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Review

Gut microbiota: next frontier in understanding human health and development of biotherapeutics

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Pages 71-86 | Published online: 11 Jul 2011

References

  • SavageDCMicrobial ecology of the gastrointestinal tractAnnu Rev Microbiol197731107133334036
  • QinJLiRRaesJA human gut microbial gene catalogue established by metagenomic sequencingNature2010464596520203603
  • BackhedFLeyRESonnenburgJLPetersonDAGordonJIHost-bacterial mutualism in the human intestineScience20053071915192015790844
  • McConnellELFaddaHMBasitAWGut instincts: Explorations in intestinal physiology and drug deliveryInt J Pharm200836421322618602774
  • MshvildadzeMNeuJThe infant intestinal microbiome: Friend or foe?Early Hum Dev201086Suppl 1677120116944
  • AdlerberthIWoldAEEstablishment of the gut microbiota in Western infantsActa Paediatr20099822923819143664
  • RumneyCJRowlandIRIn vivo and in vitro models of the human colonic floraCrit Rev Food Sci Nutr1992312993311581008
  • SekirovIRussellSLAntunesLCFinlayBBGut microbiota in health and diseasePhysiol Rev20109085990420664075
  • DethlefsenLEckburgPBBikEMRelmanDAAssembly of the human intestinal microbiotaTrends Ecol Evol20062151752316820245
  • BlautMCollinsMDWellingGWDoreJVanLJde VosWMolecular biological methods for studying the gut microbiota: The EU human gut flora projectBr J Nutr200287Suppl 2S20321112088520
  • McCartneyALApplication of molecular biological methods for studying probiotics and the gut floraBr J Nutr200288Suppl 1S29S3712215179
  • PeterHSommarugaRAn evaluation of methods to study the gut bacterial community composition of freshwater zooplanktonJ Plankton Res2008309971006
  • LefebvrePCariouBLienFKuipersFStaelsBRole of bile acids and bile acid receptors in metabolic regulationPhysiol Rev20098914719119126757
  • WongJMdeSRKendallCWEmamAJenkinsDJColonic health: Fermentation and short chain fatty acidsJ Clin Gastroenterol20064023524316633129
  • ChenWJAndersonJWJenningsDPropionate may mediate the hypocholesterolemic effects of certain soluble plant fibers in cholesterol-fed ratsProc Soc Exp Biol Med19841752152186320209
  • BerggrenAMNymanEMLundquistIBjorckIMInfluence of orally and rectally administered propionate on cholesterol and glucose metabolism in obese ratsBr J Nutr1996762872948813902
  • Tlaskalova-HogenovaHStepankovaRHudcovicTCommensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseasesImmunol Lett2004939710815158604
  • RoundJLMazmanianSKThe gut microbiota shapes intestinal immune responses during health and diseaseNat Rev Immunol2009931332319343057
  • CebraJJPeriwalSBLeeGLeeFShroffKEDevelopment and maintenance of the gut-associated lymphoid tissue (GALT): The roles of enteric bacteria and virusesDev Immunol1998613189716901
  • BouskraDBrezillonCBerardMLymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasisNature200845650751018987631
  • HaversonKRehakovaZSinkoraJSverLBaileyMImmune development in jejunal mucosa after colonization with selected commensal gut bacteria: A study in germ-free pigsVet Immunol Immunopathol200711924325317643495
  • HapfelmeierSLawsonMASlackEReversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responsesScience20103281705170920576892
  • AtarashiKTanoueTShimaTInduction of colonic regulatory T cells by indigenous Clostridium speciesScience201133133734121205640
  • MazmanianSKLiuCHTzianabosAOKasperDLAn immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune systemCell200512210711816009137
  • IvanovIIAtarashiKManelNInduction of intestinal Th17 cells by segmented filamentous bacteriaCell200913948549819836068
  • MazmanianSKRoundJLKasperDLA microbial symbiosis factor prevents intestinal inflammatory diseaseNature200845362062518509436
  • LuhrsHGerkeTMullerJGButyrate inhibits NF-kappaB activation in lamina propria macrophages of patients with ulcerative colitisScand J Gastroenterol20023745846611989838
  • MaslowskiKMVieiraATNgARegulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43Nature20094611282128619865172
  • KleessenBBlautMModulation of gut mucosal biofilmsBr J Nutr200593Suppl 1S35S4015877893
  • HamerHMJonkersDVenemaKVanhoutvinSTroostFJBrummerRJReview article: The role of butyrate on colonic functionAliment Pharmacol Ther20082710411917973645
  • SalminenSBouleyCBoutron-RuaultMCFunctional food science and gastrointestinal physiology and functionBr J Nutr199880Suppl 1S147S1719849357
