Recent advances in understanding how the mammalian immune system and intestinal microbiota functionally interact have yielded novel insights for human health and disease. Modern technologies to quantitatively measure specific members and functional characteristics of the microbiota in the gastrointestinal tract, along with fundamental and emerging concepts in the field of immunology, have revealed numerous ways in which host-microbiota interactions proceed beneficially, neutrally, or detrimentally for mammalian hosts. It is clear that the gut microbiota has a strong influence on the shape and quality of the immune system; correspondingly, the immune system guides the composition and localization of the microbiota. In the following review, we examine the evidence that these interactions encompass homeostasis and inflammation in the intestine and, in certain cases, extraintestinal tissues. Lastly, we discuss translational therapies stemming from research on host-microbiota interactions that could be used for the treatment of chronic inflammatory diseases.

The human body hosts a remarkable variety (1) and quantity (2) of microorganisms collectively referred to as the microbiota. The microbiota encompasses Archaea, Bacteria, Eukarya, and viruses that form a complex ecosystem thought to have coevolved with mammalian hosts over time. Commensal bacteria are the most well-defined member of the microbiota. Among the various body surfaces where commensal bacteria reside, the gastrointestinal (GI) tract contains the highest densities, which are estimated to range between 1011 and 1014 cells per gram of luminal content (3). This enormous cellular and genetic component of the human body is now well recognized to provide indispensible functions in digestion, nutrition status, and protection against invasive pathogens (4).

The mammalian immune system is also significantly enriched in the GI tract and engages in a complex dialogue with the microbiota to maintain a state of homeostasis that is mutually beneficial. For example, the requirement for microbiota in the proper development of the immune system was first demonstrated in animals reared in microorganism-free environments, known as germ-free. Germ-free animals display a variety of intestinal immune defects, including impaired development of GALTs, lower amounts of secreted Ig, and reduced intraepithelial CD8+ T cells (5). Additionally, evidence has supported the notion of the gut microbiota having a strong influence over the development of the immune system outside of the intestine (6). In germ-free mice, splenic CD4+ Th cells are skewed toward the Th2 cell subset and promote enhanced allergic responses and type 2 immunity (6). Germ-free mice also have decreased total numbers of peripheral CD4+ T cells, including Th17 cells (7) and regulatory T cell (Treg) compartments (8, 9). Conversely, the intestinal immune system also actively shapes the composition and compartmentalization of the microbiota through various mechanisms (1013). Overall, these observations demonstrate that the colonizing microbiota and host immune system have a complex, dynamic, and reciprocal dialogue.

Members of the microbiota are recognized by the innate immune system through their conserved pathogen-associated molecular patterns, referred to in this article as microbe-associated molecular patterns (MAMPs) (14), to encompass such ligands in normally nonpathogenic organisms of the microbiota. MAMPs are recognized by germline-encoded pattern recognition receptors distributed spatiotemporally across various cell types and tissues. Despite this ability to directly respond to microbiota-derived signals, several features of the immune system act in cooperation with the intestinal barrier to protect the body from opportunistic pathogens and to limit the immune system from overreacting to beneficial microbiota in the gut (Fig. 1A). Such features include the following: a thick mucus lining the lumen of the gut epithelial cells that physically excludes most microorganisms (15), secreted IgA that recognizes and binds microbe-specific epitopes and facilitates their removal (16), and secreted antimicrobial peptides that directly neutralize microorganisms (17, 18). In addition to their pathogen-protective effects, these features help to maintain sequestration of the microbiota, thus reducing the likelihood of the mammalian immune system mounting an overreactive response to commensal bacteria. However, when the epithelial barrier is compromised by chemical, pathogenic, or inflammatory insults, the immune system must deal with the resulting influx of commensal and opportunistic microorganisms. In most contexts, the immune system responds appropriately to protect the host from invasive microbes while maintaining long-term tolerance to the microbiota. Not surprisingly, sustained breakdown of the intestinal barrier is linked to several chronic inflammatory diseases, although the mechanisms are still being determined (19, 20) (Fig. 1B).

FIGURE 1.

Host–microbiota interactions underlie homeostasis and inflammation in the intestine and extraintestinal tissues. (A) At homeostasis, gut bacteria are compartmentalized within the lumen through exclusion by the mucus, neutralization by antimicrobial peptides produced by IECs, and release of secretory IgA (sIgA) from intestinal-resident B cells. In response to various cues, ILC3s and Th17 cells in the intestine produce IL-22, which acts on IECs to promote compartmentalization of the microbiota. Tregs produce IL-10 and are induced by microbially derived SCFAs and PSA or by the bacterial species B. fragilis and Clostridium. Intestinal activation of Tregs can protect against neuroinflammation in the CNS during EAE. (B) During chronic intestinal inflammation, loss of intestinal barrier function results in bacterial translocation across the epithelium, release of commensally derived MAMPs, proinflammatory cytokine and chemokine activation, and Th17 and B cell responses. Specific bacteria exacerbate intestinal inflammation, including Prevotellaceae, Enterobacteriaceae, and the Th17-inducing SFB. Loss of tolerance to self-Ags can occur because of lowered thresholds for autoactivation (bystander effect) that can mediate autoimmunity in extraintestinal tissues. Bystander effects initiate and exacerbate Th17-mediated inflammation in mouse models of EAE and RA. In RA, Th17 and follicular helper T cell responses aid in autoantibody production in secondary lymph nodes. Licensing of cross-reactive T cell responses that recognize microbially derived peptides and react to self-peptides can also initiate autoimmunity in extraintestinal tissues, exemplified in a mouse model of experimental autoimmune uveitis (EAU).

FIGURE 1.

Host–microbiota interactions underlie homeostasis and inflammation in the intestine and extraintestinal tissues. (A) At homeostasis, gut bacteria are compartmentalized within the lumen through exclusion by the mucus, neutralization by antimicrobial peptides produced by IECs, and release of secretory IgA (sIgA) from intestinal-resident B cells. In response to various cues, ILC3s and Th17 cells in the intestine produce IL-22, which acts on IECs to promote compartmentalization of the microbiota. Tregs produce IL-10 and are induced by microbially derived SCFAs and PSA or by the bacterial species B. fragilis and Clostridium. Intestinal activation of Tregs can protect against neuroinflammation in the CNS during EAE. (B) During chronic intestinal inflammation, loss of intestinal barrier function results in bacterial translocation across the epithelium, release of commensally derived MAMPs, proinflammatory cytokine and chemokine activation, and Th17 and B cell responses. Specific bacteria exacerbate intestinal inflammation, including Prevotellaceae, Enterobacteriaceae, and the Th17-inducing SFB. Loss of tolerance to self-Ags can occur because of lowered thresholds for autoactivation (bystander effect) that can mediate autoimmunity in extraintestinal tissues. Bystander effects initiate and exacerbate Th17-mediated inflammation in mouse models of EAE and RA. In RA, Th17 and follicular helper T cell responses aid in autoantibody production in secondary lymph nodes. Licensing of cross-reactive T cell responses that recognize microbially derived peptides and react to self-peptides can also initiate autoimmunity in extraintestinal tissues, exemplified in a mouse model of experimental autoimmune uveitis (EAU).

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In this review, we assess how functional interactions between the mammalian immune system and the microbiota in the gut can drive inflammatory diseases locally and systemically. Comparatively, we also examine settings in which host-microbiota interactions can prevent or constrain autoimmune disease. Lastly, we briefly discuss the evidence advocating for the therapeutic modulation of host immune factors, as well as the manipulation of microbiota or microbiota-derived biomolecules for treating chronic inflammatory disease.

Inflammatory bowel disease (IBD) is a family of chronic inflammatory disorders of the GI tract. In the clinic, IBD is frequently diagnosed as Crohn’s disease (CD), affecting any part of the GI tract, or ulcerative colitis, in which pathology is restricted primarily to the colon (20). As with most complex diseases, IBD is thought to occur from a combination of genetic (21, 22), environmental, and lifestyle-associated risk factors (23) that culminate in dysregulated host innate and adaptive immune responses to the intestinal microbiota. Despite the complexity of IBD’s etiology, the host-microbiota interactions that drive disease pathogenesis are becoming better understood through studies in human IBD patients and animal models of intestinal damage and inflammation.

