The Gut Microbiota
`
`REVIEW
`
`Interactions Between the Microbiota
`and the Immune System
`
`Lora V. Hooper,1* Dan R. Littman,2 Andrew J. Macpherson3
`
`The large numbers of microorganisms that inhabit mammalian body surfaces have a highly coevolved
`relationship with the immune system. Although many of these microbes carry out functions that are
`critical for host physiology, they nevertheless pose the threat of breach with ensuing pathologies.
`The mammalian immune system plays an essential role in maintaining homeostasis with resident
`microbial communities, thus ensuring that the mutualistic nature of the host-microbial relationship
`is maintained. At the same time, resident bacteria profoundly shape mammalian immunity. Here, we
`review advances in our understanding of the interactions between resident microbes and the immune
`system and the implications of these findings for human health.
`
`Complex communities of microorganisms,
`
`termed the “microbiota,” inhabit the body
`surfaces of virtually all vertebrates. In the
`lower intestine, these organisms reach extraordi-
`nary densities and have evolved to degrade a
`variety of plant polysaccharides and other dietary
`substances (1). This simultaneously enhances host
`digestive efficiency and ensures a steady nutrient
`supply for the microbes. Metabolic efficiency
`was likely a potent selective force that shaped the
`evolution of both sides of the host-microbiota
`relationship. Millions of years of coevolution,
`however, have forged pervasive interconnections
`between the physiologies of microbial commu-
`nities and their hosts that extend beyond metabolic
`functions. These interconnections are particularly
`apparent in the relationship between the microbiota
`and the immune system.
`Despite the symbiotic nature of the intestinal
`host-microbial relationship, the close association
`of an abundant bacterial community with intesti-
`nal tissues poses immense health challenges. The
`dense communities of bacteria in the lower intes-
`tine (≥1012/cm3 intestinal contents) are separated
`from body tissues by the epithelial layer (10 mm)
`over a large intestinal surface area (~200 m2 in
`humans). Opportunistic invasion of host tissue by
`resident bacteria has serious health consequences,
`including inflammation and sepsis. The immune
`system has thus evolved adaptations that work to-
`gether to contain the microbiota and preserve the
`symbiotic relationship between host and microbiota.
`The evolution of the vertebrate immune system has
`therefore been driven by the need to protect the
`
`1The Howard Hughes Medical Institute and Department of Im-
`munology, The University of Texas Southwestern Medical Center
`at Dallas, Dallas, TX 75390, USA. 2Howard Hughes Medical
`Institute and Molecular Pathogenesis Program, The Kimmel
`Center for Biology and Medicine of the Skirball Institute, New
`York University School of Medicine, New York, NY 10016, USA.
`3Maurice Müller Laboratories, University Clinic for Visceral Sur-
`gery and Medicine, University of Bern, Bern, Switzerland.
`*To whom correspondence should be addressed. E-mail:
`lora.hooper@utsouthwestern.edu
`
`host from pathogens and to foster complex micro-
`bial communities for their metabolic benefits (2).
`In this Review, we survey the state of our
`understanding of microbiota-immune system in-
`teractions. We also highlight key experimental
`challenges that must be confronted to advance
`our understanding in this area and consider how
`our knowledge of these interactions might be
`harnessed to improve public health.
`
`Tools for Analyzing the Microbiota–Immune
`System Relationship
`Much of our current understanding of microbiota–
`immune system interactions has been acquired
`from studies of germ-free animals. Such animals
`are reared in sterile isolators to control their
`exposure to microorganisms, including viruses,
`bacteria, and eukaryotic parasites. Germ-free
`animals can be studied in their microbiologically
`sterile state or can serve as living test tubes for the
`establishment of simplified microbial ecosystems
`composed of a single microbial species or defined
`species mixtures. The technology has thus come
`to be known as “gnotobiotics,” a term derived from
`Greek meaning “known life.” Gnotobiotic ani-
`mals, particularly rodents, have become critical
`experimental tools for determining which host
`immune functions are genetically encoded and
`which require interactions with microbes.
`The current impetus for gnotobiotic exper-
`imentation has been driven by several impor-
`tant technical advances. First, because any mouse
`strain can be derived to germ-free status (3), large
`numbers of genetically targeted and wild-type
`inbred isogenic mouse strains have become avail-
`able in the germ-free state. The contribution of
`different immune system constituents to host-
`microbial mutualism can thus be determined by
`comparing the effects of microbial colonization
`in genetically altered and wild-type mice (4, 5).
