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a much deeper understanding of the Key questions to guide a community structure, genetic reper- toire, metabolic products, and function better understanding of of the complex microbiome that out- numbers our somatic cells by 10-fold. host – commensal microbiota Th ese advances have depended on the unique structure of the 16s ribosomal interactions in intestinal RNA subunit, which can be used as a signature of individual bacterial species. Th ese techniques have rapidly evolved inflammation from surveys that measure the most 1 common species, such as denaturing R B S a r t o r gradient gel electrophoresis and termi- nal restriction fragment-length polymor- Co-evolution with an extremely complex commensal enteric phism, to sequencing of clone libraries, microbiota has helped shape mammalian mucosal immune to the most recent, but still rapidly evolv- responses. A yet incompletely defined subset of intestinal ing pyrosequencing techniques using increasingly rapid, fi rst-, second-, and bacteria is required to stimulate chronic, immune-mediated now third-generation parallel sequenc- intestinal inflammation, including human Crohn ’ s disease, and ers that permit deep exploration of the intestinal microbiota composition is altered in a characteristic microbiome. Th ese advances have led to manner by the inflammatory response to create a dysbiotic an unprecedented view of the gut micro- bial composition, now including viral relationship of protective vs. aggressive bacteria. We pose a and fungal profi les, as well as bacteria, number of questions regarding host interactions with the its adjuvants, antigens, and metabolic enteric microbiota, including influences of inflammation, host products. However, many questions genetics, early environmental exposure, and diet on microbial remain regarding how the diverse com- composition and function, and conversely, the effect of bacterial ponents interact to shape our immune function for homeostatic and patho- metabolism, enteric fungi and viruses, and endogenous physiological purposes, and how in protective bacterial species on host immune and inflammatory turn, the diverse components of the responses. These questions are designed to stimulate research mucosal innate and adaptive immune that will promote a better understanding of host– microbial response, immune-mediated infl amma- tion, and host genetics shape the com- interactions in the intestine and promote targeted novel position and function of the intestinal therapeutic interventions. microbiota. 1 – 3

CURRENT UNDERSTANDING OF THE COMMENSAL MICROBIOTA IN We have co-evolved with an extremely com- eff ector and homeostatic limbs of the innate INTESTINAL INFLAMMATION plex group of bacteria, fungi, and viruses and adaptive immune systems, which in Commensal intestinal bacteria are essen- that interact not only with each other turn regulate microbial growth, composi- tial stimuli for experimental chronic but also with the host to help shape our tion, and function. immune-mediated infl ammation with mucosal immune response. Th ese micro- Dramatic advances in culture-independ- strong evidence of their involvement bial signals activate and diff erentiate both ent molecular techniques have permitted in Crohn’ s disease and pouchitis, but in

1 Department of Medicine/ Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA . Correspondence: RB Sartor ([email protected] ) Received 22 July 2010; accepted 3 December 2010; published online 19 January 2011. doi: 10.1038/mi.2010.87

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addition, these agents are almost cer- Table 1 Mucosal homeostasis vs. inflammation depends on the balance of tainly involved in the pathogenesis of beneficial vs. detrimental enteric microbial species ulcerative colitis, alcoholic liver disease, Detrimental bacterial species Protective bacterial species nonalcoholic steatohepatitis, and meta- bolic syndrome. 4 – 7 Crohn’ s disease seems Bacteroides vulgatus , Bacteroides thetaiotamicron Lactobacillus species to be an inappropriately aggressive TH1 Enterococcus faecalis Bifidobacterium species and / or TH17 immune response to a Adherent / invasive Escherichia coli Nonpathogenic E. coli subset of commensal intestinal bacteria Klebsiella pneumoniae , Bifidobacterium animalis Saccharomyces boulardii in genetically susceptible hosts, which Fusobacterium varium Bacteroides fragilis is initiated and reactivated by transient Intestinal Helicobacter species Faecalibacterium prausnitzii 3,4,8,9 infectious or environmental triggers. Segmented filamentous bacteria Roseburia spp . These triggers break the mucosal bar- Ruminococcus