2024
Lubricating gel influence on vaginal microbiome sampling
Amitai Komem D, Hadar R, Paulson J, Mordechai Y, Eskandarian H, Efroni G, Amir A, Haberman Y, Tsur A. Lubricating gel influence on vaginal microbiome sampling. Scientific Reports 2024, 14: 18223. PMID: 39107405, PMCID: PMC11303677, DOI: 10.1038/s41598-024-68948-w.Peer-Reviewed Original ResearchConceptsMicrobial compositionVaginal samplesVaginal microbiome samplesBeta diversityVaginal microbiome studiesMicrobiome studiesMicrobiome samplesTaxa abundanceGynecological examinationPregnant womenLubricant gelReduce painMicrobial dataGel exposureEmergency roomSterile swabsEffect of gelMicrobial analysis
2023
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies
Kennedy K, de Goffau M, Perez-Muñoz M, Arrieta M, Bäckhed F, Bork P, Braun T, Bushman F, Dore J, de Vos W, Earl A, Eisen J, Elovitz M, Ganal-Vonarburg S, Gänzle M, Garrett W, Hall L, Hornef M, Huttenhower C, Konnikova L, Lebeer S, Macpherson A, Massey R, McHardy A, Koren O, Lawley T, Ley R, O’Mahony L, O’Toole P, Pamer E, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda D, Smith G, Sokol H, Spector T, Surette M, Tannock G, Walker A, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023, 613: 639-649. PMID: 36697862, PMCID: PMC11333990, DOI: 10.1038/s41586-022-05546-8.Peer-Reviewed Original ResearchConceptsMicrobial populationsHuman immune developmentMicrobial ecologyReproductive biologyMicrobial communitiesLow biomass environmentsMicrobial signalsMicrobial studiesDNA sequencingMicrobiome studiesDNA extractionMicrobial analysisClinical microbiologyMechanistic conceptsCautionary exampleImmune developmentRecent studiesHuman fetusesFetal tissuesMammalsGnotobiologyEcologyMicrobiologyFetal microbiomeBiology
2021
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution
Matsuo Y, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi T, Kryukov K, Fukuda A, Morimoto Y, Naito Y, Okada H, Bono H, Nakagawa S, Hirota K. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. BMC Microbiology 2021, 21: 35. PMID: 33499799, PMCID: PMC7836573, DOI: 10.1186/s12866-021-02094-5.Peer-Reviewed Original ResearchConceptsRRNA gene amplicon sequencingShort-read sequencingHuman gut microbiotaGene amplicon sequencingAmplicon sequencingRibosomal RNAGut microbiotaTaxonomic classificationBacterial communitiesBacterial compositionFull-length 16S rRNA geneShort-read sequencing methodsConventional short-read sequencing methodsDominant bacterial generaMock bacterial communityLong-read sequencingTaxonomic classification of bacteriaComplex bacterial communitiesRRNA gene analysisClassification of bacteriaComplex bacterial compositionHuman fecal samplesRRNA geneNanopore sequencingMicrobiome studies
2017
Constructing Predictive Microbial Signatures at Multiple Taxonomic Levels
Wang T, Zhao H. Constructing Predictive Microbial Signatures at Multiple Taxonomic Levels. Journal Of The American Statistical Association 2017, 112: 1022-1031. DOI: 10.1080/01621459.2016.1270213.Peer-Reviewed Original ResearchBacterial taxaTaxonomic levelsMultiple taxonomic levelsDifferent taxonomic levelsDNA sequencing technologiesHuman microbiome studiesPhylogenetic treeHost phenotypeSequencing technologiesNormal human physiologyTaxaHuman microbiomeMicrobial signaturesMicrobiome studiesMicrobiome data analysisImportant groupMicrobiome dataHigh-dimensional compositional dataHuman physiologyRecent advancesMicrobesRapid advancesMajor goalMicrobiomePhenotype
2015
Autoimmune host–microbiota interactions at barrier sites and beyond
Ruff WE, Kriegel MA. Autoimmune host–microbiota interactions at barrier sites and beyond. Trends In Molecular Medicine 2015, 21: 233-244. PMID: 25771098, PMCID: PMC5918312, DOI: 10.1016/j.molmed.2015.02.006.Peer-Reviewed Original ResearchConceptsBarrier sitesAutoimmune animal modelsPathogenesis of autoimmunityBystander activationHost-microbiota interactionsAutoimmune diseasesAdaptive immunityAnimal modelsInfectious agentsAutoimmunityGnotobiotic approachesHomeostatic conditionsInternal organsCurrent literatureMicrobiotaDetrimental effectsHuman microbiome studiesDysbiosisPathogenesisMicrobiome studiesDiseaseImmunity
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