`Second, next-generation sequencing tech-
`nologies have opened the black box of micro-
`biota complexity. Although advances in ex vivo
`culturability are still needed, the composition of
`
`human and animal microbiotas can be opera-
`tionally defined from polymorphisms of bacterial
`genes, especially those encoding the 16S ribo-
`somal RNA sequences. Such analyses have made
`possible the construction of defined microbiotas,
`whose distinct effects on host immunity can now
`be examined (6). Moreover, these advances allow
`the study of experimental animals that are both
`isobiotic and, in a defined inbred host, isogenic.
`A dominant goal of these efforts is to benefit hu-
`man health [see Blumberg and Powie (7)]. With
`the developing technology, the species differ-
`ences can be closed using mice with a defined
`humanized microbiota (8). On the horizon, there
`is even the prospect of humanized isobiotic mice
`that also have a humanized immune system (9).
`A third advance has been the development of
`experimental systems that allow the uncoupling
`of commensal effects on the immune system from
`microbial colonization. This cannot be achieved
`by antibiotic treatment alone because a small pro-
`portion of the targeted microbes will persist.
`Deletion strains of bacteria lacking the ability to
`synthesize prokaryotic-specific amino acids have
`been developed that can be grown in culture but do
`not persist in vivo, so the animals become germ-
`free again. This allows issues of mucosal immune
`induction, memory, and functional protection to
`be explored without permanent colonization (10).
`Finally, important insights about the impact of
`resident microbial communities on mammalian
`host biology have been acquired by using high-
`throughput transcriptomic and metabolomic tools
`to compare germ-free and colonized mice (11, 12).
`These tools include DNA microarrays, which have
`led to a detailed understanding of how microbiota
`shape many aspects of host physiology, includ-
`ing immunity (13, 14) and development (15), as
`well as mass spectrometry and nuclear magnetic
`resonance spectroscopy, which have provided im-
`portant insights into how microbiota influence
`metabolic signaling in mammalian hosts (12). The
`application of these new approaches to the older
`technology of gnotobiotics has revolutionized
`the study of interactions between the microbiota
`and the immune system.
`
`Looking Inside-Out: Immune System
`Control of the Microbiota
`A major driving force in the evolution of the
`mammalian immune system has been the need
`to maintain homeostatic relationships with the
`microbiota. This encompasses control of micro-
`bial interactions with host tissues as well as the
`composition of microbial consortia. Here, we dis-
`cuss recent insights into how the immune system
`exerts “inside-out” control over microbiota local-
`ization and community composition (see Fig. 1).
`Stratification and compartmentalization of the
`microbiota. The intestinal immune system faces
`unique challenges relative to other organs, as it
`must continuously confront an enormous micro-
`bial load. At the same time, it is necessary to avoid
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`pathologies arising from innate immune signaling
`or from microbiota alterations that disturb essential
`metabolic functions. An important function of the
`intestinal immune system is to control the expo-
`sure of bacteria to host tissues, thereby lessening
`the potential for pathologic outcomes. This oc-
`curs at two distinct levels: first, by minimizing
`direct contact between intestinal bacteria and the
`epithelial cell surface (stratification) and, second,
`by confining penetrant bacteria to intestinal sites
`and limiting their exposure to the systemic im-
`mune compartment (compartmentalization).
`Several immune effectors function together to
`stratify luminal microbes and to minimize bacterial-
`epithelial contact. Intestinal goblet cells secrete
`mucin glycoproteins that assemble into a ~150-mm-
`thick viscous coating at the intestinal epithelial
`cell surface. In the colon, there are two structurally
`distinct mucus layers. Although the outer mucus
`layer contains large numbers of bacteria, the inner
`mucus layer is resistant to bacterial penetration
`(16). In contrast, the small intestine lacks clearly
`distinct inner and outer mucus layers (17). Here,
`compartmentalization depends in part on antibac-
`terial proteins that are secreted by the intestinal
`epithelium. RegIIIg is an antibacterial lectin that
`is expressed in epithelial cells under the control of
`Toll-like receptors (TLRs) (18–20). RegIIIg limits
`bacterial penetration of the small intestinal mucus
`layer, thus restricting the number of bacteria that
`contact the epithelial surface (5).
