmental

influences, however, are risk factors in all of these diseases. Altered community composition

of the microbiome due to lifestyle, known as dysbiosis, may represent this disease

modifying component. An increase in pro-inflammatory microbes, for example SFBs in

animal models, may promote Th17 cell activity to increase and thus predispose genetically

susceptible people to Th17-mediated autoimmunity (B). Alternatively, a decrease or absence

in anti-inflammatory microbes, for example

B. fragilis

in animal models, may lead to an

under-development of Treg cell subsets (C). The imbalance between Th17 cells and Tregs

ultimately leads to autoimmunity.

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Fig. 3.

A model for the co-evolution of adaptive immunity with the microbiota. (

) The adaptive

immune system develops under the control of the vertebrate genome to produce various cell

types. The evolutionarily ancient molecule TGF

directs the differentiation of Foxp3

Treg

cells. Although the earliest mammals contained a gut microbiota, bacteria may or may not

have influenced features of the primordial adaptive immune system. (

) Over millennia of

co-evolution, commensal microbes (

B. fragilis

used as an example here) produced molecules

that networked with the primordial immune system to help expand various Treg cell subsets,

for example IL-10-producing Foxp3

Treg cells. This process may have evolved to allow

these microorganisms to colonize the gut by inducing antigen-specific tolerance to the

microbiota. (

) Pro-inflammatory pathobionts (such as SFBs) may have induced Th17 cell

differentiation to increase mucosal defenses against enteric pathogens. (

) The modern

adaptive immune system may have arisen from 2 distinct events: Tregs and Th17 cell types

evolved independently (A to B and A to C), or through the sequential development of Th17

cells from Treg cell precursors (A to B to C to D). This may have been achieved by a

combinatorial signal of TGF

, augmented by the addition of IL-6 to promote Th17 cell

evolution over time (inset). Together, the modulation of Tregs and Th17 cells by commensal

and pathobionts, respectively, appears to shape the immune status of the host, and thus

represents a possible risk factor for autoimmune diseases which appear to depend on

balanced Treg/Th17 proportions.

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