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`The Microbiome in Infectious
`Disease and Inflammation
`Kenya Honda1 and Dan R. Littman2,3
`1Department of Immunology, Graduate School of Medicine, The University of Tokyo,
`Tokyo 113-0033, Japan; email: kenya@m.u-tokyo.ac.jp
`2Molecular Pathogenesis Program, 3Howard Hughes Medical Institute, The Kimmel
`Center for Biology and Medicine of the Skirball Institute, New York University School of
`Medicine, New York, NY 10016; email: Dan.Littman@med.nyu.edu
`
`Annu. Rev. Immunol. 2012. 30:759–95
`
`First published online as a Review in Advance on
`January 6, 2012
`
`The Annual Review of Immunology is online at
`immunol.annualreviews.org
`
`This article’s doi:
`10.1146/annurev-immunol-020711-074937
`Copyright c(cid:2) 2012 by Annual Reviews.
`All rights reserved
`
`0732-0582/12/0423-0759$20.00
`
`Keywords
`intestinal microbiota, Th17 cells, Treg cells, innate lymphoid cells,
`segmented filamentous bacteria, Clostridium
`
`Abstract
`The mammalian alimentary tract harbors hundreds of species of
`commensal microorganisms (microbiota) that intimately interact with
`the host and provide it with genetic, metabolic, and immunological
`attributes. Recent reports have indicated that the microbiota compo-
`sition and its collective genomes (microbiome) are major factors in
`predetermining the type and robustness of mucosal immune responses.
`In this review, we discuss the recent advances in our understanding of
`host-microbiota interactions and their effect on the health and disease
`susceptibility of the host.
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`INTRODUCTION
`The tissues of the gastrointestinal tract have
`the unique property of harboring an enormous
`number of microbes within the lumen. The
`concentration of microbes that reside in the
`small intestine is estimated to be from 103 to
`109
`cells/ml, whereas
`the large intestine
`contains abundant bacteria, which achieve a
`concentration of up to 1011 or 1012 cells/g of lu-
`minal contents (1). This concentration is similar
`to or even higher than that achieved in colonies
`growing under optimum conditions on labora-
`tory plates, indicating that the colonic lumen
`provides a safe and nourishing environment and
`represents an extremely efficient natural biore-
`actor for bacteria. The estimated total number
`of bacteria carried by a healthy human in the gut
`is 1014, which, as a whole, constitutes the micro-
`biota (also referred to as the microbial flora), an
`ecosystem in dynamic equilibrium. The mem-
`bers of the intestinal microbiota can be catego-
`rized as either allochthonous or autochthonous
`(1, 2). Allochthonous bacteria
`are only
`transiently present, whereas autochthonous
`bacteria are indigenous and preferentially
`colonize physical spaces or niches in particular
`animal species. In most cases, indigenous bacte-
`ria can attach to the epithelium or mucus layer
`and form a biofilm, and thereby significantly
`affect host development and physiology.
`The microbiota allows for optimal break-
`down of
`foods, uptake of nutrients, and
`enhancement of intestinal development, which
`have led to diet diversification and increased
`evolutionary fitness. Beyond digestion and
`metabolism, the microbiota also contributes to
`development and maintenance of the intestinal
`epithelial barrier, development of the immune
`system, and competition with pathogenic
`microorganisms, thus preventing their prop-
`agation. Indeed, studies of germfree (GF)
`animals indicate that intestinal microbes pro-
`foundly affect the development of the mucosal
`immune system in terms of the organization
`of Peyer’s patches (PPs) and isolated lymphoid
`follicles
`(ILFs),
`secretion of antimicrobial
`peptides by epithelial cells, and accumulation
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`of various immunocytes at mucosal sites (3–7).
`Collectively, the gut microbiota provides an
`indispensable internal ecosystem for numer-
`ous host physiological processes and can be
`considered to have coevolved with the host to
`form a superorganism (8).
`The collective genome of intestinal mi-
`crobes, termed the microbiome, is estimated
`to contain at least 100 times more genes
`than our own genome (9). Unlike the human
`genome, which is rarely altered by xenobiotic
`intervention, the gut microbiota composition is
`readily changeable by diet, antibiotic ingestion,
`infection by pathogens, and other life events.