`Stratification of intestinal bacteria on the
`luminal side of the epithelial barrier also depends
`on secreted immunoglobulin A (IgA). IgA spe-
`cific for intestinal bacteria is produced with the
`help of intestinal dendritic cells that sample the
`small numbers of bacteria that penetrate the over-
`lying epithelium. These bacteria-laden dendritic
`cells interact with B and T cells in the Peyer’s
`patches, inducing B cells to produce IgA directed
`against intestinal bacteria (21). IgA+ B cells home
`to the intestinal lamina propria and secrete IgA
`that is transcytosed across the epithelium and
`deposited on the apical surface. The transcytosed
`IgAs bind to luminal bacteria, preventing micro-
`bial translocation across the epithelial barrier (22).
`Mucosal compartmentalization functions to
`minimize exposure of resident bacteria to the sys-
`temic immune system (Fig. 1B). Although bacteria
`are largely confined to the luminal side of the
`epithelial barrier, the sheer number of intestinal
`bacteria makes an occasional breach inevita-
`ble. Typically, commensal microorganisms that
`penetrate the intestinal epithelial cell barrier are
`phagocytosed and eliminated by lamina propria
`macrophages (23). However, the intestinal im-
`mune system samples some of the penetrant bac-
`teria, engendering specific immune responses
`that are distributed along the length of the intes-
`tine (21). Bacteria that penetrate the intestinal
`barrier are engulfed by dendritic cells (DCs) re-
`siding in the lamina propria and are carried alive
`to the mesenteric lymph nodes. However, these
`
`SPECIALSECTION
`
`bacteria do not penetrate to systemic secondary
`lymphoid tissues. Rather, the commensal-bearing
`DCs induce protective secretory IgAs (21), which
`are distributed throughout all mucosal surfaces
`by recirculation of activated B and T cells. Thus,
`distinctive anatomical adaptations in the mucosal
`immune system allow immune responses directed
`against commensals to be distributed widely while
`still being confined to mucosal tissues.
`Other immune cell populations also promote
`the containment of commensal bacteria to in-
`testinal sites. Innate lymphoid cells reside in the
`lamina propria and have effector cytokine pro-
`
`files resembling those of T helper (TH) cells (24).
`Innate lymphoid cells that produce interleukin
`(IL)–22 are essential for containment of lymphoid-
`resident bacteria to the intestine, thus preventing
`their spread to systemic sites (25).
`The compartmentalization of mucosal and
`systemic immune priming can be severely per-
`turbed in immune-deficient mice. For example,
`mice engineered to lack IgA show priming of
`serum IgG responses against commensals, indi-
`cating that these bacteria have been exposed to
`the systemic immune system (22). A similar out-
`come is observed when innate immune sensing is
`
`Fig. 1. Looking inside-out: immune system control of the microbiota. Several immune effectors function
`together to stratify luminal microbes and to minimize bacterial-epithelial contact. This includes the mucus
`layer, epithelial antibacterial proteins, and IgA secreted by lamina propria plasma cells. Compartmen-
`talization is accomplished by unique anatomic adaptations that limit commensal bacterial exposure to the
`immune system. Some microbes are sampled by intestinal DCs. The loaded DCs traffic to the mesenteric
`lymph nodes through the intestinal lymphatics but do not penetrate further into the body. This
`compartmentalizes live bacteria and induction of immune responses to the mucosal immune system.
`There is recirculation of induced B cells and some T cell subsets through the lymphatics and the
`bloodstream to home back to mucosal sites, where B cells differentiate into IgA-secreting plasma cells.
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`The Gut Microbiota
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`defective. Mice lacking MyD88 or TRIF signal-
`ing adaptors for TLR-mediated sensing of bacteria
`also produce serum IgG responses against com-
`mensals (26). This probably results from the fact
`that in these settings, large numbers of commensals
`cross the epithelial barrier and phagocytic cells
`are less able to eliminate the penetrant organisms.
`Immune system control of microbiota com-
`position. The development of high-throughput
`sequencing technologies for microbiota analysis
`has provided insight into the many factors that
`determine microbiota composition. For example
`nutrients, whether derived from the host diet
`(27) or from endogenous host sources (28), are
`critically important in shaping the structure of
`host-associated microbial communities. Recent
`evidence suggests that the immune system is also
`likely to be an important contributor to “inside-
`out” host control over microbiota composition.
