2025
Genotype-environment-driven dysbiosis in the skin microbiome of ichthyosis
Zhou W, Ring N, Caldwell R, Milstone L, Oh J. Genotype-environment-driven dysbiosis in the skin microbiome of ichthyosis. Journal Of Investigative Dermatology 2025 PMID: 40571157, DOI: 10.1016/j.jid.2025.06.1568.Peer-Reviewed Original ResearchSkin microbiomeMetabolic pathway levelTransepidermal water lossHost covariatesMetabolic potentialMicrobiome featuresPathway levelImpact hostCutaneous microbiomeMicrobiomeGroup of patientsGenotypesComplex interactionsTGM1Environmental factorsRetinoid usePhenotypeWater lossHostIchthyosisClinical treatmentDiseased skinGenotype-relatedDysbiosisSkinHierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides
Kabonick S, Verma K, Modesto J, Pearce V, Winokur K, Groisman E, Townsend G. Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides. Nature Communications 2025, 16: 4488. PMID: 40368925, PMCID: PMC12078602, DOI: 10.1038/s41467-025-59704-3.Peer-Reviewed Original ResearchConceptsFructose-1,6-bisphosphateMammalian gutGut BacteroidesBacterial phylumGut microbiomeIntestinal colonizationTranscription factorsGlycolytic pathwayBacteroides speciesCarbohydrate utilizationHost immunomodulationGutCarbohydrateCurIntestinal disordersFructoseHostRegulationAbundant amountSugarPhylumBacteroidetesMicrobiomeBacteroidesTranscriptionMapping pesticide-induced metabolic alterations in human gut bacteria
Chen L, Yan H, Di S, Guo C, Zhang H, Zhang S, Gold A, Wang Y, Hu M, Wu D, Johnson C, Wang X, Zhu J. Mapping pesticide-induced metabolic alterations in human gut bacteria. Nature Communications 2025, 16: 4355. PMID: 40348778, PMCID: PMC12065874, DOI: 10.1038/s41467-025-59747-6.Peer-Reviewed Original ResearchConceptsModulating gut microbiota compositionGut bacteria speciesGut microbial speciesHuman gut bacteriaGut microbiota compositionGut bacterial metabolismPesticide exposureHost healthGut bacteriaMicrobiota compositionMicrobial speciesBacterial metabolismBacteria speciesMolecular mechanismsComprehensive atlasLipid metabolismGutIn Vivo Mouse ModelPesticidesHostMetabolismSpeciesInteractive atlasMouse modelMetabolic changesStructural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin
Kim M, Kim J, Lee G, Olinares P, Airan Y, Chow J, Park J, Jeong Y, Park J, Chait B, Herzon S, Kim C, Kang J. Structural study on human microbiome-derived polyketide synthases that assemble genotoxic colibactin. Structure 2025 PMID: 40381618, DOI: 10.1016/j.str.2025.04.017.Peer-Reviewed Original ResearchNRPS-PKSCarrier proteinCryo-EM structurePKS enzymesPolyketide synthaseBiosynthesis mechanismBiosynthetic enzymesUpstream enzymesDimer interfaceColibactinBinding sitesDocking interactionsKetosynthasePromote colorectal cancerEnzymeStructural studiesGenomeBiosynthesisStructural detailsStructural analysisProteinGenotoxinsSynthaseHostCLBIHuman and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities
Mueller N, Dujsikova A, Singh A, Chen Y. Human and pathogen-encoded circular RNAs in viral infections: insights into functions and therapeutic opportunities. Human Molecular Genetics 2025, ddaf031. PMID: 40304711, DOI: 10.1093/hmg/ddaf031.Peer-Reviewed Original ResearchDNA virusesHost cellular machineryHost-virus interactionsCircular RNAsContribution to pathogenesisRNA biologyProtein translationCellular machineryProtein decoysRNA-based therapiesBiological rolePotential of circRNAsRegulatory moleculesRNAMicroRNA spongesViral systemsDNAViral replicationImmune evasionTherapeutic targetCircRNAsTherapeutic opportunitiesHostProteinViral diseasesInteractions Between Commensal Microbes and Mosquito-Borne Viruses.