Genetic analyses have identified loss-of-function mutations and polymorphisms in key immune tolerance–related genes and immune-response elements that can lead to early-onset IBD or increase disease susceptibility in adulthood (21, 22). Many primary immunodeficiencies first manifest in the GI tract (24). For example, individuals with loss-of-function mutations in IL-10/IL-10R signaling present with very early–onset IBD as a result of their inability to regulate inflammatory immune responses to commensal bacteria in the GI tract (2527). Indeed, several other primary immunodeficiencies, such as combined T and B cell deficiencies, are linked to early-onset GI disorders (24), and many more are continually being identified through whole exome sequencing (28). Genome-wide association studies have also identified a number of polymorphisms that are associated with an increased susceptibility to developing IBD in early life or adulthood (21, 22). The susceptibility loci include genes and gene pathways involved in intestinal barrier function, innate immune recognition, adaptive immunity, and cellular homeostasis (21). For example, genetic alterations in NOD2, an intracellular pattern recognition receptor for bacterial peptidoglycans, confer increased susceptibility to developing CD in adulthood (29, 30). To extend the genetic evidence, many of the identified genetic alterations found in IBD patients can phenocopy aspects of human disease when experimentally induced in animal models (31). These studies support the concept that diverse impairments of hematopoietic and nonhematopoietic cell signaling pathways underlie abnormal host-microbiota interactions.

Environmental and lifestyle risk factors also play a role in disease development (23), as evidenced by modest disease concordance between monozygotic twins who develop ulcerative colitis and CD in adulthood (32). For example, diet is implicated in causative and preventative roles in IBD through various mechanisms (33). Of note, short- and long-term dietary patterns can modify the composition of the gut microbiota (3436). Diet’s link to IBD, among other environmental risk factors that alter the gut microbiota, such as antibiotic use, has motivated investigation of associations between microbial dysbiosis and intestinal inflammation. Dysbiosis is defined as a microbial imbalance resulting in a shift (i.e., loss or outgrowth of a species) and overall reduction in microbial diversity. Using 16S sequencing of gut fecal content, it was observed that IBD patients have reduced colonic microbial diversity and a detectable shift in bacterial enterotypes compared with healthy individuals (37). For example, in a cohort of CD patients, Frank et al. (38) detected a relative decrease in Firmicutes and Bacteroides in the intestinal microbiota, as well as a relative increase in the proinflammatory bacteria Enterobacteriaceae, relative to controls (Fig. 1B). Additionally, fecal metabolite analysis revealed a decrease in butyrate-producing bacterium in CD patients (39, 40). However, no single bacterial strain or combinations of strains have been shown to directly cause or prevent IBD in humans.

Several animal studies have demonstrated that dysbiosis can drive inflammatory pathogenesis in the intestine. These studies involve the demonstration that a proinflammatory consortium of microbiota, generally resulting from immune impairment, can transfer disease phenotype to healthy wild-type (WT) recipient animals. For instance, one of the first animal studies to implicate an IBD-causative consortium of bacteria involved the horizontal transfer of microbiota from a spontaneous model of colitis (mice deficient in both T-bet and Rag2; referred to as TRUC mice) into a healthy recipient mouse which resulted in transfer of colitis (41). Garrett et al. (42) later identified more specifically that Klebsiella pneumoniae and Proteus mirabilis, which grow out in TRUC mice, act in conjunction with the presence of normal gut flora to drive the colitogenic effect upon transfer. In another model, NLRP6 inflammasome–deficient mice displayed spontaneous colitis that was transferrable to WT neonates or adults via cross-fostering or cohousing (43). Prevotellaceae was implicated as the primary driver of the inflammatory effect in this study (43). In another study, Couturier-Maillard et al. found that mice with a deficiency in NOD2 had a dysbiotic consortium of microbiota that could transfer colitis to healthy recipient mice (44). These studies underscore that genetic disruption of immune pathways in the intestine is sufficient to initiate colitogenic microbial dysbiosis. These microbial consortiums can then transfer disease even in the context of a functional immune system.

Specific microbial species can be characterized by their capacity to provoke inflammatory responses in the intestine. Segmented filamentous bacteria (SFB) preferentially induce the differentiation of proinflammatory CD4+ Th17 cells in the lamina propria of the ileum through the TLR5 innate pathway, serum amyloid A, and direct epithelial cell adhesion (45, 46) (Fig. 1B). Recently, it was found that a variety of bacterial species exhibiting epithelial cell adhesion (such as Citrobacter rodentium, enterohemorrhagic Escherichia coli, and Candida albicans) could similarly induce Th17 cells in the intestine (47). Epithelial adhesion was an indispensible bacterial characteristic for this effect because adhesion-defective bacterial mutants failed to induce Th17 cell responses (47). Finally, Helicobacter hepaticus also was demonstrated to induce proinflammatory innate lymphoid cell (ILC) and Th17 cell responses through the induction of cytokines IL-1β and IL-23 in the colon (48). Thus, the induction of proinflammatory immune cells and their subsequent effector functions underlie some of the pathogenic effects of these bacterial members (Fig. 1B). It is important to note that ILCs and Th17 cells also mediate protection from pathogens and proper containment of commensal bacteria, thus promoting homeostasis in the gut (49), which is examined later in this review. Furthermore, SFB were well characterized to significantly induce Th17 cell responses but also were demonstrated to promote the development of intestinal Tregs (8). Thus, a comprehensive analysis of microbiota-induced responses should carefully be considered, and single species cannot always be defined solely as pro- or anti-inflammatory. Moreover, dysbiotic blooms of bacterial species in the gut, such as Enterobacteriaceae, can be secondary to intestinal inflammation from various insults (50), which may owe to the unique ability of these bacteria to feed off the by-products of host inflammation (51). Such observations obscure cause-and-effect relationships between microbial dysbiosis and inflammation.

In summary, IBD arises from a framework of genetic predispositions, environmental risk factors, and dysbiotic microbiota that underpins its chronic nature. Continued interrogation of the complexity of host-microbiota interactions that promote or constrain IBD in the various contexts of human disease should yield more rationally informed preventative or therapeutic approaches.

In parallel with research on how host-microbiota interactions drive inflammatory diseases in the intestine, mounting evidence suggests that these interactions also impact systemic inflammatory disease (5255) (Fig. 1B). Indeed, IBD patients frequently have extraintestinal disease manifestations involving the joints, skin, and eyes (56). Multi-disease cohort genome-wide association studies have revealed significant overlap in genetic susceptibility loci for IBD with a variety of inflammatory diseases involving extraintestinal tissues (21, 57). Additionally, similar to ulcerative colitis, some autoimmune diseases, such as rheumatoid arthritis (RA), show less disease concordance between monozygotic twins than do other autoimmune diseases (58). This suggests a strong role for environmental factors in disease development. Alterations in the gut microbiota are associated with several chronic inflammatory diseases outside of the intestine (5). Although causal relationships have not been demonstrated, these observations provoke the theory that disrupted host-microbiota interactions in the gut, arising from genetic or environmental perturbations, may underlie or impact the course of systemic autoimmune diseases.

Several research efforts in animal models have illuminated how the gut microbiota can have a causative or protective role in autoimmune disease outside of the intestine. In the following sections we categorize such evidence into two, nonmutually exclusive groupings: bystander effects (Ag nonspecific) and molecular mimicry (Ag specific). Although these have already been proposed and demonstrated as ways in which infectious pathogens, such as viruses, may lead to chronic autoimmune disease in humans (59), less research has elucidated mechanisms in which resident or transient microbiota can have similar roles in systemic inflammatory diseases.

In certain contexts, gut microbiota can exert an adjuvant effect in the priming of autoreactive adaptive immune responses. Animal models support the concept that microbiota provide a necessary bystander role in initiating autoimmune diseases in extraintestinal sites (Fig. 1B). For instance, mice treated with antibiotics (60) or reared in germ-free conditions (61) show reduced induction of experimental autoimmune encephalitis (EAE). Recolonization of germ-free mice with SFB alone induces Th17 cells in the gut and enhances neurodegeneration in the CNS upon active EAE induction (61). SFB can have a similar impact, although through a different mechanism, to induce autoimmunity in a mouse model of spontaneous autoimmune arthritis (K/BxN) (62). Germ-free K/BxN mice are resistant to the development of arthritis, primarily as a result of reduced systemic germinal center formation and subsequent loss of autoantibody production. Recolonization with SFB restores autoimmune arthritis through the activation of Th17 cells in the intestine, which then traffic to the spleen to aid in germinal center formation and the production of autoantibodies that mediate disease (62). More recently, SFB colonization in K/BxN mice was found to induce the activation of follicular helper T cells in the Peyer’s patches, which subsequently egress to the spleen and aid in the production of autoantibodies (63). A unique variation of the bystander model also was demonstrated by Campisi et al. (64): C. rodentium infection causes self-antigen release from apoptotic host cells, which are then processed and presented by APCs alongside bacterial peptides, resulting in the licensing of autoreactive Th17 cells. This reinforces the concept that severe inflammation in the intestine, arising from infection in this case, can provide the initiating conditions for the development of local and systemic autoimmunity.