gnavus rier and activate an initial nonspecifi c immune response, which becomes Proteus mirabilis Abbreviation: IBD, infl ammatory bowel disease. chronic because of the constant drive of Each species has documented infl ammatory or protective activity either in rodent models or human IBD. commensal microbial antigens in hosts that have genetic defects in mucosal bar- rier function or repair, bacterial killing by innate immune cells or Paneth cells, or disease and has been reported to provide hosts respond selectively to the same bac- immunoregulation. protection in experimental colitis and terial species, 26 two diff erent commensal The profile of both fecal and muco- to predict relapse of postoperative ileal bacterial species can induce different sally associated bacteria exhibit changes Crohn ’ s disease.17,18 phenotypes of infl ammation in the same described as “ dysbiosis ” in a subset Commensal bacteria have an essen- host20 and have additive eff ects,27 and (~ 1 / 3) of inflammatory bowel disease tial role in driving immune-mediated commensal specifi c pathogen-free bac- (IBD) patients with active disease and experimental infl ammation in the dis- terial species that induce colitis in suscep- in rodents with experimental colitis that tal intestine.4,6,18 Germ-free genetically tible hosts do not cause infl ammation in are characterized by decreased bacterial susceptible mice and rats exhibit no evi- wild-type hosts.19,20 Even diff erent E. coli diversity and an altered ratio of benefi - dence of chronic colitis under germ-free strains have variable abilities to induce cial and aggressive bacterial species. 1,10 (sterile) conditions and CD4 + T cells experimental, immune-mediated colitis, These alterations include decreased produce interferon-  and interleukin-17 as adherent-invasive nontoxigenic E. coli concentrations of the Lachnospiraceae in response to cecal bacterial lysates and strains, including a human ileal Crohn ’ s subset of Clostridiales, and variable bacterial antigens in specifi c pathogen- disease isolate, induce chronic colitis, but changes in Bacteroidetes, with a con- free genetically engineered rodents and a nonadherent strain does not. 28 Th ese comitant increase in Proteobacteria and aft er selective colonization with some, observations lay the foundation for the Actinobacteria (except Bifi dobacterides). but not all, bacterial species in gnotobi- hypothesis that a subset of nonpatho- Bacterial species that are consistently otic rodents. 19,20 It is diffi cult to predict genic commensal bacteria provide the increased in human IBD and experimen- the pathophysiological effects in vivo constant antigenic drive of IBD in genet- tal colitis include Escherichia coli , spe- due to host-specifi c eff ects, as segmented ically susceptible hosts, whereas other cifi cally the B2 and D phylotypic groups fi lamentous bacterium, a noncultivatable endogenous species primarily induce and adherent / invasive strains associated commensal that induces TH17 responses protective regulatory immune responses. with ileal Crohn’ s disease. 11– 13 In addi- in wild-type noninfl amed mice 21 did not Th e relative balance of these aggressive vs. tion, experimental TH1/ TH17 activation induce colitis when monoassociated in benefi cial organisms determine infl am- and colitis in monoassociated interleukin- the SCID (severe combined immuno- mation vs. homeostasis and potentially 10-defi cient mice alter gene expression defi ciency) mouse CD45RBhigh transfer can be manipulated for therapeutic in a commensal adherent/ invasive E. coli model, 22 and Bifi dobacterium animalis , benefi t (Table 1 ). strain in preliminary experiments, with normally considered to be a protec- Th e following key questions to better upregulation of bacterial stress-response tive probiotic strain, can cause colitis in understand microbial– host interactions genes. 14 In recent studies, Rumino coccus monoassociated interleukin-10-defi cient remain unresolved. Selected illustrations gnavus , Klebsiella pneumoniae , and mice.23,24 In contrast, other commensal by currently available data are provided. Proteus mirabilis have been implicated species and their defi ned components and in Crohn ’ s disease and experimental secreted products have predominantly IS DYSBIOSIS A CAUSE OR A colitis. 15,16 Conversely, Faecalibacterium protective properties.18,25 Th ese studies CONSEQUENCE OF INTESTINAL prausnitzii , a major representative of the demonstrate both host and bacterial spe- INFLAMMATION? butyrate-producing Clostridium leptum cies specifi city, as only a relatively small Th e primary vs. secondary nature of the group of the Lachnospiraceae family, is subset of commensal bacterial species will characteristic pattern of decreased Clostri- decreased in ileal and colonic Crohn’ s induce experimental colitis,19,20 diff erent dial groups IV (including F. prausnitzii )