Zhu Y, Cao Y, Jiang L, Wang P, Cheng G. Interactions Between Commensal Microbes and Mosquito-Borne Viruses. Annual Review Of Virology 2025 PMID: 40067963, DOI: 10.1146/annurev-virology-092623-101222.Peer-Reviewed Original ResearchMosquito-Borne VirusesCommensal microbesMammalian hostsHost gut microbiotaInsect-specific virusesSymbiotic microbesEndosymbiotic bacteriaGut microbiotaRe-emerging mosquito-borne virusSkin microbiotaViral transmissionPathogenesis of viral infectionsMicrobesViral pathogenesisMicrobiotaVector competenceGlobal public healthHostMosquito-borne viral diseaseMosquito-borneImmune regulationTherapeutic approachesViral diseasesViral infectionIntricate interactionsAn Extraordinary Case of Prosthetic Joint Infection by Listeria monocytogenes and Histoplasma capsulatum
Luu T, Daddi L, Azar M, Trubin P, Molloy I, Spichler-Moffarah A. An Extraordinary Case of Prosthetic Joint Infection by Listeria monocytogenes and Histoplasma capsulatum. Cureus 2025, 17: e76901. PMID: 39906453, PMCID: PMC11791120, DOI: 10.7759/cureus.76901.Peer-Reviewed Original ResearchListeria monocytogenes</i>Gram-positive organismsProsthetic joint infectionListeria monocytogenesHistoplasma capsulatumHost conditionsImmunocompromised hostsTwo-stage exchange surgeryCases of prosthetic joint infectionJoint infectionCo-InfectionHostAntimicrobial treatmentSynovial fluid cultureEpidemiological risk factorsMonocytogenesComplication of hipFungiPathogensExchange surgeryBacteriaFluid cultureOrganizationBiofilmRemote history
2024
Diverse phage communities are maintained stably on a clonal bacterial host
Pyenson N, Leeks A, Nweke O, Goldford J, Schluter J, Turner P, Foster K, Sanchez A. Diverse phage communities are maintained stably on a clonal bacterial host. Science 2024, 386: 1294-1300. PMID: 39666794, PMCID: PMC7617280, DOI: 10.1126/science.adk1183.Peer-Reviewed Original ResearchConceptsPhage communitiesBacterial hostsPhage speciesEcology of bacteriophagesDiverse biological entitiesPhage diversityGrowth phenotypeCommunity ecologyEcological mechanismsPhageBacterial cellsPhenotypic heterogeneityHost populationsBacteriophageBiological entitiesDiversityHostSpeciesPhylogeneticallyNichePhenotypeStrainCellsCommunityA model of proximate protection against pathogenic infection through shared immunity
Nixon D, Kyza-Karavioti M, Mallick S, Daley L, Hupert N, Bachtel N, Eleftherianos I. A model of proximate protection against pathogenic infection through shared immunity. MBio 2024, 15: e03046-24. PMID: 39526781, PMCID: PMC11633142, DOI: 10.1128/mbio.03046-24.Peer-Reviewed Original ResearchDrosophila melanogaster</i>Host immune defenseTransforming biomedical researchMicrobial signalsPathogen infectionPathogen challengeAdult fliesImmunological primingInsect pathogensImmune defenseInfected hostsInnate immune primingImmune primingHostPathogensInfluence immunityBiomedical researchHealthy individualsFliesPrimed hostsProtective effectLethal doseImmunityBacteriaSpecific chemicalsMucosal sugars delineate pyrazine vs pyrazinone autoinducer signaling in Klebsiella oxytoca
Hamchand R, Wang K, Song D, Palm N, Crawford J. Mucosal sugars delineate pyrazine vs pyrazinone autoinducer signaling in Klebsiella oxytoca. Nature Communications 2024, 15: 8902. PMID: 39406708, PMCID: PMC11480411, DOI: 10.1038/s41467-024-53185-6.Peer-Reviewed Original ResearchConceptsK. oxytocaGeneral carbohydrate metabolismVirulence factor productionPLP-dependent enzymesAssociated with gutEnterobactin biosynthesisAutoinducer signalBacterial virulenceKlebsiella oxytocaSpecific carbohydratesHost immune responseCarbohydrate metabolismAutoinducerMolecular signalsVirulenceHistamine receptor H4BiosynthesisHost signalAcquisition responsesProtease inhibitorsPathwayHostLung pathologyLung isolationImmune responseμREACT: A microfluidic system for rapid evaluation of trans-kingdom interactions