  • HillDAArtisDIntestinal bacteria and the regulation of immune cell homeostasisAnnu Rev Immunol20102862366720192812
  • StappenbeckTSHooperLVGordonJIDevelopmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cellsProc Natl Acad Sci U S A200299154511545512432102
  • HawrelakJAMyersSPThe causes of intestinal dysbiosis: A reviewAltern Med Rev2004918019715253677
  • DePGNadalIMedinaMIntestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in childrenBMC Microbiol2010106320181275
  • NadalIDonatERibes-KoninckxCCalabuigMSanzYImbalance in the composition of the duodenal microbiota of children with coeliac diseaseJ Med Microbiol2007561669167418033837
  • BrugmanSKlatterFAVisserJTAntibiotic treatment partially protects against type 1 diabetes in the bio-breeding diabetes-prone rat. Is the gut flora involved in the development of type 1 diabetes?Diabetologia2006492105210816816951
  • SchwartzRFNeuJSchatzDAtkinsonMAWasserfallCAntibiotic treatment partially protects against type 1 diabetes in the bio-breeding diabetes-prone rat. Is the gut flora involved in the development of type 1 diabetes?Diabetologia20075022022117119915
  • RoeschLFLorcaGLCasellaGCulture-independent identification of gut bacteria correlated with the onset of diabetes in a rat modelISME J2009353654819225551
  • MacFarlaneSSteedHMacFarlaneGTIntestinal bacteria and inflammatory bowel diseaseCrit Rev Clin Lab Sci200946255419107650
  • WalkerAWSandersonJDChurcherCHigh-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel diseaseBMC Microbiol201111721219646
  • KangSDenmanSEMorrisonMDysbiosis of fecal microbiota in Crohn’s disease patients as revealed by a custom phylogenetic microarrayInflamm Bowel Dis2010162034204220848492
  • SjogrenYMJenmalmMCBottcherMFBjorkstenBSverremark-EkstromEAltered early infant gut microbiota in children developing allergy up to 5 years of ageClin Exp Allergy20093951852619220322
  • WatanabeJFujiwaraRSasajimaNItoSSonoyamaKAdministration of antibiotics during infancy promoted the development of atopic dermatitis-like skin lesions in NC/Nga miceBiosci Biotechnol Biochem20107435836320139606
  • GruberCvan StuijvenbergMMoscaFReduced occurrence of early atopic dermatitis because of immunoactive prebiotics among low-atopy-risk infantsJ Allergy Clin Immunol201012679179720832848
  • PendersJStobberinghEEThijsCMolecular fingerprinting of the intestinal microbiota of infants in whom atopic eczema was or was not developingClin Exp Allergy2006361602160817177684
  • VaelCNelenVVerhulstSLGoossensHDesagerKNEarly intestinal Bacteroides fragilis colonisation and development of asthmaBMC Pulm Med200881918822123
  • WatanabeSNarisawaYAraseSDifferences in fecal microflora between patients with atopic dermatitis and healthy control subjectsJ Allergy Clin Immunol200311158759112642841
  • QuigleyEMBacterial flora in irritable bowel syndrome: Role in pathophysiology, implications for managementJ Dig Dis200782717261128
  • SiJMYuYCFanYJChenSJIntestinal microecology and quality of life in irritable bowel syndrome patientsWorld J Gastroenterol2004101802180515188510
  • KassinenAKrogius-KurikkaLMakivuokkoHThe fecal microbiota of irritable bowel syndrome patients differs significantly from that of healthy subjectsGastroenterology2007133243317631127
  • TanaCUmesakiYImaokaAHandaTKanazawaMFukudoSAltered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndromeNeurogastroenterol Motil20102251251519903265
  • HildebrandtMAHoffmannCSherrill-MixSAHigh-fat diet determines the composition of the murine gut microbiome independently of obesityGastroenterology20091371716172419706296
  • LeyREBackhedFTurnbaughPLozuponeCAKnightRDGordonJIObesity alters gut microbial ecologyProc Natl Acad Sci U S A2005102110701107516033867
  • TurnbaughPJHamadyMYatsunenkoTA core gut microbiome in obese and lean twinsNature200945748048419043404
  • TurnbaughPJLeyREMahowaldMAMagriniVMardisERGordonJIAn obesity-associated gut microbiome with increased capacity for energy harvestNature20064441027103117183312
  • TurnbaughPJBackhedFFultonLGordonJIDiet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiomeCell Host Microbe2008321322318407065
  • KalliomakiMColladoMCSalminenSIsolauriEEarly differences in fecal microbiota composition in children may predict overweightAm J Clin Nutr20088753453818326589
