Role of the Gut Microbiota in Immunity and Inflammatory Disease

REVIEWS

Role of the gut microbiota in immunity and inflammatory disease

Nobuhiko Kamada1, Sang‑Uk Seo1, Grace Y. Chen2 and Gabriel Núñez1 Abstract | The mammalian intestine is colonized by trillions of microorganisms, most of which are bacteria that have co‑evolved with the host in a symbiotic relationship. The collection of microbial populations that reside on and in the host is commonly referred to as the microbiota. A principal function of the microbiota is to protect the intestine against colonization by exogenous pathogens and potentially harmful indigenous microorganisms via several mechanisms, which include direct competition for limited nutrients and the modulation of host immune responses. Conversely, pathogens have developed strategies to promote their replication in the presence of competing microbiota. Breakdown of the normal microbial community increases the risk of pathogen infection, the overgrowth of harmful pathobionts and inflammatory disease. Understanding the interaction of the microbiota with pathogens and the host might provide new insights into the pathogenesis of disease, as well as novel avenues for preventing and treating intestinal and systemic disorders.

Microbiota-dependent lymphoid development Gut-associated lymphoid The skin and mucosal surfaces of vertebrates are colo‑ tissues nized by large numbers of microorganisms, includ‑ GALTs. The study of germ-free mice led to the discov‑ (GALTs). Lymphoid structures ing bacteria, fungi, parasites and viruses, commonly ery that the gut microbiota is required for the normal and aggregates that are referred to as the microbiota. In humans, more than generation and/or maturation of GALTs. GALTs are associated with the intestinal 100 trillion microorganisms, mostly bacteria, colonize immune structures in which antigen can be taken up mucosa, specifically the tonsils, Peyer’s patches, lymphoid the oral–gastrointestinal tract, and most of these micro‑ and presented by antigen-presenting cells, and there‑ follicles, appendix or cecal organisms reside in the distal intestine. Millions of years fore these structures have important roles in lympho‑ patch, and mesenteric lymph of co‑evolution between the host and microorganisms cyte functions that lead to inflammation or tolerance. nodes. They are enriched in have led to a mutualistic relationship in which the micro‑ GALTs include the Peyer’s patches, crypt patches and conventional and 6–8 unconventional lymphocytes, biota contributes to many host physiological processes isolated lymphoid follicles (ILFs) . In the fetus, lym‑ and in specialized dendritic cell and, in turn, the host provides niches and nutrients phoid tissue inducer (LTi) cells promote the devel‑ and macrophage subsets. for microbial survival1. The main contributions of the opment of Peyer’s patches in the absence of resident microbiota to the host include the digestion and fermen‑ bacteria, although Peyer’s patches in germ-free mice are tation of carbohydrates, the production of vitamins, the smaller in size than those in specific-pathogen-free mice9. development of gut-associated lymphoid tissues (GALTs), Unlike Peyer’s patches, the maturation of ILFs and crypt 7,10 1Department of Pathology the polarization of gut-specific immune responses and patches requires stimulation by the gut microbiota . 1–3 and Comprehensive Cancer the prevention of colonization by pathogens . In turn, Specifically, incomplete maturation of ileal and colonic Center, University of gut immune responses that are induced by commensal ILFs is observed in mice that are deficient in various Michigan, Ann Arbor 48109, populations regulate the composition of the micro‑ pattern recognition receptors (PRRs) (BOX 1) that are acti‑ Michigan, USA. 2Department of Internal biota. Thus, a complex interplay between the host vated by bacterial stimuli, such as Toll-like receptor 2 Medicine and Comprehensive immune system and the microbiota is necessary for (TLR2), TLR4, and nucleotide-binding oligomerization Cancer Center, University of gut homeostasis. However, when the mutualistic rela‑ domain 2 (NOD2), and in their adaptor molecules, such Michigan, Ann Arbor 48109, tionship between the host and microbiota is disrupted, as myeloid differentiation primary-response protein 88 Michigan, USA. the gut microbiota can cause or contribute to disease4,5. (MYD88) and TIR domain-containing adaptor protein Correspondence to G.N. 8 e-mail: In this Review, we provide an overview of the current inducing IFNβ (TRIF; also known as TICAM1) . The [email protected] understanding of the dual role of the gut microbiota in development of ILFs is also tightly regulated by NOD1, doi:10.1038/nri3430 health and disease. which is a bacterial sensor that responds to bacterial

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 321

+ Box 1 | Pattern recognition receptors IL‑6 and IL‑23 production by CD11c lamina propria dendritic cells (DCs) and the subsequent induction of Pattern recognition receptors (PRRs) are receptor molecules expressed in immune 14 (FIG. 1a) TH17 cell differentiation . Likewise, luminal cells. PRRs recognize pathogen-associated molecular patterns (PAMPs), such as ATP, which is provided by commensal bacteria but not lipopolysaccharide, flagellin, bacterial DNA and RNA, and they have crucial roles in by pathogenic bacteria, promotes T 17 cell development innate immunity and protection against pathogens. In addition to pathogens, the H gut-resident microbiota contains PAMPs that are recognized by PRRs. Most PRRs through a mechanism that is distinct to that elicited by 12 fall into three families: the Toll-like receptors (TLRs), NOD-like receptors (NLRs) and SFB . However, whether SAA and ATP are required for retinoic acid-inducible gene I (RIG‑I)‑like receptors (RLRs). TH17 cell development in vivo remains unclear. IL‑1β is

TLR family members are expressed on the cell surface and in endosomes, and also crucial for TH17 cell differentiation and is specifi‑ stimulation of TLRs by bacterial components activates downstream adaptor molecules cally induced by the gut microbiota16 (FIG. 1a). Although such as myeloid differentiation primary response 88 protein (MYD88) and/or TIR domain- reconstitution of germ-free mice with the microbiota containing adaptor protein inducing IFNβ (TRIF). TLR activation results in the upregulation of conventionally raised mice rescues the development of of pro-inflammatory mediators that facilitate host immune responses. NLRs are TH17 cells in the gut, colonization with rat or human cytoplasmic proteins that regulate inflammatory and apoptotic responses. The NLRs microbiota does not17. This indicates that the microbiota nucleotide-binding oligomerization domain 1 (NOD1) and NOD2 share the downstream might regulate the development of T 17 cells in the gut adaptor molecule receptor-interacting serine/threonine kinase (RICK), which activates H in a species-specific manner. innate immunity through nuclear factor‑κB (NF‑κB) and mitogen-activated protein kinases (MAPKs). A specific subset of NLRs is involved in the formation of the + inflammasome, which activates caspase 1. These NLRs include NLRP3 (NOD-, LRR- and TReg cells. Forkhead box P3 (FOXP3) regulatory T (TReg) + pyrin domain-containing 3), NLRP1 and NLRC4 (NOD-, LRR- and CARD-containing 4), cells comprise a subset of CD4 TH cells that accumu‑ and they contain specific domains (a pyrin domain or a CARD) that assist in the late in the intestine, where they help to maintain gut

recruitment of the adaptor protein ASC, which forms an oligomeric complex with homeostasis. The depletion of TReg cells results in the caspase 1. Activation of the inflammasome and caspase 1 leads to the secretion of + abnormal expansion of CD4 TH cells expressing com‑ mature interleukin‑1β (IL‑1β) and IL‑18, which are involved in host defence and in the mensal bacteria-specific T cell receptors (TCRs); conse‑ pathogenesis of multiple autoimmune diseases. RLRs are cytoplasmic proteins that quently, intestinal inflammation ensues18. Importantly, are involved in intracellular virus recognition but have been demonstrated to also the development of peripherally derived T cells is partly be important in gut immunity and in disease pathogenesis166,167. The RLRs RIG‑I and Reg dependent on the gut microbiota, as the number of T melanoma differentiation-associated protein 5 (MDA5) recognize double-stranded Reg RNA. Another RLR member, LGP2 (also known DHX58), lacks amino‑terminal cells is greatly decreased in the colonic lamina propria 19,20 (FIG. 1a) caspase-recruitment domains and functions as a regulator of RIG‑I and MDA5 signalling. of germ-free mice . The induction of TReg cells is triggered by specific populations of commensal bac‑

teria. The accumulation of IL-10-producing TReg cells in peptidoglycan molecules8. However, although it is clear the colon is promoted by colonization of germ-free mice Germ-free mice Mice that are born and raised from studies using germ-free mice that GALT develop‑ with one of the following bacterial populations: a mix‑ in isolators, without exposure ment requires the presence of microbiota, the require‑ ture of 46 Clostridium spp. cluster IV and XIVa strains; to microorganisms. ment for specific PRRs is less clear, as these studies altered Schaedler flora (ASF), which consists of a cock‑ have been confounded by differences between mouse tail of eight defined commensal bacteria; or the human Peyer’s patches 19–21 (FIG. 1a) Collections of lymphoid tissue strains that can result in environmental alterations in commensal bacterium Bacteroides fragilis . that are located in the mucosa the microbiota, which, in turn, might affect lymphoid However, the mechanism by which specific bacterial of the small intestine. They development independently of a specific gene defect. populations induce the development of TReg cells remains have an outer epithelial layer poorly understood. consisting of specialized T 17 cells. It is now well known that the resident micro‑ epithelial cells called M cells. H Peyer’s patches consist of a biota regulates the development of specific lymphocyte IgA-producing B cells and plasma cells. A close relation‑ dome area, B cell follicles and subsets in the gut. T helper 17 (TH17) cells are a specific ship also exists between the microbiota and gut-specific interfollicular T cell areas. High + lineage of CD4 TH cells that are crucial for host defence B cell responses. IgA is a major class of immunoglobu‑ endothelial venules are present and that have a role in the development of autoimmune lin that is produced in mucosal tissues, including in the mainly in the interfollicular areas. disease by producing the pro-inflammatory cytokines intestine. In the intestinal lumen, IgA is produced as pol‑ interleukin‑17A (IL‑17A), IL‑17F and IL‑22 (REF. 11). ymeric IgA at high concentrations22 (FIG. 1b). Polymeric + Specific-pathogen-free mice Unlike other subsets of CD4 TH cells, such as TH1 and IgA is transported via the polymeric immunoglobulin Mice raised in conditions TH2 cells, TH17 cells preferentially accumulate in the receptor (pIgR) that is expressed on intestinal epithelial whereby an increasing number intestine, which indicates that the development of T 17 cells and is released into the intestinal lumen as secreted of pathogens are excluded or H 23 (FIG. 1b) eradicated from the colony. cells might be regulated by gut-intrinsic mechanisms. IgA (SIgA) . SIgA coats commensal bacteria and These animals are maintained Consistent with this hypothesis, the presence of intes‑ soluble antigens to inhibit their binding to the host epi‑ in the absence of most of the 22 tinal TH17 cells is greatly reduced in antibiotic-treated thelium and their penetration into the lamina propria . known chronic and latent or germ-free mice12–16, which shows that the microbiota Thus, SIgA promotes intestinal barrier function and persistent pathogens. Although (FIG. 1b) this enables better control of has a crucial role in TH17 cell development. In fact, a helps to maintain host–commensal mutualism . experimental conditions related particular species of Clostridia-related bacteria, called In addition, IgA has been shown to regulate the com‑ to immunity and infection, it segmented filamentous bacteria (SFB), promotes the position and the function of the gut microbiota24. For also sets apart such animal 13–15 (FIG. 1a) generation of TH17 cells in mice . The precise example, deficiency or dysfunction of IgA as a result models from pathogen-exposed mechanism by which SFB promote T 17 cell develop‑ of deficiency or mutation of activation-induced cytidine humans or non-human H deaminase primates, whose immune ment remains to be fully elucidated. The adhesion of (AID), respectively, leads to alterations in the 25,26 systems are in constant contact SFB to the host epithelium upregulates serum amyloid composition of the gut microbiota . Moreover, bind‑ with pathogens. A protein (SAA) production, which, in turn, promotes ing of IgA to the commensal Bacteroides thetaiotaomicron

322 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

a • SFB • Clostridium cluster IV • Other microbiota and XIVa strains REGIIIγ • PSA+ Bacteroides fragilis • Other microbiota Epithelial Gut lumen ATP cell

Lamina IL-1β, • PSA SAA IL-22 propria IL-6 and • Other factors? IL-23 TGFβ CD103+ DC + TH17 cell and TLR5 DC