Huang C, Yang J, Chen S, Han S, Zhang H, Samuel J, Van Schaik E, de Figueiredo P, Han A. μREACT: A microfluidic system for rapid evaluation of trans-kingdom interactions. Biosensors And Bioelectronics 2024, 267: 116838. PMID: 39393191, DOI: 10.1016/j.bios.2024.116838.Peer-Reviewed Original ResearchTrans-kingdom interactionsInterkingdom interactionsHost cellsMammalian host cellsHost cell typesPhylogenetic spectrumBacterial speciesSpectrum of microorganismsBiological networksBiological processesEcosystem dynamicsSingle-cellCell typesDielectrophoretic separationHigh-throughputMicrobial samplesAdherent microorganismsFlow cytometry systemMicroorganismsMicrofluidic systemCellsHostEndosymbiosisInterkingdomCytometry systemAnopheles gambiae lacking AgTRIO probe inefficiently on a mammalian host
Chuang Y, Dong Y, Stone H, Abouneameh S, Tang X, Raduwan H, Dimopoulos G, Fikrig E. Anopheles gambiae lacking AgTRIO probe inefficiently on a mammalian host. Cell Reports 2024, 43: 114600. PMID: 39126653, PMCID: PMC11407849, DOI: 10.1016/j.celrep.2024.114600.Peer-Reviewed Original ResearchVertebrate hostsAnopheles gambiaePlasmodium sporozoitesCRISPR-Cas9-mediated genome editingPlasmodium transmissionTransmit malariaMosquito probingMosquito salivaTransmit PlasmodiumBlood resourcesMalariaRepetitive probesBloodPlasmodiumMammalian hostsAbility of mosquitoesBlood mealGenome editingA. gambiaeKnockoutVertebratesGambiaHostMealSalivaMicrobe Profile: Bacteriophage ϕ6: a model for segmented RNA viruses and the evolutionary consequences of viral ‘sex’
Turner P, Chao L. Microbe Profile: Bacteriophage ϕ6: a model for segmented RNA viruses and the evolutionary consequences of viral ‘sex’. Microbiology 2024, 170: 001467. PMID: 39046321, PMCID: PMC11316545, DOI: 10.1099/mic.0.001467.Peer-Reviewed Original ResearchConceptsEukaryotic virusesHost-pathogen interactionsEvolution of sexDsRNA virusesEvolutionary consequencesSegment reassortmentBacterial virusesRNA virusesRate of adaptationMutation ratePhenotypic complexityMutation loadLipid envelopeBacteriophageReassortmentRNAMutationsVirusMolecular modelingDsRNAExperimental systemGeneticsTraitsHostReplicationEnvironmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages
Shridhar S, Beghini F, Alexander M, Singh A, Juárez R, Brito I, Christakis N. Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages. Cell Reports 2024, 43: 114442. PMID: 38968070, PMCID: PMC11290354, DOI: 10.1016/j.celrep.2024.114442.Peer-Reviewed Original ResearchGut microbiomeGut microbiome speciesSpecies-level profilingSequenced microbiomesMetagenomic dataMicrobiome speciesHost phenotypeBacterial speciesHuman phenotypesMesoamerican highlandsSeveral speciesGutSpeciesMicrobiomePhenotypeAssociated with body mass indexCommunity-based cohortBody mass indexConsistent with previous findingsSocioeconomic factorsIsolated villagesHousehold wealthMass indexHostStrainBorg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Schoelmerich M, Ly L, West-Roberts J, Shi L, Shen C, Malvankar N, Taib N, Gribaldo S, Woodcroft B, Schadt C, Al-Shayeb B, Dai X, Mozsary C, Hickey S, He C, Beaulaurier J, Juul S, Sachdeva R, Banfield J. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications 2024, 15: 5414. PMID: 38926353, PMCID: PMC11208441, DOI: 10.1038/s41467-024-49548-8.Peer-Reviewed Original ResearchConceptsExtrachromosomal elementsMethylation motifsPublished complete genomesCell surface proteinsShort readsComplete genomeConserved genesGenetic repertoireLinear genomeNanopore sequencingGenomic backboneStructure predictionGenomic signaturesGenomeMethane-oxidizing archaeaHost cellsSurface proteinsArchaeaGenesActivity in situPeatland soilsGenetic inheritanceMotifMethanoperedensHost3-Hydroxykynurenine targets kainate receptors to promote defense against infection
