2025
Bacterial recolonization of hospital sink biofilms
Healy H, Pawluk E, Dieter L, Roberts S, Tanner W, Mathew T, Peaper D, Martinello R, Peccia J. Bacterial recolonization of hospital sink biofilms. Journal Of Hospital Infection 2025, 162: 95-105. PMID: 40466811, DOI: 10.1016/j.jhin.2025.05.013.Peer-Reviewed Original ResearchBacterial abundanceRRNA gene amplicon sequencingHospital sink drainsGene amplicon sequencingBacterial gene copiesPathogen abundanceAmplicon sequencingMethylobacterium-MethylorubrumDrain biofilmsHealthcare-Associated InfectionsCommunity taxonomyGene copiesMicrobial communitiesSkin microbiomeCulturable bacteriaRecolonizationSink drainsBacterial recolonizationMALDI-TOFCulturable countsBacteriaHospital sinksAbundanceSphingobiumDigital droplet PCRFlgY, PflA, and PflB form a spoke–ring network in the high-torque flagellar motor of Helicobacter pylori
Tachiyama S, Rosinke K, Khan M, Zhou X, Xin Y, Botting J, Yue J, Roujeinikova A, Hoover T, Liu J. FlgY, PflA, and PflB form a spoke–ring network in the high-torque flagellar motor of Helicobacter pylori. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2421632122. PMID: 40261933, PMCID: PMC12054838, DOI: 10.1073/pnas.2421632122.Peer-Reviewed Original ResearchConceptsMS ringAccessory proteinsStator complexWild-type <i>H. pyFlagellar motorSalmonella enterica</i>Protein-protein interactionsFlagellar motilityAlphaFold-predicted structuresFlgIBiochemical approachesPflBGastric mucus layerMolecular geneticsPFLACryoelectron tomographyUnique motilityBacterial flagellar motorMucus layerMotilityBacteriaProteinHuman stomachPseudoatomic modelHelicobacter pyloriActivity of GPCR-targeted drugs influenced by human gut microbiota metabolism
Wu Q, Song D, Zhao Y, Verdegaal A, Turocy T, Duncan-Lowey B, Goodman A, Palm N, Crawford J. Activity of GPCR-targeted drugs influenced by human gut microbiota metabolism. Nature Chemistry 2025, 17: 808-821. PMID: 40181149, DOI: 10.1038/s41557-025-01789-w.Peer-Reviewed Original ResearchConceptsGut commensal bacteriaCommensal bacteriaGut microbial communityGut microbiota metabolismDrug metabolismMetabolize drugsMicrobial communitiesIndividual speciesMetabolic modeMorganella morganiiMicrobiota metabolismGPCR-targeted drugsTricyclic systemThiophene motifsBacteria mixtureBacteriaMetabolomics investigationsMetabolismTargeting GPCRsDrug metabolitesPharmacological efficacyDrug transformationDrug structureDrugMetabolitesMatrix-producing neutrophils populate and shield the skin
Vicanolo T, Özcan A, Li J, Huerta-López C, Ballesteros I, Rubio-Ponce A, Dumitru A, Nicolás-Ávila J, Molina-Moreno M, Reyes-Gutierrez P, Johnston A, Martone C, Greto E, Quílez-Alvarez A, Calvo E, Bonzon-Kulichenko E, Álvarez-Velez R, Chooi M, Kwok I, González-Bermúdez B, Malleret B, Espinosa F, Zhang M, Wang Y, Sun D, Zhen Chong S, El-Armouche A, Kim K, Udalova I, Greco V, Garcia R, Vázquez J, Dopazo A, Plaza G, Alegre-Cebollada J, Uderhardt S, Ng L, Hidalgo A. Matrix-producing neutrophils populate and shield the skin. Nature 2025, 641: 740-748. PMID: 40108463, PMCID: PMC12074881, DOI: 10.1038/s41586-025-08741-5.Peer-Reviewed Original ResearchRepertoire of proteinsExtracellular matrixInnate immune systemPopulation of neutrophilsImmune diversityPromote barrier functionBacterial invasionInnate immune cellsTGFB signalingForeign moleculesPhysical barrierRing formationBarrier functionImmune systemEnvironmental threatsDefenceDiverse strategiesToxic chemicalsNaive skinTGFBImmune cellsBacteriaNeutrophilsEnzymeProteinTopology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults
Fu J, Yu D, Zheng W, Jiang Y, Wang L, Cai H, Xia Q, Shu X, Xu W. Topology of gut Microbiota Network and Guild-Based Analysis in Chinese Adults. Phenomics 2025, 5: 91-108. PMID: 40313606, PMCID: PMC12040777, DOI: 10.1007/s43657-024-00211-8.Peer-Reviewed Original ResearchOperational taxonomic unitsGut microbiotaDiversity of OTUsCo-abundance networksTaxonomic unitsAssociated with type 2 diabetesMicrobiota networkMicrobial networksGuild structureGut bacteriaGenus classificationMicro-ecosystemMicrobiotaGuildsShanghai MeGenusGutRelevant to diabetesStructural similarityBacteriaSparse CorrelationsChinese populationCO abundanceType 2 diabetesHuman healthNon-disruptive matrix turnover is a conserved feature of biofilm aggregate growth in paradigm pathogenic species
