2024
Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients
Ho M, Nguyen H, Van Hoang M, Bui T, Vu B, Dinh T, Vo H, Blaydon D, Eldirany S, Bunick C, Bui C. Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients. Human Genomics 2024, 18: 38. PMID: 38627868, PMCID: PMC11022333, DOI: 10.1186/s40246-024-00603-x.Peer-Reviewed Original ResearchConceptsSkin microbiomeCI patientsJAK/STAT-signaling pathwayRecurrent pathogenic variantsMeta-genomeCommensal microbiotaHereditary skin disordersJAK/STAT signalingIncreased production of inflammatory cytokinesIncreased susceptibility to infectionJAK/STAT-signalingPeripheral blood mononuclear cellsPathogenic variantsAge- and gender-matched controlsSkin barrier defectsHigher colonizationResultsThis case-control studyProduction of inflammatory cytokinesMicrobial populationsBlood mononuclear cellsImproving therapeutic managementEpidermal scalesCase-control studyMicrobiomeGender-matched controls
2023
mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation
Movassagh M, Schiff S, Paulson J. mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. Bioinformatics 2023, 39: btad565. PMID: 37707523, PMCID: PMC10516520, DOI: 10.1093/bioinformatics/btad565.Peer-Reviewed Original ResearchConceptsSingle nucleotide variationsRNA sequencingMicrobial abundance dataQuantitative trait lociSingle nucleotide polymorphism dataRibosomal RNA sequencingField of genomicsWhole-genome sequencingEvidence of interplayMutational profileTrait lociMicrobial communitiesMicrobial abundancePolymorphism dataMicrobial populationsGenome sequencingAbundance dataFirst R packageHuman geneticsBioconductor packageGenetic variantsMicrobiome dataSequencingR packageAbundanceDietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species
Pearce V, Groisman E, Townsend G. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023, 15: 2221484. PMID: 37358144, PMCID: PMC10294740, DOI: 10.1080/19490976.2023.2221484.Peer-Reviewed Original ResearchConceptsMaster regulatorMicrobial populationsOrthologous transcription factorsMammalian gut microbiotaMicrobial gene expressionHuman gut symbiontHuman gut BacteroidesDistinct microbial populationsIntestinal Bacteroides speciesGut symbiontsCarbohydrate utilizationMRNA leaderTranscription factorsHost dietGut BacteroidesNutrient availabilityGene expressionMolecular pathwaysUnknown mechanismDietary sugarsBacteroides speciesFuture therapeutic interventionsRegulatorSimple sugarsPathogenic outcomesQuestioning 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
2016
Competition along trajectories governs adaptation rates towards antimicrobial resistance
Ogbunugafor C, Eppstein M. Competition along trajectories governs adaptation rates towards antimicrobial resistance. Nature Ecology & Evolution 2016, 1: 0007. PMID: 28812552, DOI: 10.1038/s41559-016-0007.Peer-Reviewed Original ResearchAntimicrobial resistanceFitness increaseEvolution of antimicrobial resistanceRate of evolutionEmpirical fitness landscapesGenotype-phenotype mapAdaptive trajectoriesCombinations of mutationsFitness landscapeSpecies of malariaAdaptive evolutionEvolutionary biologistsMicrobial populationsAllelesLandscapeDrug resistanceMutationsAdaptive fitness landscapeMicrobiome: Ecology of eczema
Odell ID, Flavell RA. Microbiome: Ecology of eczema. Nature Microbiology 2016, 1: 16135. PMID: 27562264, PMCID: PMC6035744, DOI: 10.1038/nmicrobiol.2016.135.Peer-Reviewed Original Research
2012
A Single Promoter Inversion Switches Photorhabdus Between Pathogenic and Mutualistic States
Somvanshi VS, Sloup RE, Crawford JM, Martin AR, Heidt AJ, Kim KS, Clardy J, Ciche TA. A Single Promoter Inversion Switches Photorhabdus Between Pathogenic and Mutualistic States. Science 2012, 337: 88-93. PMID: 22767929, PMCID: PMC4006969, DOI: 10.1126/science.1216641.Peer-Reviewed Original ResearchConceptsNematode intestinePromoter inversionVariable life historiesM-form cellsInsect infectionHost nematodesLife historyMicrobial populationsSecondary metabolitesAntibiotic toleranceIndividual cellsNematodesPhotorhabdusM formJuvenile offspringCellsPathogenic variantsFirst cellsDistinct formsMutualistsMutualismVariantsInsectsAvirulenceSmall cell variant
2007
Dynamic phase microscopy, a new method to detect viable and killed spores and to estimate the heterogeneity of spore populations
Tychinsky V, Mulyukin A, Lisovskii V, Nikolaev Y, Kretushev A, Vyshenskaya T, Suzina N, Duda V, El-Registan G. Dynamic phase microscopy, a new method to detect viable and killed spores and to estimate the heterogeneity of spore populations. Advances In Space Research 2007, 40: 1678-1685. DOI: 10.1016/j.asr.2007.03.090.Peer-Reviewed Original ResearchDynamic phase microscopyPT fluctuationsSpore populationDormant sporesGerminating sporesPhase microscopySearching lifePhysiological stateViability of individual cellsDead cellsHeterogeneity of microbial populationsEarly germination stageMicroscope objectiveOptical path differenceMonitoring studiesHeat-killed sporesKill sporesExtraterrestrial factorsMicroscopy methodsMicrobial populationsSpore diameterPhase thicknessEnvironmental assaultsPath differenceSpores
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