Parada-Kusz M, Clatworthy A, Goering E, Blackwood S, Shigeta J, Mashin E, Salm E, Choi C, Combs S, Lee J, Rodriguez-Osorio C, Clish C, Tomita S, Hung D. 3-Hydroxykynurenine targets kainate receptors to promote defense against infection. Nature Chemical Biology 2024, 20: 1586-1596. PMID: 38898166, PMCID: PMC12204212, DOI: 10.1038/s41589-024-01635-z.Peer-Reviewed Original ResearchKainate-sensitive glutamate receptorsHost tryptophan metabolismHost survivalBacterial infectionsPromote host survivalGlutamate receptorsLethal bacterial infectionHost-pathogenIn vivo chemical screeningTryptophan metabolismPromote defenseBacterial expansionOutcome of infectionChemical screeningZebrafish embryosAntibacterial activityKainate receptorsPathogen eradicationPathogensHostModulate immunityNervous systemInfectionMetabolismReceptorsLongitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease
Zhou X, Shen X, Johnson J, Spakowicz D, Agnello M, Zhou W, Avina M, Honkala A, Chleilat F, Chen S, Cha K, Leopold S, Zhu C, Chen L, Lyu L, Hornburg D, Wu S, Zhang X, Jiang C, Jiang L, Jiang L, Jian R, Brooks A, Wang M, Contrepois K, Gao P, Rose S, Tran T, Nguyen H, Celli A, Hong B, Bautista E, Dorsett Y, Kavathas P, Zhou Y, Sodergren E, Weinstock G, Snyder M. Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease. Cell Host & Microbe 2024, 32: 506-526.e9. PMID: 38479397, PMCID: PMC11022754, DOI: 10.1016/j.chom.2024.02.012.Peer-Reviewed Original ResearchHost healthMicrobiome dynamicsBacterial taxaBody sitesMicrobiome stabilityIndividual taxaHuman microbiomeMicrobial compositionMicrobial dynamicsMulti-OmicsNasal microbiomeMicrobiomeDisrupt interactionsMolecular markersBody-sitesTaxaHostMetabolic diseasesOral microbiomeInsulin-resistant individualsIndividual-specificTemporal dynamicsClinical featuresComprehensive viewClinical markersCorrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons
Ma Q, Srivastav S, Gamez S, Dayama G, Feitosa-Suntheimer F, Patterson E, Johnson R, Matson E, Gold A, Brackney D, Connor J, Colpitts T, Hughes G, Rasgon J, Nolan T, Akbari O, Lau N. Corrigendum: A mosquito small RNA genomics resource reveals dynamic evolution and host responses to viruses and transposons. Genome Research 2024, 34: 160-160. PMID: 38326031, PMCID: PMC10903936, DOI: 10.1101/gr.278898.123.Peer-Reviewed Original Research
2023
Signaling between mammalian adiponectin and a mosquito adiponectin receptor reduces Plasmodium transmission
Chuang Y, Stone H, Abouneameh S, Tang X, Fikrig E. Signaling between mammalian adiponectin and a mosquito adiponectin receptor reduces Plasmodium transmission. MBio 2023, 15: e02257-23. PMID: 38078744, PMCID: PMC10790699, DOI: 10.1128/mbio.02257-23.Peer-Reviewed Original ResearchBlood mealComplex life cycleMosquito fitnessMammalian hostsMammalian adiponectinPathogen infectivityLipid transportersVertebrate hostsAdiponectin receptorsHematophagous arthropodsFemale mosquitoesPlasmodium transmissionLife cycleMosquitoesImportant lipid transporterPathwayHostInfectious agentsVector-borne infectious agentsArthropodsAdiponectinReceptorsInfectionTransportersMealA Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations
Loney R, Delesalle V, Chaudry B, Czerpak M, Guffey A, Goubet-McCall L, McCarty M, Strine M, Tanke N, Vill A, Krukonis G. A Novel Subcluster of Closely Related Bacillus Phages with Distinct Tail Fiber/Lysin Gene Combinations. Viruses 2023, 15: 2267. PMID: 38005943, PMCID: PMC10674732, DOI: 10.3390/v15112267.Peer-Reviewed Original Research
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