CD11b+CD11c– Retinoic CD11b+CD11c– CD70+CD11clow DC + macrophage FOXP3 acid and macrophage and CX CR1+CD11c+ DC 3 IL-12(?) TReg cell IL-10 TH1 cell

b c SIgA REGIIIγ

TLR

TSLP FDC pDC, IL-22 IL-25 Pattern recognition BAFF TIP DC and + receptors and TLR5 DC APRIL (PRRs). Germline-encoded APRIL, BAFF, NO, receptors (such as the Toll-like BAFF, retinoic acid APRIL receptors (TLRs) and the and TNF NOD-like receptors (NLRs)) IgA that can sense pathogen- associated molecular patterns IgA+ and initiate signalling B cell B cell RORγt+ ILC3 cascades that lead to an IL-17RB+ DC innate immune response. They can be membrane-bound • ↑ AID (such as TLRs and C-type lectin • Class switching IgA+ plasma cell receptors (CLRs)) or soluble cytoplasmic receptors (such as Figure 1 | The gut microbiota-mediated development of the intestinal immune system. a | Segmented filamentous retinoic acid-inducible gene I (RIG‑I), melanoma differentiation- bacteria (SFB) and other commensal microorganisms activate lamina propria dendritic cells (DCs) and macrophages to associated protein 5 (MDA5) induce T helper 17 (TH17) cells and TH1 cells through the production of interleukin‑1β (IL‑1β), NatureIL‑6 and Reviews IL‑23 in |the Immunology case and NLRs). of TH17 cells, and possibly IL‑12 in the case of TH1 cells (although the role of IL-12 in TH1 development in vivo in the gut

remains to be confirmed). TH17 cells regulate the gut microbiota community in an IL‑22- and regenerating islet-derived + Peripherally derived TReg cells protein 3γ (REGIIIγ)-dependent manner. Clostridium spp. clusters IV and XIVa, polysaccharide A (PSA) Bacteroides fragilis A subset of forkhead box P3 and other microbiota stimulate intestinal epithelial cells, T cells, and lamina propria DCs and macrophages to promote + (FOXP3) regulatory T (TReg) + the development and/or the activation of forkhead box P3 (FOXP3) regulatory T (TReg) cells. b | The microbiota stimulates cells that are induced in the intestinal epithelial cells and DCs to promote IgA-producing B cell and plasma cell differentiation in the lamina propria. periphery and mediate their Toll-like receptor (TLR) activation on intestinal epithelial cells induces the secretion of B cell-activating factor (BAFF) and suppressive effects through the secretion of cytokines a proliferation-inducing ligand (APRIL), which promote the differentiation of IgA-producing plasma cells. Intestinal such as interleukin‑10 and epithelial cells also produce thymic stromal lymphoprotein (TSLP) to promote BAFF and APRIL expression by DCs. Various transforming growth factor‑β, types of DCs, such as plasmacytoid DCs (pDCs), TIP DCs (TNF and inducible nitric oxide synthase (iNOS)-producing DCs) which inhibit other T cells. and TLR5+ DCs secrete BAFF, APRIL, nitric oxide (NO), retinoic acid and tumour necrosis factor (TNF) to facilitate the Their role is to maintain expression of activation-induced cytidine deaminase (AID) and IgA class-switching in B cells. Follicular DCs (FDCs) also self-tolerance. induce the differentiation of IgA-producing plasma cells in Peyer’s patches and isolated lymphoid follicles. IgA that is produced by lamina propria B cells is secreted into the intestinal lumen (SIgA), where it alters microbiota composition Activation-induced cytidine and function. c | Innate lymphoid cells (ILCs) that express retinoic acid receptor-related orphan receptor-γt (RORγt) and deaminase produce IL-22 (termed ILC3s) regulate the gut microbiome through the induction of REGIII in intestinal epithelial cells. (AID). An enzyme that is γ + required for two crucial The microbiota positively regulates the production of IL‑22 by RORγt ILC3s via an unknown mechanism. In addition, the + events in the germinal centre: microbiota induces IL‑25 secretion by endothelial cells, which acts on lamina propria IL‑17 receptor B (IL‑17RB) DCs, + somatic hypermutation and and the IL‑25‑activated DC subset suppresses IL‑22 production by RORγt ILC3s. CX3CR1, CX3C-chemokine receptor 1; class-switch recombination. SAA, serum amyloid A protein; TGFβ, transforming growth factor‑β.

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 323

inhibits innate immune responses by affecting bacterial Microbiota and resistance to pathogens gene expression27. The gut microbiota also regulates IgA It has been known for many years that germ-free mice production, as the number of IgA-producing cells in are more susceptible to infection than conventionally the intestine is markedly decreased in germ-free mice22. raised mice44,45. Furthermore, treatment with antibiot‑ Although the precise mechanisms by which commensal ics is associated with increased colonization of patho‑ bacteria promote the development of IgA-producing gens in both mice and humans46–49. These observations cells remain poorly understood, bacterial recognition indicate that an important function of the indigenous through MYD88 in follicular DCs (FDCs) is known to be microbiota might be to protect the host from infection. important for the generation of IgA28 (FIG. 1b). Notably, The mechanisms by which commensal bacteria achieve for a subset of lamina propria DCs, commensal bacteria- this remain poorly understood, but there is evidence derived flagellin promotes the synthesis of retinoic acid, to indicate that both direct and indirect mechanisms which is an important molecule that facilitates the differ‑ might be involved. entiation of IgA-producing B cells29,30 (FIG. 1b). Likewise, commensal bacteria promote the expression of factors Direct competition for nutrients. Several studies have that are involved in the induction of IgA+ B cells, such shown that commensal bacteria can inhibit pathogen as tumour necrosis factor (TNF), inducible nitric oxide colonization by successfully competing for the limited synthase (iNOS; also known as NOS2), B cell activating supply of nutrients within the intestine. For example, factor (BAFF; also known as TNFSF13B) and a prolifer‑ Escherichia coli competes with enterohaemorrhagic ation-inducing ligand (APRIL; also known as TNFSF13) E. coli (EHEC; an enteric pathogen that causes substan‑ in lamina propria DCs31,32. In addition to TNF- and iNOS- tial morbidity and mortality worldwide) for organic producing (TIP) DCs, intestinal plasma cells express TNF acids, amino acids and other nutrients50–53 (FIG. 2). As and iNOS following microbial exposure, which further different commensal E. coli strains have distinct meta‑ promotes the IgA secretory function of intestinal B cells33 bolic profiles, each strain can differentially compete (FIG. 1b). Thus, the microbiota instructs lamina propria with pathogens53. Although our understanding of how DCs and/or FDCs to induce the differentiation of IgA- commensal bacteria outcompete pathogens is still producing B cells, and in turn, IgA regulates the func‑ poor, studies thus far indicate that pathogen eradica‑ tion and composition of the gut microbiota to maintain tion might be most effective with bacteria that are meta‑ mutualism between the host and the microbiota. bolically related to the pathogen. For example, E. coli, but not Bacteroides spp., can effectively outcompete the ILCs. Innate lymphoid cells (ILCs) are increasingly recog metabolically related pathogen Citrobacter rodentium, nized as innate immune cells that share functional charac‑ which is a mouse bacterium that models infection by teristics with T cells (reviewed in REFS 34,35). ILCs arise enteropathogenic E. coli (EPEC) and EHEC54. The from a common lymphoid precursor cell but differenti‑ ability of E. coli to outcompete C. rodentium is partly ate into multiple lineages on the basis of the expression mediated by competition for simple sugars that are used of specific transcriptional factors. Currently, ILCs have by both bacteria in the intestine54 (FIG. 2). been categorized into three main groups: T‑bet+ ILCs Likewise, the enteric pathogen Salmonella enteria (termed ILC1s) GATA-binding protein 3 (GATA3)+ subsp. enterica serovar Typhimurium is capable of colo‑ ILCs (termed ILC2s), and retinoic acid receptor-related nizing the intestine of mice that have been harbouring orphan receptor-γt (RORγt)+ ILCs (termed ILC3s)34–37. a limited microbiota for several weeks, but it is rapidly The role of the microbiota in the development and eradicated after co‑housing with conventionally raised the function of ILCs has been controversial. Although mice, which indicates that not all commensal bacteria some studies report that the microbiota is required for have the ability to out-compete the pathogen55. The the differentiation of ILCs and for their production of metabolic activity of the microbiota can also affect IL‑22 (REFS 38,39) (FIG. 1c), another study suggested that pathogen colonization by a mechanism that is distinct the microbiota suppressed IL‑22 production by RORγt+ from nutritional competition. The commensal bacterial ILCs40 (FIG. 1c). A crucial function of IL‑22 is to promote strain B. thetaiotaomicron produces multiple fucosidases antimicrobial peptide production by intestinal epithe‑ that generate fucose from host-derived glycans, such as lial cells. Specifically, IL‑22 induces the expression of the mucin, and this modulates the expression of EHEC viru‑ C‑type lectin antimicrobial peptides regenerating islet- lence genes through the activation of the fucose sensor derived protein 3β (REGIIIβ) and REGIIIγ, which can FusKR56 (FIG. 2). affect the gut microbiota41,42. Depletion of either IL‑22 or Pathogens, in turn, have also evolved strategies to over‑ IL‑22‑producing ILCs leads to overgrowth and/or dis‑ come competition by commensal bacteria. One strategy semination of potentially pathogenic bacteria, such as is to use nutrients that are not primarily metabolized

Follicular DCs Alcaligenes xylosoxidans, which might increase the risk by commensal bacteria. Carbohydrate usage can differ (FDCs). Specialized of subsequent intestinal damage and systemic inflamma‑ substantially between pathogenic and commensal E. coli non-haematopoietic stromal tion43. Thus, the regulation of gut-specific immune cells strains52,57. For example, EHEC, but not certain commen‑ cells that reside in the follicles by commensal bacteria has far-reaching effects that are sal E. coli strains, can use galactose, hexuronates, man‑ and germinal centres. These not limited to immune homeostasis, but also include the nose, ribose and ethanolamine, which is released into the cells possess long dendrites, but are not related to dendritic regulation of the balance between beneficial and poten‑ intestine during epithelial cell turnover, as a carbon or 52,58 cells, and carry intact antigen tially pathogenic commensals in the microbiota, and nitrogen source . Use of ethanolamine can be explained on their surface. resistance to intestinal pathology. by the presence of the ethanolamine utilization (eut)

324 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

Direct Indirect

Pathogen Commensal Pathogen Competition microbiota for nutrients

Virulence factor Fucose expression

Microbiota strategies Microbiota Killing (T6SS) Pathogen • Gut Pathogen colonization colonization • lumen Systemic translocation

Nutrients speciﬁcally SCFAs REGIIIγ Epithelial used by REGIIIγ IgA cell pathogens Pathogen strategies Pathogen Mucus

↑ Barrier function

Lamina propria Inﬂamed IL-22 epithelial cell IL-22 Plasma cell Induce B cell pro-IL-1β ILC3 Neutrophil TH1 or T 17 cell IL-1β H IL-1β and IL-23

Macrophage Figure 2 | Direct and indirect resistance of the microbiota to colonization by enteric pathogens. Direct competition between pathogens and commensal bacteria is shown on the left-hand side. Resident microorganismsNature Reviews directly | Immunology inhibit the colonization and/or the proliferation of incoming enteric pathogens. Commensal microorganisms can outcompete pathogens for shared nutrients, such as carbohydrates, amino acids and organic acids. In addition, commensal bacterial strains such as Bacteroides thetaiotaomicron catabolize mucin to produce fucose, which inhibits virulence factor expression by pathogenic Escherichia coli. Enteric pathogens have evolved strategies to overcome competition by commensal bacteria. Some pathogens can directly kill their commensal competitors through their type VI secretion system (T6SS). Pathogen-induced inflammation, which leads to increased epithelial cell turnover, provides nutrients that selectively promote the growth of pathogens. Moreover, pathogens can localize to epithelium-associated niches that are devoid of commensal bacteria and use nutrients near the epithelium to escape direct competition with resident microorganisms. Indirect mechanisms of competition between commensal bacteria and pathogens are shown on the right-hand side. Commensal bacteria catabolize polysaccharides to generate short-chain fatty acid (SCFAs), such as acetate, which enhances intestinal epithelial cell barrier function. In addition, commensal microbiota promotes the production of mucus and the release of antimicrobial peptides such as regenerating islet-derived protein 3γ (REGIIIγ) from epithelial cells to limit pathogen colonization and proliferation. Innate immune cells, such as intestinal resident macrophages, neutrophils and

some group 3 innate lymphoid cells (namely ILC3s), as well as T helper 1 (TH1) cells, TH17 cells and IgA-producing B cells and plasma cells, are also activated by the microbiota to limit pathogen colonization. IL, interleukin.

operon in the genome of the EHEC strain and not in the epithelium where commensal bacteria do not normally commensal E. coli strain58. Thus, pathogens have evolved reside54. Localization to epithelium-associated niches to use nutritional resources that are not consumed by might also allow certain pathogens such as EPEC and commensal bacteria to acquire a growth advantage. EHEC to use nutrients that are available at or near the Another strategy used by pathogens is the induction of epithelium and to escape from direct competition with inflammation by their virulence factors. For example, resident microorganisms (FIG. 2). Furthermore, certain infection by S. Typhimurium results in the production Gram-negative enteric pathogens, such as Serratia marce‑ Type IV secretion system of reactive oxygen species by neutrophils, which facili‑ scens and C. rodentium, can directly kill their commensal (T6SS). An export system that tates the conversion of endogenous thiosulphate into competitors through the expression of the type VI secretion is used by Gram-negative system 61,62 (FIG. 2) bacteria to deliver effector tetrathionate, thereby selectively promoting the growth (T6SS) . Thus, the outcome of infection 59,60 proteins to other cells in a cell of S. Typhimurium (FIG. 2). Moreover, virulence factors by pathogens is ultimately determined by both host and contact-dependent manner. such as intimin allow C. rodentium to attach to the host commensal bacterial factors.