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and XIVa, and in some studies, Bacteroi- older children and adults remains specu- complex microbiota over time. 47,48 Ini- detes, with increased concentrations lative at present. tial colonization depends on mode of of Proteobacteria (including E. coli ), delivery, with vaginally delivered infants R. gnavus, and Actinobacteria that is WHAT ARE THE RELATIVE INFLUENCES acquiring microbial communities resem- associated with IBD is unclear. Trans- OF GENETICS VS. ENVIRONMENTAL bling their mother’ s vaginal microbiota mission of colitis 16,29 and metabolic FACTORS IN SHAPING THE INTESTINAL dominated by Lactobacillus , Prevotella , syndrome5 by fecal transplants from MICROBIOME? or Sneathia spp., whereas infants deliv- affected to wild-type recipient mice Multiple factors contribute to the devel- ered by Cesarian section acquired skin that are normally not susceptible pro- opment of the intestinal microbiota, organisms, including Staphylococcus , vides evidence for an etiological role for including maternal transmission, early life Corynebacterium, and Propionibac- abnormal commensal bacteria. How- exposures, diet, and genetics.1,41 However, terium spp. 49 Initial communities are ever, the fi nding of very similar dysbio- the relative roles of environmental vs. aerobic, transitioning gradually to the sis patterns in intestinal infl ammation genetic infl uences are not yet well under- anaerobic complex microbiota. Mater- in widely diverse hosts, including mice, stood. In a seminal metagenomic study, nal and paternal infl uences are evident humans, and dogs, 13,30,31 disparities Turnbaugh et al. 42 demonstrated that the in twin studies, with shared environ- between the microbiota in active vs. degree of similarity between monozygotic ment more important than genetic infl u- quiescent IBD,17,32,33 and similarities and dizygotic twin pairs was not signifi - ences.42 Dominant maternal infl uences of microbiota alterations in infections, cantly diff erent, although monozygotic on transmitted bacterial communities are and chemically and genetically induced twins had a trend toward greater similar- confi rmed by mouse studies. 46 Dietary gut infl ammation34,35 strongly support ity, and that bacterial communities were regulation is important, with domina- nonspecifi c alterations as a consequence more similar within family members than tion of the preweaning microbiota by the of the infl ammatory milieu. Th is funda- between diff erent families, suggesting a lactose-responsive Bifi dobacterium and mental issue has profound implications primary role for early shared exposure Lactobacillus spp. and rapid diversifi ca- for proposed therapeutic strategies, such rather than genetic direction of microbial tion of bacterial communities aft er wean- as fecal transplants. composition. In contrast, Frank et al.43 ing. 50 Somewhat surprisingly, cultivatable reported that the NOD 2 (nucleotide- bacterial communities do not seem to be CAN THE COMMENSAL MICROBIOTA binding oligomerization domain con- influenced heavily by breast vs. bottle BE ALTERED PERMANENTLY BY taining 2) composite genotype, ATG 16L1 feeding, with the exception of Lactoba- THERAPEUTIC INTERVENTIONS? polymorphisms, and ileal disease location cillus rhamnosus. 47,48 As atopic disorders Th is question is integral to the duration were associated with mucosal dysbiosis appear to be linked to early ( < 6 months of microbial-based therapies, including in patients with Crohn ’ s disease. Simi- of age) microbiota composition, 51 mul- fecal transplant. Although an indivi dual ’ s larly, NOD 2 defi ciency in mice resulted tiple investigators have explored early fecal microbiota changes daily with die- in decreased F. prausnitzii ileal mucosal probiotic intervention in infants or tary and environmental shift s, there is concentrations.44 Similarly, monoassocia- even mothers with atopic conditions in a remarkable long-term stability of the tion of 23 inbred mouse strains with the the third trimester of pregnancy, usu- intestinal bacterial population. 