Molecular mimicry, or an adaptive response that recognizes and responds to foreign-derived non-self and self-antigens, also has been proposed as a general mechanism for autoimmunity (65, 66). Understandably, cross-reactivity of adaptive responses has direct benefit to the host when it results in broader protection against phylogenically related pathogens; in contrast, it can adversely result in an inappropriate response to self-antigens. Using mouse models, several groups have provided evidence that microbiota-derived Ags may provide the antigenic basis for the initiation of systemic autoimmune disease (55). The seminal observation that molecular mimicry to common microbial peptides can induce autoimmunity came from a series of experiments demonstrating that structurally related microbial peptides could activate MBP-specific T cells (in the Ob TCR-DR2b mouse model), which then induce neurodegeneration in mice (67). More recently, Horai et al. (68) showed that gut microbiota can provide the antigenic material for cross-reactivity to a self-antigen. Using a spontaneous model of autoimmune uveitis (TCR transgenic for the retinal protein IRBP), the investigators found that IRBP-specific CD4+ T cells are first activated in the gut, migrate to the eye, and drive pathogenic autoimmune uveitis (68). Interestingly, Kadowaki et al. (69) demonstrated that myelin protein (MOG)-specific CD4+ intraepithelial lymphocytes can be activated and proliferate in response to gut Ags. In this context, CD4+ T cells differentiate into a regulatory Th17 cell phenotype that expresses CTLA4 and TGFBR1. Upon transfer into WT mice, MOG-specific CD4+ intraepithelial lymphocytes infiltrate the CNS and upregulate LAG3 expression, reducing neuroinflammation (69). These experiments demonstrate that molecular mimicry can activate proinflammatory and immunoregulatory pathways that influence autoimmune disease in extraintestinal sites.

Despite the correlative evidence that commensal bacteria can directly initiate autoimmunity in extraintestinal tissues, no single bacterium or consortium of bacteria has been specifically identified in humans. Additional research and experimental tools are warranted to clarify the mechanisms of bystander effects and molecular mimicry in extraintestinal autoimmune disease settings. Recently published articles demonstrated systematic approaches to identify commensal bacteria that incite colitis (70) or diet-dependent enteropathy (71). These approaches consist of sequencing IgA-targeted bacterial taxa from the fecal microbiota and then validating the bacterium’s immunological impact in gnotobiotic mice, which may prove useful for the identification of specific intestinal commensal bacteria involved in autoimmune diseases outside of the gut. Furthermore, stratification of IgA sequencing into T cell–independent and T cell–dependent IgA-production mechanisms (72) may help to delineate bacterial members that have the strongest capacity to invoke autoreactive T cell responses.

In addition to the detrimental outcomes of host-microbiota interactions, attention has focused on interactions that lead to beneficial physiological states associated with mammalian health. Recently identified mechanisms including microbiota-derived metabolites, regulatory immune cell types, systemic Ig, and intrinsic immune functions that coordinate to enforce peripheral tolerance have been elucidated from experimental models of inflammatory diseases.

The presence of microbiota in the gut of conventionalized mice was shown to have an essential role in generating the CD4+ Foxp3+ Treg compartment (73), a key cellular mediator of regulatory immune responses. Several research groups have identified specific species of commensal bacteria, or consortia of commensal bacteria, that regulate the number, quality, and TCR repertoire of intestinal Tregs. As reviewed recently (74), it is clear that many members of the commensal microbiota have a Treg-inducing capacity; well-documented examples include Bacteroides fragilis (75) and Clostridium (9) (Fig. 1A). Recently, Faith et al. (76) devised a systematic approach to elucidate combinations of human-associated microbial species that can promote intestinal Treg responses in gnotobiotic mice. This method may permit the identification of new immunoregulatory phenotypes that are associated with particular members of the human microbiota.

In parallel with the identification of groups or specific members of the microbiota, more reductionist approaches have identified microbiota-derived molecules and metabolites that stimulate Treg responses. The best-characterized molecules by which the microbiota promote Treg differentiation are bacterial-derived polysaccharide A (PSA) and short-chain fatty acids (SCFAs) (Fig. 1A). PSA was the first documented microbiota-derived molecule that directs the development of a balanced T cell compartment in mice (6). Later, it was found that colonization of mice with PSA-sufficient strains of the commensal B. fragilis or purified PSA protect against experimentally induced colitis and that the protective effect required the presence of a functional IL-10–producing CD4+ T cell compartment (6). Furthermore, prophylactic or therapeutic administration of PSA could protect mice from the induction of EAE, which was dependent on an IL-10–producing Treg population (77). This suggests that the effects of PSA-mediated Treg induction can have a systemic influence over peripheral tolerance in tissues outside of the intestine. SCFAs are another group of immunoregulatory molecules that are primarily derived from the microbiota-mediated digestion of dietary fiber and promote the differentiation of peripheral Tregs (7880). Interestingly, SCFAs, such as acetate, can be detected in the blood circulation (81), suggesting that microbiota-derived SCFAs can have far-ranging effects outside of the intestine.

Along with the well-documented role of Tregs, other recently identified cell types and cytokine–cytokine receptor pathways that connect hematopoietic and nonhematopoietic cells mediate tolerance at the intestinal barrier. For example, ILCs maintain dialogue with intestinal epithelial cells (IECs), intestinal dendritic cells, and other cell types to coordinate protective and regulatory immune responses (82, 83). Of note, group 3 ILCs (ILC3s) can modify the composition and anatomical localization of the microbiota. ILC3s respond to a variety of inflammatory cytokines (i.e., IL-1β, IL-23, IL-6) and microbiota-derived metabolites (i.e., aryl hydrocarbon receptor [AhR] ligands) (83). Following activation, ILC3s produce multiple effector molecules, including the cytokine IL-22, which acts directly on IECs to produce antimicrobial peptides, increase mucus production from goblet cells, and increase fucosylation of the mucus (8486). During steady-state, the physiological outcome of this response is to maintain proper localization and composition of commensal bacteria (87, 88). In response to breakdown of the intestinal barrier from various insults, such as infection with C. rodentium, this pathway reinforces compartmentalization of the pathogen to prevent its systemic dissemination from the intestine (89, 90).

Recently, it was demonstrated that microbiota-derived indole metabolites of tryptophan in the diet can target AhR in Th17 cells and ILC3s to promote production of IL-22 (91). Mice deficient for the adaptor protein CARD9 develop spontaneous colitis and display a loss of bacterial species able to convert tryptophan into ligands for AhR. Supplementation of three Lactobacillus strains capable of metabolizing tryptophan into AhR ligands protected CARD9−/− mice against inflammation in the colon (91). These results expand the evidence that particular metabolites in the gut microenvironment are key to the proper regulation of gut homeostasis. Notably, ILC3s can also directly limit microbiota-specific T cell responses to maintain intestinal homeostasis through Ag presentation on MHC class II (92, 93). Future investigation of ILC3s and other regulatory pathways that influence host-microbiota interactions in the GI tract could provoke the development of novel treatment options for inflammatory disease.

Systemic Ig responses to commensal microbiota also were found to be essential for the maintenance of beneficial host-microbiota interactions. For example, maternally acquired IgA and IgG in neonatal mice leads to dampened T cell–dependent immune responses against commensal bacteria (94). Additionally, systemic IgG responses to Gram-negative bacterial commensals, acquired early and over the course of life, were shown to provide cross-protection against Gram-negative pathogens, such as E. coli and Salmonella, in mice (95). These observations reinforce the concept that microbial composition and the timing of host-commensal interactions provide the foundation for balanced immunity in the intestine. Lastly, the microbiota was observed to promote its own compartmentalization within the intestinal lumen, as well as provide protection to the host from pathogens (96, 97). Recent identification of the gut–vascular barrier system in the small intestine (98), which restricts dissemination of gut bacteria, should provide a new therapeutic framework for constraining disease manifestations that are due to bacterial translocation across the intestinal epithelium.