`The plasticity of the microbiome has been
`implicated in numerous disease conditions, and
`an unfavorable alteration of the gut microbiota
`composition is called dysbiosis, which includes
`an outgrowth of potential pathogenic bacteria
`(pathobionts) and a decrease in the number
`of beneficial bacteria (10, 11). Multiple recent
`reports have shown a link between dysbiosis
`and immune disorders. Crohn’s disease and
`ulcerative colitis are two chronic intestinal
`inflammatory conditions referred to as in-
`flammatory bowel disease (IBD). IBD is a
`disease with an elusive etiology, and although
`many potential triggers have been invoked,
`one attractive hypothesis is that IBD may be
`a result of dysbiosis in the intestinal microbial
`community that promotes the overgrowth of
`bacteria that aberrantly stimulate the intestinal
`immune system. Indeed, many reports have
`shown that the microbial populations in the in-
`testine of IBD patients are different from those
`of healthy individuals (12–14). Accumulating
`evidence suggests that a change in the gut
`microbiota composition has a key role not only
`in IBD, but also in the development of systemic
`immune diseases, such as rheumatoid arthritis
`(15, 16), encephalomyelitis (17, 18), type 1
`diabetes (19, 20), and allergic diseases (21, 22).
`The microbiota affects the host immune sys-
`tem through multiple factors, which include
`microbial components and their metabolites.
`The immune system recognizes these factors
`mostly through innate immune receptors. Con-
`stitutive signaling induced by the microbiota
`
`GF: germfree
`PP: Peyer’s patch
`ILF: isolated
`lymphoid follicle
`Microbiome:
`a genetic catalog of the
`microbial species that
`inhabit a defined
`environment such as
`the human body
`Dysbiosis:
`a condition with
`imbalance in the
`composition of the
`bacterial microbiota;
`this includes an
`outgrowth of
`potentially pathogenic
`bacteria and/or a
`decrease in bacterial
`diversity and bacteria
`beneficial to the host
`Pathobiont:
`a symbiont or a
`commensal that is able
`to promote pathology
`only when genetic or
`environmental
`conditions are altered
`in the host
`IBD: inflammatory
`bowel disease
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`LTi: lymphoid tissue
`inducer
`Gnotobiote:
`gnotobiotic comes
`from the Greek
`“known life” and refers
`to animals with defined
`microbiological status
`MetaHIT
`(Metagenomics of
`the Human
`Intestinal Tract)
`consortium: the
`MetaHIT project aims
`to understand the role
`of the human intestinal
`microbiota in health
`and disease; the
`consortium involves 13
`research centers from
`eight countries
`
`keeps the intestinal mucosa in a state of phys-
`iological inflammation, with continuous pro-
`duction of tissue repair factors, antimicrobial
`proteins, and immunoglobulin A (IgA) that, to-
`gether, maintain intestinal barrier integrity and
`provide beneficial functions to the microbiota
`(23–25). Without constitutive innate signaling,
`intestinal barrier injury and bacterial translo-
`cation may occur. Innate immune recognition
`of the microbiota leads to the establishment of
`an arsenal of unique and diverse intestinal im-
`mune cell populations. IgA-producing plasma
`cells, intraepithelial lymphocytes (IELs), and
`T cell receptor (TCR) γδ-expressing T cells
`(γδ T cells) are the classically known lym-
`phocytes unique to the mucosa. Recent stud-
`ies have shown the presence of innate immune
`lymphocytes, such as CD4+CD3− lymphoid
`tissue–inducer cells (LTi cells) and interleukin
`(IL)-22-producing natural killer (NK)-like cells
`(26, 27). Furthermore, CD4+ T cells in the
`intestinal mucosa comprise significant num-
`bers of IL-17-expressing cells (Th17 cells) and
`forkhead box P3 (Foxp3)-expressing regulatory
`T cells (Treg cells) (28). All these cells are
`particularly abundant in the intestinal mucosa,
`even under steady-state conditions, and their
`accumulation and function are deeply affected
`by the presence of the microbiota.