36 Pro- defi ned altered Schaedler fl ora indicated ally with little success.52 Although most biotic administration only transiently important genetic eff ects,45 although the authors state that the human microbiota alters fecal bacterial composition due to a lack of diff erences in the fecal microbiota is stabilized by 12 months of age, trans- lack of long-term colonization, with in two diff erent mouse strains implanted plantation of the human microbiota to reversion to baseline within 2 weeks into a foster mother demonstrated germ-free (sterile) adult mice shows that of ceasing therapy.37 However, despite lasting effects of maternal microbiota the absence of competing organisms can earlier evidence to the contrary, recent transmission.46 Th ese and other studies obviate age eff ects.53 data indicate long-term changes in have revealed that both genotype and Th ese studies suggest that the poten- microbial composition and diversity aft er environmental infl uences, mostly diet tial of targeting infants at high risk for antibiotic therapy, particularly if adminis- and early microbial exposure, combine developing immunological diseases for tered cyclically.38 – 40 Th ese observations, to shape enteric microbiota composi- constitution with the “ healthy ” micro- along with transfer of colitis 16,29 and tion, which remains quite stable once biota to prevent the onset of disease has metabolic syndrome5 by fecal inocula- developed. not yet been achieved. Th is potentially tion and activation of ileal interleukin-17 important area of investigation needs to responses by colonization with a specifi c DOES INITIAL BACTERIAL COLONIZA- be further explored in rodent models, in bacterial species (segmented fi lamentous TION AND EARLY ENVIRONMENTAL which consequences of experimentation bacterium), 21 suggest that immunologi- EXPOSURES DETERMINE LIFE-LONG are acceptable and mechanistic studies cal eff ects of commensal bacterial trans- BACTERIAL COMPOSITION? can be performed. Early intervention fer may be sustained over at least several Transition from the sterile amniotic sac to in infancy or during pregnancy could months. The prospect of permanently the external environment is accompanied be a very physiological and nontoxic changing the intestinal microbiota in by progressive transition to increasingly approach to altering life-long risk of

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familial infl ammatory / allergic conditions, nor viral infection alone was suffi cient activity of endogenous butyrate-pro- given the apparent importance of early to induce the Paneth cell phenotype or ducing bacterial species, provides great infant colonization on adult microbial potentiate toxin-induced colitis; only promise for an extremely physiological communities. the interaction of the viral trigger with and cost-eff ective approach to modify genetic defect enhanced colitis. the intestinal microbiome in order to INFECTIOUS AGENTS: TRIGGERS OR treat and prevent infl ammatory diseases CHRONIC STIMULI? CAN ENDOGENOUS PROTECTIVE in high-risk individuals.4,63,64 Although the essential role for the com- COMMENSAL BACTERIAL SPECIES mensal microbiota as antigenic stimuli MORE EFFECTIVELY TREAT AND PREVENT WHAT ARE THE EFFECTS OF MICROBIAL of eff ector immune responses in chronic INFLAMMATORY DISEASES THAN WILL METABOLITES ON EFFECTOR AND intestinal inflammation is broadly TRADITIONAL PROBIOTIC SPECIES? REGULATORY MUCOSAL IMMUNE accepted, the importance of traditional Traditional probiotic species are an FUNCTION AND INFLAMMATION? and opportunistic pathogens in IBD attractive potential treatment of intes- Intestinal bacteria are metabolically remains quite controversial. An etiologi- tinal infl ammation, but results to date active and greatly contribute to the gut cal role for MAP ( Mycobacterium avium have not lived up to their promise, metabolome. Th ese organisms use either subspecies paratuberculosis ) in Crohn’ s despite well-documented immunosup- dietary or host-derived carbohydrate disease is not widely supported, but the pressive eff ects.58,59 In addition to their substrates, the availability of which can intriguing possibility that an obligate immunoregulatory activity, at least one almost immediately alter bacterial gene intracellular opportunistic pathogen probiotic species strongly infl uences gene expression to upregulate or downregulate such as MAP or adherent / invasive E. coli expression and metabolism of commen- various bacterial genes and metabolic selectively persists within macrophages sal bacteria. 60 An important limitation of pathways.62 Nonabsorbed dietary carbo- of individuals with genetic defects in the currently available probiotic prepa- hydrates (fi ber, prebiotics) are substrates intracellular microbial clearance, such as rations, which are traditionally derived used by subsets of enteric anaerobic bac- NOD 2, ATG 16L1, and IGRM, must be from fermented foods rather than com- teria to produce benefi cial short-chain considered.4 Chronic infections can cause mensal enteric bacterial species, is their fatty acids, most notably butyrate, which persistent enterocolitis in normal hosts, inability to colonize the distal intestine is the primary energy substrate for distal with potentiation of injury in susceptible and persist aft er administration ceases. 4,59 colonocytes and suppresses immune acti- hosts, as illustrated by enterotoxigenic A potential solution is to use commen- vation. Recent studies indicate multiple Bacteroides fragilis . 54 Transient infection sal protective bacterial species, such as mechanisms and immunosuppression by by traditional enteric pathogens can trig- F. prausnitzii , B. fragilis, host-derived butyrate, including inhibition of histone ger chronic, immune-mediated experi- Lactobacillus, Bifidobacterium, and deacetylases and induction of apopto- mental intestinal infl ammation6 and is E. coli strains, which exhibit protective sis.65,66 In contrast, bacterial production linked to human IBD in epidemiological activities in experimental murine studies. of toxic metabolites, such as hydrogen studies. 55 Potential mechanisms include Th is strategy is particularly appealing as sulfi de, nitrous oxide, and reactive oxy- breaking the mucosal barrier and /or acti- a means to correct specifi c defi ciencies in gen metabolites, can injure epithelial cells vating pathogenic immune responses protective commensal bacterial concen- and potentially induce chronic intestinal that are subsequently perpetuated by trations in an individual, such as selective infl ammation.67 commensal enteric antigens in geneti- replacement of low numbers of mucos- cally susceptible hosts who are unable to ally adherent F. prausnitzii, which is a HOW DO COMMENSAL FUNGI AND repair epithelial breaches or downregu- risk factor for postoperative recurrence VIRUSES AFFECT INTESTINAL IMMUNE late the infl ammatory response. An alter- of Crohn ’s disease.18 FUNCTION, INFLAMMATORY native mechanism is priming of adaptive PROCESSES, AND BACTERIAL immune responses to commensal bacte- WHAT IS THE ROLE OF DIET IN SHAPING COMPOSITION AND FUNCTION? ria, as documented for Helicobacter bilis56 AND MANIPULATING ENTERIC Another virtually unexplored frontier and cytomegalovirus 57 infection. Cadwell BACTERIAL COMPOSITION, FUNCTION, of the gut microbiota is the lush fungal et al.9 recently provided powerful proof of AND METABOLISM? and viral elements that can directly aff ect the concept that infectious triggers can An extremely important yet vastly under- intestinal epithelial cells and mucosal interact with host genetic susceptibility explored fi eld is the eff ect of diet on the immune responses and can influence to induce disease. Noravirus infection gut microbiome. Nascent studies clearly intestinal bacterial populations and func- induced a characteristic abnormality in demonstrate the ability of various human tion. Bacteriophages off er an opportunity Paneth cell granules in ATG 16L1 mutant diets to alter enteric bacterial composi- to modulate specifi c bacterial populations mice, similar to those in Crohn’ s disease tion, gene expression, and metabolic because of their selective tropism. Recent patients with ATG 16L1 polymorphisms, activity in reconstituted gnotobiotic molecular surveys identify abundant and potentiated acute toxin-induced coli- mice.61,62 Dietary manipulation, which commensal viruses mainly targeting com- tis, which was driven in part by commen- includes the use of prebiotic substances mensal bacteria. 68 As mentioned above, sal bacteria. Neither the genetic defect that foster the growth and metabolic noravirus can induce aberrant Paneth cell

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6 . Nell , S . , Suerbaum , S . & Josenhans , C . The impact of the microbiota on the pathogenesis of IBD: lessons from mouse infection models . Nat. Rev. Microbiol. 8 , 564 – 577 ( 2010 ). 7 . Purohit , V. et al. Alcohol, intestinal bacterial growth, intestinal permeability to endotoxin, and medical consequences of a symposium . Alcohol 42 , 349 – 361 ( 2008 ). 8 . Xavier , R. J . & Podolsky , D. K . Unravelling the pathogenesis of infl ammatory bowel disease . Nature 448 , 427 – 434 ( 2007 ). 9 . Cadwell , K. et al. Virus-plus-susceptibility gene interaction determines Crohn’s disease gene Atg16L1 phenotypes in intestine . Cell 141, 1135 – 1145 ( 2010 ). 10 . Frank , D. N . et al. Molecular-phylogenetic characterization of microbial community imbalances in human infl ammatory bowel diseases . Proc. Natl Acad. Sci. USA 104 , 13780 – 13785 ( 2007 ). 11 . Darfeuille-Michaud , A . et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease . Gastroenterology 127, 412 – 421 ( 2004 ). 