Established immunosuppressive medicines, such as glucocorticoids, still represent effective front-line therapies to treat inflammatory disease (99), but they have clear disadvantages as a long-term treatment option. Not surprisingly, the medical and biotechnology sectors have taken an interest in translating knowledge of host-microbiota interactions into better standards of care and medicines to treat autoimmune diseases. For example, therapies aiming to adoptively transfer Tregs or promote their in vivo induction in patients are being explored as therapeutic approaches for IBD (100). Additionally, mAbs have been developed to block cytokine pathways implicated in chronic inflammation. For instance, blockade of the Th1 and Th17 cell pathways by targeting the shared anti-p40 subunit of IL-12/IL-23 with the mAb ustekinumab is rapidly advancing through clinical trials as a novel treatment for moderate-to-severe CD (101, 102). ILCs have received increasing attention as novel targets for the treatment of inflammatory diseases given some of their analogous signaling pathways with T cells (103). Clinical investigation on how specific subsets of ILCs respond to approved mAb therapies that target cytokine/cytokine receptor pathways, or novel small molecules targeting transcriptional regulators, will extend and refine the paradigm of ILC involvement in provoking and resolving inflammatory disease in the intestine and in extraintestinal tissues (104106).

In parallel with therapeutic strategies of directly modulating host immune factors, recent approaches have used mechanistic understanding of intestinal microbiota, or microbiota-derived products, for the development of novel treatments (107109). Among others, proposed and emerging therapies include modification of diet (81, 110), more targeted antibiotics to preserve microbiota integrity (111), supplementation of immunoregulatory metabolites, administration of live biotherapeutic products (112), and fecal microbiota transplant therapy (FMT) (113116). Although FMT studies have reported promising results in preclinical and clinical settings for infectious diseases, such as Clostridium difficile, preliminary clinical trials of FMT for IBD revealed limited efficacy (114, 117). No microbiota-based or microbiota-derived medical product has been approved by governmental regulatory agencies for the prevention or treatment of inflammatory disease.

Among other challenges faced (107), a prerequisite for translational development includes distinguishing the temporal and kinetic influences of the microbiota on the host immune system (118). Animal studies emphasize that the functions of several immune cell types arise during a critical period in infancy (118). For example, a subset of RORγt+ Tregs arises in the colon early after birth and prior to weaning (119121). Additionally, germ-free mice display increased frequencies of invariant NKT cells in the colon, which predisposes the mice to environmentally triggered colitis (122). Hyperresponsive invariant NKT cell responses in germ-free mice are reversible through administration of a normal microbiota, or B. fragilis–derived Ags, but only during the first 2 wk of life (122). Nevertheless, many beneficial influences of the microbiota and microbiota-derived biomolecules on immune cell subsets are age independent (118) and conceivably represent the most appropriate treatment options for reversing immune defects present in adulthood.

Interrogation of host-microbiota interactions in the intestine has revealed unexpected and novel insights into human health and disease. Human genetic, epidemiologic, and microbial analyses, paired with complementary animal disease models, support the concept that disrupted host-microbiota interactions with the immune system underlie the chronic nature of many inflammatory diseases. Furthermore, rationally designed therapies that modulate or re-establish beneficial interactions are a promising approach for the treatment of intestinal and extraintestinal inflammatory diseases. Emergent technologies aim to focus research efforts on identifying the scope and relevance of these interactions more systematically and unambiguously.

We thank members of the Sonnenberg Laboratory for discussions and critical reading of the manuscript.

This work was supported by National Institutes of Health Grants DP5OD012116, R01AI123368, R21DK110262, and U01AI095608, the National Institute of Allergy and Infectious Diseases Mucosal Immunology Studies Team, the Crohn’s and Colitis Foundation of America, the Searle Scholars Program, and an American Asthma Foundation Scholar Award.

Abbreviations used in this article:

AhR

aryl hydrocarbon receptor

CD

Crohn’s disease

EAE

experimental autoimmune encephalitis

FMT

fecal microbiota transplant therapy

GI

gastrointestinal

IBD

inflammatory bowel disease

IEC

intestinal epithelial cell

ILC

innate lymphoid cell

ILC3

group 3 ILC

MAMP

microbe-associated molecular pattern

PSA

polysaccharide A

RA

rheumatoid arthritis

SCFA

short-chain fatty acid

SFB

segmented filamentous bacteria

Treg

regulatory T cell

WT

wild-type.