`Although it is not fully understood why and
`how the intestinal microbiota generates such
`a large variety of immune cell populations, re-
`cent studies using gnotobiotes (animals with a
`defined microbiological status) have suggested
`that specific components of the microbiota
`induce specific populations of immune cells.
`Below, we summarize the recent findings on
`how members of the microbiota provide an
`intestinal environment uniquely suited for the
`well-balanced development of the innate and
`adaptive immune system and discuss the role
`of the microbiota in infectious diseases and
`inflammation.
`
`COMPOSITION OF
`THE MICROBIOME
`The establishment of the intestinal microbiota
`occurs progressively, beginning immediately
`
`after birth. The initial infant gut microbiota
`has a relatively simple composition, which is af-
`fected in large part by the maternal microbiota.
`Vaginally delivered infants acquire bacterial
`communities resembling their own mother’s
`vaginal microbiota, dominated by Lactobacillus,
`Prevotella, or Sneathia spp., whereas infants de-
`livered by Cesarean section harbor bacterial
`communities similar to those found on the skin
`surface, dominated by Staphylococcus, Corynebac-
`terium, and Propionibacterium spp. (29). These
`pioneer bacteria may affect the composition of
`adult flora. After the weaning period, however,
`the microbiota markedly changes, and obligate
`anaerobes become prominent, with much lower
`numbers of facultative anaerobes.
`Only four phyla dominate adult human in-
`testinal habitats (30). Most (>90%) of them be-
`long to Bacteroidetes (including Bacteroides) and
`Firmicutes (including Clostridium, Lactobacillus,
`and Bacillus). Firmicute bacteria in the gut
`include two major clostridial groups, namely
`the clostridial clusters IV and XIVa that com-
`prise the Lachnospiraceae. Lower-abundance
`phyla are mainly composed of Proteobacteria
`(including Escherichia) and Actinobacteria (in-
`cluding Bifidobacterium). The mouse intestinal
`microbiota is similar to the human microbiota
`in broad terms. Such limited phylum predomi-
`nance suggests the presence of strong selective
`forces over thousands, perhaps even millions,
`of years of coevolution. Notably, certain mem-
`bers of the Firmicutes, such as Clostridium and
`Bacillus genera, are found in a state of vegetative
`growth or as spores. The ability to make spores
`may be of ecological advantage to the organ-
`ism as it enables it to survive under adverse
`conditions to efficiently colonize the intestine.
`At lower taxonomic levels, there is consid-
`erable interindividual variation. Metagenomic
`approaches using massive parallel sequencing
`allow for the direct enumeration of the micro-
`biota without having to isolate and cultivate
`bacteria. Using this technology, the interna-
`tional MetaHIT (Metagenomics of the Human
`Intestinal Tract) project has recently reported
`that each human individual carries on average
`540,000 common genes in the intestine (9).
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`This estimate suggests that only approximately
`35% of bacterial genes are shared between
`individuals.
`Interestingly,
`the results
`from
`the MetaHIT consortium also suggested the
`existence of at least three enterotypes in the
`human population (31). Enterotypes, which
`can be compared to blood types, are defined by
`characteristic populations of bacterial species
`and the genes that they encode. It is not yet
`known how enterotypes affect metabolism or
`immune system homeostasis in the host.
`The microbiome is adaptable to environ-
`mental changes and host genotypes. Recent
`studies have shown that community mem-
`bership and function of the microbiota can
`change owing to numerous variables including
`lifestyle, hygiene, diet, and use of antibiotics
`(32). Furthermore, it has recently become clear
`that the composition of the microbiota can
`influence onset and/or progression of several
`diseases. Indeed, the respective levels of the two
`main intestinal phyla, the Bacteroidetes and
`Firmicutes, are linked to obesity and metabolic
`disorders, both in humans and mice (33, 34).
