2024
Integrating the gut microbiome and pharmacology
Verdegaal A, Goodman A. Integrating the gut microbiome and pharmacology. Science Translational Medicine 2024, 16: eadg8357. PMID: 38295186, DOI: 10.1126/scitranslmed.adg8357.Peer-Reviewed Original Research
2023
Cross-feeding in the gut microbiome: Ecology and mechanisms
Culp E, Goodman A. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host & Microbe 2023, 31: 485-499. PMID: 37054671, PMCID: PMC10125260, DOI: 10.1016/j.chom.2023.03.016.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionGastrointestinal MicrobiomeHost Microbial InteractionsMammalsMicrobiotaSymbiosisConceptsHost healthHost-microbe interactionsSpecies fitnessMicrobe-microbeEvolutionary implicationsMicrobial inhabitantsGut communitiesTrophic networksMicrobial communitiesTrophic levelsMammalian gutPrimary fermentersMetabolic outputDifferent microbesAmino acidsGut commensalsCooperative interactionsGut microbiomeNegative interactionsFitnessMutualismEcologyMicrobesEmergent roleCofactorBacteria require phase separation for fitness in the mammalian gut
Krypotou E, Townsend G, Gao X, Tachiyama S, Liu J, Pokorzynski N, Goodman A, Groisman E. Bacteria require phase separation for fitness in the mammalian gut. Science 2023, 379: 1149-1156. PMID: 36927025, PMCID: PMC10148683, DOI: 10.1126/science.abn7229.Peer-Reviewed Original ResearchConceptsMammalian gutTranscription termination factor RhoTermination factor RhoGene regulationTranscription terminationMechanisms bacteriaBacteria interactionsHuman commensalValuable targetBacteriaRhoGut microbiotaFitnessNovel clinical applicationsTherapeutic manipulationGutHuman healthCommensalRegulation
2019
Mapping human microbiome drug metabolism by gut bacteria and their genes
Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 2019, 570: 462-467. PMID: 31158845, PMCID: PMC6597290, DOI: 10.1038/s41586-019-1291-3.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteriaBacteroides thetaiotaomicronDiltiazemFemaleGastrointestinal MicrobiomeGenome, BacterialGerm-Free LifeHumansMaleMicePharmaceutical PreparationsSubstrate SpecificityConceptsHuman gut bacteriaGut bacteriaHigh-throughput genetic analysisMicrobial gene productsDiverse cladeGene contentGenomic contentGene productsGenetic analysisMolecular mechanismsDrug metabolismBacteriaMultiple disease indicationsMetabolic activityDrug-metabolizing activityGut microbiomeMicrobiomeMetabolismDrug developmentMedical therapyTreatment delayMass spectrometryCladeDisease indicationsAdverse effectsSeparating host and microbiome contributions to drug pharmacokinetics and toxicity
Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Separating host and microbiome contributions to drug pharmacokinetics and toxicity. Science 2019, 363 PMID: 30733391, PMCID: PMC6533120, DOI: 10.1126/science.aat9931.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteroides thetaiotaomicronBiological AvailabilityBiotransformationBromodeoxyuridineClonazepamGastrointestinal MicrobiomeGerm-Free LifeMiceConceptsMicrobiome contributionDrug metabolismFunction of bioavailabilityDrug-metabolizing activitySame metabolic transformationsMetabolism of drugsSystemic drugsMetabolite exposureMetabolite absorptionGut microbiotaDrug pharmacokineticsDrug efficacyPharmacokinetic modelDrugsMedical drugsTransit kineticsMetabolismInterpersonal variationMetabolic transformationToxicityMetabolic routesPharmacokineticsMice
2017
An insider's perspective: Bacteroides as a window into the microbiome
Wexler AG, Goodman AL. An insider's perspective: Bacteroides as a window into the microbiome. Nature Microbiology 2017, 2: 17026. PMID: 28440278, PMCID: PMC5679392, DOI: 10.1038/nmicrobiol.2017.26.Peer-Reviewed Original ResearchMeSH KeywordsBacteroidesFirmicutesGastrointestinal MicrobiomeGastrointestinal TractGenomicsHigh-Throughput Nucleotide SequencingHumansMetagenomeMicrobiotaSymbiosisConceptsGut bacteriumHuman gut BacteroidesModel organismsMicrobial communitiesMetagenome sequencesGut BacteroidesClose relativesGut microorganismsEscherichia coliCommensal microorganismsCentury of studyBacteriumMicroorganismsGut microbiotaImportant insightsBacteroidesSheer diversityHuman healthGenomicsEcologyOrganismsEcosystemsDiversityMicrobiomeColiEngineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut
Lim B, Zimmermann M, Barry NA, Goodman AL. Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. Cell 2017, 169: 547-558.e15. PMID: 28431252, PMCID: PMC5532740, DOI: 10.1016/j.cell.2017.03.045.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteroidesGastrointestinal MicrobiomeGene ExpressionGenetic EngineeringHumansMiceNeuraminidasePromoter Regions, GeneticConceptsGene expressionModulate gene expressionAbsence of inducerCommunity assemblyAddition of inducerGenetic toolsInducible promoterGene productsExpression platformHost physiologyPromoter activityHuman commensalGenus BacteroidesSynthetic inducersGut anaerobesInducerSialidase activityExpressionNumerous aspectsGut microbiotaSialic acidGutPromoterValuable toolCommensal
2016
Human symbionts inject and neutralize antibacterial toxins to persist in the gut
Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL. Human symbionts inject and neutralize antibacterial toxins to persist in the gut. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 3639-3644. PMID: 26957597, PMCID: PMC4822603, DOI: 10.1073/pnas.1525637113.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacteroides fragilisFemaleGastrointestinal MicrobiomeGenome, BacterialGerm-Free LifeHumansMaleMiceModels, AnimalPhylogenySymbiosisType VI Secretion SystemsConceptsHuman gut symbiontGut symbiontsMicrobial communitiesProminent Human Gut SymbiontHundreds of speciesHuman gut commensalGut microbial communityContact-dependent killingHuman gut microbiomeAntibacterial toxinsInterbacterial interactionsInteraction assaysCommunity compositionInterbacterial antagonismEffector lociImmunity genesMajor phylaSecretome studiesHuman symbiontsSymbiontsMicrobiome manipulationGut microbesGut commensalsMultiple mouse modelsGut microbiome