1
Human Microbiome Project Consortium
.
2012
.
Structure, function and diversity of the healthy human microbiome.
Nature
486
:
207
214
.
2
Sender
R.
,
Fuchs
S.
,
Milo
R.
.
2016
.
Are we really vastly outnumbered? revisiting the ratio of bacterial to host cells in humans.
Cell
164
:
337
340
.
3
Hill
D. A.
,
Artis
D.
.
2010
.
Intestinal bacteria and the regulation of immune cell homeostasis.
Annu. Rev. Immunol.
28
:
623
667
.
4
Round
J. L.
,
Mazmanian
S. K.
.
2009
.
The gut microbiota shapes intestinal immune responses during health and disease.
Nat. Rev. Immunol.
9
:
313
323
.
5
Kamada
N.
,
Seo
S. U.
,
Chen
G. Y.
,
Núñez
G.
.
2013
.
Role of the gut microbiota in immunity and inflammatory disease.
Nat. Rev. Immunol.
13
:
321
335
.
6
Mazmanian
S. K.
,
Liu
C. H.
,
Tzianabos
A. O.
,
Kasper
D. L.
.
2005
.
An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system.
Cell
122
:
107
118
.
7
Ivanov
I. I.
,
Frutos
Rde. L.
,
Manel
N.
,
Yoshinaga
K.
,
Rifkin
D. B.
,
Sartor
R. B.
,
Finlay
B. B.
,
Littman
D. R.
.
2008
.
Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine.
Cell Host Microbe
4
:
337
349
.
8
Gaboriau-Routhiau
V.
,
Rakotobe
S.
,
Lécuyer
E.
,
Mulder
I.
,
Lan
A.
,
Bridonneau
C.
,
Rochet
V.
,
Pisi
A.
,
De Paepe
M.
,
Brandi
G.
, et al
.
2009
.
The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses.
Immunity
31
:
677
689
.
9
Atarashi
K.
,
Tanoue
T.
,
Shima
T.
,
Imaoka
A.
,
Kuwahara
T.
,
Momose
Y.
,
Cheng
G.
,
Yamasaki
S.
,
Saito
T.
,
Ohba
Y.
, et al
.
2011
.
Induction of colonic regulatory T cells by indigenous Clostridium species.
Science
331
:
337
341
.
10
Brown
E. M.
,
Sadarangani
M.
,
Finlay
B. B.
.
2013
.
The role of the immune system in governing host-microbe interactions in the intestine.
Nat. Immunol.
14
:
660
667
.
11
Fung
T. C.
,
Artis
D.
,
Sonnenberg
G. F.
.
2014
.
Anatomical localization of commensal bacteria in immune cell homeostasis and disease.
Immunol. Rev.
260
:
35
49
.
12
Zhang
H.
,
Sparks
J. B.
,
Karyala
S. V.
,
Settlage
R.
,
Luo
X. M.
.
2015
.
Host adaptive immunity alters gut microbiota.
ISME J.
9
:
770
781
.
13
Dollé
L.
,
Tran
H. Q.
,
Etienne-Mesmin
L.
,
Chassaing
B.
.
2016
.
Policing of gut microbiota by the adaptive immune system.
BMC Med.
14
:
27
.
14
Ausubel
F. M.
2005
.
Are innate immune signaling pathways in plants and animals conserved?
Nat. Immunol.
6
:
973
979
.
15
Hansson
G. C.
2012
.
Role of mucus layers in gut infection and inflammation.
Curr. Opin. Microbiol.
15
:
57
62
.
16
Mantis
N. J.
,
Rol
N.
,
Corthésy
B.
.
2011
.
Secretory IgA’s complex roles in immunity and mucosal homeostasis in the gut.
Mucosal Immunol.
4
:
603
611
.
17
Bevins
C. L.
,
Salzman
N. H.
.
2011
.
Paneth cells, antimicrobial peptides and maintenance of intestinal homeostasis.
Nat. Rev. Microbiol.
9
:
356
368
.
18
Mukherjee
S.
,
Hooper
L. V.
.
2015
.
Antimicrobial defense of the intestine.
Immunity
42
:
28
39
.
19
Maynard
C. L.
,
Elson
C. O.
,
Hatton
R. D.
,
Weaver
C. T.
.
2012
.
Reciprocal interactions of the intestinal microbiota and immune system.
Nature
489
:
231
241
.
20
Maloy
K. J.
,
Powrie
F.
.
2011
.
Intestinal homeostasis and its breakdown in inflammatory bowel disease.
Nature
474
:
298
306
.
21
Khor
B.
,
Gardet
A.
,
Xavier
R. J.
.
2011
.
Genetics and pathogenesis of inflammatory bowel disease.
Nature
474
:
307
317
.
22
Liu
T. C.
,
Stappenbeck
T. S.
.
2016
.
Genetics and pathogenesis of inflammatory bowel disease.
Annu. Rev. Pathol.
11
:
127
148
.
23
Ananthakrishnan
A. N.
2015
.
Epidemiology and risk factors for IBD.
Nat. Rev. Gastroenterol. Hepatol.
12
:
205
217
.
24
Agarwal
S.
,
Mayer
L.
.
2013
.
Diagnosis and treatment of gastrointestinal disorders in patients with primary immunodeficiency.
Clin. Gastroenterol. Hepatol.
11
:
1050
1063
.
25
Glocker
E. O.
,
Kotlarz
D.
,
Boztug
K.
,
Gertz
E. M.
,
Schäffer
A. A.
,
Noyan
F.
,
Perro
M.
,
Diestelhorst
J.
,
Allroth
A.
,
Murugan
D.
, et al
.
2009
.
Inflammatory bowel disease and mutations affecting the interleukin-10 receptor.
N. Engl. J. Med.
361
:
2033
2045
.
26
Shah
N.
,
Kammermeier
J.
,
Elawad
M.
,
Glocker
E. O.
.
2012
.
Interleukin-10 and interleukin-10-receptor defects in inflammatory bowel disease.
Curr. Allergy Asthma Rep.
12
:
373
379
.
27
Engelhardt
K. R.
,
Grimbacher
B.
.
2014
.
IL-10 in humans: lessons from the gut, IL-10/IL-10 receptor deficiencies, and IL-10 polymorphisms.
Curr. Top. Microbiol. Immunol.
380
:
1
18
.
28
Kelsen
J. R.
,
Baldassano
R. N.
,
Artis
D.
,
Sonnenberg
G. F.
.
2015
.
Maintaining intestinal health: the genetics and immunology of very early onset inflammatory bowel disease.
Cell Mol. Gastroenterol. Hepatol.
1
:
462
476
.
29
Hugot
J. P.
,
Chamaillard
M.
,
Zouali
H.
,
Lesage
S.
,
Cézard
J. P.
,
Belaiche
J.
,
Almer
S.
,
Tysk
C.
,
O’Morain
C. A.
,
Gassull
M.
, et al
.
2001
.
Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn’s disease.
Nature
411
:
599
603
.
30
Ogura
Y.
,
Bonen
D. K.
,
Inohara
N.
,
Nicolae
D. L.
,
Chen
F. F.
,
Ramos
R.
,
Britton
H.
,
Moran
T.
,
Karaliuskas
R.
,
Duerr
R. H.
, et al
.
2001
.
A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease.
Nature
411
:
603
606
.
31
Mizoguchi
A.
,
Takeuchi
T.
,
Himuro
H.
,
Okada
T.
,
Mizoguchi
E.
.
2016
.
Genetically engineered mouse models for studying inflammatory bowel disease.
J. Pathol.
238
:
205
219
.
32
Spehlmann
M. E.
,
Begun
A. Z.
,
Burghardt
J.
,
Lepage
P.
,
Raedler
A.
,
Schreiber
S.
.
2008
.
Epidemiology of inflammatory bowel disease in a German twin cohort: results of a nationwide study.
Inflamm. Bowel Dis.
14
:
968
976
.
33
Lee
D.
,
Albenberg
L.
,
Compher
C.
,
Baldassano
R.
,
Piccoli
D.
,
Lewis
J. D.
,
Wu
G. D.
.
2015
.
Diet in the pathogenesis and treatment of inflammatory bowel diseases.
Gastroenterology
148
:
1087
1106
.
34
De Filippo
C.
,
Cavalieri
D.
,
Di Paola
M.
,
Ramazzotti
M.
,
Poullet
J. B.
,
Massart
S.
,
Collini
S.
,
Pieraccini
G.
,
Lionetti
P.
.
2010
.
Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.
Proc. Natl. Acad. Sci. USA
107
:
14691
14696
.
35
Wu
G. D.
,
Chen
J.
,
Hoffmann
C.
,
Bittinger
K.
,
Chen
Y. Y.
,
Keilbaugh
S. A.
,
Bewtra
M.
,
Knights
D.
,
Walters
W. A.
,
Knight
R.
, et al
.
2011
.
Linking long-term dietary patterns with gut microbial enterotypes.
Science
334
:
105
108
.
36
David
L. A.
,
Maurice
C. F.
,
Carmody
R. N.
,
Gootenberg
D. B.
,
Button
J. E.
,
Wolfe
B. E.
,
Ling
A. V.
,
Devlin
A. S.
,
Varma
Y.
,
Fischbach
M. A.
, et al
.
2014
.
Diet rapidly and reproducibly alters the human gut microbiome.
Nature
505
:
559
563
.
37
Manichanh
C.
,
Rigottier-Gois