`Certain secreted antibacterial proteins produced
`by epithelial cells can shape the composition of in-
`testinal microbial communities. a-defensins are
`small (2 to 3 kD) antibacterial peptides secreted by
`Paneth cells of the small intestinal epithelium. Anal-
`ysis of the microbiota in mice that were either de-
`ficient in functional a-defensins or that overexpressed
`human a-defensin-5 showed that although there
`was no impact on total numbers of colonizing bacte-
`ria, there were substantial a-defensin–dependent
`changes in community composition, with reciprocal
`differences observed in the two mouse strains (29).
`An interesting question is how far secreted in-
`nate immune effectors “reach” into the luminal
`microbial consortia. For example, the impact of hu-
`man a-defensin-5 on luminal community composi-
`tion contrasts with the antibacterial lectin RegIIIg,
`which limits penetration of bacteria to the epithelial
`surface but does not alter luminal communities (5).
`This suggests that some antimicrobial proteins, such
`as a-defensins, reach into the lumen to shape overall
`community composition, whereas others, such as
`RegIIIg, have restricted effects on surface-associated
`bacteria and thus control microbiota location relative
`to host surface tissues. Questions remain as to ex-
`actly how a-defensin-5 controls luminal community
`composition, however. In one scenario, these small
`antimicrobial peptides diffuse through the mucus
`layer and directly act on bacteria that inhabit the lu-
`men. Another possibility is that a-defensin-5 exerts
`its antibacterial activity on bacteria that are trapped in
`the outer reaches of the mucus layer, with those bac-
`teria acting as reservoirs that seed luminal commu-
`nities and thus dictate their composition. Answering
`these questions will require improved tools for fine-
`mapping microbiota composition and consortia from
`the surface of the intestine to the interior of the lumen.
`The impact of the immune system on micro-
`biota composition is also suggested by several im-
`mune deficiencies that alter microbial communities
`in ways that predispose to disease. For example,
`Garrett et al. studied mice that lack the transcription
`factor T-bet (encoded by Tbx21), which governs
`inflammatory responses in cells of both the innate
`
`and the adaptive immune system (30). When
`Tbx21–/– mice were crossed onto Rag2–/– mice,
`which lack adaptive immunity, the Tbx21–/–/Rag2–/–
`progeny developed ulcerative colitis in a microbiota-
`dependent manner (30). Remarkably, this colitis
`phenotype was transmissible to wild-type mice by
`adoptive transfer of the Tbx21–/–/Rag2–/– micro-
`biota. This demonstrated that altered microbiota
`were sufficient to induce disease and could thus be
`considered “dysbiotic.” Similarly, mice lacking the
`bacterial flagellin receptor TLR5 exhibit a syn-
`drome encompassing insulin resistance, hyper-
`lipidemia, and increased fat deposition associated
`with alterations in microbiota composition (31).
`These metabolic changes are transferable to wild-
`type mice that acquire the Tlr5–/– gut microbiota.
`A third example of immune-driven dysbiosis is
`seen in mice deficient for epithelial cell expres-
`sion of the inflammasome component NLRP6.
`These mice develop an altered microbiota with
`increased abundance of members of the Bacte-
`roidetes phylum associated with increased intes-
`tinal inflammatory cell recruitment and susceptibility
`to chemically induced colitis. Again, there is evi-
`dence that dysbiosis alone is sufficient to drive the
`intestinal inflammation, because conventionally
`raised wild-type mice that acquire the dysbiotic
`microbiota show similar immunopathology (32).
`Together, these findings suggest that the im-
`mune system affords mammalian hosts some con-
`trol over the composition of their resident microbial
`communities. It is also clear that these commu-
`nities can be perturbed by defects in the host im-
`mune system. This leads to the idea of the immune
`system as a form of ecosystem management that
`exerts critical control over microbiota compo-
`sition, diversity, and location [see Costello et al.
`(33)]. However, a number of questions remain.
`First, although it is apparent that the immune sys-
`tem shapes community composition at the species
`level, it is not yet clear whether the immune sys-
`tem shapes the genetics and physiology of indi-
`vidual microbial species. Second, how much does
`the immune system combine with gastric acid and
`intestinal motility to control the longitudinal dis-
`tribution of microbial species in the gastrointes-
`tinal tract? Finally, it will be important to determine
`the extent to which the immune system also con-
`trols microbial community composition and loca-
`tion in other organ systems, such as the respiratory
`tract, urogenital tract, and skin.