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 325

Commensal bacteria promote mucosal barrier function. via the NLRC4 (NOD-, LRR- and CARD-containing 4) The attachment of pathogens to the surface of the intes‑ inflammasome71. Unlike commensal bacteria, these patho‑ tinal epithelium is a crucial initial step for infection to gens are capable of activating the NLRC4 inflammasome occur. As a defence mechanism, the epithelium produces to produce IL‑1β because they express a type III secretion mucus and antimicrobial molecules to inhibit pathogen system, which allows the transfer of the NLRC4 agonist invasion. In the colon, the mucus layer forms a strong bar‑ flagellin into the host cytosol71. Consequently, BALB/c rier against both pathogens and commensal bacteria63,64. mice that are deficient in NLRC4 or in the IL‑1 receptor In the small and large intestines, the inner mucus layer (IL‑1R) are highly susceptible to orogastric infection with near the epithelium is devoid of commensal bacteria63,64. S. Typhimurium71. The protective role of IL‑1β in intesti‑ However, the mucus layer in germ-free mice is much nal immunity is, at least partly, mediated by its ability to thinner than that in conventionally raised mice, which induce the expression of endothelial adhesion molecules indicates that the microbiota might contribute to mucus that contribute to neutrophil recruitment and pathogen production65 (FIG. 2). Consistent with this hypothesis, the clearance in the intestine. Thus, NLRC4‑dependent IL‑1β thickness of the mucus layer of germ-free mice can be production by resident phagocytes represents a specific restored to normal by oral administration of the bacterial response that can discriminate between pathogenic and products lipopolysaccharide (LPS) and peptidoglycan65. commensal bacteria. The microbiota also contributes to the production of The intestinal microbiota also promotes immunity antimicrobial molecules by epithelial cells of the small through the production of IL‑22 by ILC3s38. Germ-free and large intestines (FIG. 2). For example, REGIIIγ and mice show impaired intestinal production of IL‑22, which REGIIIβ that are contained in Paneth cell granules indicates that there might be a requirement for commen‑ are released into the lumen to regulate host–bacte‑ sal bacteria or their metabolites16. Mice with defects in ria interactions through their antimicrobial activity66. IL‑22‑expressing cells exhibit increased susceptibility to Epithelium-intrinsic deletion of MYD88 impairs the C. rodentium infection, which indicates that commen‑ production of REGIIIγ and REGIIIβ; therefore, it seems sal bacterial-driven IL‑22 that is produced by ILC3s is that recognition of the microbiota by TLRs medi‑ important for protection against infectious pathogens38,73,74. ates the expression of these antimicrobial peptides42,66. Consistent with this idea, administration of IL‑22 to Importantly, the impaired production of REGIIIγ and aryl hydrocarbon receptor (Ahr)−/− mice, which exhibit REGIIIβ increases the susceptibility of mice to infection impaired IL‑22 production, provides protection against by enteric pathogens including Listeria monocytogenes, C. rodentium infection74. Taken together, these results Yersinia pseudotuberculosis and S. enterica subsp. enterica indicate that commensal bacteria might also promote host serovar Enteritidis67–69. defence by stimulating ILCs to produce IL‑22 (FIG. 2). The microbiota can also enhance epithelial barrier function through the production of metabolites. For The microbiota promotes adaptive immunity. As men‑ instance, short-chain fatty acids (SCFAs), especially tioned above, specific commensal bacteria promote acetate, produced by Bifidobacterium spp. act on the epi‑ the generation of different T cell subsets in the intes‑ 12,14,19–21,75 Inflammasome thelium to inhibit the translocation of Shiga toxin that is tine that have unique roles during pathogen (REF. 45) (FIG. 2) (FIG. 2) A molecular complex of several produced by E. coli O157:H7 . The precise infection . For instance, TH17 cell differentiation proteins, including a NOD-like signalling mechanism by which bacterial products and that is induced by SFB colonization facilitates protec‑ receptor (NLR), the adaptor metabolites enhance epithelial defence, and how this tion against C. rodentium infection14. Likewise, micro‑ protein ASC and a caspase, mutually affects the microbiota and the host, remains biota-induced T cells attenuate intestinal damage that that, upon assembly, cleaves Reg pro‑interleukin‑1β (pro-IL‑1β) to be elucidated. is caused by exaggerated immune responses against and pro‑IL‑18, thereby infectious pathogens. Specifically, B. fragilis promotes producing mature IL‑1 and β The microbiota enhances innate immunity to patho- IL‑10‑producing TReg cells that protect against Helicobacter IL‑18. gens. Mononuclear phagocytes, such as macrophages hepaticus infection21,76, and Bifidobacterium infantis

Aryl hydrocarbon receptor and DCs, are located in the lamina propria and promote increases the number of TReg cells that attenuate intes‑ (AHR). A cytosolic, immunological unresponsiveness to commensal bacteria, tinal disease severity following S. Typhimurium infec‑ ligand-dependent transcription which is important for maintaining gut homeostasis70,71. tion77. Commensal bacteria also induce specific immune factor that translocates to the Specifically, gut-resident phagocytes are hyporespon‑ responses, including IgA production and the generation nucleus following the binding sive to microbial ligands and commensal bacteria, and of CD4+ T cells, that are directed against their own anti‑ of specific ligands, which 78–80 include dietary and microbial they do not produce biologically significant levels of gens . Although the precise role of commensal bacte‑ 70–72 metabolites. AHR participates pro-inflammatory molecules upon stimulation . ria-specific adaptive immunity against invasive pathogens in the differentiation of However, the microbiota is essential for upregulating remains poorly understood, there is evidence indicating regulatory T cells, T helper 17 the production of pro‑IL‑1β, the precursor to IL‑1β, in that it is important for limiting the systemic dissemination (TH17) cells and intraepithelial 71 81 intestinal T cells, and it is resident mononuclear phagocytes . Under steady-state of commensal bacteria . The induction of this ‘firewall’ required for the secretion of conditions when the epithelial barrier is intact, resident function of the adaptive immune system by the micro‑ interleukin‑22 by TH17 cells. commensal bacteria cannot also induce the processing of biota might prevent collateral damage — which could be More recently, AHR has been pro‑IL‑1β into biologically active mature IL‑1β and thus a caused by the translocation of indigenous bacteria — that shown to have crucial roles in state of hyporesponsiveness is maintained71. By contrast, is often associated with pathogen infection and epithelial the development and function of group 3 innate lymphoid infection by enteric pathogens such as S. Typhimurium barrier disruption. In addition, it might contribute to the cells, including lymphoid tissue and Pseudomonas aeruginosa can induce the processing elimination of pathogens through opsonization or other inducer (LTi) cells and ILC3s. of pro‑IL‑1β by promoting the activation of caspase 1 immune mechanisms.

326 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

Protective role of the commensal microbiota against sys- abrogated if mice also have a deficiency in individual temic infection. The mechanism by which the micro‑ TLRs or in MYD88. For example, spontaneous coli‑ biota promotes systemic pathogen eradication is poorly tis that develops in Il10−/− mice, in conditional signal understood. Pretreatment of germ-free mice with LPS transducer and activator of transcription 3 (Stat3)−/− induces pro-inflammatory cytokine production and mice or in mice with a deletion in inhibitor of nuclear neutrophil recruitment, and can prevent systemic bac‑ factor-κB kinase-γ (IKKγ; also known as NEMO) spe‑ terial infection82. This observation indicates that com‑ cifically in intestinal epithelial cells (NEMOΔIEC mice) mensal bacteria might, at least partly, promote host is reversed when these mice also lack TLRs or MYD88 defence at distant sites through the release of microbial (REFS 98–101). However, Il2−/− mice that are deficient in molecules. Consistent with this hypothesis, peptido MYD88 still develop spontaneous colitis99. In this model, glycan molecules that are derived from the microbiota the microbiota might drive colitis through the promo‑ 12 are found in the periphery and can prime peripheral tion of inflammatory TH17 cell responses that occur blood neutrophils to facilitate their bactericidal capacity independently of MYD88. via NOD1 signalling83. This neutrophil priming effect, Similar to mice, human intestinal mononuclear which is presumably induced by intestinal bacteria, phagocytes show hyporesponsiveness to microbial stim‑ enhances host defence against systemic infection with ulation under steady-state conditions102,103. However, in Streptococcus pneumoniae83. patients with IBD, intestinal mononuclear phagocytes The microbiota might also have an important role in robustly respond to microbial products and to the resi‑ systemic antiviral immune responses. Germ-free mice dent bacteria, which results in the production of large and antibiotic-treated mice show reduced innate and amounts of pro-inflammatory cytokines such as TNF adaptive immune responses to influenza virus, which and IL‑23, as occurs in IBD-prone mice103. Thus, the Inflammatory bowel disease results in increased viral loads in their tissues84,85. The abnormal activation of resident intestinal mononuclear (IBD). Immune-mediated inflammation of the bowel. microbiota might enhance antiviral immunity through phagocytes by commensal bacteria might facilitate the There are two main forms: the inflammasome and the production of innate development or persistence of intestinal inflammation in Crohn’s disease, which is a cytokines that are required for optimal immune responses IBD. Consistent with this idea, intestinal macrophages granulomatous segmental against viruses84. For example, the microbiota promotes isolated from Il10−/− mice robustly respond to gut bac‑ inflammation affecting any part of the intestine; and ulcerative type I interferon (IFN) production by macrophages teria, whereas wild-type intestinal macrophages are 70–72 colitis, which is a mucosal and the subsequent IFN-priming of natural killer (NK) hyporesponsive . However, the increased production inflammation involving the cells, which is important for protection against infection of pro-inflammatory molecules by intestinal phagocytes rectum and extending for a with mouse cytomegalovirus and lymphocytic chorio might also reflect the activity of recruited monocytes variable distance along the meningitis virus86. Moreover, the gut microbiota induces in areas of infection or inflammation. colon. In developed countries, the incidence of inflammatory intestinal TLR-dependent DC activation and inhibits There is genetic evidence showing that the impaired 87 bowel disease is approximately systemic parasitic infection . Recent studies also indicate recognition and killing of commensal bacteria also con‑ one in 50,000. It usually starts that commensal bacteria might provide tissue-specific tributes to IBD development, as has been suggested by in early adult life and continues defence mechanisms, as has been demonstrated by the the fact that many of the identified IBD-susceptibility afterwards with a relapsing, 104 remitting course. protection provided by resident skin bacteria against genes regulate host–microbial interactions . NOD2, local pathogen infection88. which is an intracellular sensor of bacterial peptidog‑ SAMP1/yit mice Taken together, these studies using different infection lycan, was identified as a susceptibility gene for Crohn’s A mutant mouse strain that models show a protective effect of the microbiota against disease, and Crohn’s disease-associated NOD2 muta‑ spontaneously develops a systemic infection; however, additional studies are nec‑ tions are associated with a loss of function of the pro‑ chronic intestinal inflammation 105–107 autophagy that is mainly localized in the essary to identify the underlying mechanisms as well as tein . Mutations in the regulatory genes terminal ileum. the relative contributions of host defence mechanisms autophagy related gene 16‑like 1 (ATG16L1) and immu‑ that are promoted by the microbiota of specific tissues nity-related GTPase family M (IRGM) are also linked Autophagy such as the skin or the respiratory tract. It is also impor‑ to Crohn’s disease108,109, and autophagy dysfunction is An evolutionarily conserved 110–112 process in which acidic tant to note that commensal bacteria do not always pro‑ associated with defects in bacterial killing . In addi‑ double-membrane vacuoles tect against pathogenic infection and in certain contexts tion, NOD2 and autophagy proteins regulate the func‑ sequester intracellular they can facilitate it (as discussed below)89–91. tion of Paneth cells, which release granules containing contents (such as damaged antimicrobial peptides in response to bacteria113. NOD2 organelles and The microbiota and intestinal disease is highly expressed in Paneth cells, and some studies macromolecules) and target ‑defensins them for degradation through The microbiota contributes to IBD. The gut micro‑ report diminished expression of Paneth cell α fusion to secondary lysosomes. biota is essential for triggering or enhancing chronic in individuals with Crohn’s disease-associated NOD2 intestinal inflammation in various inflammatory bowel mutations114,115. Nod2−/− mice have impaired antimicro‑ α-defensins disease (IBD)-prone mouse strains (TABLE 1). Under bial functions in Paneth cells, resulting in the accumu‑ One subset of defensin −/− −/− proteins. Defensins and germ-free conditions, Il10 or Tcra mice, as well as lation of ileal bacteria, which might contribute to IBD 116 HM cathelicidins are members of a transgenic rats that have been engineered to overexpress pathogenesis . Atg16l1‑mutant (Atg16l1 ) mice show family of small antimicrobial HLA‑B27 and human β2 microglobulin, do not develop abnormal granule formation in Paneth cells, which is polypeptides that are colitis92–95. In Il2−/− or SAMP1/yit mice, although sponta‑ also observed in patients with Crohn’s disease who abundant in neutrophils and neous intestinal inflammation occurs even under germ- have homozygous mutations in ATG16L1 (REF. 117). In epithelial cells. They contribute HM to host defence by disrupting free conditions ,symptoms are attenuated compared Atg16l1 mice this abnormality can be triggered by 96,97 the cytoplasmic membrane of with conventionally raised mutant mice . In many enteric viral infection (for example, by murine noro‑ microorganisms. spontaneous colitis models, intestinal inflammation is virus) and is associated with increased susceptibility

