FEMSMicrobiologyReviews,fuw045,41,2017,182–199doi:10.1093/femsre/fuw045AdvanceAccessPublicationDate:9February2017ReviewarticleREVIEWARTICLEIntestinalmicrobiomelandscaping:insightincommunityassemblageandimplicationsformicrobialmodulationstrategiesSudarshanA.Shetty1,∗,FloorHugenholtz1,LeoLahti1,2,3,HaukeSmidt1andWillemM.deVos1,41LaboratoryofMicrobiology,WageningenUniversity,Stippeneng4,Building124,6708WEWageningen,theNetherlands,2VIBLabforBioinformaticsand(Eco-)systemsBiology,KULeuven,CampusGasthuisberg,3000Leuven,Belgium,3DepartmentofMathematicsandStatistics,UniversityofTurku,20014Turku,Finlandand4ResearchProgrammeUnitImmunobiology,DepartmentofBacteriologyandImmunology,HelsinkiUniversity,P.O.Box21,00014Helsinki,Finland∗Correspondingauthor:LaboratoryofMicrobiology,WageningenUniversity,Stippeneng4,Building124,6708WEWageningen,theNetherlands.Tel:+0317480059;E-mail:sudarshan.shetty@wur.nlOnesentencesummary:Ameta-analysis-basedreviewdiscussesthekeyfeaturesofhumanintestinalmicrobiome,i.e.thecompositionalandfunctional‘core’,communitytypes,andtheexistenceofalternativestablestatesandhowtheseconceptscanbeusedtoimprovehosthealth.Editor:AntoineDanchin†LeoLahti,http://orcid.org/0000-0001-5537-637XABSTRACTHighindividuality,largecomplexityandlimitedunderstandingofthemechanismsunderlyinghumanintestinalmicrobiomefunctionremainthemajorchallengesfordesigningbeneficialmodulationstrategies.ExemplifiedbytheanalysisofintestinalbacteriainathousandWesternadults,wediscusskeyconceptsofthehumanintestinalmicrobiomelandscape,i.e.thecompositionalandfunctional‘core’,thepresenceofcommunitytypesandtheexistenceofalternativestablestates.Genomicinvestigationofcoretaxarevealedfunctionalredundancy,whichisexpectedtostabilizetheecosystem,aswellastaxawithspecializedfunctionsthathavethepotentialtoshapethemicrobiomelandscape.ThecontrastbetweenPrevotella-andBacteroides-dominatedsystemshasbeenwelldescribed.However,lessknownistheeffectofnotsoabundantbacteria,forexample,Dialisterspp.thathavebeenproposed...