L.
,
Bonnaud
E.
,
Gloux
K.
,
Pelletier
E.
,
Frangeul
L.
,
Nalin
R.
,
Jarrin
C.
,
Chardon
P.
,
Marteau
P.
, et al
.
2006
.
Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach.
Gut
55
:
205
211
.
38
Frank
D. N.
,
St Amand
A. L.
,
Feldman
R. A.
,
Boedeker
E. C.
,
Harpaz
N.
,
Pace
N. R.
.
2007
.
Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases.
Proc. Natl. Acad. Sci. USA
104
:
13780
13785
.
39
Fujimoto
T.
,
Imaeda
H.
,
Takahashi
K.
,
Kasumi
E.
,
Bamba
S.
,
Fujiyama
Y.
,
Andoh
A.
.
2013
.
Decreased abundance of Faecalibacterium prausnitzii in the gut microbiota of Crohn’s disease.
J. Gastroenterol. Hepatol.
28
:
613
619
.
40
Wang
W.
,
Chen
L.
,
Zhou
R.
,
Wang
X.
,
Song
L.
,
Huang
S.
,
Wang
G.
,
Xia
B.
.
2014
.
Increased proportions of Bifidobacterium and the Lactobacillus group and loss of butyrate-producing bacteria in inflammatory bowel disease.
J. Clin. Microbiol.
52
:
398
406
.
41
Garrett
W. S.
,
Lord
G. M.
,
Punit
S.
,
Lugo-Villarino
G.
,
Mazmanian
S. K.
,
Ito
S.
,
Glickman
J. N.
,
Glimcher
L. H.
.
2007
.
Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system.
Cell
131
:
33
45
.
42
Garrett
W. S.
,
Gallini
C. A.
,
Yatsunenko
T.
,
Michaud
M.
,
DuBois
A.
,
Delaney
M. L.
,
Punit
S.
,
Karlsson
M.
,
Bry
L.
,
Glickman
J. N.
, et al
.
2010
.
Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis.
Cell Host Microbe
8
:
292
300
.
43
Elinav
E.
,
Strowig
T.
,
Kau
A. L.
,
Henao-Mejia
J.
,
Thaiss
C. A.
,
Booth
C. J.
,
Peaper
D. R.
,
Bertin
J.
,
Eisenbarth
S. C.
,
Gordon
J. I.
,
Flavell
R. A.
.
2011
.
NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis.
Cell
145
:
745
757
.
44
Couturier-Maillard
A.
,
Secher
T.
,
Rehman
A.
,
Normand
S.
,
De Arcangelis
A.
,
Haesler
R.
,
Huot
L.
,
Grandjean
T.
,
Bressenot
A.
,
Delanoye-Crespin
A.
, et al
.
2013
.
NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer.
J. Clin. Invest.
123
:
700
711
.
45
Ivanov
I. I.
,
Atarashi
K.
,
Manel
N.
,
Brodie
E. L.
,
Shima
T.
,
Karaoz
U.
,
Wei
D.
,
Goldfarb
K. C.
,
Santee
C. A.
,
Lynch
S. V.
, et al
.
2009
.
Induction of intestinal Th17 cells by segmented filamentous bacteria.
Cell
139
:
485
498
.
46
Sano
T.
,
Huang
W.
,
Hall
J. A.
,
Yang
Y.
,
Chen
A.
,
Gavzy
S. J.
,
Lee
J. Y.
,
Ziel
J. W.
,
Miraldi
E. R.
,
Domingos
A. I.
, et al
.
2015
.
An IL-23R/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses. [Published erratum appears in 2016 Cell 164(1–2): 324.]
Cell
163
:
381
393
.
47
Atarashi
K.
,
Tanoue
T.
,
Ando
M.
,
Kamada
N.
,
Nagano
Y.
,
Narushima
S.
,
Suda
W.
,
Imaoka
A.
,
Setoyama
H.
,
Nagamori
T.
, et al
.
2015
.
Th17 cell induction by adhesion of microbes to intestinal epithelial cells.
Cell
163
:
367
380
.
48
Coccia
M.
,
Harrison
O. J.
,
Schiering
C.
,
Asquith
M. J.
,
Becher
B.
,
Powrie
F.
,
Maloy
K. J.
.
2012
.
IL-1β mediates chronic intestinal inflammation by promoting the accumulation of IL-17A secreting innate lymphoid cells and CD4(+) Th17 cells.
J. Exp. Med.
209
:
1595
1609
.
49
Sonnenberg
G. F.
,
Artis
D.
.
2012
.
Innate lymphoid cell interactions with microbiota: implications for intestinal health and disease.
Immunity
37
:
601
610
.
50
Lupp
C.
,
Robertson
M. L.
,
Wickham
M. E.
,
Sekirov
I.
,
Champion
O. L.
,
Gaynor
E. C.
,
Finlay
B. B.
.
2007
.
Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae.
Cell Host Microbe
2
:
119
129
.
51
Winter
S. E.
,
Winter
M. G.
,
Xavier
M. N.
,
Thiennimitr
P.
,
Poon
V.
,
Keestra
A. M.
,
Laughlin
R. C.
,
Gomez
G.
,
Wu
J.
,
Lawhon
S. D.
, et al
.
2013
.
Host-derived nitrate boosts growth of E. coli in the inflamed gut.
Science
339
:
708
711
.
52
Wu
H. J.
,
Wu
E.
.
2012
.
The role of gut microbiota in immune homeostasis and autoimmunity.
Gut Microbes
3
:
4
14
.
53
Ferreira
C. M.
,
Vieira
A. T.
,
Vinolo
M. A.
,
Oliveira
F. A.
,
Curi
R.
,
Martins
Fdos. S.
.
2014
.
The central role of the gut microbiota in chronic inflammatory diseases.
J. Immunol. Res.
2014
:
689492
.
54
Ho
J. T.
,
Chan
G. C.
,
Li
J. C.
.
2015
.
Systemic effects of gut microbiota and its relationship with disease and modulation.
BMC Immunol.
16
:
21
.
55
Zárate-Bladés
C. R.
,
Horai
R.
,
Caspi
R. R.
.
2016
.
Regulation of autoimmunity by the microbiome.
DNA Cell Biol.
35
:
455
458
.
56
Vavricka
S. R.
,
Schoepfer
A.
,
Scharl
M.
,
Lakatos
P. L.
,
Navarini
A.
,
Rogler
G.
.
2015
.
Extraintestinal manifestations of inflammatory bowel disease.
Inflamm. Bowel Dis.
21
:
1982
1992
.
57
Richard-Miceli
C.
,
Criswell
L. A.
.
2012
.
Emerging patterns of genetic overlap across autoimmune disorders.
Genome Med.
4
:
6
.
58
Bogdanos
D. P.
,
Smyk
D. S.
,
Rigopoulou
E. I.
,
Mytilinaiou
M. G.
,
Heneghan
M. A.
,
Selmi
C.
,
Gershwin
M. E.
.
2012
.
Twin studies in autoimmune disease: genetics, gender and environment.
J. Autoimmun.
38
:
J156
J169
.
59
Getts
D. R.
,
Chastain
E. M.
,
Terry
R. L.
,
Miller
S. D.
.
2013
.
Virus infection, antiviral immunity, and autoimmunity.
Immunol. Rev.
255
:
197
209
.
60
Ochoa-Repáraz
J.
,
Mielcarz
D. W.
,
Ditrio
L. E.
,
Burroughs
A. R.
,
Foureau
D. M.
,
Haque-Begum
S.
,
Kasper
L. H.
.
2009
.
Role of gut commensal microflora in the development of experimental autoimmune encephalomyelitis.
J. Immunol.
183
:
6041
6050
.
61
Lee
Y. K.
,
Menezes
J. S.
,
Umesaki
Y.
,
Mazmanian
S. K.
.
2011
.
Proinflammatory T-cell responses to gut microbiota promote experimental autoimmune encephalomyelitis.
Proc. Natl. Acad. Sci. USA
108
(
Suppl. 1
):
4615
4622
.
62
Wu
H. J.
,
Ivanov
I. I.
,
Darce
J.
,
Hattori
K.
,
Shima
T.
,
Umesaki
Y.
,
Littman
D. R.
,
Benoist
C.
,
Mathis
D.
.
2010
.
Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells.
Immunity
32
:
815
827
.
63
Teng
F.
,
Klinger
C. N.
,
Felix
K. M.
,
Bradley
C. P.
,
Wu
E.
,
Tran
N. L.
,
Umesaki
Y.
,
Wu
H. J.
.
2016
.
Gut microbiota drive autoimmune arthritis by promoting differentiation and migration of Peyer’s patch T follicular helper cells.
Immunity
44
:
875
888
.
64
Campisi
L.
,
Barbet
G.
,
Ding
Y.
,
Esplugues
E.
,
Flavell
R. A.
,
Blander
J. M.
.
2016
.
Apoptosis in response to microbial infection induces autoreactive TH17 cells.
Nat. Immunol.
17
:
1084
1092
.
65
Oldstone
M. B.
1987
.
Molecular mimicry and autoimmune disease.
Cell
50
:
819
820
.
66
Yurkovetskiy
L. A.
,
Pickard
J. M.
,
Chervonsky
A. V.
.
2015
.
Microbiota and autoimmunity: exploring new avenues.
Cell Host Microbe
17
:
548
552
.
67
Harkiolaki
M.
,
Holmes
S. L.
,
Svendsen
P.
,
Gregersen
J. W.
,
Jensen
L. T.
,
McMahon
R.
,
Friese
M. A.
,
van Boxel
G.
,
Etzensperger
R.
,
Tzartos
J. S.
, et al
.
2009
.