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 327

Table 1 | Role of the gut microbiota in the protection or induction of IBD Commensal bacterium Host Genotype Disease Receptors Possible mechanism Refs Commensal microbiota that protect against IBD 19 Clostridium spp. clusters Mouse Wild-type DSS colitis Unknown Induction of TReg cells IV and XIVa 20 Altered Schaedler flora Mouse Wild-type DSS colitis MYD88 and Induction of TReg cells TRIF 21 Bacteroides fragilis Mouse Wild-type TNBS colitis TLR2, MYD88 Induction of TReg cells via polysaccharide A Bacteroides vulgatus Mouse Il2−/− Spontaneous colitis Unknown Suppression of Escherichia coli- 120 triggered colitis in Il2−/− mice Faecalibacterium Human NA IBD Unknown Induction of IL‑10 by PBMCs 148 prausnitzii Commensal microbiota that promote the development of IBD E. coli Mouse Il10−/− Spontaneous colitis Unknown Monocolonization of germ-free 119 mice induces colitis E. coli Mouse Il2−/− Spontaneous colitis Unknown Monocolonization of germ-free 96, 120 mice induces colitis Enterococcus faecalis Mouse Il10−/− Spontaneous colitis Unknown Monocolonization of germ-free 119 mice induces colitis B. vulgatus Rat HLA‑B27–B2m Spontaneous colitis Unknown Monocolonization of germ-free 96 transgenic rats induces colitis B. vulgatus Mouse Il10r2−/−Tgfbr2−/− Spontaneous colitis Unknown Colonization of antibiotic- 122 treated mice triggers colitis Bacteroides Mouse Il10r2−/–Tgfbr2−/− Spontaneous colitis Unknown Colonization of antibiotic-treated 122 thetaiotaomicron mice triggers colitis B. thetaiotaomicron Rat HLA‑B27–B2m Spontaneous colitis Unknown Monocolonization of germ-free 95 transgenic rats induces colitis Bacteroides unifirmatis Mouse Il10r2−/− Tgfbr2−/− Spontaneous colitis Unknown Colonization of antibiotic-treated 122 mice triggers colitis Klebsiella pneumoniae*‡ Mouse Tbx21−/−Rag2−/− Spontaneous colitis Unknown Other commensal bacteria are 123,124 required for the induction of colitis Proteus mirabilis*‡ Mouse Tbx21−/−Rag2−/− Spontaneous colitis Unknown Other commensal bacteria are 123,124 required for the induction of colitis Helicobacter typhlonius* Mouse Tbx21−/−Rag2−/− Spontaneous colitis Unknown Transmissible to non-colitogenic 125 TRUC mice Prevotellaceae*‡ Mouse Nlrp6−/−, Asc−/− or DSS colitis Unknown Impaired IL‑18 signalling promotes 126 Casp1−/− pathobiont expansion TM7*‡ Mouse Nlrp6−/−, Asc−/− or DSS colitis Unknown Impaired IL‑18 signalling promotes 126 Casp1−/− pathobiont expansion Bilophila wadsworthia Mouse Il10−/− Spontaneous colitis Unknown Consumption of a diet composed 128 of milk-derived fat induces pathobiont expansion B2m, gene encoding β2‑microglobulin; Casp1, caspase 1; DSS, dextran-sulphate sodium; IBD, inflammatory bowel disease; IL, interleukin; MYD88, myeloid differentiation primary-response protein 88; NA, not applicable; Nlrp6, NOD-, LRR- and pyrin domain-containing 6; PBMCs, peripheral blood mononuclear cells; Rag2, recombination-activating gene 2; Tbx21, T-box 21 (encodes T‑bet); Tgfbr2, transforming growth factor‑β receptor 2; TLR, Toll-like receptor; TNBS, −/− −/− 2,4,6‑trinitrobenzene sulphonic acid; TReg cell, regulatory T cell; TRIF, TIR domain-containing adaptor protein inducing IFNβ; TRUC, Tbx21 Rag2 mice. *Transmissable to mutant hosts. ‡Transmissable to wild-type hosts.

to chemically induced colitis118. Thus, defects in host The role of the pathobiont in IBD. As non-pathogenic mechanisms that recognize and clear bacteria are symbionts, the gut microbiota derives nutritional ben‑ associated with the development of human IBD. How efits from the host and help to maintain gut homeostasis. genetic defects lead to chronic colitis in patients with However, under certain conditions, particular bacterial IBD remains unknown, but it is possible that impaired populations that are typically found in very low abun‑ NOD2 or autophagy function might result in the accu‑ dance can acquire pathogenic properties. These condi‑ mulation of intestinal commensal bacteria that have the tions include inherent immune defects as well as changes capacity to locally invade the intestinal mucosa and to in diet and/or acute inflammation, and can result in trigger an abnormal inflammatory response. the disruption of the normal balanced state of the gut

328 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

Homeostasis Inﬂammatory bowel disease

Genetic factors (for example, mutations in Environmental factors Nod2, Atg16I1 and Il23r) (diet, stress and infection)

Transmissable to healthy host Symbiont Dysbiosis Unclassiﬁed Beneﬁcial Pathobionts bacteria bacteria

Gut lumen

Lamina • ↑↑↑ TH17 cells • ↓ TReg cells propria • ↑↑↑ TH1 cells • ↓ IL-10 • ↓ REGIIIγ • GALT development • ↑ TReg cell Unknown • ↑ TH17 and TH1 cells • ↑ IL-10 contribution Chronic inﬂammation • ↑ Barrier function • ↑ REGIIIγ • ↑ REGIIIγ Homeostasis Figure 3 | Protective and pathogenic role of the gut microbiota in IBD. During homeostasis (left-hand side), the gut microbiota has important roles in the development of intestinal immunity. Beneficial subsets of commensal bacteria tend to have anti-inflammatory activities. Pathobionts that are colitogenic are directly suppressed by beneficial commensal Nature Reviews | Immunology bacteria partly through the induction of regulatory immune responses, involving regulatory T (TReg) cells, interleukin‑10 (IL‑10) and regenerating islet-derived protein 3γ (REGIIIγ). In inflammatory bowel disease (IBD) (right-hand side), a combination of genetic factors (for example, mutations in nucleotide-binding oligomerization domain 2 (Nod2), autophagy-related gene 16‑like 1 (Atg16l1) and interleukin‑23 receptor (Il23r)) and environmental factors (such as infection, stress and diet) result in disruption of the microbial community structure, a process termed dysbiosis. Dysbiosis results in a loss of protective bacteria and/or in the accumulation of colitogenic pathobionts, which leads to chronic

inflammation involving hyperactivation of T helper 1 (TH1) and TH17 cells. Dashed line shows that that the suppression of pathobionts by beneficial bacteria is diminished. In certain contexts, pathobionts can be transferred to the host and can cause disease without the host having a predisposing genetic susceptibility. It is unknown whether unclassified bacteria have a role in the pathogenesis of IBD. GALT, gut-associated lymphoid tissue.

microbiota, which is referred to as dysbiosis5. Dysbiosis Mice that have only innate immune cells with a defi‑ involves the abnormal accumulation or increased viru‑ ciency in T‑bet (Tbx21−/− (gene encoding T-bet) Rag−/− lence of certain commensal populations of bacteria, mice; also known as TRUC mice) develop spontaneous thereby transforming former symbionts into ‘patho‑ ulcerative colitis-like inflammation123. This colitis is trans‑ bionts’ (FIG. 3). Pathobionts are typically colitogenic in missible to T‑bet-sufficient Rag−/− mice and even to that they can trigger intestinal inflammation; therefore, wild-type mice through co‑housing, which indicates that there has been considerable interest in the identification impaired T‑bet signalling in innate immune cells leads to of pathobionts to understand the pathogenesis of IBD. the overgrowth of pathobionts that cause disease123. Indeed, Colitogenic pathobionts have been identified using the analysis of gut microbial communities in TRUC mice rodent models of spontaneous colitis (TABLE 1). For exam‑ showed that Klebsiella pneumoniae and Proteus mirabilis, ple, colonization of germ-free Il10−/− or Il2−/− mice with one both of which are found in very low abundance in healthy of several particular E. coli or Enterococcus faecalis strains, mice, accumulate in the guts of TRUC mice124. These bac‑ but not with Bacteroides vulgatus, induces colitis119–121. teria can trigger colitis in T‑bet-sufficient Rag−/− mice and By contrast, B. vulgatus, but not E. coli, triggers colitis in in wild-type mice, which indicates that they can function HLA‑B27‑transgenic rats94,95. The differential colitogenic as pathobionts. Interestingly, although K. pneumoniae or capacity of these bacteria cannot be merely explained P. mirabilis can induce colitis in healthy mice, mono- Rag by differences in the host species (mouse versus rat), as or dual-colonization of germ-free TRUC mice with these Recombinase activating genes; Rag1and Rag2 are expressed B. vulgatus, but not E. coli, induces intestinal inflamma‑ bacteria does not, which indicates that interactions with in developing lymphocytes. tion in mice that are deficient in both IL‑10R2 and TGFβ additional commensal bacteria are required to actually Mice that are deficient in either receptor 2 (REF. 122). These findings indicate that specific trigger inflammation124. The proteobacterium Helicobacter of these genes fail to produce immune defects in the host might determine the ability typhlonius also accumulates in colitic TRUC mice, and B or T cells owing to a of individual commensal bacteria to trigger colitis (FIG. 3). oral administration of the bacterium is sufficient to developmental block in the gene rearrangement that is However, the physiological relevance of these findings induce colitis in non-colitic TRUC mice, but not in T‑bet- −/− 125 necessary for receptor remains unclear because monocolonization of germ-free sufficient Rag mice . Similarly, the colitis induced expression. mice does not mimic the normal complex gut ecosystem. by H. typhlonius is not transmissible to wild-type mice125.

