2024
A host–microbiota interactome reveals extensive transkingdom connectivity
Sonnert N, Rosen C, Ghazi A, Franzosa E, Duncan-Lowey B, González-Hernández J, Huck J, Yang Y, Dai Y, Rice T, Nguyen M, Song D, Cao Y, Martin A, Bielecka A, Fischer S, Guan C, Oh J, Huttenhower C, Ring A, Palm N. A host–microbiota interactome reveals extensive transkingdom connectivity. Nature 2024, 628: 171-179. PMID: 38509360, DOI: 10.1038/s41586-024-07162-0.Peer-Reviewed Original ResearchNiche colonizationHost–microorganism interactionsHost-microbiota interactionsInvade host tissuesStrain-specific interactionsHost cells in vitroConspecific strainsEffect of indigenous microorganismsHost biologyHost proteinsSecreted proteinsCommensal microorganismsExoproteinsBacterial strainsDiverse phylogenyMolecular basisMyriad microorganismsTissue of originTissue isolationCells in vitroInteractomeBinding patternsHost tissuesBiological logicHost immune system in vivo
2022
Commensal 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 spectrumDamageInterspecies commensal interactions have nonlinear impacts on host immunity
Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW. Interspecies commensal interactions have nonlinear impacts on host immunity. Cell Host & Microbe 2022, 30: 988-1002.e6. PMID: 35640610, PMCID: PMC9283318, DOI: 10.1016/j.chom.2022.05.004.Peer-Reviewed Original ResearchConceptsImmunological outcomesCell activationIntestinal epithelial cell activationInflammatory bowel disease patientsBowel disease patientsDendritic cell activationMesenteric lymph nodesSystemic antibody responsesEpithelial cell activationImmunological milieuLymph nodesAntibody responseDisease patientsAkkermansia muciniphilaGnotobiotic miceHost immunityCommensal microbesHuman cohortsHuman gut bacteriaGut bacteriaMiceAllobaculumMuciniphilaDiseaseIncomplete penetrance
2020
Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition
Chen JW, Rice TA, Bannock JM, Bielecka AA, Strauss JD, Catanzaro JR, Wang H, Menard LC, Anolik JH, Palm NW, Meffre E. Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition. Science 2020, 369: 320-325. PMID: 32675374, DOI: 10.1126/science.aay9733.Peer-Reviewed Original ResearchConceptsB cell toleranceB cellsCell toleranceEarly human fetal lifeHuman fetal B cellsPolyreactive B cellsHuman fetal lifeApoptotic cellsFetal B cellsHuman fetal liverB cell specificitySingle B cellsAbundant autoantibodiesGut microbiota assemblyNewborn seraFetal lifeBone marrowFetal developmentHealthy adultsCommensal bacteriaRepertoire breadthMicrobiota assemblyFetal liverPreimmune repertoireCell specificityEnteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity
Jarret A, Jackson R, Duizer C, Healy ME, Zhao J, Rone JM, Bielecki P, Sefik E, Roulis M, Rice T, Sivanathan KN, Zhou T, Solis AG, Honcharova-Biletska H, Vélez K, Hartner S, Low JS, Qu R, de Zoete MR, Palm NW, Ring AM, Weber A, Moor AE, Kluger Y, Nowarski R, Flavell RA. Enteric Nervous System-Derived IL-18 Orchestrates Mucosal Barrier Immunity. Cell 2020, 180: 50-63.e12. PMID: 31923399, PMCID: PMC7339937, DOI: 10.1016/j.cell.2019.12.016.Peer-Reviewed Original ResearchConceptsEnteric nervous systemSingle-cell sequencingMucosal barrier immunitySingle-molecule fluorescenceIL-18Non-redundant roleSitu mRNA hybridization studiesEpithelial cellsUnbiased RNA sequencingRNA sequencingProtein responseBarrier immunityNervous systemConfocal microscopyCytokine IL-18Hybridization studiesInvasive bacterial infectionsSalmonella typhimurium infectionSequencingProfound consequencesIntestinal neuronsEnteric neuronsIntestinal immunityMucosal barrierTyphimurium infection
2016
Signaling via pattern recognition receptors NOD2 and TLR2 contributes to immunomodulatory control of lethal pneumovirus infection.
Rice TA, Brenner TA, Percopo CM, Ma M, Keicher JD, Domachowske JB, Rosenberg HF. Signaling via pattern recognition receptors NOD2 and TLR2 contributes to immunomodulatory control of lethal pneumovirus infection. Antiviral Res 2016, 132: 131-40. PMID: 27312104, DOI: 10.1016/j.antiviral.2016.06.002.Peer-Reviewed Original Research