REVIEWOpenAccessUnderstandingtheimpactofantibioticperturbationonthehumanmicrobiomeD.J.Schwartz1,2*†,A.E.Langdon2,3†andG.Dantas2,3,4,5*AbstractThehumangutmicrobiomeisadynamiccollectionofbacteria,archaea,fungi,andvirusesthatperformsessentialfunctionsforimmunedevelopment,pathogencolonizationresistance,andfoodmetabolism.Perturbationofthegutmicrobiome’secologicalbalance,commonlybyantibiotics,cancauseandexacerbatediseases.Topredictandsuccessfullyrescuesuchperturbations,first,wemustunderstandtheunderlyingtaxonomicandfunctionaldynamicsofthemicrobiomeasitchangesthroughoutinfancy,childhood,andadulthood.Weofferanoverviewofthehealthygutbacterialarchitectureovertheselifestagesandcommentonvulnerabilitytoshortandlongcoursesofantibiotics.Second,theresilienceofthemicrobiomeafterantibioticperturbationdependsonkeycharacteristics,suchasthenature,timing,duration,andspectrumofacourseofantibiotics,aswellasmicrobiomemodulatoryfactorssuchasage,travel,underlyingillness,antibioticresistancepattern,anddiet.Inthisreview,wediscussacuteandchronicantibioticperturbationstothemicrobiomeandresistomeinthecontextofmicrobiomestabilityanddynamics.Wespecificallydiscusskeytaxonomicandresistancegenechangesthataccompanyantibiotictreatmentofneonates,children,andadults.Restorationofahealthygutmicrobialecosystemafterroutineantibioticswillrequirerationallymanagedexposuretospecificantibioticsandmicrobes.Tothatend,wereviewtheuseoffecalmicrobiotatransplantationandprobioticstodirectrecolonizationofthegutecosystem.Weconcludewithourperspectivesonhowbesttoassess,predict,andaidrecoveryofthemicrobiomeafterantibioticperturbation.Keywords:Gutmicrobiome,Resistome,Antibiotics,Perturbation,Resilience,Dynamics,RecolonizationIntroductionThehumangutmicrobiomeconsistsofbacteria,vi-ruses,andfungiideallylivingsymbioticallywiththeirhumanhost,thoughthisreviewwillfocusexclusivelyonbacterialresidentswithinthegutmicrobiome[1].Individualspeciesandcollectivebacterialfunctionswithinthegutmicrobiomeconfermanybenefitsthroughoutlifeincl...