`There has also been a substantial increase in
`the number of reports showing the relationship
`between the microbiota composition and the
`incidence of chronic inflammatory disease,
`including allergic conditions and autoimmune
`disorders
`(15–22). Furthermore,
`transplan-
`tation experiments in which the microbiota
`of diseased animals is grafted into healthy
`recipients have demonstrated the transfer of
`several disease phenotypes. These include obe-
`sity, metabolic disorders, and chronic colitis
`(35–37), all of which have complex etiologies
`affected by host genetic and environmental
`factors. Therefore, a better understanding of
`the functional properties of individual mem-
`bers of the microbiota is increasingly relevant
`to the treatment of complex chronic diseases.
`
`Factors that Affect Community
`Membership of Microbiota
`Diet. Diet
`important
`is one of
`the most
`factors shaping microbial diversity in the gut.
`Because members of
`the microbiota have
`their own substrate preference and there is
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`intense competition for resources, alterations
`in the components of the diet, particularly
`the type and quantity of
`fat and polysac-
`charides, result
`in changes
`in community
`composition and function of the microbiota.
`Mouse studies revealed that
`feeding mice
`with a high-fat and high-carbohydrate diet
`(Western diet) resulted in an increase in the
`number of bacteria of the Firmicutes phylum
`and a decrease in that of bacteria of the
`Bacteroidetes phylum (38, 39). This increase
`in the number of Firmicutes was mainly due to
`the proliferation of the Erysipelotrichaceae
`family (38, 39). The abundance of this family
`of bacteria immediately diminished when the
`diet was changed to a diet low in fat and rich in
`plant polysaccharides. The decrease in the pro-
`portion of Firmicutes after a low-calorie diet
`was similarly observed in humans (40). Another
`human study of 19 obese volunteers showed
`that a decreased carbohydrate intake led to a
`decrease in the number of bacteria within a
`specific group of Firmicutes that included Rose-
`buria spp. and Eubacterium rectale (41). Diet also
`influences fecal community enterotypes in hu-
`man subjects (42). Individuals with long-term
`diets rich in protein and animal fat had an
`enterotype dominated by Bacteroides, whereas
`those on high carbohydrate diets had a preva-
`lence of Prevotella. Although change in diet
`resulted in a rapid change in microbiota, this
`was not sufficient to shift the enterotype during
`a 10-day course. A similar distribution of fecal
`enterotypes was observed in a comparison of
`European and African children, who have diets
`rich in protein/animal fat and carbohydrates,
`respectively (43). Whether enterotypes asso-
`ciated with long-term diets can be reversed by
`changes in the diet remains to be determined.
`Changes
`in the diet and accompanied
`alterations in community membership of the
`microbiota, whether chronic or short-term,
`lead to changes in the gene expression profiles
`of the microbiota. For instance, alterations
`in availability of diet polysaccharides result in
`changes in the expression of genes for carbo-
`hydrate active enzymes (CAZymes), including
`glycoside
`hydrolases
`and
`polysaccharide
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`SCFA: short-chain
`fatty acid
`DC: dendritic cell
`
`lyases, in members of the microbiota, such as
`thetaiotaomicron (44). Seaweeds
`Bacteroides
`are major components of the Japanese diet;
`Bacteroides plebeius residing in the gut of
`Japanese individuals acquired the genes of
`enzymes
`that can metabolize the sulfated
`polysaccharide porphyran of marine algae
`through the horizontal transfer from marine
`bacteria naturally colonizing dietary seaweeds
`(45). These changes in gene expression of
`constituents of the microbiota likely ensure
`that the microbial community can adapt to
`dietary changes and maximize energy harvest,
`while contributing to host fitness.
`In some cases, changes in the diet and
`subsequent alterations in the microbiome may
`exert a detrimental effect on host physiology.
`Indeed, in individuals having a high-fat and
`high-carbohydrate diet, the microbiota is more
`heavily enriched with bacteria of the phylum
`Firmicutes and less with those of the phylum
`Bacteroidetes, and this condition may be more
`efficient at extracting energy from a given diet
`compared with the microbiota of lean indi-
`viduals (33). This suggests a positive-feedback
`mechanism,
`in which an obesity-inducing
`diet can change the composition of the gut
`microbiota, which results in a shape of the
`microbiome more capable of extracting energy
`from the diet, thereby helping perpetuate obe-
`sity. It has been postulated that changes in the
`diet and associated changes in the gut micro-
`biota may also lead to immune disorders (46). In
`fact, allergies and asthma are almost completely
`nonexistent in certain rural African communi-
`ties, where people eat diets low in protein and
`animal fat and high in plant polysaccharides.
