2024
Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles
Chang D, Gupta V, Hur B, Cobo-López S, Cunningham K, Han N, Lee I, Kronzer V, Teigen L, Karnatovskaia L, Longbrake E, Davis J, Nelson H, Sung J. Gut Microbiome Wellness Index 2 enhances health status prediction from gut microbiome taxonomic profiles. Nature Communications 2024, 15: 7447. PMID: 39198444, PMCID: PMC11358288, DOI: 10.1038/s41467-024-51651-9.Peer-Reviewed Original ResearchConceptsMicrobiome taxonomic profilingTaxonomic profilesOpen-source command-line toolGut microbiome researchGut microbial compositionGut microbiome signaturesFecal microbiota transplantationCommand-line toolShotgun metagenomicsTaxonomic signalMicrobiome researchMicrobial compositionMicrobiome signaturesGut healthMicrobiota transplantationGutPublished datasetsMultiple diseasesAntibiotic exposureEffects of dietMetagenomicsHigh confidencePhenotypeCross-validated balanced accuracyImpact of Latino ethnicity on the gut microbiome composition of patients with metastatic renal cell cancer (mRCC).
Barragán Carrillo R, Dizman N, Ebrahimi H, Meza L, Bergerot P, Dorff T, Hsu J, Zengin Z, Salgia N, Chehrazi-Raffle A, Tripathi A, Castro D, Mercier B, Caporaso G, Lee K, Pal S. Impact of Latino ethnicity on the gut microbiome composition of patients with metastatic renal cell cancer (mRCC). Journal Of Clinical Oncology 2024, 42: 4521-4521. DOI: 10.1200/jco.2024.42.16_suppl.4521.Peer-Reviewed Original ResearchMetastatic renal cell cancerImmune checkpoint inhibitionGut microbiome compositionBeta diversityBacterial speciesANCOM-BCAbundance of bacterial speciesWhole metagenome sequencingF/B ratioRatio of Firmicutes/BacteroidetesStool specimensShannon diversity indexR. inulinivoransE. rectaleRenal cell cancerTaxonomic profilesMetagenomic sequencingAlpha diversityGut microbiotaGut microbiomeMicrobiome compositionBray-CurtisDiversity indexComposition of patientsGut dysbiosisEvolution of the functionality of microbial communities in patients with metastatic renal cell carcinoma (mRCC) receiving cabozantinib (cabo)/nivolumab (nivo) with or without CBM588: A randomized clinical trial.
Ebrahimi H, Meza L, Lee K, Malhotra J, Alcantara M, Zengin Z, Dizman N, Hsu J, Llamas-Quitiquit M, Castro D, Mercier B, Barragan-Carrillo R, Chawla N, Li X, Liu S, Chehrazi-Raffle A, Dorff T, Frankel P, Tripathi A, Pal S. Evolution of the functionality of microbial communities in patients with metastatic renal cell carcinoma (mRCC) receiving cabozantinib (cabo)/nivolumab (nivo) with or without CBM588: A randomized clinical trial. Journal Of Clinical Oncology 2024, 42: 460-460. DOI: 10.1200/jco.2024.42.4_suppl.460.Peer-Reviewed Original ResearchMetastatic renal cell carcinomaMetabolic pathwaysClinical outcomesAnnotated open reading framesFunction of microbial communitiesMetatranscriptomic sequencing dataWhole metagenome sequencingOpen reading frameGut microbial functionsGut microbiome functionsResponse rate to sorafenibExperimental armElectron transfer chainCancer cell typesAssociated with clinical outcomesRenal cell carcinomaReading frameSequence dataTaxonomic profilesBiosynthesis pathwayMetagenomic sequencingMicrobiome functionMicrobial functionsMolecular functionsRandomized clinical trials
2012
Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability
Filkins L, Hampton T, Gifford A, Gross M, Hogan D, Sogin M, Morrison H, Paster B, O'Toole G. Prevalence of Streptococci and Increased Polymicrobial Diversity Associated with Cystic Fibrosis Patient Stability. Journal Of Bacteriology 2012, 194: 4709-4717. PMID: 22753064, PMCID: PMC3415522, DOI: 10.1128/jb.00566-12.Peer-Reviewed Original ResearchConceptsDiverse microbial communitiesHigher bacterial diversityCystic fibrosis lung environmentQuantitative PCRGenomic DNA samplesCystic fibrosis patientsMicrobial communitiesRRNA geneBacterial communitiesBacterial diversityOverall diversityTaxonomic profilesGroup speciesMicroarray analysisDominant organismsPseudomonas aeruginosaPatient stabilityPredominant generaFibrosis patientsSpeciesHypervariable regionSpecies of StreptococcusCurrent dogmaStable lung diseaseDiversityA framework for human microbiome research
Methé B, Nelson K, Pop M, Creasy H, Giglio M, Huttenhower C, Gevers D, Petrosino J, Abubucker S, Badger J, Chinwalla A, Earl A, FitzGerald M, Fulton R, Hallsworth-Pepin K, Lobos E, Madupu R, Magrini V, Martin J, Mitreva M, Muzny D, Sodergren E, Versalovic J, Wollam A, Worley K, Wortman J, Young S, Zeng Q, Aagaard K, Abolude O, Allen-Vercoe E, Alm E, Alvarado L, Andersen G, Anderson S, Appelbaum E, Arachchi H, Armitage G, Arze C, Ayvaz T, Baker C, Begg L, Belachew T, Bhonagiri V, Bihan M, Blaser M, Bloom T, Bonazzi V, Brooks P, Buck G, Buhay C, Busam D, Campbell J, Canon S, Cantarel B, Chain P, Chen I, Chen L, Chhibba S, Chu K, Ciulla D, Clemente J, Clifton S, Conlan S, Crabtree J, Cutting M, Davidovics N, Davis C, DeSantis T, Deal C, Delehaunty K, Dewhirst F, Deych E, Ding Y, Dooling D, Dugan S, Dunne W, Durkin A, Edgar R, Erlich R, Farmer C, Farrell R, Faust K, Feldgarden M, Felix V, Fisher S, Fodor A, Forney L, Foster L, Di Francesco V, Friedman J, Friedrich D, Fronick C, Fulton L, Gao H, Garcia N, Giannoukos G, Giblin C, Giovanni M, Goldberg J, Goll J, Gonzalez A, Griggs A, Gujja S, Haas B, Hamilton H, Harris E, Hepburn T, Herter B, Hoffmann D, Holder M, Howarth C, Huang K, Huse S, Izard J, Jansson J, Jiang H, Jordan C, Joshi V, Katancik J, Keitel W, Kelley S, Kells C, Kinder-Haake S, King N, Knight R, Knights D, Kong H, Koren O, Koren S, Kota K, Kovar C, Kyrpides N, La Rosa P, Lee S, Lemon K, Lennon N, Lewis C, Lewis L, Ley R, Li K, Liolios K, Liu B, Liu Y, Lo C, Lozupone C, Lunsford R, Madden T, Mahurkar A, Mannon P, Mardis E, Markowitz V, Mavrommatis K, McCorrison J, McDonald D, McEwen J, McGuire A, McInnes P, Mehta T, Mihindukulasuriya K, Miller J, Minx P, Newsham I, Nusbaum C, O’Laughlin M, Orvis J, Pagani I, Palaniappan K, Patel S, Pearson M, Peterson J, Podar M, Pohl C, Pollard K, Priest M, Proctor L, Qin X, Raes J, Ravel J, Reid J, Rho M, Rhodes R, Riehle K, Rivera M, Rodriguez-Mueller B, Rogers Y, Ross M, Russ C, Sanka R, Sankar P, Sathirapongsasuti J, Schloss J, Schloss P, Schmidt T, Scholz M, Schriml L, Schubert A, Segata N, Segre J, Shannon W, Sharp R, Sharpton T, Shenoy N, Sheth N, Simone G, Singh I, Smillie C, Sobel J, Sommer D, Spicer P, Sutton G, Sykes S, Tabbaa D, Thiagarajan M, Tomlinson C, Torralba M, Treangen T, Truty R, Vishnivetskaya T, Walker J, Wang L, Wang Z, Ward D, Warren W, Watson M, Wellington C, Wetterstrand K, White J, Wilczek-Boney K, Wu Y, Wylie K, Wylie T, Yandava C, Ye L, Ye Y, Yooseph S, Youmans B, Zhang L, Zhou Y, Zhu Y, Zoloth L, Zucker J, Birren B, Gibbs R, Highlander S, Weinstock G, Wilson R, White O. A framework for human microbiome research. Nature 2012, 486: 215-221. PMID: 22699610, PMCID: PMC3377744, DOI: 10.1038/nature11209.Peer-Reviewed Original ResearchConceptsHigh-throughput metagenomic dataRibosomal RNA genesMicrobial taxonomic profilesHuman microbiome researchMetagenomic dataRNA genesTaxonomic profilesMetagenomic sequencingMetagenomics protocolHuman microbiomeMicrobiome researchMicrobial communitiesMicrobiomeGenesDistinct typesBody sitesSequenceHuman healthProject consortiumAbundanceStrain
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply