2025
Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease
Yang Y, Duan Y, Lang S, Fondevila M, Schöler D, Harberts A, Cabré N, Chen S, Shao Y, Vervier K, Miyamoto Y, Zhang X, Chu H, Yang L, Tan C, Eckmann L, Bosques-Padilla F, Verna E, Abraldes J, Brown R, Vargas V, Altamirano J, Caballería J, Shawcross D, Louvet A, Lucey M, Mathurin P, Garcia-Tsao G, Bataller R, Stärkel P, Lawley T, Schnabl B. Targeted inhibition of pathobiont virulence factor mitigates alcohol-associated liver disease. Cell Host & Microbe 2025, 33: 957-972.e6. PMID: 40441146, PMCID: PMC12162233, DOI: 10.1016/j.chom.2025.05.003.Peer-Reviewed Original ResearchConceptsEthanol-induced liver diseaseAlcohol-associated liver diseaseAlcohol-associated hepatitisLiver diseaseGenome of Escherichia coliE. coliMetagenomic sequencing of fecal samplesInternational cohort of patientsGenetic manipulation of bacteriaGnotobiotic mouse modelOutcomes of patientsManipulation of bacteriaCohort of patientsScavenger receptor MARCOGlobal health burdenVirulence factorsMetagenomic sequencingGut microbiotaGenetic manipulationDisease progressionMouse modelKupffer cellsKpsMBacterial spreadInternational cohortIndole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming
Zhou S, Wang K, Huang J, Xu Z, Yuan Q, Liu L, Wang Z, Miao J, Wang H, Wang T, Guan W, Ding C. Indole-3-lactic acid suppresses colorectal cancer via metabolic reprogramming. Gut Microbes 2025, 17: 2508949. PMID: 40409349, PMCID: PMC12118437, DOI: 10.1080/19490976.2025.2508949.Peer-Reviewed Original ResearchConceptsIndole-3-lactic acidColorectal cancer patientsColorectal cancerAryl hydrocarbon receptorDownregulated glucose metabolismPotential clinical therapeutic targetsAnti-apoptotic capabilityInfluence tumor progressionGut microbiota metabolismTumor cell proliferationMetagenomic sequencingPhosphorylation sitesXenograft mouse modelGut microbiotaClinical therapeutic targetMetabolic reprogrammingMicrobiota metabolismP-STAT3Tumor progressionTumor malignancyMouse modelTryptophan metabolismCancer cellsIn vitro experimentsCRC developmentRapid Metagenomic Sequencing (RaMSes) of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients with Hematologic Malignancies and Pulmonary Complications
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Shlomchik W, Methé B, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing (RaMSes) of Bronchoalveolar Lavage Fluid for Diagnosis of Infection in Patients with Hematologic Malignancies and Pulmonary Complications. CHEST Pulmonary 2025, 100173. DOI: 10.1016/j.chpulm.2025.100173.Peer-Reviewed Original ResearchPulmonary complicationsHematologic malignanciesRespiratory pathogensCulture-independent sequencing approachesDetection of fungal pathogensNon-infectious pulmonary complicationsSuspected lower respiratory tract infectionLower respiratory tract infectionsCulture-independent sequencing methodsRespiratory tract infectionsBronchoalveolar lavage fluidDiagnosis of infectionEmpirical antimicrobialsPCR-based testsTract infectionsFungal pathogensMetagenomic sequencingClinical manifestationsSequencing approachLavage fluidMicrobial communitiesCohort studySequencing methodsPatientsComplications
2024
Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes
Peng X, Li S, Dou W, Li M, Gontcharov A, Peng Z, Qi B, Wang Q, Li Y. Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes. Microorganisms 2024, 12: 2540. PMID: 39770743, PMCID: PMC11677963, DOI: 10.3390/microorganisms12122540.Peer-Reviewed Original ResearchCommunity compositionMicrobial functional profilesHost-specific selectionMicrobial community compositionCharacteristics of microbiotaCulture-based studiesSpecies of bacteriaBacteria community compositionPhagocytosis of bacteriaFunctional traitsMetagenomic sequencingMyxomycete speciesAssociated microbiomeAmplicon sequencingFunctional redundancyMetagenomic insightsMicrobial communitiesMyxomycetesSpecies-specificBacteria speciesDominant bacteriaBacteriaFunctional roleFunctional analysisPlasmodiaA virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon
Petrone M, Charon J, Grigg M, William T, Rajahram G, Westaway J, Piera K, Shi M, Anstey N, Holmes E. A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon. Virus Evolution 2024, 10: veae091. PMID: 39619416, PMCID: PMC11605544, DOI: 10.1093/ve/veae091.Peer-Reviewed Original ResearchViral taxaRNA virusesAnalysis of metagenomic dataPlasmodium speciesSingle-celled eukaryotesHuman-infecting Plasmodium speciesPathogen life cycleGenome architectureGroup of virusesMetagenomic dataMetagenomic sequencingDisease-causingVirus discoveryTaxaViral diversityParasite PlasmodiumRNAInfecting protozoaPlasmodium knowlesiViromeHuman malariaParasite fitnessSpeciesApicomplexaInfect humansImpact 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 dysbiosisRapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy
Hensley M, Sayed K, Haidar G, Wang X, Benos P, Ito S, Im A, Geramita E, Dela Cruz C, Morris A, Kitsios G. Rapid Metagenomic Sequencing (RaMSes) for Comprehensive Detection of Respiratory Pathogens in Patients With Hematologic Malignancy. 2024, a2915-a2915. DOI: 10.1164/ajrccm-conference.2024.209.1_meetingabstracts.a2915.Peer-Reviewed Original ResearchMetagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice
Chen H, Huang S, Zhao Y, Sun R, Wang J, Yao S, Huang J, Yu Z. Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice. Microbiology Spectrum 2024, 12: e03735-23. PMID: 38441977, PMCID: PMC10986500, DOI: 10.1128/spectrum.03735-23.Peer-Reviewed Original ResearchConceptsTaxonomic compositionGut microbiomeIntestinal microbiomeFunctional genesKEGG OrthologyMetagenomic analysisIntestinal microbiotaRegulatory mechanismsFunction of gut microbiomeComposition of gut microbiotaAbundance of functional genesMetagenomic sequencingGene functionGut microbiotaPotential regulatory mechanismSpecies levelIntervention of probioticsBacillus amyloliquefaciensMicrobiomeGenesMicrobiotaHost immune responseProbiotic interventionMetabolic reactionsSchistosoma japonicum</i>Gut Microbiome of Patients With Breast Cancer in Vietnam
Nguyen S, Tran H, Long J, Shrubsole M, Cai H, Yang Y, Nguyen L, Nguyen G, Nguyen C, Ta T, Wu J, Cai Q, Zheng W, Tran T, Shu X. Gut Microbiome of Patients With Breast Cancer in Vietnam. JCO Global Oncology 2024, 10: e2300234. PMID: 38359370, PMCID: PMC10881109, DOI: 10.1200/go.23.00234.Peer-Reviewed Original ResearchConceptsGut microbiome health indexGut microbiomeTaxa abundanceA-diversityUnhealthy gut microbiomeGut microbiome of patientsStool samplesShotgun metagenomic sequencingGut microbial diversityAbundance of speciesBreast cancerMicrobiome of patientsMetagenomic sequencingInvestigated taxaGut microbiotaB-diversityMicrobial diversityDiagnosis delayDecreased abundanceIncreased abundanceMicrobiomeHigher intake of fiberGutIntake of fiberTaxaEvolution 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
2022
Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease
Liang T, Li D, Zunong J, Li M, Amaerjiang N, Xiao H, Khattab N, Vermund S, Hu Y. Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease. Nutrients 2022, 14: 4641. PMID: 36364902, PMCID: PMC9657134, DOI: 10.3390/nu14214641.Peer-Reviewed Original ResearchConceptsNonalcoholic fatty liver diseaseFatty liver diseaseHigher lymphocyte countsLymphocyte countGut microbiotaLiver diseaseHealthy childrenGut microbiota dysbiosisEffect of lymphocytesProinflammatory bacteriaMicrobiota dysbiosisRisk factorsIntestinal microbiotaAbundance of BacteroidetesLymphocytesMicrobiotaChildrenOpportunistic pathogenDiseaseCountMetagenomic sequencingLow numberHigher numberDysbiosisGroupSeasonal Dynamics of Mosquito-Borne Viruses in the Southwestern Florida Everglades, 2016, 2017.