`Actinobacteria and Bacteroidetes are more
`abundant in African (Burkina Faso) than in
`EU children’s microbiota, whereas Firmicutes
`and Proteobacteria are more abundant in EU
`than in African children (43). Importantly,
`the microbiome of African children exhibits
`a higher microbial richness and biodiversity
`than that of EU children. The African sam-
`ples, but not the EU samples, contain two
`bacterial genera, Prevotella and Xylanibacter
`(43). These findings are consistent with the
`
`above-described diet/enterotype concept (42)
`and suggest that the African microbiomes are
`dominated by the Prevotella enterotype driven
`by the low-fat/high-fiber diet. Prevotella and
`Xylanibacter have enzymes necessary for the hy-
`drolysis of cellulose and xylan and contribute to
`the production of high amounts of short-chain
`fatty acids (SCFAs) (43). As discussed below,
`SCFAs contribute to the maintenance of im-
`mune homeostasis in the intestine. Therefore,
`changes in the diet and gut microbial ecology
`are likely to affect the metabolic predisposition
`and immune status of the host.
`
`Inflammation. Alterations
`community
`in
`membership can also be induced by inflam-
`mation. In mice, enteric pathogens such as
`Citrobacter rodentium and Salmonella enterica
`subspecies 1 serovar Typhimurium actively
`induce intestinal inflammation, which then al-
`ters the composition of indigenous microbiota,
`reducing the number of strict anaerobes such
`as the Firmicutes and allowing proteobacteria
`to proliferate (47, 48). Intestinal inflammation
`caused by either a chemical inducer, such as
`dextran sulfate sodium (DSS), or a genetic
`deficiency, such as Il10 deficiency, can also alter
`the composition of the intestinal microbiota,
`resulting in a reduction in both the total
`number of resident
`intestinal bacteria and
`bacterial diversity (47). Studies have shown a
`change in composition of the microbiota in
`T-bet−/− Rag2−/− ulcerative colitis (TRUC)
`mice, which have a T-bet deficiency in the
`innate immune system and develop spon-
`taneous colitis with high penetrance on a
`BALB/c background (36, 49). TRUC colitis
`is attributed to the hyperproduction of tumor
`necrosis factor (TNF)-α by dendritic cells
`(DCs), because T-bet is a negative regulator
`of TNF-α transcription (36). The colitis in
`TRUC mice is accompanied by a considerable
`alteration in microbial composition. TRUC
`colitis can be transmitted to wild-type mice
`when they are cross-fostered or cohoused
`with TRUC mice (36). Detailed analysis
`of altered microbiota has revealed a lower
`proportional
`representation of Firmicutes,
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`Probiotics: live
`microorganisms that,
`when administered in
`adequate amounts,
`confer a health benefit
`to the host
`IEC: intestinal
`epithelial cell
`TLR: Toll-like
`receptor
`
`764
`
`including Clostridium spp., and the constitutive
`presence of colitogenic bacteria, such as Proteus
`mirabilis and Klebsiella pneumoniae (50), which
`are otherwise transient allochthonous bacteria
`and constitute very minor, if any, components
`of
`the microbiota. Interestingly, colitis in
`TRUC mice is improved by the consumption
`of a fermented milk product containing a
`probiotic strain, Bifidobacterium lactis
`(51).
`Consumption of B. lactis results in a change
`in the structure of the microbiota, namely, an
`increase in the number of lactate-consuming
`Desulfovibrio spp. and the butyrate-producing
`Anaerostipes caccae subgroup and Eubacterium
`hallii, accompanied by a decrease in cecal
`pH and increases in acetic, propionic, and
`butyric acid levels. These conditions provide a
`nonpermissive environment for the colitogenic
`Proteus and Klebsiella in TRUC mice. These
`results suggest that inflammation mediated by
`the overproduction of inflammatory cytokines,
`such as TNF-α, leads to an increase in pH
`and a decrease in the amount of SCFAs in
`the intestinal lumen, resulting in an altered
`microbial community, including outgrowth of
`potentially pathogenic bacteria. Collectively,
`much like the positive-feedback mechanism
`in diet-mediated obesity described above,
`intestinal inflammation caused by infection or
`genetic predisposition can render the shape
`of the microbiome more prone to induce
`inflammation. This vicious cycle of dysbiosis
`and inflammation may be operative in IBD
`patients.
