2025
Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model
Ashton P, Mageiros L, Meiring J, Chunga-Chirambo A, Khanam F, Dongol S, Banda H, Karkey A, Preciado-Llanes L, Thomaides-Brears H, Gibani M, Rajib N, Rahman N, Biswas P, Bhuiyan M, Kay S, Auger K, Seret O, Thomson N, Pollard A, Baker S, Basnyat B, Clemens J, Dolecek C, Dunstan S, Dougan G, Heyderman R, Pitzer V, Qadri F, Gordon M, Holt K, Darton T. Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model. Microbiome 2025, 13: 168. PMID: 40696437, PMCID: PMC12281769, DOI: 10.1186/s40168-025-02125-7.Peer-Reviewed Original ResearchConceptsMetabolic gene clustersShort-chain fatty acidsTyphoid fever patientsS. typhiGut microbiomeTyphoid feverShort-chain fatty acid metabolismInfection modelAsymptomatic household contactsHuman infection modelPotential functional roleGene clusterShotgun metagenomicsInvasive SalmonellaFever patientsBacterial diversityMicrobiota characteristicsAssociated with typhoid feverBackgroundTyphoid feverStool microbiomeBacterial speciesClade ADevelopment of clinical infectionSCFA metabolismIngestion of contaminated food
2024
Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis
Tang H, Du S, Niu Z, Zhang D, Tang Z, Chen H, Chen Z, Zhang M, Xu Y, Sun Y, Fu X, Norback D, Shao J, Zhao Z. Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis. BMC Microbiology 2024, 24: 505. PMID: 39614169, PMCID: PMC11606197, DOI: 10.1186/s12866-024-03668-9.Peer-Reviewed Original ResearchConceptsSpecies levelBacterial speciesAR childrenNasal cavityMethodsIn this case–control studyBody sitesControl groupBacterial diversityCase-control studyB-diversityOral swab samplesS. epidermidisStaphylococcus epidermidisStaphylococcus aureusBacterial characterizationMicrobesAllergic rhinitisSpeciesHealthy subjectsBackgroundAllergic rhinitisSwab samplesHealthy onesConclusionsOur studyMicroorganismsRhinitis
2023
Association between intra-tumoral microbiome and clinical benefit (CB) from immunotherapy (IO) in patients with metastatic renal cell carcinoma (mRCC).
Meza L, Choi Y, Zhang J, Dizman N, Zengin Z, Ebrahimi H, Barragan-Carrillo R, Hsu J, Chawla N, Chehrazi-Raffle A, Tripathi A, Castro D, Mercier B, Govindarajan A, Chan A, Schork N, Byron S, Pal S. Association between intra-tumoral microbiome and clinical benefit (CB) from immunotherapy (IO) in patients with metastatic renal cell carcinoma (mRCC). Journal Of Clinical Oncology 2023, 41: 4561-4561. DOI: 10.1200/jco.2023.41.16_suppl.4561.Peer-Reviewed Original ResearchMetastatic renal cell carcinomaClinical benefitLine immunotherapyMicrobial diversityNivolumab/ipilimumabStart of immunotherapyBacterial diversityClear cell histologyPD-L1 expressionRenal cell carcinomaRelative abundanceAvailable RNA sequencing dataRelative microbial abundanceParaffin-embedded samplesRNA sequencing dataRNA-seq readsCell histologyCommon regimenMedian ageLine treatmentCell carcinomaPoor riskShannon diversity indexRCC tumorsImmunotherapyExperimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation
Burmeister A, Tzintzun-Tapia E, Roush C, Mangal I, Barahman R, Bjornson R, Turner P. Experimental Evolution of the TolC-Receptor Phage U136B Functionally Identifies a Tail Fiber Protein Involved in Adsorption through Strong Parallel Adaptation. Applied And Environmental Microbiology 2023, 89: e00079-23. PMID: 37191555, PMCID: PMC10304864, DOI: 10.1128/aem.00079-23.Peer-Reviewed Original ResearchConceptsExperimental evolutionPhage populationsParallel molecular evolutionWhole-population sequencingAntibiotic resistance proteinsTail fiber proteinE. coli hostPhage evolutionEvolutionary potentialMolecular evolutionPhage genotypesTolC proteinParallel adaptationProtein geneAntibiotic resistanceExperimental populationsBacterial diversitySelection pressureBacterial hostsColi hostFiber proteinBacterial populationsBacterial cellsPhage resistancePhage dynamics
2022
Diversity of bacterial communities in the plasmodia of myxomycetes
