计算生物学论文：Adapting Functional Genomic Tools to Metag

Adaptingfunctionalgenomictoolstometagenomicanalyses:investigatingtheroleofgutbacteriainrelationtoobesityYuanhuaLiu,ChenhongZhang,LipingZhaoandChristineNardiniAbstractWiththeexpandingavailabilityofsequencingtechnologies,researchpreviouslycenteredonthehumangenomecannowaffordtoincludethestudyofhumans’internalecosystem(humanmicrobiome).Giventhescaleofthedatainvolvedinthismetagenomicresearch(twoordersofmagnitudelargerthanthehumangenome)andtheirimportanceinrelationtohumanhealth,itiscrucialtoguarantee(alongwiththeappropriatedatacollectionandtax-onomy)propertoolsfordataanalysis.Weproposetoadapttheapproachesdefinedfortheanalysisofgene-expressionmicroarrayinordertoinferinformationinmetagenomics.Inparticular,weappliedSAM,abroad-lyusedtoolfortheidentificationofdifferentiallyexpressedgenesamongdifferentsamplesclasses,toareporteddatasetonaresearchmodelwithmiceoftwogenotypes(ahighdensitylipoproteinknockoutmouseanditswild-typecounterpart).Thedatacontaintwodifferentdiets(high-fatornormal-chow)toensuretheonsetofobesity,prodromeofmetabolicsyndromes(MS).Byusing16SrRNAgeneasagenomicdiversitymarker,weillustratehowthisapproachcanidentifybacterialpopulationsdifferentiallyenrichedamongdifferentgeneticanddietaryconditionsofthehost.Thisapproachfaithfullyreproduceshighly-relevantresultsfromphylogeneticandstandardstatisticalana-lyses,usedtoexplaintheroleofthegutmicrobiomeinrelationtoobesity.Thisrepresentsapromisingproof-of-principleforusingfunctionalgenomicapproachesinthefastgrowingareaofmetagenomics,andwarrantstheavailabilityofalargebodyofthoroughlytestedandtheoreticallysoundmethodologiestothisexcitingnewfield.Keywords:humanmicrobiome;functionalgenomic;metagenomicsINTRODUCTIONThemicroorganismcommunityinthehumangastrointestinal(GI)tractcontainsmorethan1000specieswhoseaccumulatedgenomesmayhave100timesmoregenesthanthehumangenome.Inthisperspective,gutmicrobiotacanbeviewedasanorganthatregulatesitshost’smetabolicandimmunesystems[1,2].Gutintestinal(GI)micro-organismsareinfactknowntocontributetodiversehumanprocesses,suchaspreventingthecolonizationandattacksofpathogens,regulatingtheimmunesystemthroughanumberofsignalmoleculesandmetabolites,aidingthedevelopmentofintestinalmicrovilli,breakingdownnon-digestiblepolysac-charides,andensuringanaerobicmetabolismofpep-tidesandproteinswhichresultsinrecoveryofmetabolicenergyforthehost[3,4].Althoughde-finitiveproofsremainstobeprovided,growingLiuYuanhuaisamemberofresearchstaffintheClinicalGenomicGroupattheMaxPlanck—ChineseAcademyofSciencesPartnerInstituteforComputationalBiology(MPG-CASPICB),Shanghai.ChenhongZhangisaPhDstudentattheSchoolofLifeSciencesandBiotechnologyatJiaoTongUniversity,Shanghai.LipingZhaoisProfessorofMicrobiology,AssociateDeanoftheSchoolofLifeSciencesandBiotechnology,andAssociateDirectorofShanghaiCenterforSystemsBiomedicineatJiaoTongUniversity,Shanghai.ChristineNardiniisPrincipalInvestigatoratMPG-CASPICB.Correspondingauthor.ChristineNardini,ClinicalGenomicNetwork,CAS-MPGPartnerInstituteandKeyLaboratoryforComputationalBiology,ShanghaiInstitutesforBiologicalSciences,ChineseAcademyofSciences,Shanghai,People’sRepublicofChina.Tel:þ862154920485;Fax:þ862154920451;E-mail:[e-mail]1of7doi:10.1093/bfgp/elq011TheAuthor2010.PublishedbyOxfordUniversityPress.Allrightsreserved.Forpermissions,pleaseemail:[e-mail]GenomicsAdvanceAccesspublishedMay6,2010atMainLibraryL610LawrenceLivermoreNatLabonJanuary3,2011bfg.oxfordjournals.orgDownloadedfromevidenceindicatesthatGImicrobiotaplayacrucialroleintheprogressofhumandiseasesandinparticu-larformetabolicsyndromes(MS),suchasobesity,diabetesandhypertension[5–7].ToenhancetheunderstandingofthemechanismsofMSdevelopment,earlyresearchhasdevotedcon-siderableeffortstothestudyofthehostgenomicvariations.Nowadays,giventheindicationthatGIisinvolvedtosomeextentinsuchdiseases,moreattentionhasbeenpaidtoexploringthedisruptionofgutmicrobiota.Thismetagenomicapproachtodiseaseschallengesresearchersinmanyways,fromashiftinparadigmthatmodifiestheprevalenceofgenomicetiologyofdiseases,tomorepracticalissuesrelatedtothecomplexityandvastnessofGImicro-biotadata.TheactualconnectionbetweenvariationsintheGIandonsetofobesityandothermorecomplexMSisstillunderhugedebateamongscientists,andisnottheobjectofthispaper.Inthisstudy,weconcentrateinparticularontheidentificationofmethodologiesthatareabletohighlightrelationshipsbetweenthevariationsintheGIcompositionandobesity(awellknownconsequenceoffatfeeding,relatedtoMS[8–12]),asitismeasuredintermsofimpairedglucoseintoleranceandfatmassdevelopment,makinguseoftoolsthatarebothwell-developedandvalidatedinotherareasofresearch.BasedontheobservationthatcomplexityandvastnessoftheGImicrobiotadataaretraitssharedwithhigh-throughputtranscriptionaldata,whicharetheobjectofstudyoffunctionalgenomics,wesoughttoadaptsomeofthewell-testedandmuch-usedtoolsforgeneexpressionanalysisofDNAmicroarraydatatometagenomicstudies.Toclarifythisconcept,Figure1indicatesschematicallyhowthetwotypesofdat