  • SchwiertzATarasDSchaferKMicrobiota and short-chain fatty acid in lean and overweight healthy subjectsObesity (Silver Spring)20101819019519498350
  • LarsenNVogensenFKvan den BergFWGut microbiota in human adults with type 2 diabetes differs from non-diabetic adultsPLoS One20105e908520140211
  • WuXMaCHanLMolecular characterisation of the faecal microbiota in patients with type II diabetesCurr Microbiol2010611697820087741
  • MutluEKeshavarzianAEngenPForsythCBSikaroodiMGillevetPIntestinal dysbiosis: A possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in ratsAlcohol Clin Exp Res2009331836184619645728
  • LuppCRobertsonMLWickhamMEHost-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of EnterobacteriaceaeCell Host Microbe2007211912918005726
  • HopkinsMJMacfarlaneGTChanges in predominant bacterial populations in human faeces with age and with Clostridium difficile infectionJ Med Microbiol20025144845411990498
  • SnoverDCUpdate on the serrated pathway to colorectal carcinomaHum Pathol20114211020869746
  • VannucciLStepankovaRKozakovaHFiserovaARossmannPTlaskalova-HogenovaHColorectal carcinogenesis in germ-free and conventionally reared rats: Different intestinal environments affect the systemic immunityInt J Oncol20083260961718292938
  • KadoSUchidaKFunabashiHIntestinal microflora are necessary for development of spontaneous adenocarcinoma of the large intestine in T-cell receptor beta chain and p53 double-knockout miceCancer Res2001612395239811289103
  • UronisJMMuhlbauerMHerfarthHHRubinasTCJonesGSJobinCModulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibilityPLoS One20094e602619551144
  • WuSRheeKJAlbesianoEA human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responsesNat Med2009151016102219701202
  • BalamuruganRRajendiranEGeorgeSSamuelGVRamakrishnaBSReal-time polymerase chain reaction quantification of specific butyrate-producing bacteria, Desulfovibrio and Enterococcus faecalis in the feces of patients with colorectal cancerJ Gastroenterol Hepatol2008231298130318624900
  • SobhaniITapJRoudot-ThoravalFMicrobial dysbiosis in colorectal cancer (CRC) patientsPLoS One20116e1639321297998
  • OkadaHKuhnCFeilletHBachJFThe ‘hygiene hypothesis’ for autoimmune and allergic diseases: An updateClin Exp Immunol20101601920415844
  • RoduitCWohlgensingerJFreiRPrenatal animal contact and gene expression of innate immunity receptors at birth are associated with atopic dermatitisJ Allergy Clin Immunol201112717918521112617
  • PhipatanakulWCeledonJCRabyBAEndotoxin exposure and eczema in the first year of lifePediatrics2004114131815231902
  • LikeAAGuberskiDLButlerLInfluence of environmental viral agents on frequency and tempo of diabetes mellitus in BB/Wor ratsDiabetes1991402592621899407
  • WenLLeyREVolchkovPYInnate immunity and intestinal microbiota in the development of Type 1 diabetesNature20084551109111318806780
  • CaniPDAmarJIglesiasMAMetabolic endotoxemia initiates obesity and insulin resistanceDiabetes2007561761177217456850
  • CaniPDNeyrinckAMFavaFSelective increases of bifidobacteria in gut microflora improve high-fat-diet-induced diabetes in mice through a mechanism associated with endotoxaemiaDiabetologia2007502374238317823788
  • SzaboGBalaSAlcoholic liver disease and the gut-liver axisWorld J Gastroenterol2010161321132920238398
  • ThuySLadurnerRVolynetsVNonalcoholic fatty liver disease in humans is associated with increased plasma endotoxin and plasminogen activator inhibitor 1 concentrations and with fructose intakeJ Nutr20081381452145518641190
  • SabateJMJouetPHarnoisFHigh prevalence of small intestinal bacterial overgrowth in patients with morbid obesity: A contributor to severe hepatic steatosisObes Surg20081837137718286348
  • CaniPDBibiloniRKnaufCChanges in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in miceDiabetes2008571470148118305141
  • CaniPDPossemiersSVan de WieleTChanges in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeabilityGut2009581091110319240062
  • Attene-RamosMSNavaGMMuellnerMGWagnerEDPlewaMJGaskinsHRDNA damage and toxicogenomic analyses of hydrogen sulfide in human intestinal epithelial FHs 74 Int cellsEnviron Mol Mutagen20105130431420120018
  • HopeMEHoldGLKainREl-OmarEMSporadic colorectal cancer – role of the commensal microbiotaFEMS Microbiol Lett20052441715727814
  • PayneCMCrowley-SkillicornCBernsteinCHolubecHMoyerMPBernsteinHHydrophobic bile acid-induced micronuclei formation, mitotic perturbations, and decreases in spindle checkpoint proteins: Relevance to genomic instability in colon carcinogenesisNutr Cancer20106282584020661832