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 329

There is increasing evidence that defects in the NOD- which the microbiota mediates resistance against the like receptor (NLR) family of proteins are associated with development of colitis through TLR signalling remain dysbiosis. For example, Nlrp6−/− mice have impaired IL‑18 unclear. Administration of LPS (a TLR4 ligand) or CpG production, which is associated with an abnormal expan‑ (a TLR9 ligand) protects mice from colitis by promoting sion of the commensal bacterial species Prevotellaceae and epithelial barrier function following the upregulation of the candidate division TM7 (REF. 126). Although Nlrp6−/− cytoprotective heat shock proteins or by the induction mice do not develop spontaneous colitis, these mice have of type I IFN production, respectively138,139,143. In addi‑ an increased susceptibility to dextran sulphate sodium tion, the production of protective IgA and IgM suppresses (DSS)-induced colitis, and this phenotype is transmis‑ the harmful dissemination of commensal bacteria after sible to wild-type mice by co-housing126. This study colonic damage through MYD88 signalling in B cells140. demonstrates a correlation between the accumulation of The human commensal bacterium B. fragilis also pro‑ Prevotellaceae and TM7, as well as DSS-induced colitis tects mice from colitis by promoting the accumulation of 76,144 susceptibility, but whether these bacteria are the direct IL‑10‑producing TReg cells in the colon . This protective cause of this susceptibility and whether their accumu‑ effect is mediated by the outer membrane polysaccharide A lation is indeed NLRP6‑dependent remain to be deter‑ (PSA) of B. fragilis76,144. TLR2‑mediated internalization mined. Similarly, bacterial genomic sequencing shows of PSA into DCs, followed by its surface presentation, −/− 145,146 that Nod2 mice, which have an increased susceptibility activates IL‑10‑producing TReg cells . Commensal to DSS-induced colitis, have an altered microbiota that bacterial stimulation through MYD88 also limits the + can be transferred to wild-type mice to increase dis‑ trafficking of CX3CR1 mononuclear phagocytes that ease susceptibility127. However, the specific pathobionts capture luminal non-invasive bacteria to the mesenteric involved have not yet been identified. lymph nodes (MLNs)147. Consequently, disruption of the Diet has a considerable effect on the composition of commensal microbiota and/or MYD88 signalling results microbial communities and can lead to the expansion in excessive B and T cell stimulation in the MLNs, which of pathobionts. For instance, a diet rich in saturated milk might contribute to the development of IBD. fats, but not in polyunsaturated vegetable oil fats, induces It has also been reported that the microbiota protects dysbiosis and expansion of Bilophila wadsworthia, which against colitis through TLR-independent mechanisms. is a hydrogen-consuming, sulphite-reducing commen‑ For example, the colonization of neonatal germ-free sal bacterium. This intestinal bacterium promotes pro- mice with whole microbiota results in decreased hyper‑

inflammatory TH1 immunity and exacerbates colitis methylation of the CXC-chemokine ligand 16 (Cxcl16) in IBD-prone Il10−/− mice but not in wild-type mice128. gene75. This epigenetic modification of the Cxcl16 gene Although further studies are necessary, the increase in reduces CXCL16 expression and CXCL16‑mediated taurine conjugation of hepatic bile acids might stimulate accumulation of iNKT cells that can contribute to colitis the growth of sulphite-reducing microorganisms such as development75. Clostridium spp. (clusters IV and XIVa) B. wadsworthia, which promote harmful inflammation and ASF also promote the development of FOXP3+ 128 via mechanisms that remain to be elucidated . TReg cells, which can protect against chemically induced 19,20 (FIG. 3) Taken together, these observations indicate that colitis . Differentiation of TReg cells that are defects in the immune system and/or changes in diet induced by Clostridium spp. (clusters IV and XIV) is can trigger dysbiosis, which results in the accumulation independent of NOD1, NOD2, caspase-recruitment of pathobionts that promote transmissible or non-trans‑ domain-containing protein 9 (CARD9; a signalling missible colitis (FIG. 3). There is increasing evidence that molecule downstream of Dectin-1) and MYD88 sig‑ 19 dysbiosis affects susceptibility to developing not only nalling ; however, the induction of TReg cells by ASF IBD but also colitis-associated colon cancer in mouse requires MYD88–TRIF signalling20. Intestinal commen‑ models, as well as colon cancer in humans127,129–133. The sal bacteria can also exert protective anti-inflammatory role of commensal bacteria in intestinal cancer has been effects through their production of metabolites, such as recently reviewed134 and is not discussed here. SCFAs136. Likewise, numbers of Faecalibacterium praus‑ nitzii, a principal member of the phylum Firmicutes, are Protective effect of the microbiota in IBD. Although reduced in patients with Crohn’s disease. Culture super‑ colitogenic pathobionts promote the development natants of F. prausnitzii containing secreted metabolites of IBD, commensal bacteria are also crucial for reducing exhibit anti-inflammatory effects on human epithelial IBD susceptibility, and this has generated considerable cell lines in vitro, and they decrease the susceptibility of interest in the development of probiotic approaches to mice to chemically induced colitis in vivo, although it is prevent IBD (TABLE 1). The protective effect of com‑ unclear whether these effects are TLR-independent148. iNKT cells mensal bacteria is evident from studies using germ-free Thus, commensal bacteria and their products have activ‑ Invariant natural killer (iNKT) cells; a population of cells that mice, which are more susceptible to DSS-induced colitis ities that can protect the host against inflammation by 135–137 are thought to be particularly than conventionally housed mice . Consistent with different mechanisms (FIG. 3). important in bridging the these observations, deficiency in TLR2, TLR4, TLR9 or innate and adaptive immune MYD88 are all associated with increased susceptibility to Microbiota and extra-intestinal diseases responses. iNKT cells are DSS-induced colitis138–140. Tlr5−/− mice also develop spon‑ Multiple sclerosis. The gut microbiota has the capacity typified by a capacity for self-recognition and rapid taneous colitis in certain mouse housing facilities, which to affect the development of autoimmune central nerv‑ release of cytokines such as strongly indicates that the microbiota might affect disease ous system (CNS) disorders. Broad-spectrum antibi‑ interferon‑γ. susceptibility141,142. However, the precise mechanisms by otics are given orally to mice reduce the symptoms of

330 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

experimental autoimmune encephalomyelitis 149 + Experimental autoimmune (EAE) . In induces FOXP3 TReg cell differentiation, can prevent encephalomyelitis one model of multiple sclerosis, mice are immunized EAE symptoms152 (FIG. 4). Thus, the pathogenesis of CNS (EAE). An experimental model with the self antigen myelin oligodendrocyte glyco‑ disorders might ultimately depend on the balance of of multiple sclerosis that is protein (MOG) in complete Freund’s adjuvant (CFA). different community members in the gut microbiota. induced by immunization of susceptible animals with Disease symptoms in either MOG–CFA-induced EAE or myelin-derived antigens, in a spontaneous EAE mouse model are reduced when Arthritis. Autoimmune arthritis, such as rheumatoid such as myelin basic protein, the mice are housed under germ-free conditions150,151. arthritis, is a systemic inflammatory disease that pri‑ proteolipid protein or myelin Monocolonization of germ-free mice with SFB results marily affects the joints but can also affect other parts oligodendrocyte glycoprotein. in an increase in the number of TH17 cells in both the of the body. The events that trigger the development of K/BxN transgenic mice intestinal lamina propria and the CNS, which results in autoimmune arthritis remains unknown. However, in 150 (FIG. 4) Mice formed by crossing severe EAE . Thus, SFB-enhanced TH17 cell- mouse models, the gut microbiota contributes to disease non-obese diabetic (NOD)/Lt mediated inflammation might contribute to EAE exac‑ symptoms. Arthritis symptoms in K/BxN transgenic mice mice with KRN T cell receptor- erbation. However, it is unclear whether the disease is are reduced in a germ-free environment136,153. As in EAE, transgenic mice on the C57BL/6 background. As the KRN caused by the migration of SFB-specific TH17 cells into TH17 cell responses are implicated in promoting disease, receptor on T cells recognizes a the CNS or by the expansion of pathogenic autoantigen- and SFB-mediated enhancement of TH17 cell immunity peptide from the autoantigen specific T cells that are promoted by intestinal TH17 stimulates autoantibody production by B cells, which glucose-6‑phosphate (FIG. 4) 153 (FIG. 4) cell responses . By contrast, certain populations leads to arthritic symptoms . TH17 cell immunity isomerase, these mice develop of commensal bacteria are capable of attenuating CNS is also a key factor in spontaneous rheumatoid arthri‑ an arthritis that is mediated, + −/− and transferable, by circulating inflammation. For example, PSA B. fragilis, which tis in IL‑1R antagonist (Il1rn) mice, which exhibit antibodies against glucose-6‑ phosphate isomerase.

CNS Joint Multiple sclerosis Arthritis EAE

TH17 cell TH17 cell IL-1R TReg cell antagonist IL-1β

TH17 cell Beneﬁcial commensal bacteria Gut Lamina lumen propria

SFB IgE Peripheral blood

↓ Firmicutes B cell Basophil ↑ Bacteroidetes iNKT cell

Type 1 diabetes Allergic Pancreatitis inﬂammation Pancreas Lungs Figure 4 | Gut microbiota affects extra-intestinal autoimmune diseases. Segmented filamentous bacteria (SFB)

colonization induces T helper 17 (TH17) cell development in the intestine. These TH17 cells might migrate to the periphery

to affect systemic and central nervous system (CNS) immunity; increased intestinal TH17 cells enhance the expansion of pathogenic autoantigen-specific T cells in the intestine and cause inflammation in the CNS.Nature By contrast, Reviews ‘beneficial’ | Immunology + commensal bacteria can attenuate CNS inflammation through the induction of forkhead box P3 (FOXP3) regulatory T (TReg)

cells. Induced TH17 cells can also promote autoimmune arthritis by facilitating autoantibody production by B cells (not shown). In addition, microbiota-induced interleukin‑1β (IL‑1β) signalling participates in the development of rheumatoid

arthritis through the induction of TH17 cells. The IL‑1 receptor (IL‑1R) antagonist blocks IL‑1β signalling and abrogates joint inflammation. Balance in the microbial community also determines susceptibility to type 1 diabetes. A decreased Firmicutes/Bacteroidetes ratio as a result of a deficiency in myeloid differentiation primary-response protein 88 (MYD88)

in non-obese diabetic mice is associated with an attenuated risk of type 1 diabetes. SFB-induced TH17 cells protect the host against type 1 diabetes development by an unknown mechanism. Finally, exposure to microorganisms in neonatal, but not adult, life decreases the accumulation of invariant natural killer T (iNKT) cells in the gut, which results in protection against allergic inflammation in the lungs. In addition, microbial compounds stimulate peripheral B cells through B cell-intrinsic MYD88 signalling and inhibit IgE production. Decreased levels of peripheral IgE result in decreased numbers of basophils, and attenuate the risk of allergic airway inflammation. EAE, experimental autoimmune encephalomyelitis.

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 331

excessive IL‑1 signalling, enhanced IL‑17 expression treated with antibiotics have an expansion of basophils and increased arthritic symptoms154. Similar to K/BxN in the peripheral blood as well as increased serum IgE mice, arthritic symptoms in Il1rn−/− mice are diminished levels160 (FIG. 4). The expansion of basophils as a result when the mice are housed in germ-free conditions, which of microbiota depletion exacerbates the allergic airway indicates that the microbiota might be essential for the inflammation that is triggered by exposure to house progression of arthritis in this model, although whether dust mite allergen160. The microbiota is directly sensed SFB are involved is unclear155 (FIG. 4). Together with the by B cells and activates MYD88 signalling to limit IgE

observation that IL‑1β signalling is essential for TH17 cell class-switching in B cells. As CpG stimulation alone can differentiation16, these results indicate that the microbiota prevent IgE production by B cells, the TLR9–MYD88 is involved in the pathogenesis of rheumatoid arthritis axis might have a crucial role in IgE responses that can 160 partly through the promotion of TH17 cell responses. lead to allergic inflammation . Consistent with this idea, allergic responses to food T1D. Type 1 diabetes (T1D) is an autoimmune disorder antigens are aggravated in antibiotic-treated mice or in that results in the destruction of insulin-producing cells Tlr4−/− mice, but are ameliorated by CpG treatment161. in the pancreas. Recent studies with NOD mice, which Thus, exposure to microorganisms that stimulate TLR have been used to model this disease, have provided some signalling might be important in reducing the develop‑

insights into how the gut microbiota can affect the devel‑ ment of allergic inflammation by the promotion of TH1

opment of T1D. Diabetes in NOD mice is ameliorated in rather than TH2 cell polarization. A recent study dem‑ the absence of MYD88 (REF. 156). However, protection onstrated that neonatal colonization of the gut micro‑ against diabetes in Myd88−/− NOD mice is abrogated by biota is essential for reducing numbers of iNKT cells in antibiotic treatment and in germ-free conditions156. These the intestine, and iNKT cells have been implicated in data indicate that commensal bacteria might be impor‑ mediating allergic responses in the lungs75 (FIG. 4). Taken tant for reducing disease susceptibility in this model. together, the essential role of the gut microbiota in regu‑ Indeed, 16S ribosomal RNA sequencing showed altera‑ lating immune balance in the intestine might explain its tions in the composition of the microbiota in Myd88−/− ability to influence susceptibility to allergies. These find‑ NOD mice compared with their Myd88‑sufficient NOD ings support the hygiene hypothesis, which arose from littermates. These alterations were characterized by a the observation that early exposure to bacteria during lower Firmicutes/Bacteroides ratio on a phylum level infancy is associated with a reduced incidence of allergic and indicate that certain bacterial populations might diseases. contribute to protection against T1D (FIG. 4). As it has been recently demonstrated that deficiencies in MYD88 Other extra-intestinal diseases. Systemic dissemination or individual TLRs alone do not affect the composition of the gut microbiota has a crucial role in the develop‑ of the gut microbiota157, it is possible that the genetic ment of severe acute pancreatitis162. Cerulein-induced background of the NOD mice contributes to the effect of pancreatitis is dramatically reduced in Nod1−/− mice, MYD88 deficiency on microbiota composition. which indicates that there might be an important role Interestingly, SFB has also been implicated in pro‑ for commensal bacteria-mediated NOD1 activation in tection against T1D, which indicates that intestinal the development of pancreatitis163. NOD1 stimulation