Li S, Qi B, Wang W, Peng X, Gontcharov A, Liu B, Wang Q, Li Y. Diversity of bacterial communities in the plasmodia of myxomycetes. BMC Microbiology 2022, 22: 314. PMID: 36544088, PMCID: PMC9773492, DOI: 10.1186/s12866-022-02725-5.Peer-Reviewed Original ResearchConceptsOperational taxonomic unitsBacterial communitiesBacterial operational taxonomic unitsDiversity of bacterial communitiesGroups of eukaryotesFruiting body stageBacterial community compositionCommunity functional compositionResultsThe bacterial communityRRNA amplicon sequencingAssociated with bacteriaDistinctive life cycleTaxonomic unitsMyxomycete speciesCommunity compositionAmplicon sequencingBacterial diversityUnique bacteriaBacteria diversityDominant phylaMyxomycetesGram-negativeMyxomycete plasmodiaBacteriaFunctional composition
2020
Predicting BPD: Lessons Learned From the Airway Microbiome of Preterm Infants
Gentle S, Lal C. Predicting BPD: Lessons Learned From the Airway Microbiome of Preterm Infants. Frontiers In Pediatrics 2020, 7: 564. PMID: 32117822, PMCID: PMC7011099, DOI: 10.3389/fped.2019.00564.Peer-Reviewed Original ResearchBronchopulmonary dysplasiaPreterm infantsAirway microbiomeChronic lung disease of prematurityLung disease of prematurityDiagnosis of bronchopulmonary dysplasiaPrediction of bronchopulmonary dysplasiaMicrobiome-mediated therapeuticsDisease of prematurityBronchopulmonary dysplasia developmentChronic lung diseaseAirways of newbornsHost immune systemTime of birthSystems biology approachBPD developmentClinical phenotypeMultifactorial etiologyAirwayImmune systemBacterial diversityInfantsMicrobiome signaturesBiology approachLow biomass
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 diseaseDiversity
2008
Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics
Koeppel A, Perry E, Sikorski J, Krizanc D, Warner A, Ward D, Rooney A, Brambilla E, Connor N, Ratcliff R, Nevo E, Cohan F. Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 2504-2509. PMID: 18272490, PMCID: PMC2268166, DOI: 10.1073/pnas.0712205105.Peer-Reviewed Original ResearchConceptsBacterial systematicsNatural communitiesSequence-based approachesEvolution CanyonBacterial domainEcotype SimulationSuch ecotypesMicrobial ecologyDistinct lineagesMultiple ecotypesEvolutionary dynamicsBacterial diversityDifferent solar exposureTraditional speciesBacterial populationsBacterial ecologyEcotypesBacterial cellsEcologyDistinct rolesSystematicsFundamental unitDiverse setCladeLineages
2007
A Systematics for Discovering the Fundamental Units of Bacterial Diversity
Cohan F, Perry E. A Systematics for Discovering the Fundamental Units of Bacterial Diversity. Current Biology 2007, 17: r373-r386. PMID: 17502094, DOI: 10.1016/j.cub.2007.03.032.Peer-Reviewed Original ResearchConceptsBacterial diversityHistory of coexistenceBacterial evolutionBacterial systematistsMicrobial worldSpecies unitsBacterial systematicsEvolutionary dynamicsDNA sequencesBiological diversityFundamental unitTremendous diversitySequence clustersBacterial speciesEvolutionary propertiesEvolutionary theoryMolecular techniquesDiversitySpeciesSystematistsDistinct groupsSystematicsPlantsSequenceMicrobiologists
2006
Identifying the Fundamental Units of Diversity Among Bacillus Isolates From "Evolution Canyon" III
Perry E, Koeppel A, Krizanc D, Rooney A, Sikorski J, Nevo E, Cohan F. Identifying the Fundamental Units of Diversity Among Bacillus Isolates From "Evolution Canyon" III. Israel Journal Of Ecology And Evolution 2006, 52: 543-552. DOI: 10.1560/ijee_52_3-4_543.Peer-Reviewed Original ResearchBacterial systematicsEvolution CanyonDistinct populationsSequence diversity patternsDNA sequence diversityLineage-specific ratesSingle bacterial speciesEcological distinctnessFundamental unitPutative ecotypesMicrobial ecologistsDiversity patternsDistinct lineagesEcological diversityDifferent microhabitatsSequence evolutionSequence dataSequence diversityBacterial diversityCladeSequence clustersBacterial speciesBacillus subtilisBacillus isolatesEvolutionary simulations
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