12 . Kotlowski , R . , Bernstein , C .N . , Sepehri , S. & Krause , D. O . High prevalence of Escherichia coli belonging to the B2+D phylogenetic group in infl ammatory bowel disease . Gut 56 , Figure 1 Chronic IBD depends on an interaction of at least four components, which alone are 669 – 675 ( 2007 ). not sufficient to cause disease. IBD, inflammatory bowel diseases; NSAID, nonsteroidal 13 . Baumgart , M . et al. Culture independent anti-inflammatory drug. analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum . granule morphology and potentiate acute will lay the foundation for novel thera- ISME J. 1 , 403 – 418 ( 2007 ). experimental colitis.9 peutic interventions that extend beyond 14 . Patwa , L. G. , Sartor , R. B . & Hansen , J. J. Deletion of genes encoding E. coli small heat our current reliance on probiotics arising shock proteins ibpA/B worsens experimental CONCLUSIONS AND FUTURE from fermented dairy products. colitis in E. coli monoassociated IL-10-defi cient DIRECTIONS mice . Gastroenterology 138 ( 2010 ) (abstract) . ACKNOWLEDGMENTS 15 . Willing , B . et al. A pyrosequencing study in Commensal enteric bacteria provide We thank Susie May for expert secretarial twins shows that GI microbial profi les vary with an essential role in the pathogenesis assistance and Jonathan Hansen, MD, PhD, infl ammatory bowel disease phenotypes . of Crohn’ s disease and probably other for creating Figure 1 . The original research Gastroenterology 139 , 1844 – 1854 ( 2010 ). was supported by the Crohn’ s and Colitis 16 . Garrett , W .S . et al. Enterobacteriaceae act in chronic, immune-mediated infl ammatory concert with the gut microbiota to induce Foundation of America and by the NIH conditions in the intestine and liver, and spontaneous and maternally transmitted grants RO1 DK53347, RO1 DK 40249, P30 also provide obligate stimuli for the nor- colitis . Cell Host. Microbe 8 , 292 – 300 ( 2010 ). DK34987, and P40 RR018603. 17 . Sokol , H . et al. Low counts of Faecalibacterium mal development and diff eren tiation of prausnitzii in colitis microbiota . Infl amm. Bowel. mucosal immune responses. IBD requires DISCLOSURE Dis. 15 , 1183 – 1189 ( 2009 ). interactions between genetic susceptibil- Dr Sartor has received funding from the 18 . Sokol , H . et al. Faecalibacterium prausnitzii is Advisory Board of Dannon/ Yakult Educational an antiinfl ammatory commensal bacterium ity, environmental triggers, enteric micro- Foundation. identifi ed by gut microbiota analysis of Crohn’s biota, and eff ector and regulatory immune disease patients . Proc. Natl Acad. Sci. USA responses, as outlined in Figure 1 . © 2011 Society for Mucosal Immunology 105 , 16731 – 16736 ( 2008 ). 19 . Sellon , R .K . et al. Resident enteric bacteria are Although recent breakthroughs in molec- necessary for development of spontaneous ular techniques have led to a rapid evolu- REFERENCES colitis and immune system activation in tion in our understanding of the enteric 1 . Hansen , J. , Gulati , A . & Sartor , R. B . The role interleukin-10-defi cient mice . Infect. Immun. of mucosal immunity and host genetics in 66 , 5224 – 5231 ( 1998 ). bacterial composition, many questions defi ning intestinal commensal bacteria . 20 . Kim , S .C . et al. Variable phenotypes of remain regarding their function and Curr. Opin. Gastroenterol. 26 , 564 – 571 ( 2010 ). enterocolitis in interleukin 10-defi cient mice their complex mutualistic interplay with 2 . Garrett , W .S . , Gordon , J. I . & Glimcher , L .H . monoassociated with two different commensal Homeostasis and infl ammation in the intestine . bacteria . Gastroenterology 128 , 891 – 906 the host. Answering the questions posed Cell 140 , 859 – 870 ( 2010 ). ( 2005 ). in this commentary will begin to address 3 . Abraham , C. & Cho , J. H. Infl ammatory bowel 21 . Ivanov , I . I . et al. Induction of intestinal Th17 some of the most obvious gaps in our disease . N. Engl. J. Med. 361 , 2066 – 2078 cells by segmented fi lamentous bacteria . ( 2009 ). Cell 139 , 485 – 498 ( 2009 ). knowledge of host – microbial interactions 4 . Sartor , R. B. Microbial infl uences in 22 . Stepankova , R . et al. Segmented fi lamentous that determine chronic immune-medi- infl ammatory bowel diseases . bacteria in a defi ned bacterial cocktail induce ated infl ammation vs. mucosal homeo- Gastroenterology 134 , 577 – 594 ( 2008 ). intestinal infl ammation in SCID mice 5 . Vijay-Kumar , M . et al. Metabolic syndrome and reconstituted with CD45RBhigh CD4+ stasis and peaceful coexistence with our altered gut microbiota in mice lacking Toll-like T cells . Infl amm. Bowel. Dis. 13 , 1202 – 1211 complex gut microbiota. Th is knowledge receptor 5 . Science 328 , 228 – 231 ( 2010 ). ( 2007 ).