  • OnoueMKadoSSakaitaniYUchidaKMorotomiMSpecific species of intestinal bacteria influence the induction of aberrant crypt foci by 1,2-dimethylhydrazine in ratsCancer Lett19971131791869065820
  • EllmerichSSchollerMDurantonBPromotion of intestinal carcinogenesis by Streptococcus bovisCarcinogenesis20002175375610753212
  • BackhedFDingHWangTThe gut microbiota as an environmental factor that regulates fat storageProc Natl Acad Sci U S A2004101157181572315505215
  • SamuelBSShaitoAMotoikeTEffects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41Proc Natl Acad Sci U S A2008105167671677218931303
  • BackhedFManchesterJKSemenkovichCFGordonJIMechanisms underlying the resistance to diet-induced obesity in germ-free miceProc Natl Acad Sci U S A200710497998417210919
  • DumasMEBartonRHToyeAMetabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant miceProc Natl Acad Sci U S A2006103125111251616895997
  • Food and Agriculture Organization/World Health OrganizationHealth and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria Report of a joint FAO/WHO expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteriaBasel, SwitzerlandWorld Health Organization2001
  • FalagasMEBetsiGIAthanasiouSProbiotics for prevention of recurrent vulvovaginal candidiasis: A reviewJ Antimicrob Chemother20065826627216790461
  • MshvildadzeMNeuJProbiotics and prevention of necrotizing enterocolitisEarly Hum Dev200985S71S7419781874
  • ReiffCKellyDInflammatory bowel disease, gut bacteria and probiotic therapyInt J Med Microbiol2010300253319800289
  • PreidisGAVersalovicJTargeting the human microbiome with antibiotics, probiotics, and prebiotics: Gastroenterology enters the metagenomics eraGastroenterology20091362015203119462507
  • PrakashSJonesMLArtificial cell therapy: New strategies for the therapeutic delivery of live bacteriaJ Biomed Biotechnol2005456
  • PrakashSMartoniCToward a new generation of therapeutics: Artificial cell targeted delivery of live cells for therapyAppl Biochem Biotechnol200612812216415477
  • GibsonGRRoberfroidMBDietary modulation of the human colonic microbiota: Introducing the concept of prebioticsJ Nutr1995125140114127782892
  • CaniPDLecourtEDewulfEMGut microbiota fermentation of prebiotics increases satietogenic and incretin gut peptide production with consequences for appetite sensation and glucose response after a mealAm J Clin Nutr2009901236124319776140
  • StrowskiMZWiedenmannBProbiotic carbohydrates reduce intestinal permeability and inflammation in metabolic diseasesGut2009581044104519592687
  • RafterJBennettMCaderniGDietary synbiotics reduce cancer risk factors in polypectomized and colon cancer patientsAm J Clin Nutr20078548849617284748
  • GillSRPopMDeboyRTMetagenomic analysis of the human distal gut microbiomeScience20063121355135916741115
  • MartoniCBhathenaJJonesMLUrbanskaAMChenHPrakashSInvestigation of microencapsulated BSH active lactobacillus in the simulated human GI tractJ Biomed Biotechnol200713684
  • MartoniCBhathenaJUrbanskaAMPrakashSMicroencapsulated bile salt hydrolase producing Lactobacillus reuteri for oral targeted delivery in the gastrointestinal tractAppl Microbiol Biotechnol20088122523318719901
  • BhathenaJKulamarvaAUrbanskaAMMartoniCPrakashSMicroencapsulated bacterial cells can be used to produce the enzyme feruloyl esterase: Preparation and in-vitro analysisAppl Microbiol Biotechnol2007751023102917483939
  • BhathenaJMartoniCKulamarvaAUrbanskaAMMalhotraMPrakashSOrally delivered microencapsulated live probiotic formulation lowers serum lipids in hypercholesterolemic hamstersJ Med Food20091231031919459731
  • ChenHOuyangWJonesMHaqueTLawuyiBPrakashSIn-vitro analysis of APA microcapsules for oral delivery of live bacterial cellsJ Microencapsul20052253954716361197
  • OuyangWChenHJonesMLNovel multi-layer APPPA microcapsules for oral delivery: Preparation condition, stability and permeabilityIndian J Biochem Biophys20094649149720361712
  • UrbanskaAMBhathenaJMartoniCPrakashSEstimation of the potential antitumor activity of microencapsulated Lactobacillus acidophilus yogurt formulation in the attenuation of tumorigenesis in Apc(Min/+) miceDig Dis Sci20095426427318633708
  • LiMWangBZhangMSymbiotic gut microbes modulate human metabolic phenotypesProc Natl Acad Sci U S A20081052117212218252821