Letterhttps://doi.org/10.1038/s41586-018-0620-2Thehumangutmicrobiomeinearly-onsettype1diabetesfromtheTEDDYstudytommiVatanen1*,ericA.Franzosa1,2,randallSchwager2,Suryatripathi1,timothyD.Arthur1,KendraVehik3,ÅkeLernmark4,WilliamA.Hagopian5,MarianJ.rewers6,Jin-XiongShe7,Jormatoppari8,9,Anette-G.Ziegler10,11,12,BeenaAkolkar13,JeffreyP.Krischer3,ChristopherJ.Stewart14,15,NadimJ.Ajami14,JosephF.Petrosino14,DirkGevers1,19,HarriLähdesmäki16,HeraVlamakis1,CurtisHuttenhower1,2,20*&ramnikJ.Xavier1,17,18,20*Type1diabetes(T1D)isanautoimmunediseasethattargetspancreaticisletbetacellsandincorporatesgeneticandenvironmentalfactors1,includingcomplexgeneticelements2,patientexposures3andthegutmicrobiome4.Viralinfections5andbroadergutdysbioses6havebeenidentifiedaspotentialcausesorcontributingfactors;however,humanstudieshavenotyetidentifiedmicrobialcompositionalorfunctionaltriggersthatarepredictiveofisletautoimmunityorT1D.Hereweanalyse10,913metagenomesinstoolsamplesfrom783mostlywhite,non-Hispanicchildren.Thesampleswerecollectedmonthlyfromthreemonthsofageuntiltheclinicalendpoint(isletautoimmunityorT1D)intheTheEnvironmentalDeterminantsofDiabetesintheYoung(TEDDY)study,tocharacterizethenaturalhistoryoftheearlygutmicrobiomeinconnectiontoisletautoimmunity,T1Ddiagnosis,andothercommonearlylifeeventssuchasantibiotictreatmentsandprobiotics.Themicrobiomesofcontrolchildrencontainedmoregenesthatwererelatedtofermentationandthebiosynthesisofshort-chainfattyacids,butthesewerenotconsistentlyassociatedwithparticulartaxaacrossgeographicallydiverseclinicalcentres,suggestingthatmicrobialfactorsassociatedwithT1Daretaxonomicallydiffusebutfunctionallymorecoherent.Whenweinvestigatedthebroaderestablishmentanddevelopmentoftheinfantmicrobiome,bothtaxonomicandfunctionalprofilesweredynamicandhighlyindividualized,anddominatedinthefirstyearoflifebyoneofthreelargelyexclusiveBifidobacteriumspecies(B.bifidum,B.breveorB.longum)orbythephylumProteobacteria.Inparticular,thestrain-specificcarriageofgenesfortheutilizationo...