`
`Looking Outside-In: How Microbiota
`Shape Immunity
`The earliest comparisons of germ-free and colonized
`mice revealed a profound effect of microbial colo-
`nization on the formation of lymphoid tissues and
`subsequent immune system development. It was
`thus quickly apparent that the microbiota influ-
`ence the immune system from “outside-in.” Recent
`studies have greatly amplified this understanding
`and have revealed some of the cellular and mo-
`lecular mediators of these interactions (see Fig. 2).
`
`The impact of the microbiota on lymphoid
`structure development and epithelial function.
`The tissues of the gastrointestinal tract are rich in
`myeloid and lymphoid cells, many of which
`reside in organized lymphoid tissues. It has long
`been appreciated that the gut microbiota have a
`critical role in the development of organized lym-
`phoid structures and in the function of immune
`system cells. For example, isolated lymphoid fol-
`licles in the small intestine do not develop in
`germ-free mice, and such mice are also deficient
`in secretory IgA and CD8ab intraepithelial lym-
`phocytes. The specific microbial molecules en-
`dowed with this inductive function have not yet
`been described, however.
`Sensing of commensal microbiota through the
`TLR-MyD88 signaling pathway triggers several
`responses that are critical for maintaining host-
`microbial homeostasis. The microbiota induce
`repair of damaged intestinal epithelium through a
`MyD88-dependent process that can be rescued in
`microbe-depleted animals by gavage with bacterial
`lipopolysaccharide (LPS). The innate signals, con-
`veyed largely through myeloid cells, are required to
`enhance epithelial cell proliferation (34, 35). As
`discussed above, MyD88-dependent bacterial sig-
`nals are also required for the induction of epithelial
`antimicrobial proteins such as RegIIIg (5, 19). This
`expression can be induced by LPS (19, 20 ) or flagel-
`lin (36). The flagellin signals are relayed through
`TLR5 expressed by CD103+CD11b+ dendritic cells
`in the lamina propria, stimulating production of IL-
`23 that, in turn, promotes the expression of IL-22
`by innate lymphoid cells (37). IL-22 then stimu-
`lates production of RegIIIg, which is also secreted
`upon direct activation of MyD88 in epithelial
`cells (5, 20). This is one clear example of the
`importance of commensals in the induction of host
`innate responses, but it likely represents a tiny
`fraction of the multitude of effects of microbiota on
`the host immune system.
`Microbiota shaping of T cell subsets. It has
`recently become evident that individual commensal
`species influence the makeup of lamina propria T
`lymphocyte subsets that have distinct effector func-
`tions. Homeostasis in the gut mucosa is maintained
`by a system of checks and balances between poten-
`tially proinflammatory cells, which include TH1 cells
`that produce interferon-g; TH17 cells that produce
`IL-17a, IL-17f, and IL-22; diverse innate lymphoid
`cells with cytokine effector features resembling
`TH2 and TH17 cells; and anti-inflammatory Foxp3+
`regulatory T cells (Tregs). Colonization of mice with
`segmented filamentous bacteria (SFB) results in
`accumulation of TH17 cells and, to a lesser extent, in
`an increase in TH1 cells (38, 39). SFB appear able to
`penetrate the mucus layer overlying the intestinal
`epithelial cells in the terminal ileum, and they in-
`teract closely with the epithelial cells, inducing host
`cell actin polymerization at the site of interaction
`and, presumably, signaling events that result in a
`TH17 polarizing environment within the lamina
`propria. There is little known about host cell
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`signaling pathways initiated by SFB. It is possible
`that SFB influence epithelial gene expression, re-
`sulting, for example, in expression of antimicro-
`bial proteins such as RegIIIg and of molecules
`that participate in TH17 cell polarization. SFB
`may also act directly on cells of the immune sys-
`tem, either through interactions with myeloid cells
`that extend processes through the epithelium to
`the mucus layer or by production of metabolites
`that act on various receptors expressed by host cells.
`Other bacteria have been shown to enhance the
`anti-inflammatory branches of the adaptive immune
`system by directing the differentiation of Tregs or by
`inducing IL-10 expression. For example, coloniza-
`tion of gnotobiotic mice with a complex cocktail of
`46 mouse Clostridial strains, originally isolated from
`mouse feces and belonging mainly to cluster IVand
`XIVa of the Clostridium genus, results in the
`expansion of lamina propria and systemic Tregs.