`IBD patients exhibit substantial changes
`in the composition of
`the microbiota. A
`decrease in the numbers of bifidobacteria and
`lactobacilli in IBD patients has been known for
`many years (52). Overgrowth of Escherichia coli,
`the so-called adherent-invasive E. coli (AIEC)
`in particular, is frequently observed in human
`IBD patients and is considered to lead to the ag-
`gravation of disease symptoms. AIECs interact
`intimately with the inflamed ileal mucosa and
`even invade intestinal epithelial cells (IECs)
`(53, 54). Recent studies using high-throughput
`sequence analysis of 16S rRNA genes have
`shown that there is a decrease in Bacteroidetes
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`and Firmicutes frequencies and an increase in
`Actinobacteria and Proteobacteria frequencies
`in IBD patients. In particular, it was shown
`that the family Lachnospiraceae, which com-
`prises the Clostridium clusters IV and XIVa [also
`known as Clostridium leptum and coccoides groups
`(55)], was significantly less abundant in IBD
`patients than in healthy subjects (13). Other
`reports have provided data showing a reduction
`in the number of bacteria within the Clostridium
`cluster IV, particularly the species Faecalibac-
`terium prausnitzii, in the gut of IBD patients
`(56, 57) and a correlation between low counts of
`F. prausnitzii and postsurgical recurrence (58).
`Importantly, individuals with chronic in-
`flammation have a lower bacterial diversity of
`the microbiota than healthy individuals. The
`MetaHIT consortium reported that IBD pa-
`tients harbored, on average, 25% fewer genes
`than individuals not suffering from IBD (9). Al-
`though it remains unclear whether the decrease
`in microbial membership is a causative factor
`or a consequence of chronic inflammation in
`IBD patients, maintaining the diversity of the
`gut microbial community is likely a prerequisite
`for a stable and healthy gastrointestinal tract.
`
`Host genotype. Host genotype can intrinsi-
`cally affect the composition of the microbiota.
`For instance, genetically obese mice, such as
`ob/ob mice (leptin gene deficiency), have an
`altered microbiota with increased Firmicutes
`and decreased Bacteroidetes frequencies (33).
`Importantly, gut microbiota transferred from
`ob/ob mice to wild-type GF mice can induce
`obesity, presumably owing to the fact that
`obesity-associated microbes can extract more
`energy from the diet, which suggests that
`a change in the microbiota by leptin gene
`deficiency may precede the obesity phenotype
`of ob/ob mice (33). Mice deficient in Toll-
`like receptor 5 (Tlr5−/−) similarly exhibit a
`change in the shape of the microbiota (35).
`Tlr5−/− mice display hyperphagia and signs
`of metabolic syndrome,
`including insulin
`resistance and increased adiposity. Wild-type
`mice inoculated with Tlr5−/− microbiota
`the Tlr5−/− mice, displaying
`phenocopy
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`LP: lamina propria
`
`hyperphagia and obesity, suggesting that the
`Tlr5−/− phenotype is primarily due to the
`changes in the microbiota. NLRP6, a sensor of
`endogenous or exogenous stress, induces the
`formation of a multimolecular inflammasome
`complex upon binding of unknown ligand,
`leading to activation of caspase-1 and cleavage
`of pro-IL-1β and pro-IL-18 (37). In IECs, the
`inflammasome-mediated constitutive produc-
`tion of IL-18 is required for the maintenance
`of epithelial cell barrier function and regener-
`ation. NLRP6−/− mice exhibit reduced IL-18
`levels in IECs and are highly susceptible to DSS
`colitis (37). Importantly, NLRP6−/− mice show
`quantitative and qualitative changes in the
`microbiota, including increased representation
`of members of Prevotellaceae and TM7, and
`reductions in members of the genus Lactobacil-
`lus in the Firmicutes phylum. The transmission
`of this microbiota community confers similar
`susceptibility to DSS colitis onto wild-type
`mice. As described above, T-bet−/− Rag2−/−
`TRUC mice also have an abnormal microbial
`composition, and TRUC colitis is transmissible
`to wild-type mice (36). These reports indicate
`that obesogenic or colitogenic microbiota can
`arise in the host depending on the genotype.