T cell-mediated autoimmune disease due to low-affinity crossreactivity to common microbial peptides.
Immunity
30
:
348
357
.
68
Horai
R.
,
Zárate-Bladés
C. R.
,
Dillenburg-Pilla
P.
,
Chen
J.
,
Kielczewski
J. L.
,
Silver
P. B.
,
Jittayasothorn
Y.
,
Chan
C. C.
,
Yamane
H.
,
Honda
K.
,
Caspi
R. R.
.
2015
.
Microbiota-dependent activation of an autoreactive T cell receptor provokes autoimmunity in an immunologically privileged site.
Immunity
43
:
343
353
.
69
Kadowaki
A.
,
Miyake
S.
,
Saga
R.
,
Chiba
A.
,
Mochizuki
H.
,
Yamamura
T.
.
2016
.
Gut environment-induced intraepithelial autoreactive CD4(+) T cells suppress central nervous system autoimmunity via LAG-3.
Nat. Commun.
7
:
11639
.
70
Palm
N. W.
,
de Zoete
M. R.
,
Cullen
T. W.
,
Barry
N. A.
,
Stefanowski
J.
,
Hao
L.
,
Degnan
P. H.
,
Hu
J.
,
Peter
I.
,
Zhang
W.
, et al
.
2014
.
Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease.
Cell
158
:
1000
1010
.
71
Kau
A. L.
,
Planer
J. D.
,
Liu
J.
,
Rao
S.
,
Yatsunenko
T.
,
Trehan
I.
,
Manary
M. J.
,
Liu
T. C.
,
Stappenbeck
T. S.
,
Maleta
K. M.
, et al
.
2015
.
Functional characterization of IgA-targeted bacterial taxa from undernourished Malawian children that produce diet-dependent enteropathy.
Sci. Transl. Med.
7
:
276ra24
.
72
Bunker
J. J.
,
Flynn
T. M.
,
Koval
J. C.
,
Shaw
D. G.
,
Meisel
M.
,
McDonald
B. D.
,
Ishizuka
I. E.
,
Dent
A. L.
,
Wilson
P. C.
,
Jabri
B.
, et al
.
2015
.
Innate and adaptive humoral responses coat distinct commensal bacteria with immunoglobulin A.
Immunity
43
:
541
553
.
73
Strauch
U. G.
,
Obermeier
F.
,
Grunwald
N.
,
Gürster
S.
,
Dunger
N.
,
Schultz
M.
,
Griese
D. P.
,
Mähler
M.
,
Schölmerich
J.
,
Rath
H. C.
.
2005
.
Influence of intestinal bacteria on induction of regulatory T cells: lessons from a transfer model of colitis.
Gut
54
:
1546
1552
.
74
Tanoue
T.
,
Atarashi
K.
,
Honda
K.
.
2016
.
Development and maintenance of intestinal regulatory T cells.
Nat. Rev. Immunol.
16
:
295
309
.
75
Round
J. L.
,
Lee
S. M.
,
Li
J.
,
Tran
G.
,
Jabri
B.
,
Chatila
T. A.
,
Mazmanian
S. K.
.
2011
.
The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota.
Science
332
:
974
977
.
76
Faith
J. J.
,
Ahern
P. P.
,
Ridaura
V. K.
,
Cheng
J.
,
Gordon
J. I.
.
2014
.
Identifying gut microbe-host phenotype relationships using combinatorial communities in gnotobiotic mice.
Sci. Transl. Med.
6
:
220ra11
.
77
Ochoa-Repáraz
J.
,
Mielcarz
D. W.
,
Wang
Y.
,
Begum-Haque
S.
,
Dasgupta
S.
,
Kasper
D. L.
,
Kasper
L. H.
.
2010
.
A polysaccharide from the human commensal Bacteroides fragilis protects against CNS demyelinating disease.
Mucosal Immunol.
3
:
487
495
.
78
Smith
P. M.
,
Howitt
M. R.
,
Panikov
N.
,
Michaud
M.
,
Gallini
C. A.
,
Bohlooly-Y
M.
,
Glickman
J. N.
,
Garrett
W. S.
.
2013
.
The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis.
Science
341
:
569
573
.
79
Arpaia
N.
,
Campbell
C.
,
Fan
X.
,
Dikiy
S.
,
van der Veeken
J.
,
deRoos
P.
,
Liu
H.
,
Cross
J. R.
,
Pfeffer
K.
,
Coffer
P. J.
,
Rudensky
A. Y.
.
2013
.
Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation.
Nature
504
:
451
455
.
80
Furusawa
Y.
,
Obata
Y.
,
Fukuda
S.
,
Endo
T. A.
,
Nakato
G.
,
Takahashi
D.
,
Nakanishi
Y.
,
Uetake
C.
,
Kato
K.
,
Kato
T.
, et al
.
2013
.
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
Nature
504
:
446
450
.
81
Richards
J. L.
,
Yap
Y. A.
,
McLeod
K. H.
,
Mackay
C. R.
,
Mariño
E.
.
2016
.
Dietary metabolites and the gut microbiota: an alternative approach to control inflammatory and autoimmune diseases.
Clin. Transl. Immunology
5
:
e82
.
82
Sonnenberg
G. F.
,
Artis
D.
.
2015
.
Innate lymphoid cells in the initiation, regulation and resolution of inflammation.
Nat. Med.
21
:
698
708
.
83
Klose
C. S.
,
Artis
D.
.
2016
.
Innate lymphoid cells as regulators of immunity, inflammation and tissue homeostasis.
Nat. Immunol.
17
:
765
774
.
84
Pickard
J. M.
,
Maurice
C. F.
,
Kinnebrew
M. A.
,
Abt
M. C.
,
Schenten
D.
,
Golovkina
T. V.
,
Bogatyrev
S. R.
,
Ismagilov
R. F.
,
Pamer
E. G.
,
Turnbaugh
P. J.
,
Chervonsky
A. V.
.
2014
.
Rapid fucosylation of intestinal epithelium sustains host-commensal symbiosis in sickness.
Nature
514
:
638
641
.
85
Pham
T. A.
,
Clare
S.
,
Goulding
D.
,
Arasteh
J. M.
,
Stares
M. D.
,
Browne
H. P.
,
Keane
J. A.
,
Page
A. J.
,
Kumasaka
N.
,
Kane
L.
, et al
Sanger Mouse Genetics Project
.
2014
.
Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.
Cell Host Microbe
16
:
504
516
.
86
Goto
Y.
,
Obata
T.
,
Kunisawa
J.
,
Sato
S.
,
Ivanov
I. I.
,
Lamichhane
A.
,
Takeyama
N.
,
Kamioka
M.
,
Sakamoto
M.
,
Matsuki
T.
, et al
.
2014
.
Innate lymphoid cells regulate intestinal epithelial cell glycosylation.
Science
345
:
1254009
.
87
Sonnenberg
G. F.
,
Monticelli
L. A.
,
Alenghat
T.
,
Fung
T. C.
,
Hutnick
N. A.
,
Kunisawa
J.
,
Shibata
N.
,
Grunberg
S.
,
Sinha
R.
,
Zahm
A. M.
, et al
.
2012
.
Innate lymphoid cells promote anatomical containment of lymphoid-resident commensal bacteria.
Science
336
:
1321
1325
.
88
Fung
T. C.
,
Bessman
N. J.
,
Hepworth
M. R.
,
Kumar
N.
,
Shibata
N.
,
Kobuley
D.
,
Wang
K.
,
Ziegler
C. G.
,
Goc
J.
,
Shima
T.
, et al
.
2016
.
Lymphoid-tissue-resident commensal bacteria promote members of the IL-10 cytokine family to establish mutualism.
Immunity
44
:
634
646
.
89
Zheng
Y.
,
Valdez
P. A.
,
Danilenko
D. M.
,
Hu
Y.
,
Sa
S. M.
,
Gong
Q.
,
Abbas
A. R.
,
Modrusan
Z.
,
Ghilardi
N.
,
de Sauvage
F. J.
,
Ouyang
W.
.
2008
.
Interleukin-22 mediates early host defense against attaching and effacing bacterial pathogens.
Nat. Med.
14
:
282
289
.
90
Sonnenberg
G. F.
,
Monticelli
L. A.
,
Elloso
M. M.
,
Fouser
L. A.
,
Artis
D.
.
2011
.
CD4(+) lymphoid tissue-inducer cells promote innate immunity in the gut.
Immunity
34
:
122
134
.
91
Lamas
B.
,
Richard
M. L.
,
Leducq
V.
,
Pham
H. P.
,
Michel
M. L.
,
Da Costa
G.
,
Bridonneau
C.
,
Jegou
S.
,
Hoffmann
T. W.
,
Natividad
J. M.
, et al
.
2016
.
CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.
Nat. Med.
22
:
598
605
.
92
Hepworth
M. R.
,
Monticelli
L. A.
,
Fung
T. C.
,
Ziegler
C. G.
,
Grunberg
S.
,
Sinha
R.
,
Mantegazza
A. R.
,
Ma
H. L.
,
Crawford
A.
,
Angelosanto
J. M.
, et al
.
2013
.
Innate lymphoid cells regulate CD4+ T-cell responses to intestinal commensal bacteria.
Nature
498
:
113
117
.
93
Hepworth
M. R.
,
Fung
T. C.
,
Masur
S. H.
,
Kelsen
J. R.
,
McConnell
F. M.
,
Dubrot
J.
,
Withers
D. R.
,
Hugues
S.
,
Farrar
M. A.
,
Reith
W.
, et al
.
2015
.
Immune tolerance. Group 3 innate lymphoid cells mediate intestinal selection of commensal bacteria-specific CD4+ T cells.
Science
348
:
1031
1035
.
94
Koch
M. A.
,