`These have a phenotype characteristic of Tregs in-
`duced in the periphery in response to transforming
`growth factor (TGF)–b and retinoic acid [in contrast
`to thymic-derived natural (n) Tregs (40)], and many
`
`of these inducible Tregs (iTregs) express IL-10. The
`exact Clostridial strains within the complex exper-
`imental mixture that drive this regulatory response
`remain to be defined. Furthermore, polysaccharide
`A (PSA) of Bacteroides fragilis induces an IL-10
`response in intestinal T cells, which prevents the
`expansion of TH17 cells and potential damage to the
`mucosal barrier (41). In contrast, mutant B. fragilis
`lacking PSA has a proinflammatory profile and fails
`to induce IL-10. Production of PSA by B. fragilis
`has been proposed to be instrumental for the bac-
`terium’s success as a commensal.
`Within the intestine, the balance of effector lym-
`phoid cells and Treg cells can have a profound in-
`fluence on how the mucosa responds to stresses that
`elicit damage. The relative roles of commensal-
`regulated T cells differ according to the models used
`to study inflammation. For example, in mice sub-
`jected to chemical or pathogen-induced damage to
`the mucosa, TH17 cells have a beneficial effect that
`promotes healing. In contrast, TH1 and TH17 cells,
`as well as IL-23–dependent innate lymphoid cells,
`promote colitis in models in which Treg cells are
`
`Fig. 2. Looking outside-in: how microbiota shape host immunity. Some of the many ways that intestinal
`microbiota shape host immunity are depicted. These include microbiota effects on mucosal as well as
`systemic immunity. ILFs, isolated lymphoid follicles.
`
`SPECIALSECTION
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`depleted. It is likely that inflammatory bowel dis-
`eases in humans can be similarly triggered by
`commensal-influenced imbalance of lymphoid cell
`subsets. This is supported by numerous observations,
`including the strong linkage of IL23R polymor-
`phisms with Crohn’s disease, a serious condition
`with relapsing intestinal inflammation and a risk of
`malignancy, and the severe enterocolitis associated
`with IL10 and IL10R mutations (42, 43).
`Microbiota effects on systemic immunity. The
`influence of commensal bacteria on the balance of
`T cell subsets is now known to extend well beyond
`the intestinal lamina propria. Homeostatic T cell
`proliferation itself is driven by the microbiota or
`their penetrant molecules (44). Systemic auto-
`immune diseases have long been suggested to have
`links to infections, but firm evidence for causality
`has been lacking. Recent studies in animal models,
`however, have reinforced the notion that commen-
`sal microbiota contribute to systemic autoimmune
`and allergic diseases at sites distal to the intestinal
`mucosa. Several mouse models for autoimmunity
`are dependent on colonization status. Thus, germ-
`free mice have marked attenuation of disease in
`models of arthritis and experimental autoimmune
`encephalomyelitis (EAE), as well as in various
`colitis models. In models of TH17 cell–dependent
`arthritis and EAE, monoassociation with SFB is
`sufficient to induce disease (42, 45, 46). In all of
`these models, induction of TH17 cells in the in-
`testine has a profound influence on systemic dis-
`ease. Exacerbation of arthritis and EAE is likely the
`consequence of an increase in the number of
`arthritogenic or encephalitogenic TH17 cells that
`traffic out of the lamina propria. The antigen spec-
`ificity of such cells remains to be examined.
`Induction of iTregs by the cluster IV and XIVa
`Clostridia also has a systemic effect on inflamma-
`tory processes. Colonization of germ-free mice with
`these bacteria not only results in attenuated disease
`after chemical damage of the gut epithelium but
`also reduces the serum IgE response after immuni-
`zation with antigen under conditions that favor a
`TH2 response (40). As with pathogenic TH17 cells,
`the antigen specificity of the commensal-induced
`iTregs that execute systemic anti-inflammatory func-
`tions is not yet known, although at least some of the
`Tregs in the gut have T cell receptors with specificity
`for distinct commensal bacteria (47).
`Finally, B. fragilis PSA affects the develop-
`ment of systemic T cell responses. Colonization of
`germ-free mice with PSA-producing B. fragilis
`results in higher numbers of circulating CD4+ T
`cells compared to mice colonized with B. fragilis
`lacking PSA. PSA-producing B.
