2023
Infection leaves a genetic and functional mark on the gut population of a commensal bacterium
Tawk C, Lim B, Bencivenga-Barry N, Lees H, Ramos R, Cross J, Goodman A. Infection leaves a genetic and functional mark on the gut population of a commensal bacterium. Cell Host & Microbe 2023, 31: 811-826.e6. PMID: 37119822, PMCID: PMC10197903, DOI: 10.1016/j.chom.2023.04.005.Peer-Reviewed Original ResearchConceptsRapid genetic adaptationSingle nucleotide variantsMultiple phylaGenetic adaptationFunctional marksStable marksEnteric infectionsGene expressionPopulation dynamicsGut commensalsCommensal populationsMicrobiome compositionAbsence of infectionRapid selectionCitrobacter rodentiumFitnessGut populationsCommensal bacteriumInfected miceGastrointestinal infectionsGnotobiotic miceCommensalGut lumenDirect administrationVitamin B6Cross-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 ResearchConceptsHost healthHost-microbe interactionsSpecies fitnessMicrobe-microbeEvolutionary implicationsMicrobial inhabitantsGut communitiesTrophic networksMicrobial communitiesTrophic levelsMammalian gutPrimary fermentersMetabolic outputDifferent microbesAmino acidsGut commensalsCooperative interactionsGut microbiomeNegative interactionsFitnessMutualismEcologyMicrobesEmergent roleCofactor
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 ResearchConceptsGut bacteriumHuman gut BacteroidesModel organismsMicrobial communitiesMetagenome sequencesGut BacteroidesClose relativesGut microorganismsEscherichia coliCommensal microorganismsCentury of studyBacteriumMicroorganismsGut microbiotaImportant insightsBacteroidesSheer diversityHuman healthGenomicsEcologyOrganismsEcosystemsDiversityMicrobiomeColi
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 ResearchConceptsHuman 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
2015
Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation
Cullen TW, Schofield WB, Barry NA, Putnam EE, Rundell EA, Trent MS, Degnan PH, Booth CJ, Yu H, Goodman AL. Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. Science 2015, 347: 170-175. PMID: 25574022, PMCID: PMC4388331, DOI: 10.1126/science.1260580.Peer-Reviewed Original Research
2009
Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat
Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI. Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat. Cell Host & Microbe 2009, 6: 279-289. PMID: 19748469, PMCID: PMC2895552, DOI: 10.1016/j.chom.2009.08.003.Peer-Reviewed Original ResearchConceptsHuman gut symbiontHuman gut bacteriumHuman gut commensalAdjacent chromosomal DNAGut symbiontsHuman gut microbiotaGenomic locationMicrobial genesCommunity compositionTransposon mutantsMicrobial adaptationChromosomal DNAHuman symbiontsParallel sequencingGut bacteriumBacteroides thetaiotaomicronRelative abundanceGenetic determinantsGut commensalsSymbiontsVivo selectionMetabolic organCellular compositionGnotobiotic miceGut microbiota