MucosalImmunology | VOLUME 4 NUMBER 2 | MARCH 2011 131 COMMENTARIES nature publishing group

23 . Moran , J. P. , Walter , J. , Tannock , G. W . , patients with ulcerative colitis . Aliment. Systematic Review Article number: CD006475 Tonkonogy , S. L . & Sartor , R. B . Bifi dobacterium Pharmacol. Ther. 13 , 1103 – 1108 ( 1999 ). ( 2007 ). animalis causes extensive duodenitis and 38 . Dethlefsen , L. & Relman , D .A . Microbes and 53 . Faith , J. J. et al. Creating and characterizing mild colonic infl ammation in monoassociated Health Sackler Colloquium: incomplete communities of human gut microbes in interleukin-10-defi cient mice . Infl amm. Bowel recovery and individualized responses of the gnotobiotic mice . ISME J. 4 , 1094 – 1098 Dis. 15 , 1022 – 1031 ( 2009 ). human distal gut microbiota to repeated ( 2010 ). 24 . Veiga , P. et al. Bifi dobacterium animalis subsp. antibiotic perturbation . Proc. Natl Acad. Sci. 54 . Rhee , K .J . et al. Induction of persistent colitis lactis fermented milk product reduces USA , e-pub ahead of print 16 September by a human commensal, enterotoxigenic infl ammation by altering a niche for colitogenic 2010 . Bacteroides fragilis , in wild-type C57BL/6 microbes . Proc. Natl Acad. Sci. USA 107 , 39 . Antonopoulos , D .A . et al. Reproducible mice . Infect. Immun. 77 , 1708 – 1718 ( 2009 ). 18132 – 18137 ( 2010 ). community dynamics of the gastrointestinal 55 . Gradel , K . O. et al. Increased short- and long- 25 . Round , J. L. & Mazmanian , S. K . Inducible microbiota following antibiotic perturbation . term risk of infl ammatory bowel disease after Foxp3+ regulatory T-cell development by a Infect. Immun. 77 , 2367 – 2375 ( 2009 ). salmonella or campylobacter gastroenteritis . commensal bacterium of the intestinal 40 . Swidsinski , A. , Loening-Baucke , V . , Bengmark , Gastroenterology 137 , 495 – 501 ( 2009 ). microbiota . Proc. Natl Acad. Sci. USA 107 , S. , Scholze , J. & Doerffel , Y . Bacterial biofi lm 56 . Jergens , A. E . et al. Helicobacter bilis triggers 12204 – 12209 ( 2010 ). suppression with antibiotics for ulcerative and persistent immune reactivity to antigens 26 . Kim , S. C . , Tonkonogy , S. L . , Albright , C. A . & indeterminate colitis: consequences of derived from the commensal bacteria in Sartor , R. B . Different host genetic backgrounds aggressive treatment . Arch. Med. Res. 39 , gnotobiotic C3H/HeN mice . Gut 56 , 934 – 940 determine disease phenotypes induced by 198 – 204 ( 2008 ). ( 2007 ). selective bacterial colonization . 41 . Sartor , R. B . Genetics and environmental 57 . Onyeagocha , C. et al. Latent cytomegalovirus Gastroenterology 128 , A512 ( 2005 ) . interactions shape the intestinal microbiome infection exacerbates experimental colitis . Am. 27 . Kim , S. C . , Tonkonogy , S. L . , Karrasch , T. , to promote IBD vs. mucosal homeostasis . J. Pathol. 175 , 2034 – 2042 ( 2009 ). Jobin , C. & Sartor , R . B . Dual association of Gastroenterology 139 , 1816 – 1819 ( 2010 ). 58 . Hormannsperger , G. & Haller , D . Molecular gnotobiotic IL-10-/- mice with two 42 . Turnbaugh , P. J . et al. A core gut microbiome in crosstalk of probiotic bacteria with the intestinal nonpathogenic commensal bacteria induces obese and lean twins . Nature 457 , 480 – 484 immune system: clinical relevance in the aggressive pancolitis . Infl amm. Bowel Dis. 13 , ( 2009 ). context of infl ammatory bowel disease . 1457 – 1466 ( 2007 ). 43 . Frank , D .N . et al. Clinical phenotype and Int. J. Med. Microbiol. 300 , 63 – 73 ( 2010 ). 28 . Kim , S. C . , Tonkonogy , S. L . , Jarvis , H. W . , genetic factors are associated with shifts in 59 . Gulati , A. S. & Dubinsky , M .C . Probiotics in Darfeuille-Michaud , A. & Sartor , R. B . mucosal-associated microbiota in infl am- pediatric infl ammatory bowel diseases . Curr. Escherichia coli strains differentially induce matory bowel diseases . Infl amm. Bowel. Dis. Gastroenterol. Rep. 11 , 238 – 247 ( 2009 ). colitis in IL-10 gene defi cient mice . 17 , 179 – 184 ( 2011 ). 60 . Sonnenburg , J. L. , Chen , C. T . & Gordon , J. I. Gastroenterology 134 , A23 ( 2008 ) . 44 . Gulati , A. S. , Kruek , L. & Sartor , R. B . Infl uence Genomic and metabolic studies of the impact 29 . Garrett , W. S . et al. Communicable ulcerative of NOD 2 on the protective intestinal of probiotics on a model gut symbiont and colitis induced by T-bet defi ciency in the commensal bacterium Faecalibacterium host . PLoS Biol. 4 , e413 ( 2006 ). innate immune system . Cell 131 , 33 – 45 prausnitzii . Gastroenterology 138 (Issue 5, 61 . Turnbaugh , P. J . et al. The effect of diet on the ( 2007 ). Suppl. 