TH17 cells in certain contexts might be protective, despite induces CC-chemokine ligand 2 (CCL2) production, their link to autoimmunity158 (FIG. 4). SFB-mediated pro‑ thereby promoting the recruitment of CCR2+ monocytes NOD mice tection against T1D seems to be gender-specific: male that facilitate pancreatitis163. Non-obese diabetic (NOD) mice spontaneously develop NOD mice with SFB have a lower incidence of T1D than Intestinal dysbiosis might also be linked to the 158 type 1 diabetes as a result of their female counterparts . Furthermore, the microbiota pathogenesis of cystic fibrosis, as mice with cystic autoreactive T cell-mediated in male NOD mice is distinct from that in females and fibrosis-like disease exhibit an increased abundance destruction of pancreatic it contributes to increased testosterone levels, which are of Mycobacteriaceae spp., Enterobacteriaceae spp., β‑islet cells. associated with protection against T1D159. Indeed, trans‑ Clostridaceae spp., and B. fragilis164. However, the pre‑ Hygiene hypothesis ferring the microbiota from male into female NOD mice cise mechanisms by which a dysbiotic microbiota affects This hypothesis originally results in increased levels of testosterone and reduced the pathophysiology of cystic fibrosis still remains to be stated that the increased susceptibility to T1D in female NOD mice159. Much elucidated. incidence of atopic diseases in work remains to be done to understand the complexities westernized countries was a Perspectives consequence of living in an of TH17 cell responses and the mechanisms by which the overly clean environment, gut microbiota contributes to the development of T1D. The gut microbiota has been studied for more than a which resulted in an century; however, recent studies have shown ever- understimulated immune Allergic inflammation. Under germ-free conditions, expanding roles for these microscopic organisms in system that responded 17 inappropriately to harmless host immune responses are TH2‑biased . Restoration health and disease. Despite the complexity of the gut antigens. More recently it has of the gut microbiota in germ-free mice results in microbiota, there is a delicate balance in bacterial popu‑ been proposed that an an increase in TH1 and TH17 cells and a reduction of lations such that any disruption in this balance leads to absence of exposure to TH2‑type responses to levels that are observed in conven‑ dysbiosis and, consequently, to decreased resistance to pathogens, in particular tionally housed mice17. This indicates that the microbi‑ pathogen colonization, to the favoured growth of patho‑ helminths, might predispose individuals to both increased ota might be important in maintaining balance in TH cell bionts and to pathological immune responses. Although allergy and autoimmune responses. The mechanism by which the microbiota the association of dysbiosis with disease pathogenesis disease. achieves this is still unclear. Germ-free mice or mice has become evident, it is still largely unknown which

332 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

factors are important in triggering dysbiosis. Obviously, system. Given the importance of the gut microbiota and both genetic and environmental factors are important in dysbiosis in disease pathogenesis, targeting the micro‑ shaping the microbiota; however, the relative contribu‑ biota is an attractive therapeutic approach. In fact, faecal tions of these two groups of factors, and the mechanism microbiota transplantation (FMT) has been highly effec‑ by which they interact to lead to dysbiosis, remain areas tive in the treatment of Clostridium difficile infection165, of active investigation. which indicates that the correction of dysbiosis might Other questions that need to be further addressed are be a valid approach for reducing susceptibility to other whether dysbiosis is disease-specific and whether the diseases, including IBD. Clearly, much work remains to timing with which dysbiosis occurs during the lifetime be done not only to achieve a deeper understanding of of the host is important for disease pathogenesis, espe‑ host–microbial relationships but also to establish the cially as microbiota colonization early in life is crucial for best way to use that relationship to prevent or to treat the optimal development and function of the immune diseases within and outside the intestine.

1. Hooper, L. V. & Macpherson, A. J. Immune 19. Atarashi, K. et al. Induction of colonic regulatory 37. Spits, H. & Di Santo, J. P. The expanding family of adaptations that maintain homeostasis with the T cells by indigenous Clostridium species. Science innate lymphoid cells: regulators and effectors of intestinal microbiota. Nature Rev. Immunol. 10, 331, 337–341 (2011). immunity and tissue remodeling. Nature Immunol. 12, 159–169 (2010). In this study, the authors identify a cocktail of 46 21–27 (2011). 2. Renz, H., Brandtzaeg, P. & Hornef, M. The impact of strains of Clostridium spp. that efficiently induce 38. Satoh-Takayama, N. et al. Microbial flora drives perinatal immune development on mucosal the development of peripherally derived FOXP3+ interleukin 22 production in intestinal NKp46+ cells

homeostasis and chronic inflammation. Nature Rev. TReg cells in the colon, which are important for that provide innate mucosal immune defense. Immunol. 12, 9–23 (2011). preventing intestinal inflammation and allergy. Immunity 29, 958–970 (2008). 3. Stecher, B. & Hardt, W. D. Mechanisms controlling 20. Geuking, M. B. et al. Intestinal bacterial colonization 39. Sanos, S. L. et al. RORγt and commensal microflora pathogen colonization of the gut. Curr. Opin. induces mutualistic regulatory T cell responses. are required for the differentiation of mucosal Microbiol. 14, 82–91 (2011). Immunity 34, 794–806 (2011). interleukin 22‑producing NKp46+ cells. Nature 4. Littman, D. R. & Pamer, E. G. Role of the commensal 21. Round, J. L. et al. The Toll-like receptor 2 pathway Immunol. 10, 83–91 (2009). microbiota in normal and pathogenic host immune establishes colonization by a commensal of the 40. Sawa, S. et al. RORγt+ innate lymphoid cells regulate responses. Cell Host Microbe 10, 311–323 human microbiota. Science 332, 974–977 (2011). intestinal homeostasis by integrating negative signals (2011). 22. Fagarasan, S., Kawamoto, S., Kanagawa, O. & from the symbiotic microbiota. Nature Immunol. 12, 5. Honda, K. & Littman, D. R. The microbiome in Suzuki, K. Adaptive immune regulation in the gut: 320–326 (2011). infectious disease and inflammation. Annu. Rev. T cell-dependent and T cell-independent IgA 41. Zheng, Y. et al. Interleukin‑22 mediates early host Immunol. 30, 759–795 (2012). synthesis. Annu. Rev. Immunol. 28, 243–273 (2010). defense against attaching and effacing bacterial 6. Gordon, H. A., Bruckner-Kardoss, E. & 23. Strugnell, R. A. & Wijburg, O. L. The role of secretory pathogens. Nature Med. 14, 282–289 (2008). Wostmann, B. S. Aging in germ-free mice: life tables antibodies in infection immunity. Nature Rev. 42. Vaishnava, S. et al. The antibacterial lectin RegIIIγ and lesions observed at natural death. J. Gerontol. Microbiol. 8, 656–667 (2010). promotes the spatial segregation of microbiota and 21, 380–387 (1966). 24. Macpherson, A. J., Geuking, M. B. & McCoy, K. D. host in the intestine. Science 334, 255–258 (2011). 7. Hamada, H. et al. Identification of multiple isolated Homeland security: IgA immunity at the frontiers of In this study, the authors demonstrate that lymphoid follicles on the antimesenteric wall of the the body. Trends Immunol. 33, 160–167 (2012). bacterial stimuli from commensal microbiota mouse small intestine. J. Immunol. 168, 57–64 25. Fagarasan, S. et al. Critical roles of activation-induced promote the production of the antimicrobial (2002). cytidine deaminase in the homeostasis of gut flora. molecule REGIIIγ by the epithelium in a 8. Bouskra, D. et al. Lymphoid tissue genesis induced Science 298, 1424–1427 (2002). MYD88‑dependent process. REGIIIγ functions as by commensals through NOD1 regulates intestinal This report shows that intestinal IgA responses an additional barrier against the microbiota. homeostasis. Nature 456, 507–510 (2008). can shape the commensal bacterial community. 43. Sonnenberg, G. F. et al. Innate lymphoid cells promote 9. Moreau, M. C. & Corthier, G. Effect of the 26. Wei, M. et al. Mice carrying a knock‑in mutation of anatomical containment of lymphoid-resident gastrointestinal microflora on induction and Aicda resulting in a defect in somatic hypermutation commensal bacteria. Science 336, 1321–1325 maintenance of oral tolerance to ovalbumin in C3H/ have impaired gut homeostasis and compromised (2012). HeJ mice. Infect. Immun. 56, 2766–2768 (1988). mucosal defense. Nature Immunol. 12, 264–270 44. Osawa, N. & Mitsuhashi, S. Infection of germfree mice 10. Pabst, O. et al. Adaptation of solitary intestinal (2011). with Shigella flexneri 3A. Jpn J. Exp. Med. 34, 77–80 lymphoid tissue in response to microbiota and 27. Peterson, D. A., McNulty, N. P., Guruge, J. L. & (1964). chemokine receptor CCR7 signaling. J. Immunol. 177, Gordon, J. I. IgA response to symbiotic bacteria as a 45. Fukuda, S. et al. Bifidobacteria can protect from 6824–6832 (2006). mediator of gut homeostasis. Cell Host Microbe 2, enteropathogenic infection through production of 11. Littman, D. R. & Rudensky, A. Y. Th17 and regulatory 328–339 (2007). acetate. Nature 469, 543–547 (2011). T cells in mediating and restraining inflammation. 28. Suzuki, K. et al. The sensing of environmental stimuli 46. Bohnhoff, M., Drake, B. L. & Miller, C. P. Effect of Cell 140, 845–858 (2010). by follicular dendritic cells promotes immunoglobulin A streptomycin on susceptibility of intestinal tract to 12. Atarashi, K. et al. ATP drives lamina propria generation in the gut. Immunity 33, 71–83 (2010). experimental Salmonella infection. Proc. Soc. Exp.

TH17 cell differentiation. Nature 455, 808–812 29. Mora, J. R. et al. Generation of gut-homing IgA- Biol. Med. 86, 132–137 (1954). (2008). secreting B cells by intestinal dendritic cells. 47. Hentges, D. J. & Freter, R. In vivo and in vitro 13. Ivanov, I. I. et al. Specific microbiota direct the Science 314, 1157–1160 (2006). antagonism of intestinal bacteria against Shigella differentiation of IL‑17‑producing T‑helper cells in the 30. Uematsu, S. et al. Regulation of humoral and cellular flexneri I. Correlation between various tests. mucosa of the small intestine. Cell Host Microbe 4, gut immunity by lamina propria dendritic cells J. Infect. Dis. 110, 30–37 (1962). 337–349 (2008). expressing Toll-like receptor 5. Nature Immunol. 9, 48. Lawley, T. D. et al. Antibiotic treatment of Clostridium 14. Ivanov, I. I. et al. Induction of intestinal Th17 cells by 769–776 (2008). difficile carrier mice triggers a supershedder state, segmented filamentous bacteria. Cell 139, 485–498 31. Tezuka, H. et al. Regulation of IgA production by spore-mediated transmission, and severe disease in (2009). naturally occurring TNF/iNOS-producing dendritic immunocompromised hosts. Infect. Immun. 77, This study identifies SFB as a main driver of cells. Nature 448, 929–933 (2007). 3661–3669 (2009).

intestinal TH17 cell differentiation, which can 32. Tezuka, H. et al. Prominent role for plasmacytoid 49. Rupnik, M., Wilcox, M. H. & Gerding, D. N. protect the host against enteric pathogen dendritic cells in mucosal T cell-independent IgA Clostridium difficile infection: new developments in infection. induction. Immunity 34, 247–257 (2011). epidemiology and pathogenesis. Nature Rev. 15. Gaboriau-Routhiau, V. et al. The key role of segmented 33. Fritz, J. H. et al. Acquisition of a multifunctional Microbiol. 7, 526–536 (2009). filamentous bacteria in the coordinated maturation of IgA+ plasma cell phenotype in the gut. Nature 481, 50. Momose, Y., Hirayama, K. & Itoh, K. Competition for gut helper T cell responses. Immunity 31, 677–689 199–203 (2011). proline between indigenous Escherichia coli and (2009). 34. Walker, J. A., Barlow, J. L. & McKenzie, A. N. E. coli O157:H7 in gnotobiotic mice associated with 16. Shaw, M. H., Kamada, N., Kim, Y. G. & Nunez, G. Innate lymphoid cells — how did we miss them? infant intestinal microbiota and its contribution to the Microbiota-induced IL‑1β, but not IL‑6, is critical for Nature Rev. Immunol. 13, 75–87 (2013). colonization resistance against E. coli O157:H7.

the development of steady-state TH17 cells in the 35. Sonnenberg, G. F. & Artis, D. Innate lymphoid cell Antonie Van Leeuwenhoek 94, 165–171 (2008). intestine. J. Exp. Med. 209, 251–258 (2012). interactions with microbiota: implications for 51. Momose, Y., Hirayama, K. & Itoh, K. Effect of organic 17. Chung, H. et al. Gut immune maturation depends on intestinal health and disease. Immunity 37, 601–610 acids on inhibition of Escherichia coli O157:H7 colonization with a host-specific microbiota. Cell 149, (2012). colonization in gnotobiotic mice associated with infant 1578–1593 (2012). 36. Cella, M. et al. A human natural killer cell subset intestinal microbiota. Antonie Van Leeuwenhoek 93, 18. Powrie, F., Leach, M. W., Mauze, S., Caddle, L. B. & provides an innate source of IL‑22 for mucosal 141–149 (2008). Coffman, R. L. Phenotypically distinct subsets of immunity. Nature 457, 722–725 (2009). 52. Fabich, A. J. et al. Comparison of carbon nutrition for CD4+ T cells induce or protect from chronic intestinal In this report, the authors identify IL‑22‑producing pathogenic and commensal Escherichia coli strains in inflammation in C. B-17 scid mice. Int. Immunol. 5, ILC3s in mucosal tissues, including the intestine, in the mouse intestine. Infect. Immun. 76, 1143–1152 1461–1471 (1993). both mice and humans. (2008).