Reichhardt C, Matwichuk M, Lewerke L, Jacobs H, Yan J, Parsek M. Non-disruptive matrix turnover is a conserved feature of biofilm aggregate growth in paradigm pathogenic species. MBio 2025, 16: e03935-24. PMID: 39982068, PMCID: PMC11898600, DOI: 10.1128/mbio.03935-24.Peer-Reviewed Original ResearchConceptsSynthesize EPSBiofilm aggregatesBiofilm matrixBiofilm matrix exopolysaccharidesBiofilm-forming speciesBiofilm matrix compositionStudy of biofilmsMatrix exopolysaccharidesVibrio cholerae</i>.Cellular biomassPathogenic speciesModel organismsBacterial speciesExtracellular DNAExopolysaccharideBiofilm stabilityMulticellular aggregatesCell-free matricesBiofilmCell-free formSpeciesMatrix turnoverAggregate peripheryBacteriaMatrix componentsProtein Quality Control is a Master Modulator of Molecular Evolution in Bacteria
Arenas C, Alvarez M, Wilson R, Shakhnovich E, Ogbunugafor C. Protein Quality Control is a Master Modulator of Molecular Evolution in Bacteria. Genome Biology And Evolution 2025, 17: evaf010. PMID: 39837347, PMCID: PMC11789785, DOI: 10.1093/gbe/evaf010.Peer-Reviewed Original ResearchConceptsProtein quality controlMolecular evolutionProtein translation machineryProteome homeostasisTranslation machineryHost-parasite interactionsProtein spaceOrganismal developmentProtein foldingBacterial systemsCellular processesPromote proteostasisEvolutionary biologyMechanistic basesProteostasisProteinQuality controlEpistasisChaperoneProteomicsGenesBacteriaProteaseMachineryPhenotypeAn 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
Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis
Bigdeli A, Ghaderi-Zefrehei M, Lesch B, Behmanesh M, Arab S. Bioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis. PLOS ONE 2024, 19: e0308817. PMID: 39775333, PMCID: PMC11684644, DOI: 10.1371/journal.pone.0308817.Peer-Reviewed Original ResearchConceptsBile salt hydrolaseMyelin oligodendrocyte glycoproteinBioinformatics approachProtein structureMyelin basic proteinIn silico bioinformatics approachesAmino acidsIdentical amino acidsAmino acid sequenceCapsid protein structureCentral nervous systemAspergillus speciesAcid sequenceBacterial proteinsMultiple sclerosisMyelin sheath componentsBiological insightsGut flora metabolitesBioinformatics analysisMOG proteinPathogenesis of multiple sclerosisCNS diseaseWzyBacteriaProteinMicroscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells
Antani J, Ward T, Emonet T, Turner P. Microscopic phage adsorption assay: High-throughput quantification of virus particle attachment to host bacterial cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 2024, 121: e2410905121. PMID: 39700139, PMCID: PMC11670125, DOI: 10.1073/pnas.2410905121.Peer-Reviewed Original ResearchConceptsBacterial cellsViruses of bacteriaHost bacterial cellsTarget bacterial strainsEnumeration of bacteriaPhage biologyPhage attachmentHigh-throughput quantificationPhage libraryBacterial pathogensHigh-throughput screeningPhageBacterial strainsSingle-virusVirus particlesIndividual virus particlesFluorescence microscopyBacteriaEarth's biosphereParticle trackingCellsLow throughputBacteriumRate constantsPathogensMetagenomic 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 analysisPlasmodiaBacterial Organelles in Iron Physiology
Ferrara K, Gupta K, Pi H. Bacterial Organelles in Iron Physiology. Molecular Microbiology 2024, 122: 914-928. PMID: 39545931, PMCID: PMC11659020, DOI: 10.1111/mmi.15330.Peer-Reviewed Original ResearchMembrane-bound organellesBacterial organellesFerritin-like proteinsEukaryotic organellesProtein-lipid monolayersEukaryotic cellsProteinaceous shellSpecies-specificBacterial cellsOrganellesProtecting cellsLife formsBiochemical reactionsPhysiological functionsDiverse arrayIron physiologyEnvironmental conditionsLipid bilayerBacteriaEssential micronutrientCellsSpecial structureBiogenesisGeneticsProteinA 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 chemicalsBacterial cell surface characterization by phage display coupled to high-throughput sequencing