`Nonobese diabetic mice lacking Myd88, an
`adaptor molecule for TLRs and IL-1 receptor
`(IL-1R), did not develop type 1 diabetes when
`reared in specific pathogen–free (SPF) con-
`ditions, but littermate Myd88-sufficient mice
`exhibited diabetes under the same conditions
`(19). However, when rendered GF, Myd88−/−
`nonobese diabetic mice developed severe dia-
`betes. Therefore, the attenuated phenotype of
`SPF Myd88−/− nonobese diabetic mice is not
`simply due to a defect in IL-1R or TLR signal-
`ing, but indicates a key role for the microbiota.
`Further analysis revealed that Myd88-deficient
`nonobese diabetic mice exhibit changes in the
`composition of the distal gut microbiota: a sig-
`nificantly lower Firmicutes/Bacteroidetes ratio
`compared with that of Myd88-sufficient con-
`trol mice (19). Therefore, MyD88-dependent
`signaling affects the composition of the gut
`microbiota, and thereby affects the nonobese
`diabetic phenotype.
`
`The lack of activation-induced cytidine
`deaminase (AID), which results in defective
`class switch recombination and thereby lack
`of IgA-producing plasma cells in the intestine,
`leads to the excessive proliferation of anaero-
`bic bacteria in the small intestine, particularly
`the segmented filamentous bacteria (SFB), ac-
`companied by hyperplasia of ILFs (59). The
`addition of IgA prevented the aberrant SFB
`expansion and ILF hyperplasia in the mutant
`mice. Antimicrobial peptides produced by IECs
`also have important roles in controlling the
`growth of components of the microbiota. Thus,
`α-defensin deficiency was associated with de-
`creased Bacteroidetes and increased Firmicutes
`frequencies, whereas the transgenic expression
`of human defensin 5 (HD5) in mice led to
`the reverse shift (60). Transgenic expression of
`HD5 also led to the loss of SFB, with a conse-
`quent decrease in the number of Th17 cells in
`the lamina propria (LP) of the small intestine
`(60) (discussed below).
`including
`Collectively, many diseases,
`metabolic diseases and chronic inflammatory
`conditions, may not be simply associated with
`host genetics, but may be mediated indirectly
`by the change in the microbiota (Figure 1).
`Recent
`genome-wide
`association
`studies
`(GWAS) have revealed more than 100 genetic
`loci that have significant association with IBD
`(61, 62). Several of these genes likely have
`a primary role in shaping the gut microbial
`community, which then affects IBD pathology.
`
`MICROBIAL SIGNALING
`THROUGH THE HOST INNATE
`IMMUNE SYSTEM
`The gut mucosa has evolved multiple layers
`of protection to prevent the translocation of
`pathogenic as well as indigenous microbes. The
`intestinal epithelium is covered with layers of
`mucus, which is composed of mucin glycopro-
`teins synthesized and secreted by goblet cells.
`The inner layer of the mucus gel in the colon
`is densely packed and firmly attached to the ep-
`ithelium and creates a strict barrier that pre-
`vents large particles, including most bacteria,
`
`www.annualreviews.org • Microbiome and Inflammation
`
`765
`
`Genome Ex. 1036
`Page 7 of 39
`
`

`

`IY30CH28-Littman
`
`ARI
`
`17 February 2012
`
`15:18
`
`Causes
`
`Diet
`
`Inflammation
`(Infection, etc.)
`
`Host genotype
`(cid:129)ATG16L1
`(cid:129)NLRP6
`(cid:129)NOD2
`(cid:129)IL-10
`(cid:129)IL-23, etc.