Reiner
G. L.
,
Lugo
K. A.
,
Kreuk
L. S.
,
Stanbery
A. G.
,
Ansaldo
E.
,
Seher
T. D.
,
Ludington
W. B.
,
Barton
G. M.
.
2016
.
Maternal IgG and IgA antibodies dampen mucosal T helper cell responses in early life.
Cell
165
:
827
841
.
95
Zeng
M. Y.
,
Cisalpino
D.
,
Varadarajan
S.
,
Hellman
J.
,
Warren
H. S.
,
Cascalho
M.
,
Inohara
N.
,
Núñez
G.
.
2016
.
Gut microbiota-induced immunoglobulin G controls systemic infection by symbiotic bacteria and pathogens.
Immunity
44
:
647
658
.
96
Diehl
G. E.
,
Longman
R. S.
,
Zhang
J. X.
,
Breart
B.
,
Galan
C.
,
Cuesta
A.
,
Schwab
S. R.
,
Littman
D. R.
.
2013
.
Microbiota restricts trafficking of bacteria to mesenteric lymph nodes by CX(3)CR1(hi) cells.
Nature
494
:
116
120
.
97
Knoop
K. A.
,
McDonald
K. G.
,
Kulkarni
D. H.
,
Newberry
R. D.
.
2016
.
Antibiotics promote inflammation through the translocation of native commensal colonic bacteria.
Gut
65
:
1100
1109
.
98
Spadoni
I.
,
Zagato
E.
,
Bertocchi
A.
,
Paolinelli
R.
,
Hot
E.
,
Di Sabatino
A.
,
Caprioli
F.
,
Bottiglieri
L.
,
Oldani
A.
,
Viale
G.
, et al
.
2015
.
A gut-vascular barrier controls the systemic dissemination of bacteria.
Science
350
:
830
834
.
99
Coutinho
A. E.
,
Chapman
K. E.
.
2011
.
The anti-inflammatory and immunosuppressive effects of glucocorticoids, recent developments and mechanistic insights.
Mol. Cell. Endocrinol.
335
:
2
13
.
100
Geem
D.
,
Harusato
A.
,
Flannigan
K.
,
Denning
T. L.
.
2015
.
Harnessing regulatory T cells for the treatment of inflammatory bowel disease.
Inflamm. Bowel Dis.
21
:
1409
1418
.
101
O’Toole
A.
,
Moss
A. C.
.
2015
.
Optimizing biologic agents in ulcerative colitis and Crohn’s disease.
Curr. Gastroenterol. Rep.
17
:
32
.
102
Simon
E. G.
,
Ghosh
S.
,
Iacucci
M.
,
Moran
G. W.
.
2016
.
Ustekinumab for the treatment of Crohn’s disease: can it find its niche?
Therap. Adv. Gastroenterol.
9
:
26
36
.
103
Goldberg
R.
,
Prescott
N.
,
Lord
G. M.
,
MacDonald
T. T.
,
Powell
N.
.
2015
.
The unusual suspects--innate lymphoid cells as novel therapeutic targets in IBD.
Nat. Rev. Gastroenterol. Hepatol.
12
:
271
283
.
104
Perry
J. S.
,
Han
S.
,
Xu
Q.
,
Herman
M. L.
,
Kennedy
L. B.
,
Csako
G.
,
Bielekova
B.
.
2012
.
Inhibition of LTi cell development by CD25 blockade is associated with decreased intrathecal inflammation in multiple sclerosis.
Sci. Transl. Med.
4
:
145ra106
.
105
Villanova
F.
,
Flutter
B.
,
Tosi
I.
,
Grys
K.
,
Sreeneebus
H.
,
Perera
G. K.
,
Chapman
A.
,
Smith
C. H.
,
Di Meglio
P.
,
Nestle
F. O.
.
2014
.
Characterization of innate lymphoid cells in human skin and blood demonstrates increase of NKp44+ ILC3 in psoriasis.
J. Invest. Dermatol.
134
:
984
991
.
106
Withers
D. R.
,
Hepworth
M. R.
,
Wang
X.
,
Mackley
E. C.
,
Halford
E. E.
,
Dutton
E. E.
,
Marriott
C. L.
,
Brucklacher-Waldert
V.
,
Veldhoen
M.
,
Kelsen
J.
, et al
.
2016
.
Transient inhibition of ROR-γt therapeutically limits intestinal inflammation by reducing TH17 cells and preserving group 3 innate lymphoid cells.
Nat. Med.
22
:
319
323
.
107
Olle
B.
2013
.
Medicines from microbiota.
Nat. Biotechnol.
31
:
309
315
.
108
Marchesi
J. R.
,
Adams
D. H.
,
Fava
F.
,
Hermes
G. D.
,
Hirschfield
G. M.
,
Hold
G.
,
Quraishi
M. N.
,
Kinross
J.
,
Smidt
H.
,
Tuohy
K. M.
, et al
.
2016
.
The gut microbiota and host health: a new clinical frontier.
Gut
65
:
330
339
.
109
Scott
K. P.
,
Antoine
J. M.
,
Midtvedt
T.
,
van Hemert
S.
.
2015
.
Manipulating the gut microbiota to maintain health and treat disease.
Microb. Ecol. Health Dis.
26
:
25877
.
110
Olendzki
B. C.
,
Silverstein
T. D.
,
Persuitte
G. M.
,
Ma
Y.
,
Baldwin
K. R.
,
Cave
D.
.
2014
.
An anti-inflammatory diet as treatment for inflammatory bowel disease: a case series report.
Nutr. J.
13
:
5
.
111
Yao
J.
,
Carter
R. A.
,
Vuagniaux
G.
,
Barbier
M.
,
Rosch
J. W.
,
Rock
C. O.
.
2016
.
A pathogen-selective antibiotic minimizes disturbance to the microbiome.
Antimicrob. Agents Chemother.
60
:
4264
4273
.
112
Ross
J. J.
,
Boucher
P. E.
,
Bhattacharyya
S. P.
,
Kopecko
D. J.
,
Sutkowski
E. M.
,
Rohan
P. J.
,
Chandler
D. K.
,
Vaillancourt
J.
.
2008
.
Considerations in the development of live biotherapeutic products for clinical use.
Curr. Issues Mol. Biol.
10
:
13
16
.
113
Borody
T. J.
,
Khoruts
A.
.
2011
.
Fecal microbiota transplantation and emerging applications.
Nat. Rev. Gastroenterol. Hepatol.
9
:
88
96
.
114
Moayyedi
P.
,
Surette
M. G.
,
Kim
P. T.
,
Libertucci
J.
,
Wolfe
M.
,
Onischi
C.
,
Armstrong
D.
,
Marshall
J. K.
,
Kassam
Z.
,
Reinisch
W.
,
Lee
C. H.
.
2015
.
Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial.
Gastroenterology
149
:
102
109.e6
.
115
Anderson
J. L.
,
Edney
R. J.
,
Whelan
K.
.
2012
.
Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease.
Aliment. Pharmacol. Ther.
36
:
503
516
.
116
Suskind
D. L.
,
Brittnacher
M. J.
,
Wahbeh
G.
,
Shaffer
M. L.
,
Hayden
H. S.
,
Qin
X.
,
Singh
N.
,
Damman
C. J.
,
Hager
K. R.
,
Nielson
H.
,
Miller
S. I.
.
2015
.
Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease.
Inflamm. Bowel Dis.
21
:
556
563
.
117
Rossen
N. G.
,
Fuentes
S.
,
van der Spek
M. J.
,
Tijssen
J. G.
,
Hartman
J. H.
,
Duflou
A.
,
Lowenberg
M.
,
van den Brink
G. R.
,
Mathus-Vliegen
E. M.
,
de Vos
W. M.
, et al
.
2015
.
Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis.
Gastroenterology
149
:
110
118.e4
.
118
Gensollen
T.
,
Iyer
S. S.
,
Kasper
D. L.
,
Blumberg
R. S.
.
2016
.
How colonization by microbiota in early life shapes the immune system.
Science
352
:
539
544
.
119
Kim
K. S.
,
Hong
S. W.
,
Han
D.
,
Yi
J.
,
Jung
J.
,
Yang
B. G.
,
Lee
J. Y.
,
Lee
M.
,
Surh
C. D.
.
2016
.
Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine.
Science
351
:
858
863
.
120
Ohnmacht
C.
,
Park
J. H.
,
Cording
S.
,
Wing
J. B.
,
Atarashi
K.
,
Obata
Y.
,
Gaboriau-Routhiau
V.
,
Marques
R.
,
Dulauroy
S.
,
Fedoseeva
M.
, et al
.
2015
.
The microbiota regulates type 2 immunity through RORγt+ T cells.
Science
349
:
989
993
.
121
Sefik
E.
,
Geva-Zatorsky
N.
,
Oh
S.
,
Konnikova
L.
,
Zemmour
D.
,
McGuire
A. M.
,
Burzyn
D.
,
Ortiz-Lopez
A.
,
Lobera
M.
,
Yang
J.
, et al
.
2015
.
Individual intestinal symbionts induce a distinct population of RORγ+ regulatory T cells.
Science
349
:
993
997
.
122
Olszak
T.
,
An
D.
,
Zeissig
S.
,
Vera
M. P.
,
Richter
J.
,
Franke
A.
,
Glickman
J. N.
,
Siebert
R.
,
Baron
R. M.
,
Kasper
D. L.
,
Blumberg
R. S.
.
2012
.
Microbial exposure during early life has persistent effects on natural killer T cell function.
Science
336
:
489
493
.

The authors have no financial conflicts of interest.