Grun C, Jain R, Schniederberend M, Shoemaker C, Nelson B, Kazmierczak B. Bacterial cell surface characterization by phage display coupled to high-throughput sequencing. Nature Communications 2024, 15: 7502. PMID: 39209859, PMCID: PMC11362561, DOI: 10.1038/s41467-024-51912-7.Peer-Reviewed Original ResearchConceptsBacterial cell surfaceCell surfacePhage displayP. aeruginosa virulence factorsHigh-throughput DNA sequencingHigh-throughput sequencingPhage display panningCapacity of bacteriaCamelid single-domain antibodiesVirulence factorsDNA sequencesBacterial genotypesPhageSingle-domain antibodiesPseudomonas aeruginosaHost defenseBiological informationAntimicrobial resistanceLiving cellsSequenceChronic infectionCell surface characterizationAdaptive changesCellsBacteriaThe Human Skin Microbiome in Health: CME Part 1
MacGibeny M, Adjei S, Pyle H, Bunick C, Ghannoum M, Grada A, Harris-Tryon T, Tyring S, Kong H. The Human Skin Microbiome in Health: CME Part 1. Journal Of The American Academy Of Dermatology 2024 PMID: 39168311, PMCID: PMC11912297, DOI: 10.1016/j.jaad.2024.07.1498.Peer-Reviewed Original ResearchHuman skin microbiomeSkin microbiomeMicrobiome-host interactionsMicrobiome-based therapiesMyriad of microorganismsMicrobial ecologyCommensal microbesMicrobiomeMicrobiome alterationsOverall homeostasisAssociated with skin diseasesMicroorganismsIn vitroIntrinsic factorsCME seriesFungiMicrobesAnimal studiesSkin healthBacteriaSkin diseasesEcologyHomeostasisSkinHuman skinThe profile of blood microbiome in new-onset type 1 diabetes children
Yuan X, Yang X, Xu Z, Li J, Sun C, Chen R, Wei H, Chen L, Du H, Li G, Yang Y, Chen X, Cui L, Fu J, Wu J, Chen Z, Fang X, Su Z, Zhang M, Wu J, Chen X, Zhou J, Luo Y, Zhang L, Wang R, Luo F. The profile of blood microbiome in new-onset type 1 diabetes children. IScience 2024, 27: 110252. PMID: 39027370, PMCID: PMC11255850, DOI: 10.1016/j.isci.2024.110252.Peer-Reviewed Original ResearchBlood microbiomeRRNA gene sequencesMicrobiome of patientsGene sequencesOral microbiomePICRUSt analysisMicrobial featuresMicrobiome signaturesPathogenic bacteriaMicrobiomeTranslocation of bacteriaPotential translocationBacteriaRandom forest analysisType 1 diabetic childrenGutNew-onset T1DDiscriminatory powerType 1 diabetesForest analysisOral cavityIncreasing diversityInduce inflammationPICRUStGenusDraft genome sequences of antibiotic-resistant Serratia and Enterobacter species isolated from imported fresh produce in Georgia, USA
Kassem I, Wang J, Tajani A, Esseili M, Hassan J, Yassine I, Osman M, Bisha B. Draft genome sequences of antibiotic-resistant Serratia and Enterobacter species isolated from imported fresh produce in Georgia, USA. Microbiology Resource Announcements 2024, 13: e01139-23. PMID: 38695584, PMCID: PMC11237534, DOI: 10.1128/mra.01139-23.Peer-Reviewed Original ResearchTopical Clindamycin in the Management of Acne Vulgaris: Current Perspectives and Recent Therapeutic Advances.
Del Rosso J, Bunick C, Kircik L, Bhatia N. Topical Clindamycin in the Management of Acne Vulgaris: Current Perspectives and Recent Therapeutic Advances. Journal Of Drugs In Dermatology 2024, 23: 438-445. PMID: 38834223, DOI: 10.36849/jdd.8318.Peer-Reviewed Original ResearchConceptsAcne vulgarisTopical clindamycinTreatment of acne vulgarisManagement of acne vulgarisEmergence of antibiotic-resistant bacteriaAntibiotic-resistant bacteriaTopical agentsAnti-inflammatory propertiesTherapeutic advancesClindamycinClinical studiesTherapeutic outcomesClinical applicationAntimicrobial profileGram-positive bacteriaAnaerobic bacteriaMode of actionVulgarisMonotherapyPublished dataBacteriaTherapyAcneAntibioticsRecent developments, opportunities, and challenges in the study of mRNA pseudouridylation
Gilbert W. Recent developments, opportunities, and challenges in the study of mRNA pseudouridylation. RNA 2024, 30: rna.079975.124. PMID: 38531650, PMCID: PMC11019745, DOI: 10.1261/rna.079975.124.Peer-Reviewed Original ResearchWidespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE
Portela P, Shipps C, Shen C, Srikanth V, Salgueiro C, Malvankar N. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nature Communications 2024, 15: 2434. PMID: 38509081, PMCID: PMC10954620, DOI: 10.1038/s41467-024-46192-0.Peer-Reviewed Original ResearchConceptsExtracellular electron transferExtracellular electron transfer pathwaysHeme reduction potentialEfficient extracellular electron transferInner membraneBiotechnological applicationsPeriplasmic cytochromesMicrobial nanowiresElectron transfer pathwayPpcABCDEPathwayEET pathwayCytochromePeriplasmEnvironmental processesMicrobesElectron transferBacteriaGeobacterTransfer pathwayReduction potential
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