Anderson J, Fish D, Armstrong P, Misencik M, Bransfield A, Ferrandino F, Andreadis T, Stenglein M, Kapuscinski M. Seasonal Dynamics of Mosquito-Borne Viruses in the Southwestern Florida Everglades, 2016, 2017. American Journal Of Tropical Medicine And Hygiene 2022, 106: 610-622. PMID: 35008051, PMCID: PMC8832897, DOI: 10.4269/ajtmh.20-1547.Peer-Reviewed Original ResearchConceptsSpecies of virusesSpecies of mosquitoesGumbo LimboShotgun metagenomic sequencingShark RiverSpecies complexWest Nile virusHardwood hammocksEverglades virusNotable speciesMosquito-Borne VirusesMetagenomic sequencingAnopheles speciesNile virusSeasonal dynamicsSpeciesFlorida EvergladesTensaw virusCulex nigripalpusEvergladesPools of CxCypress swampsNigripalpusMosquitoesAnopheles cruciansMetagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus
Keeler E, Vukmirovic M, Yan X, Gulino K, Ghedin E, Kaminski N, Sullivan K, Bushman F, Collman R, Rosenbach M. Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus. Sarcoidosis, Vasculitis, And Diffuse Lung Diseases 2022, 39: e2022040. PMID: 36533601, PMCID: PMC9798337, DOI: 10.36141/svdld.v39i4.13407.Peer-Reviewed Original ResearchSarcoidosis patientsRubella virusBronchoalveolar lavageMultisystem granulomatous inflammatory diseaseImmune-competent patientsRubella virus infectionGranulomatous inflammatory diseaseCutaneous sarcoidosisAntigenic triggerBAL cellsUnclear etiologyRubella virus genomeInflammatory diseasesCutaneous granulomasGranulomatous lesionsVirus infectionVirus gene expressionLung samplesAcellular fluidCompetent patientsPatientsSarcoidosisOverlapping featuresMetagenomic sequencingVirus
2021
CHARACTERIZING REPRODUCTIVE TRACT MICROBIOME THROUGH SHOTGUN METAGENOMIC SEQUENCING AT TIME OF IVF, A PILOT STUDY
Bardos J, O'Connor G, Karipcin F, DeCherney A, Hill M, Daunert S, Hernendez-Reys A, Paidas M. CHARACTERIZING REPRODUCTIVE TRACT MICROBIOME THROUGH SHOTGUN METAGENOMIC SEQUENCING AT TIME OF IVF, A PILOT STUDY. Fertility And Sterility 2021, 116: e112. DOI: 10.1016/j.fertnstert.2021.07.314.Peer-Reviewed Original ResearchTime of IVFReproductive tractPilot studyShotgun metagenomic sequencingMetagenomic sequencingIVFTractLung microbiome alterations in NSCLC patients
Zheng L, Sun R, Zhu Y, Li Z, She X, Jian X, Yu F, Deng X, Sai B, Wang L, Zhou W, Wu M, Li G, Tang J, Jia W, Xiang J. Lung microbiome alterations in NSCLC patients. Scientific Reports 2021, 11: 11736. PMID: 34083661, PMCID: PMC8175694, DOI: 10.1038/s41598-021-91195-2.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerNon-small cell lung cancer patientsRare speciesOral taxaLung microbiotaDiverse array of microbesNon-cancer controlsLobectomy samplesArray of microbesGlobal microbial compositionAssociated with lung cancer progressionLung cancerLung microbiome compositionBronchoscopy samplesPseudomonas entomophilaMetagenomic sequencingBronchoalveolar lavageLactobacillus rossiaeBacteroides pyogenesMicrobiota dysbiosisMicrobial communitiesMicrobiome compositionPaenibacillus odoriferMicrobial compositionLung microbiota dysbiosis
2020
The Problem of Microbial Dark Matter in Neonatal Sepsis - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC
Sinnar S, Schiff S. The Problem of Microbial Dark Matter in Neonatal Sepsis - Volume 26, Number 11—November 2020 - Emerging Infectious Diseases journal - CDC. Emerging Infectious Diseases 2020, 26: 2543-2548. PMID: 33080169, PMCID: PMC7588532, DOI: 10.3201/eid2611.200004.Peer-Reviewed Original ResearchConceptsNeonatal sepsisCausative pathogenInfectious Diseases journal - CDCCulture recovery ratesAntimicrobial therapyBlood culturesTimely diagnosisAntimicrobial stewardshipWorldwide deathsMost blood culturesUnidentified pathogensTransmission patternsDeathPathogen discoveryWhole metagenomic sequencingPathogensEffective diagnosticsMetagenomic sequencingSepsisPatientsInfantsTherapyDiagnosisRecovery rate
2018
Discovering antibiotics from the global microbiome
Lam YC, Crawford JM. Discovering antibiotics from the global microbiome. Nature Microbiology 2018, 3: 392-393. PMID: 29588534, DOI: 10.1038/s41564-018-0135-5.Peer-Reviewed Original Research
2012
A 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
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