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
2022
Subdoligranulum chews up joints: how a gut pathobiont can instigate arthritis
Kriegel M. Subdoligranulum chews up joints: how a gut pathobiont can instigate arthritis. Trends In Immunology 2022, 44: 4-6. PMID: 36494272, DOI: 10.1016/j.it.2022.11.006.Commentaries, Editorials and LettersConceptsRheumatoid arthritisSystemic autoimmune responseCertain autoimmune diseasesGnotobiotic mouse modelGut pathobiontSynovial inflammationAutoimmune responseAutoimmune diseasesMouse modelMonoclonal autoantibodiesArthritisGut commensalsHuman gut commensalAutoantibodiesOrigin hypothesisInflammationPathobiontsDiseaseSubdoligranulumCommensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites
Cao Y, Oh J, Xue M, Huh WJ, Wang J, Gonzalez-Hernandez JA, Rice TA, Martin AL, Song D, Crawford JM, Herzon SB, Palm NW. Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. Science 2022, 378: eabm3233. PMID: 36302024, PMCID: PMC9993714, DOI: 10.1126/science.abm3233.Peer-Reviewed Original ResearchConceptsColorectal cancerInflammatory bowel disease patientsBowel disease patientsInflammatory bowel diseaseIndigenous gut microbesBowel diseaseDisease patientsCommensal microbiotaDNA damageColon tumorigenesisElicit DNA damageGut microbesGenotoxic metabolitesGut commensalsMorganella morganiiPatientsGenotoxic chemicalsDiseaseMicrobiotaMetabolitesGenotoxicityCancerMiceFull spectrumDamageWithin-host evolution of a gut pathobiont facilitates liver translocation
Yang Y, Nguyen M, Khetrapal V, Sonnert ND, Martin AL, Chen H, Kriegel MA, Palm NW. Within-host evolution of a gut pathobiont facilitates liver translocation. Nature 2022, 607: 563-570. PMID: 35831502, PMCID: PMC9308686, DOI: 10.1038/s41586-022-04949-x.Peer-Reviewed Original ResearchConceptsHost evolutionGene expression programsCell wall structureNon-synonymous mutationsComparative genomicsIndependent lineagesExperimental evolutionExpression programsDivergent evolutionRegulatory genesBacterial behaviorCritical regulatorBacterial translocationGut commensalsTranslocationE. gallinarumMesenteric lymph nodesInitiation of inflammationImmune evasionWall structureEvade DetectionMucosal nicheLactobacillus reuteriCommensalGut microbiotaGut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins
Putnam EE, Abellon-Ruiz J, Killinger BJ, Rosnow JJ, Wexler AG, Folta-Stogniew E, Wright AT, van den Berg B, Goodman AL. Gut Commensal Bacteroidetes Encode a Novel Class of Vitamin B12-Binding Proteins. MBio 2022, 13: e02845-21. PMID: 35227073, PMCID: PMC8941943, DOI: 10.1128/mbio.02845-21.Peer-Reviewed Original ResearchConceptsComplex microbial communitiesHuman gut commensalTerminal globular domainModel organismsGut microbiomeMicrobial communitiesCompetitive fitnessTransport systemStructural homologsAccessory proteinsNew proteinsAdditional proteinsTransport proteinsGlobular domainUnknown functionMultiple transport systemsSystem lociKey roleGut commensalsProteinDiverse repertoireRelated moleculesMajor groupsFitnessOrganisms
2020
An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint
Ramanan D, Sefik E, Galván-Peña S, Wu M, Yang L, Yang Z, Kostic A, Golovkina T, Kasper D, Mathis D, Benoist C. An Immunologic Mode of Multigenerational Transmission Governs a Gut Treg Setpoint. Cell 2020, 181: 1276-1290.e13. PMID: 32402238, PMCID: PMC7393667, DOI: 10.1016/j.cell.2020.04.030.Peer-Reviewed Original ResearchConceptsDouble-negative feedback loopTreg proportionImmunological modeGut immune responseGut commensalsControlling gut inflammationSpecies levelInbred mouse strainsMulti-generational transmissionTreg-dependent mannerCellular perturbationsRegulatory T cellsDisease susceptibilityNon-epigeneticMaternal transmissionInflammatory disease susceptibilityNon-geneticGut inflammationT cellsGenetic tuningMouse strainsImmune responseMultiple generationsImmune systemFeedback loop
2019
Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity
Ruff WE, Dehner C, Kim WJ, Pagovich O, Aguiar CL, Yu AT, Roth AS, Vieira SM, Kriegel C, Adeniyi O, Mulla MJ, Abrahams VM, Kwok WW, Nussinov R, Erkan D, Goodman AL, Kriegel MA. Pathogenic Autoreactive T and B Cells Cross-React with Mimotopes Expressed by a Common Human Gut Commensal to Trigger Autoimmunity. Cell Host & Microbe 2019, 26: 100-113.e8. PMID: 31227334, PMCID: PMC8194364, DOI: 10.1016/j.chom.2019.05.003.Peer-Reviewed Original ResearchConceptsAntiphospholipid syndromePathogenic monoclonal antibodyHuman autoimmune diseasesGut commensalsB-cell autoepitopesHuman gut commensalGPI IgGAPS patientsIgG titersOral gavageMemory TSusceptible miceAntigenic loadAutoimmune diseasesAutoimmune pathologyTrigger autoimmunityHuman autoimmunityGlycoprotein IGPI autoantibodiesAutoimmunityMonoclonal antibodiesCell clonesCross reactMimotopesAutoantibodies
2018
Dietary sugar silences a colonization factor in a mammalian gut symbiont
Townsend GE, Han W, Schwalm ND, Raghavan V, Barry NA, Goodman AL, Groisman EA. Dietary sugar silences a colonization factor in a mammalian gut symbiont. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 116: 233-238. PMID: 30559205, PMCID: PMC6320540, DOI: 10.1073/pnas.1813780115.Peer-Reviewed Original ResearchCommensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus
Greiling TM, Dehner C, Chen X, Hughes K, Iñiguez AJ, Boccitto M, Ruiz DZ, Renfroe SC, Vieira SM, Ruff WE, Sim S, Kriegel C, Glanternik J, Chen X, Girardi M, Degnan P, Costenbader KH, Goodman AL, Wolin SL, Kriegel MA. Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus. Science Translational Medicine 2018, 10 PMID: 29593104, PMCID: PMC5918293, DOI: 10.1126/scitranslmed.aan2306.Peer-Reviewed Original ResearchConceptsLupus patientsGlomerular immune complex depositsPositive lupus patientsImmune complex depositsGerm-free miceSigns of autoimmunityB cell responsesT cell clonesNovel treatment approachesTriggers of autoimmunityCommensal bacterial speciesEarliest autoantibodiesChronic autoimmunityAutoimmune diseasesHealthy controlsT cellsTreatment approachesSusceptible individualsAutoimmunityCell responsesCommensal speciesLupusPatientsCell clonesGut commensals
2017
Autoantibody cross-reactivity with a microbial protein from a prevalent human gut commensal in antiphospholipid syndrome
ruff W, Roth A, Dehner C, Vieira S, Goodman A, Kriegel M. Autoantibody cross-reactivity with a microbial protein from a prevalent human gut commensal in antiphospholipid syndrome. The Journal Of Immunology 2017, 198: 58.4-58.4. DOI: 10.4049/jimmunol.198.supp.58.4.Peer-Reviewed Original ResearchAntiphospholipid syndromeAPS patientsGut commensalsBALB/cJ miceMajor B-cell epitopeGut commensal bacteriaAnti-B2GPI antibodiesB-cell epitopesInfectious triggerAutoantibody productionIgG autoantibodiesAntigenic sourceUnknown etiologyAutoantibody reactivityControl antibodyCell epitopesGut microbiotaCommensal bacteriaMajor autoantigenLow titersAutoantibodiesHuman stoolMonoclonal antibodiesVivo studiesPersistent stimulus
2016
Lupus T and B cell cross-reactivity between the human Ro60 autoantigen and Ro60 orthologs from the human microbiota
Greiling T, Dehner C, Renfroe S, Chen X, Vieira S, Ruff W, Goodman A, Wolin S, Kriegel M. Lupus T and B cell cross-reactivity between the human Ro60 autoantigen and Ro60 orthologs from the human microbiota. The Journal Of Immunology 2016, 196: 124.16-124.16. DOI: 10.4049/jimmunol.196.supp.124.16.Peer-Reviewed Original ResearchLupus patientsAnti-Ro60 antibodiesB cellsP. propionicumGerm-free miceGut commensalsHuman lupus patientsHuman microbiotaT cell clonesNovel therapeutic approachesSubset of skinAutoimmune TEarliest autoantibodiesLupus TRo60 antibodiesIgA antibodiesChronic autoimmunityMemory TSystemic autoimmunityHealthy controlsT cellsTherapeutic approachesPatientsSusceptible individualsAutoimmunityHuman 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
A common gut commensal as a cross-reactive candidate in antiphospholipid syndrome (HUM3P.250)
Dehner C, Ruff W, VIEIRA S, Goodman A, Kriegel M. A common gut commensal as a cross-reactive candidate in antiphospholipid syndrome (HUM3P.250). The Journal Of Immunology 2015, 194: 121.10-121.10. DOI: 10.4049/jimmunol.194.supp.121.10.Peer-Reviewed Original ResearchAntiphospholipid syndromeGut commensalsCD4 memory T cellsB-cell immunodominant epitopesWestern blottingIL-17 secretionMemory T cellsB cell responsesAdaptive immune responsesCommon gut commensalPatient plasma samplesAPS patientsIL-10IL-2IL-4T cellsImmune responseImmunodominant epitopesGut microbiotaTh1 clonesMajor autoantigenMolecular mimicryCell responsesPlasma samplesAntigenic potentialCross‐reactivity of Gut Commensals and Autoantigen in Antiphospholipid Syndrome
Dehner C, Ruff W, Vieira S, Goodman A, Kriegel M. Cross‐reactivity of Gut Commensals and Autoantigen in Antiphospholipid Syndrome. The FASEB Journal 2015, 29 DOI: 10.1096/fasebj.29.1_supplement.142.4.Peer-Reviewed Original ResearchAntiphospholipid syndromeMemory T cellsAutoimmune disease modelsGut commensalsAdaptive immune responsesB cell reactivityB-cell epitopesPatient plasma samplesAPS pathogenesisAPS patientsPatient PBMCsUnknown etiologyCell reactivityControl subjectsT cellsImmune responseCell epitopesT cell librariesB cellsGut microbiotaWestern blot experimentsWestern blottingHuman autoantigensDisease modelsPlasma samples
2014
Diet, microbiota and autoimmune diseases
Vieira S, Pagovich O, Kriegel M. Diet, microbiota and autoimmune diseases. Lupus 2014, 23: 518-526. PMID: 24763536, PMCID: PMC4009622, DOI: 10.1177/0961203313501401.Peer-Reviewed Original ResearchConceptsAutoimmune diseasesGut microbial communityGerm-free mouse modelDevelopment of autoimmunityDiet-derived metabolitesType 1 diabetesSeverity of diseaseLife-prolonging effectAdaptive immune systemAntiphospholipid syndromeAutoimmune modelSystemic lupusMultiple sclerosisGastrointestinal tractMurine modelMouse modelRodent modelsImmunomodulatory potentialCommensal bacteriaImmune systemCaloric restrictionGut microbiomeDietary changesLupusGut commensals
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
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