`fragilis also
`elicits higher TH1 cell frequencies in the circulation
`(48). Together, these findings show that commen-
`sal bacteria have a general impact on immunity
`that reaches well beyond mucosal tissues.
`Microbiota influences on invariant T cells and
`innate lymphoid cells. A recent study extends the
`role of microbiota to the control of the function
`invariant natural killer T cells (iNKT cells), which
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`bear an invariant T cell receptor specific for lipid
`antigens presented by the atypical class I mol-
`ecule CD1d. Germ-free mice were found to have
`increased susceptibility to iNKT cell–mediated
`oxazolone-induced colitis and ovalbumin-induced
`asthma. Unexpectedly, this effect could be reversed
`only if mice were exposed to microbiota in the
`neonatal period. The regulation of iNKT cell ex-
`pansion was ascribed to reduced expression of the
`chemokine CXCL16 in the presence of microbiota.
`Thus, signals elicited by commensals may repress
`systemic expression by epithelial cells of a chemo-
`kine that interacts with CCR6 that is selectively
`expressed by iNKT cells (49).
`Innate lymphoid cells that produce either
`IL-17 or IL-22 are protective against damage in
`an innate model of colitis and during Citrobacter
`rodentium enteric infection (50, 51). The extent
`to which innate lymphoid cells are regulated by
`the microbiota is not yet clear (52–54), but cryp-
`topatches, which are formed by a subset of innate
`lymphoid cells in the small intestine, differenti-
`ate into isolated lymphoid follicles only when
`commensals are present (55). Thus, it is likely
`that, even if innate lymphoid cell numbers are
`not influenced by commensals, their function
`may be subject to microbiota signals.
`Microbiota can trigger inflammation in immu-
`nocompromised hosts. The commensal microbiota
`clearly have important effects on the normal
`development of immunity. However, commensal
`bacteria can also trigger inflammatory responses in
`immunodeficient hosts. For example, defective
`signaling through the phosphatase SHP-1 causes a
`microbiota-dependent autoinflammatory syndrome
`with lesions on the feet, salivary glands, and lungs;
`such inflammation also occurs in mice without B or
`T lymphocytes (56, 57). There are a series of mono-
`genic conditions of the nucleotide-binding oligo-
`merization domain (NOD) receptor family (58)
`considered to be autoinflammatory. One of the best
`characterized of these is in the NLRP3 inflamma-
`some protein (59). Depending on the exact acti-
`vating mutation involved, the clinical spectrum in
`humans encompasses urticaria triggered by the cold,
`episodic fevers occurring with unknown triggers,
`and neonatal onset multisystem inflammatory dis-
`ease (60). Although the exact cause of these patholo-
`gies is not yet clear, these outcomes are consistent
`with studies in mice showing that NLRP3-deficiency
`can cause dysbiosis of the intestinal microbiota
`(61), as well as studies showing that TLR ligands
`can trigger proinflammatory IL-1b secretion in the
`presence of activating NLRP3 mutations (62, 63).
`Another NOD family member, NOD2 (CARD15),
`a receptor for the muramyl dipeptide structural unit
`of bacterial peptidoglycan, was the first susceptibil-
`ity gene identified for Crohn’s disease (64, 65). This
`reinforced early clinical observations of the benefits
`of surgically diverting the intestinal stream or treat-
`ing with antibiotics, thus implicating intestinal mi-
`crobes in the etiology (66, 67). More recent genetic
`data from genome-wide association studies (GWAS)
`
`of human inflammatory bowel disease have re-
`vealed a highly polygenic picture, with more than
`70 loci described for Crohn’s disease alone. These
`include modulators of the mucosal immune re-
`sponse, proteins functioning in the epithelial stress
`response, and the IL23R polymorphisms described
`above (68, 69). However, the sum total of the con-
`tributions of these loci to overall disease incidence
`leaves a considerable gap. It is clear that some cases
`can be explained by phenotypes from private mu-
`tations, such as those affecting IL-10 signaling (43),
`that are too infrequent to be detected by GWAS but
`that disrupt host-microbial mutualism in animal
`models (70).
`Microbiota can protect against autoimmune
`disease. Type 1 diabetes (T1D) results from auto-
`immune damage to the insulin-secreting islets of
`Langerhans in the pancreas. This autoimmune con-
`dition is also shaped by the interactions between
`immunity and the microbiota, but unlike EAE and
`arthritis, where SFB drive autoimmunity, the micro-
`biota can protect from T1D. The nonobe