1) , S-14 ( 2010 ) . human gut microbiome: a metagenomic 30 . Simpson , K .W . et al. Adherent and invasive 45 . Alexander , D .A . et al. Quantitative PCR assays analysis in humanized gnotobiotic mice . Sci. Escherichia coli is associated with for mouse enteric fl ora reveal strain-dependent Transl. Med. 1 , 6ra14 ( 2009 ). granulomatous colitis in boxer dogs . Infect. differences in composition that are infl uenced 62 . Sonnenburg , J. L. et al. Glycan foraging in vivo Immun. 74 , 4778 – 4792 ( 2006 ). by the microenvironment . Mamm. Genome 17 , by an intestine-adapted bacterial symbiont . 31 . Suchodolski , J. S. , Xenoulis , P. G . , Paddock , 1093 – 1104 ( 2006 ). Science 307 , 1955 – 1959 ( 2005 ). C. G . , Steiner , J. M . & Jergens , A. E . Molecular 46 . Friswell , M . K . et al. Site and strain-specifi c 63 . Preidis , G. A . & Versalovic , J. Targeting the analysis of the bacterial microbiota in duodenal variation in gut microbiota profi les and human microbiome with antibiotics, probiotics, biopsies from dogs with idiopathic metabolism in experimental mice . PLos One 5 , and prebiotics: gastroenterology enters the infl ammatory bowel disease . Vet. Microbiol. e8584 ( 2010 ). metagenomics era . Gastroenterology 136 , 142 , 394 – 400 ( 2010 ). 47 . Adlerberth , I. & Wold , A. E . Establishment of the 2015 – 2031 (2009 ). 32 . Petersen , A . M . et al. A phylogenetic group gut microbiota in Western infants . Acta. 64 . Quigley , E. M . Prebiotics and probiotics; of Escherichia coli associated with active l Paediatr. 98 , 229 – 238 ( 2009 ). modifying and mining the microbiota . eft-sided infl ammatory bowel disease . 48 . Vael , C. & Desager , K . The importance of the Pharmacol. Res. 61 , 213 – 218 ( 2010 ). BMC Microbiol. 9 , 171 ( 2009 ). development of the intestinal microbiota in 65 . Singh , N. et al. Blockade of dendritic cell 33 . Swidsinski , A. et al. Mucosal fl ora in infancy . Curr. Opin. Pediatr. 21 , 794 – 800 development by bacterial fermentation infl ammatory bowel disease . Gastroenterology ( 2009 ). products butyrate and propionate through a 122 , 44 – 54 ( 2002 ). 49 . Dominguez-Bello , M .G . et al. Delivery mode transporter (Slc5a8)-dependent inhibition of 34 . Hoffmann , C . et al. Community-wide response shapes the acquisition and structure of the histone deacetylases . J. Biol. Chem 285 , of the gut microbiota to enteropathogenic initial microbiota across multiple body habitats 27601 – 27608 ( 2010 ). Citrobacter rodentium infection revealed by deep in newborns . Proc. Natl Acad. Sci. USA 107 , 66 . Bailon , E. et al. Butyrate in vitro immune- sequencing . Infect. Immun. 77, 4668 – 4678 11971 – 11975 ( 2010 ). modulatory effects might be mediated through ( 2009 ). 50 . Palmer , C. , Bik , E. M . , DiGiulio , D .B . , Relman , a proliferation-related induction of apoptosis . 35 . Lupp , C. et al. Host-mediated infl ammation D .A . & Brown , P. O . Development of the human Immunobiology 215 , 863 – 873 ( 2010 ). disrupts the intestinal microbiota and promotes infant intestinal microbiota . PLoS Biol. 5 , e177 67 . Strus , M . et al. Effect of hydrogen peroxide of the overgrowth of Enterobacteriaceae . ( 2007 ). bacterial origin on apoptosis and necrosis of Cell Host Microbe 2 , 119 – 129 ( 2007 ). 51 . Penders , J. , Stobberingh, E. E . , van den gut mucosa epithelial cells as a possible 36 . Costello , E. K . et al. Bacterial community Brandt , P. A . & Thijs , C. The role of the intestinal pathomechanism of infl ammatory bowel variation in human body habitats across space microbiota in the development of atopic disease and cancer . J. Physiol. Pharmacol. 60 and time . Science 326 , 1694 – 1697 ( 2009 ). disorders . Allergy 62 , 1223 – 1236 ( 2007 ). (Suppl 6) , 55 – 60 ( 2009 ). 37 . Venturi , A. et al. Impact on the composition of 52 . Osborn , D .A . & Sinn , J. K . Probiotics in infants 68 . Reyes , A. et al. Viruses in the faecal microbiota the faecal fl ora by a new probiotic preparation: for prevention of allergic disease and food of monozygotic twins and their mothers . preliminary data on maintenance treatment of hypersensitivity . Cochrane Database Nature 466 , 334 – 338 ( 2010 ).

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