`
`Dysbiosis
`
`Reduced diversity of the
`microbiota
`(cid:129)Decrease of Bacteroidetes
`and Firmicutes
`(cid:129)Increase of Actinobacteria
`and Proteobacteria
`
`Propagation of
`potentially
`pathogenic bacteria
`(cid:129)Adherent-invasive E. coli
`(AIEC)
`(cid:129)Enterotoxigenic strains of
`B. fragilis (ETBF)
`(cid:129)Klebsiella pneumoniae
`(cid:129)Proteus mirabilis
`(cid:129)Prevotellaceae
`(cid:129)TM7
`
`Immunological outcomes
`
`Aberrant activation of
`immune system
`(Activation of Th1,
`Th17, γδ T, and innate
`lymphocytes)
`
`Repression of immune
`regulatory mechanisms
`(Decrease of Treg, Tr1,
`IgA, IL-10 and TGF-β)
`
`Aberrant immune
`responses against
`commensal
`
`microbiota and diet
`
`Chronic inflammation (IBD)
`
`Figure 1
`Causes and pathological outcomes of dysbiosis. The composition of the gut microbiota is readily affected by diet, inflammation
`(including infection by pathogens), and host genotypes. An unfavorable alteration of the community structure of the gut microbiota is
`termed dysbiosis, which includes an outgrowth of potential pathogenic bacteria (pathobionts) and a reduced diversity of the community
`structure of the microbiota. Dysbiosis is associated with the increased predisposition to immune system activation, which leads to
`aberrant immune responses against the commensal microbiota and diet. The dysregulated activation of the immune system leads to the
`worsening of the dysfunction of the microbiota, which may result in sustained inflammation in the intestine (i.e., IBD) and other organs.
`
`from directly contacting the epithelial cells (63).
`The intestinal epithelium is tightly sealed by
`tight junctions and subjacent adherens junc-
`tions, which play critical roles in the prevention
`of microbe invasion (64). The small intestinal
`epithelium contains Paneth cells at the base of
`the crypts, which contribute to innate immunity
`by secreting a diverse repertoire of antimicro-
`bial proteins. Beneath the epithelium, the LP
`contains DCs, which extend their dendrites be-
`tween epithelial cells to continuously monitor
`the gut lumen content and activate LP lympho-
`cytes. These in toto constitute the firewall that
`prevents the systemic penetration and spread of
`microbes (7, 65).
`In the past, immune responses to commensal
`bacteria were considered to be completely pre-
`vented because of the sequestration of micro-
`biota by physical barrier systems. Recent results
`have suggested, however, that constitutive and
`physiological inflammation induced by com-
`mensal microbes through pattern-recognition
`receptors (PRRs) is operative and is required
`for epithelial barrier functions and normal
`host-commensal homeostasis.
`
`Honda· Littman
`
`Constitutive Activation
`of TLRs by Microbiota
`and
`TLRs
`expressed
`by
`hematopoietic
`nonhematopoietic cells are involved in the
`recognition of the microbiota. When mice
`kept
`in SPF conditions are treated with
`broad-spectrum antibiotics,
`they become
`highly susceptible to DSS-induced intestinal
`inflammation (24). This is, at least in part, due
`to reduced constitutive TLR signaling in re-
`sponse to the microbiota, as oral administration
`of lipopolysaccharide (LPS, a TLR4 ligand)
`or lipoteichoic acid (a TLR2 ligand) restores
`resistance of antibiotic-treated mice to DSS-
`associated injury of the colonic epithelium (24).
`Mice lacking either Tlr2, Tlr4, Tlr9, or Myd88
`are highly susceptible to DSS colitis (24, 66).
`Depending on the rearing conditions, mice
`lacking Tlr5 develop spontaneous colitis, and
`bacterial translocation to the spleen and liver
`occurs (67). The absence of MyD88 signaling in
`IECs is associated with a decreased production
`of cytoprotective factors such as IL-6, KC-1,
`and heat shock proteins in IECs (24). TLR2
`
`Pattern-recognition
`receptors (PRRs):
`receptors that
`recognize m