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 333

53. Leatham, M. P. et al. Precolonized human commensal 72. Kamada, N. et al. Abnormally differentiated subsets 96. Schultz, M. et al. IL‑2‑deficient mice raised under Escherichia coli strains serve as a barrier to E. coli of intestinal macrophage play a key role in germfree conditions develop delayed mild focal O157:H7 growth in the streptomycin-treated mouse Th1‑dominant chronic colitis through excess intestinal inflammation. Am. J. Physiol. 276, intestine. Infect. Immun. 77, 2876–2886 (2009). production of IL‑12 and IL‑23 in response to bacteria. G1461–G1472 (1999). 54. Kamada, N. et al. Regulated virulence controls the J. Immunol. 175, 6900–6908 (2005). 97. Bamias, G. et al. Commensal bacteria exacerbate ability of a pathogen to compete with the gut 73. Kiss, E. A. et al. Natural aryl hydrocarbon receptor intestinal inflammation but are not essential for the microbiota. Science 336, 1325–1329 (2012). ligands control organogenesis of intestinal lymphoid development of murine ileitis. J. Immunol. 178, This study demonstrates the importance of follicles. Science 334, 1561–1565 (2011). 1809–1818 (2007). commensal bacteria in eradicating pathogens by 74. Qiu, J. et al. The aryl hydrocarbon receptor regulates 98. Kobayashi, M. et al. Toll-like receptor-dependent competing for shared nutrients. The expression of gut immunity through modulation of innate lymphoid production of IL‑12p40 causes chronic enterocolitis virulence factors by the pathogen allows it to cells. Immunity 36, 92–104 (2012). in myeloid cell-specific Stat3‑deficient mice. localize to the epithelium as a means of escaping 75. Olszak, T. et al. Microbial exposure during early life J. Clin. Invest. 111, 1297–1308 (2003). nutritional competition by the microbiota. has persistent effects on natural killer T cell function. 99. Rakoff-Nahoum, S., Hao, L. & Medzhitov, R. 55. Endt, K. et al. The microbiota mediates pathogen Science 336, 489–493 (2012). Role of Toll-like receptors in spontaneous clearance from the gut lumen after non-typhoidal 76. Mazmanian, S. K., Round, J. L. & Kasper, D. L. commensal-dependent colitis. Immunity 25, Salmonella diarrhea. PLoS Pathog. 6, e1001097 A microbial symbiosis factor prevents intestinal 319–329 (2006). (2010). inflammatory disease. Nature 453, 620–625 (2008). 100. Hoshi, N. et al. MyD88 signalling in colonic 56. Pacheco, A. R. et al. Fucose sensing regulates bacterial In this study, the authors report that a human mononuclear phagocytes drives colitis in intestinal colonization. Nature 492, 113–117 commensal bacterium, B. fragilis, protects against IL‑10‑deficient mice. Nature Commun. 3, 1120 (2012). pathobiont-induced intestinal inflammation, and (2012). 57. Le Bouguenec, C. & Schouler, C. Sugar metabolism, that the PSA in its capsule is sufficient for this 101. Nenci, A. et al. Epithelial NEMO links innate an additional virulence factor in enterobacteria. protection. Specifically, PSA induces IL‑10 immunity to chronic intestinal inflammation. Int. J. Med. Microbiol. 301, 1–6 (2010). production from CD4+ T cells that protect against Nature 446, 557–561 (2007). 58. Bertin, Y. et al. Enterohaemorrhagic Escherichia coli intestinal inflammation. 102. Smythies, L. E. et al. Human intestinal macrophages gains a competitive advantage by using ethanolamine 77. O’Mahony, C. et al. Commensal-induced regulatory display profound inflammatory anergy despite avid as a nitrogen source in the bovine intestinal content. T cells mediate protection against pathogen-stimulated phagocytic and bacteriocidal activity. J. Clin. Invest. Environ. Microbiol. 13, 365–377 (2011). NF‑κB activation. PLoS Pathog. 4, e1000112 (2008). 115, 66–75 (2005). 59. Winter, S. E. et al. Gut inflammation provides a 78. Macpherson, A. J. et al. A primitive T cell-independent 103. Kamada, N. et al. Unique CD14 intestinal respiratory electron acceptor for Salmonella. mechanism of intestinal mucosal IgA responses to macrophages contribute to the pathogenesis of Nature 467, 426–429 (2010). commensal bacteria. Science 288, 2222–2226 Crohn disease via IL‑23/IFN-γ axis. J. Clin. Invest. This study demonstrates that an enteric pathogen (2000). 118, 2269–2280 (2008). acquires a growth advantage in the presence of 79. Lathrop, S. K. et al. Peripheral education of the 104. Cho, J. H. The genetics and immunopathogenesis of intestinal inflammation. Pathogen-induced immune system by colonic commensal microbiota. inflammatory bowel disease. Nature Rev. Immunol. inflammation promotes neutrophil recruitment Nature 478, 250–254 (2011). 8, 458–466 (2008). and the conversion of a commensal metabolite 80. Hand, T. W. et al. Acute gastrointestinal infection 105. Ogura, Y. et al. A frameshift mutation in NOD2 to a form that can be used by the pathogen. induces long-lived microbiota-specific T cell responses. associated with susceptibility to Crohn’s disease. 60. Thiennimitr, P. et al. Intestinal inflammation allows Science 337, 1553–1556 (2012). Nature 411, 603–606 (2001). Salmonella to use ethanolamine to compete with the 81. Slack, E. et al. Innate and adaptive immunity 106. Hugot, J. P. et al. Association of NOD2 leucine-rich microbiota. Proc. Natl Acad. Sci. USA 108, cooperate flexibly to maintain host-microbiota repeat variants with susceptibility to Crohn’s disease. 17480–17485 (2011). mutualism. Science 325, 617–620 (2009). Nature 411, 599–603 (2001). 61. Murdoch, S. L. et al. The opportunistic pathogen 82. Fagundes, C. T. et al. Transient TLR activation restores 107. Inohara, N. et al. Host recognition of bacterial Serratia marcescens utilizes type VI secretion to inflammatory response and ability to control muramyl dipeptide mediated through NOD2. target bacterial competitors. J. Bacteriol. 193, pulmonary bacterial infection in germfree mice. Implications for Crohn’s disease. J. Biol. Chem. 278, 6057–6069 (2011). J. Immunol. 188, 1411–1420 (2012). 5509–5512 (2003). 62. Gueguen, E. & Cascales, E. Promoter swapping 83. Clarke, T. B. et al. Recognition of peptidoglycan from 108. Hampe, J. et al. A genome-wide association scan of unveils the role of the Citrobacter rodentium CTS1 the microbiota by Nod1 enhances systemic innate nonsynonymous SNPs identifies a susceptibility type VI secretion system in interbacterial immunity. Nature Med. 16, 228–231 (2010). variant for Crohn disease in ATG16L1. Nature Genet. competition. Appl. Environ. Microbiol. 79, 32–38 84. Ichinohe, T. et al. Microbiota regulates immune 39, 207–211 (2007). (2013). defense against respiratory tract influenza A virus 109. Parkes, M. et al. Sequence variants in the autophagy 63. Johansson, M. E. et al. The inner of the two Muc2 infection. Proc. Natl Acad. Sci. USA 108, 5354–5359 gene IRGM and multiple other replicating loci mucin-dependent mucus layers in colon is devoid of (2011). contribute to Crohn’s disease susceptibility. bacteria. Proc. Natl Acad. Sci. USA 105, 85. Abt, M. C. et al. Commensal bacteria calibrate the Nature Genet. 39, 830–832 (2007). 15064–15069 (2008). activation threshold of innate antiviral immunity. 110. Travassos, L. H. et al. Nod1 and Nod2 direct 64. Bergstrom, K. S. et al. Muc2 protects against lethal Immunity 37, 158–170 (2012). autophagy by recruiting ATG16L1 to the plasma infectious colitis by disassociating pathogenic and 86. Ganal, S. C. et al. Priming of natural killer cells by membrane at the site of bacterial entry. Nature commensal bacteria from the colonic mucosa. nonmucosal mononuclear phagocytes requires Immunol. 11, 55–62 (2010). PLoS Pathog. 6, e1000902 (2010). instructive signals from commensal microbiota. 111. Cooney, R. et al. NOD2 stimulation induces 65. Petersson, J. et al. Importance and regulation of the Immunity 37, 171–186 (2012). autophagy in dendritic cells influencing bacterial colonic mucus barrier in a mouse model of colitis. 87. Benson, A., Pifer, R., Behrendt, C. L., Hooper, L. V. & handling and antigen presentation. Nature Med. 16, Am. J. Physiol. Gastrointest. Liver Physiol. 300, Yarovinsky, F. Gut commensal bacteria direct a 90–97 (2010). G327–G333 (2010). protective immune response against Toxoplasma 112. Homer, C. R., Richmond, A. L., Rebert, N. A., 66. Cash, H. L., Whitham, C. V., Behrendt, C. L. & gondii. Cell Host Microbe 6, 187–196 (2009). Achkar, J. P. & McDonald, C. ATG16L1 and NOD2 Hooper, L. V. Symbiotic bacteria direct expression of 88. Naik, S. et al. Compartmentalized control of skin interact in an autophagy-dependent antibacterial an intestinal bactericidal lectin. Science 313, immunity by resident commensals. Science 337, pathway implicated in Crohn’s disease pathogenesis. 1126–1130 (2006). 1115–1119 (2012). Gastroenterology 139, 1630–1641.e2 (2010). 67. Brandl, K., Plitas, G., Schnabl, B., DeMatteo, R. P. & 89. Giel, J. L., Sorg, J. A., Sonenshein, A. L. & Zhu, J. 113. Bevins, C. L. & Salzman, N. H. Paneth cells, Pamer, E. G. MyD88‑mediated signals induce the Metabolism of bile salts in mice influences spore antimicrobial peptides and maintenance of intestinal bactericidal lectin RegIIIγ and protect mice against germination in Clostridium difficile. PLoS ONE 5, homeostasis. Nature Rev. Microbiol. 9, 356–368 intestinal Listeria monocytogenes infection. e8740 (2010). (2011). J. Exp. Med. 204, 1891–1900 (2007). 90. Kane, M. et al. Successful transmission of a retrovirus 114. Ogura, Y. et al. Expression of NOD2 in Paneth cells: 68. Dessein, R. et al. Toll-like receptor 2 is critical for depends on the commensal microbiota. Science 334, a possible link to Crohn’s ileitis. Gut 52, 1591–1597 induction of Reg3β expression and intestinal 245–249 (2011). (2003). clearance of Yersinia pseudotuberculosis. Gut 58, 91. Kuss, S. K. et al. Intestinal microbiota promote 115. Wehkamp, J. et al. NOD2 (CARD15) mutations in 771–776 (2009). enteric virus replication and systemic pathogenesis. Crohn’s disease are associated with diminished 69. van Ampting, M. T. et al. Intestinally secreted C‑type Science 334, 249–252 (2011). mucosal α-defensin expression. Gut 53, 1658–1664 lectin Reg3β attenuates salmonellosis but not 92. Sellon, R. K. et al. Resident enteric bacteria are (2004). listeriosis in mice. Infect. Immun. 80, 1115–1120 necessary for development of spontaneous colitis and 116. Petnicki-Ocwieja, T. et al. Nod2 is required for the (2012). immune system activation in interleukin-10‑deficient regulation of commensal microbiota in the intestine. 70. Denning, T. L., Wang, Y. C., Patel, S. R., Williams, I. R. mice. Infect. Immun. 66, 5224–5231 (1998). Proc. Natl Acad. Sci. USA 106, 15813–15818 (2009). & Pulendran, B. Lamina propria macrophages and 93. Dianda, L. et al. T cell receptor-α β-deficient mice fail 117. Cadwell, K. et al. A key role for autophagy and the dendritic cells differentially induce regulatory and to develop colitis in the absence of a microbial autophagy gene Atg16l1 in mouse and human interleukin 17‑producing T cell responses. Nature environment. Am. J. Pathol. 150, 91–97 (1997). intestinal Paneth cells. Nature 456, 259–263 Immunol. 8, 1086–1094 (2007). 94. Taurog, J. D. et al. The germfree state prevents (2008). 71. Franchi, L. et al. NLRC4‑driven production of IL‑1β development of gut and joint inflammatory disease 118. Cadwell, K. et al. Virus-plus-susceptibility gene discriminates between pathogenic and commensal in HLA‑B27 transgenic rats. J. Exp. Med. 180, interaction determines Crohn’s disease gene Atg16L1 bacteria and promotes host intestinal defense. 2359–2364 (1994). phenotypes in intestine. Cell 141, 1135–1145 Nature Immunol. 13, 449–456 (2012). 95. Rath, H. C., Wilson, K. H. & Sartor, R. B. Differential (2010). This study demonstrates that NLRC4 selectively induction of colitis and gastritis in HLA‑B27 transgenic 119. Kim, S. C. et al. Variable phenotypes of enterocolitis in recognizes pathogenic, but not commensal, rats selectively colonized with Bacteroides vulgatus or interleukin 10‑deficient mice monoassociated with two bacteria and that it promotes protective immunity Escherichia coli. Infect. Immun. 67, 2969–2974 different commensal bacteria. Gastroenterology 128, against pathogens via induction of mature IL‑1β. (1999). 891–906 (2005).

334 | MAY 2013 | VOLUME 13 www.nature.com/reviews/immunol

120. Waidmann, M. et al. Bacteroides vulgatus protects 136. Maslowski, K. M. et al. Regulation of inflammatory 155. Abdollahi-Roodsaz, S. et al. Stimulation of TLR2 and against Escherichia coli-induced colitis in gnotobiotic responses by gut microbiota and chemoattractant TLR4 differentially skews the balance of T cells in a interleukin-2‑deficient mice. Gastroenterology 125, receptor GPR43. Nature 461, 1282–1286 (2009). mouse model of arthritis. J. Clin. Invest. 118, 162–177 (2003). 137. Saha, S. et al. Peptidoglycan recognition proteins 205–216 (2008). 121. Bohn, E. et al. Host gene expression in the colon of protect mice from experimental colitis by promoting 156. Wen, L. et al. Innate immunity and intestinal gnotobiotic interleukin-2‑deficient mice colonized with normal gut flora and preventing induction of microbiota in the development of type 1 diabetes. commensal colitogenic or noncolitogenic bacterial interferon-γ. Cell Host Microbe 8, 147–162 (2010). Nature 455, 1109–1113 (2008). strains: common patterns and bacteria strain specific 138. Rakoff-Nahoum, S., Paglino, J., Eslami-Varzaneh, F., This report demonstrates that altered microbial signatures. Inflamm. Bowel Dis. 12, 853–862 Edberg, S. & Medzhitov, R. Recognition of communities in MYD88‑deficient NOD mice (2006). commensal microflora by toll-like receptors is prevent the development of T1D, which indicates 122. Bloom, S. M. et al. Commensal Bacteroides species required for intestinal homeostasis. Cell 118, that certain subsets of commensal microbiota induce colitis in host-genotype-specific fashion in a 229–241 (2004). might have the capacity to protect against the mouse model of inflammatory bowel disease. 139. Lee, J. et al. Maintenance of colonic homeostasis by development of T1D. Cell Host Microbe 9, 390–403 (2011). distinctive apical TLR9 signalling in intestinal epithelial 157. Ubeda, C. et al. Familial transmission rather than 123. Garrett, W. S. et al. Communicable ulcerative colitis cells. Nature Cell Biol. 8, 1327–1336 (2006). defective innate immunity shapes the distinct induced by T‑bet deficiency in the innate immune 140. Kirkland, D. et al. B cell-intrinsic MyD88 signaling intestinal microbiota of TLR-deficient mice. system. Cell 131, 33–45 (2007). prevents the lethal dissemination of commensal J. Exp. Med. 209, 1445–1456 (2012). In this study, the authors show that colitogenic bacteria during colonic damage. Immunity 36, This study indicates that differences in bacterial pathobionts can accumulate in genetically 228–238 (2012). communities in mice that are deficient in individual susceptible mice and can transmit disease to 141. Vijay-Kumar, M. et al. Deletion of TLR5 results in TLRs or MYD88 are more strongly related to wild-type mice. spontaneous colitis in mice. J. Clin. Invest. 117, maternal transmission and cage effects than to 124. Garrett, W. S. et al. Enterobacteriaceae act in concert 3909–3921 (2007). an inherent genetic susceptibility. with the gut microbiota to induce spontaneous and 142. Carvalho, F. A. et al. Interleukin‑1β (IL‑1β) promotes 158. Kriegel, M. A. et al. Naturally transmitted segmented maternally transmitted colitis. Cell Host Microbe 8, susceptibility of Toll-like receptor 5 (TLR5) deficient filamentous bacteria segregate with diabetes 292–300 (2010). mice to colitis. Gut 61, 373–384 (2012). protection in nonobese diabetic mice. Proc. Natl Acad. 125. Powell, N. et al. The transcription factor T‑bet 143. Katakura, K. et al. Toll-like receptor 9‑induced type I Sci. USA 108, 11548–11553 (2011). regulates intestinal inflammation mediated by IFN protects mice from experimental colitis. 159. Markle, J. G. et al. Sex differences in the gut interleukin‑7 receptor+ innate lymphoid cells. J. Clin. Invest. 115, 695–702 (2005). microbiome drive hormone-dependent regulation of Immunity 37, 674–684 (2012). 144. Round, J. L. & Mazmanian, S. K. Inducible Foxp3+ autoimmunity. Science 339, 1084–1088 (2013). 126. Elinav, E. et al. NLRP6 inflammasome regulates regulatory T‑cell development by a commensal 160. Hill, D. A. et al. Commensal bacteria-derived signals colonic microbial ecology and risk for colitis. Cell 145, bacterium of the intestinal microbiota. Proc. Natl regulate basophil hematopoiesis and allergic 745–757 (2011). Acad. Sci. USA 107, 12204–12209 (2010). inflammation. Nature Med. 18, 538–546 (2012). This report demonstrates that impaired NLRP6 145. Mazmanian, S. K., Liu, C. H., Tzianabos, A. O. & 161. Bashir, M. E., Louie, S., Shi, H. N. & Nagler- signalling and IL‑18 production is associated with Kasper, D. L. An immunomodulatory molecule of Anderson, C. Toll-like receptor 4 signaling by intestinal the development of dysbiosis and the accumulation symbiotic bacteria directs maturation of the host microbes influences susceptibility to food allergy. of potentially colitogenic pathobionts. immune system. Cell 122, 107–118 (2005). J. Immunol. 172, 6978–6987 (2004). 127. Couturier-Maillard, A. et al. NOD2‑mediated 146. Shen, Y. et al. Outer membrane vesicles of a human 162. Frossard, J. L., Steer, M. L. & Pastor, C. M. dysbiosis predisposes mice to transmissible colitis and commensal mediate immune regulation and disease Acute pancreatitis. Lancet 371, 143–152 (2008). colorectal cancer. J. Clin. Invest. 123, 700–711 protection. Cell Host Microbe 12, 509–520 163. Tsuji, Y. et al. Sensing of commensal organisms by the (2013). (2012). intracellular sensor NOD1 mediates experimental 128. Devkota, S. et al. Dietary-fat-induced taurocholic 147. Diehl, G. E. et al. Microbiota restricts trafficking of pancreatitis. Immunity 37, 326–338 (2012). acid promotes pathobiont expansion and colitis in bacteria to mesenteric lymph nodes by CX3CR1hi cells. 164. Lynch, S. V. et al. Cystic fibrosis transmembrane Il10−/− mice. Nature 487, 104–108 (2012). Nature 494, 116–120 (2013). conductance regulator knockout mice exhibit aberrant In this study, the authors show that a milk-derived 148. Sokol, H. et al. Faecalibacterium prausnitzii is an gastrointestinal microbiota. Gut Microbes 4, 41–47 fat diet increases the level of bile acids in the anti-inflammatory commensal bacterium identified (2013). intestine, which results in the accumulation of by gut microbiota analysis of Crohn disease patients. 165. Borody, T. J. & Khoruts, A. Fecal microbiota colitogenic pathobionts in genetically susceptible Proc. Natl Acad. Sci. USA 105, 16731–16736 transplantation and emerging applications. Nature IBD-prone mice. (2008). Rev. Gastroenterol. Hepatol. 9, 88–96 (2011). 129. Lowe, E. L. et al. Toll-like receptor 2 signaling protects 149. Ochoa-Reparaz, J. et al. Role of gut commensal 166. Li, X. D. et al. Mitochondrial antiviral signaling protein mice from tumor development in a mouse model of microflora in the development of experimental (MAVS) monitors commensal bacteria and induces an colitis-induced cancer. PLoS ONE 5, e13027 (2010). autoimmune encephalomyelitis. J. Immunol. 183, immune response that prevents experimental colitis. 130. Chen, G. Y., Shaw, M. H., Redondo, G. & Nunez, G. 6041–6050 (2009). Proc. Natl Acad. Sci. USA 108, 17390–17395 (2011). The innate immune receptor Nod1 protects the 150. Lee, Y. K., Menezes, J. S., Umesaki, Y. & 167. Negishi, H. et al. Essential contribution of IRF3 to intestine from inflammation-induced tumorigenesis. Mazmanian, S. K. Proinflammatory T‑cell responses to intestinal homeostasis and microbiota-mediated Tslp Cancer Res. 68, 10060–10067 (2008). gut microbiota promote experimental autoimmune gene induction. Proc. Natl Acad. Sci. USA 109, 131. Wu, S. et al. A human colonic commensal promotes encephalomyelitis. Proc. Natl Acad. Sci. USA 108, 21016–21021 (2012). colon tumorigenesis via activation of T helper type 17 S4615–S4622 (2011). T cell responses. Nature Med. 15, 1016–1022 151. Berer, K. et al. Commensal microbiota and myelin Acknowledgements (2009). autoantigen cooperate to trigger autoimmune This work is supported by grants from the US National 132. Arthur, J. C. et al. Intestinal inflammation targets demyelination. Nature 479, 538–541 (2011). Institutes of Health and the Bill & Melinda Gates Foundation, cancer-inducing activity of the microbiota. Science 152. Ochoa-Reparaz, J. et al. A polysaccharide from the USA. N.K. is supported by a Research Fellowship from the 338, 120–123 (2012). human commensal Bacteroides fragilis protects Crohn’s and Colitis Foundation of America. 133. Kostic, A. D. et al. Genomic analysis identifies against CNS demyelinating disease. Mucosal association of Fusobacterium with colorectal Immunol. 3, 487–495 (2010). Competing interests statement carcinoma. Genome Res. 22, 292–298 (2012). 153. Wu, H. J. et al. Gut-residing segmented filamentous The authors declare no competing financial interests. 134. Hajishengallis, G., Darveau, R. P. & Curtis, M. A. bacteria drive autoimmune arthritis via T helper 17 The keystone–pathogen hypothesis. Nature Rev. cells. Immunity 32, 815–827 (2010). Microbiol. 10, 717–725 (2012). 154. Nakae, S. et al. IL‑17 production from activated FURTHER INFORMATION 135. Kitajima, S., Morimoto, M., Sagara, E., Shimizu, C. & T cells is required for the spontaneous development Gabriel Núñez’s homepage: http://www.med.umich.edu/ Ikeda, Y. Dextran sodium sulfate-induced colitis in of destructive arthritis in mice deficient in IL‑1 immprog/faculty/nunezg.htm germ-free IQI/Jic mice. Exp. Anim. 50, 387–395 receptor antagonist. Proc. Natl Acad. Sci. USA 100, ALL LINKS ARE ACTIVE IN THE ONLINE PDF (2001). 5986–5990 (2003).

NATURE REVIEWS | IMMUNOLOGY VOLUME 13 | MAY 2013 | 335