2025
High-throughput cryo-electron tomography enables multiscale visualization of the inner life of microbes
Heydari S, Liu J. High-throughput cryo-electron tomography enables multiscale visualization of the inner life of microbes. Current Opinion In Structural Biology 2025, 93: 103065. PMID: 40381356, DOI: 10.1016/j.sbi.2025.103065.Peer-Reviewed Original ResearchCryo-ETCryo-electron tomographyCryo-ET workflowsParticle cryo-electron microscopyCryo-electron microscopyLife of microbesHigh-throughput cryo-electron tomographyCryo-EMMicrobial architectureCellular biologyVisualization of biological structuresNative stateBiological researchData acquisitionBiomedical discoveriesField of life sciencesResolutionMicrobesImaging techniquesLow resolutionInteractions 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 affinity-based depletion strategy for evaluating the effects of ergothioneine on bacterial physiology
Seminara A, Hatzios S. An affinity-based depletion strategy for evaluating the effects of ergothioneine on bacterial physiology. Cell Chemical Biology 2025, 32: 486-497.e7. PMID: 40068683, PMCID: PMC12057763, DOI: 10.1016/j.chembiol.2025.02.004.Peer-Reviewed Original ResearchConceptsGastric pathogen Helicobacter pyloriHost-associated microbesOuter membrane transportersWild-type H. pyloriTransporter-deficient strainsPathogen Helicobacter pyloriNutrient-rich mediumBacterial physiologyMicrobial physiologyErgothioneine biosynthesisBacterial speciesMicrobial strainsComplex mediaCulture H. pyloriErgothioneineStrainHelicobacter pyloriPhysiologyH. pyloriComplicating effortsBiosynthesisTranscriptionFungalMicrobesHuman dietSynthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16
Nakamura A, Fulk E, Johnson C, Isaacs F. Synthetic Genetic Elements Enable Rapid Characterization of Inorganic Carbon Uptake Systems in Cupriavidus necator H16. ACS Synthetic Biology 2025, 14: 943-953. PMID: 40048245, PMCID: PMC11934965, DOI: 10.1021/acssynbio.4c00869.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsExpression of heterologous pathwaysUptake systemCupriavidus necator H16Genome engineering technologiesHeterologous pathwaysHeterotrophic conditionsGenetic elementsChromosomal expressionTunable expressionInducible promoterGenetic engineering technologyModel microbesCarbon sourceGene expressionFacultative chemolithotrophsUptake pathwayH16PathwayLanding padExpressionGenomeGenesMicrobesChemolithotrophsA human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability
Lim B, Xu J, Wierzbicki I, Gonzalez C, Chen Z, Gonzalez D, Gao X, Goodman A. A human gut bacterium antagonizes neighboring bacteria by altering their protein-folding ability. Cell Host & Microbe 2025, 33: 200-217.e24. PMID: 39909037, PMCID: PMC11931560, DOI: 10.1016/j.chom.2025.01.008.Peer-Reviewed Original ResearchConceptsHuman gut microbesChaperone complexGut microbesCommunity dynamicsHuman gut bacteriumProtein folding abilityProtein folding capacityHuman gut microbiomeMicrobial community dynamicsGut metagenomesNeighboring bacteriaExpression strainGut bacteriumMammalian gutFitness advantageGut microbiomeAllelic variationGenetic characterizationPathogen-induced inflammationSubstrate aggregationAntagonistic interactionsMicrobesRecipient cellsGutNeighboring cells
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 studyMicroorganismsRhinitisMicrobial transformation of dietary xenobiotics shapes gut microbiome composition
Culp E, Nelson N, Verdegaal A, Goodman A. Microbial transformation of dietary xenobiotics shapes gut microbiome composition. Cell 2024, 187: 6327-6345.e20. PMID: 39321800, PMCID: PMC11531382, DOI: 10.1016/j.cell.2024.08.038.Peer-Reviewed Original ResearchGut microbiomeHuman gut microbesGut microbiome compositionDiet-microbiome interactionsGut microbesCommunity compositionMicrobiome compositionMicrobial metabolismResponse to dietInterindividual variationMicrobiomeDietary xenobioticsMap interactionsGutMetabolic activityEnzymeXenobioticsDetoxificationGenesMicrobesResveratrolRemodelingTraitsInteractionVariationThe 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 skinMETAGENOMICS FOR PATHOGEN DETECTION DURING A MASS MORTALITY EVENT IN SONGBIRDS
Mwakibete L, Greening S, Kalantar K, Ahyong V, Anis E, Miller E, Needle D, Oglesbee M, Thomas W, Sevigny J, Gordon L, Nemeth N, Ogbunugafor C, Ayala A, Faith S, Neff N, Detweiler A, Baillargeon T, Tanguay S, Simpson S, Murphy L, Ellis J, Tato C, Gagne R. METAGENOMICS FOR PATHOGEN DETECTION DURING A MASS MORTALITY EVENT IN SONGBIRDS. Journal Of Wildlife Diseases 2024, 60: 362-374. PMID: 38345467, DOI: 10.7589/jwd-d-23-00109.Peer-Reviewed Original ResearchConceptsMass mortality eventsMortality eventsWildlife mortality eventsAffected birdsOcular dischargeClinical signsSubclinical infectionNext-generation sequencingMetagenomic next-generation sequencingSwollen conjunctivaBirdsMetagenomic approachPathogen detectionPathogenic microbesEastern USCongruent resultsDetect microbesMolecular laboratoryNutritional deficienciesMicrobesWildlifeEnvironmental contaminationPathogensDiagnostic investigationsPasserinesWidespread 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 potentialAdvances in understanding bat infection dynamics across biological scales
Sánchez C, Phelps K, Frank H, Geldenhuys M, Griffiths M, Jones D, Kettenburg G, Lunn T, Moreno K, Mortlock M, Vicente-Santos A, Víquez-R L, Kading R, Markotter W, Reeder D, Olival K. Advances in understanding bat infection dynamics across biological scales. Proceedings Of The Royal Society B 2024, 291: 20232823. PMID: 38444339, PMCID: PMC10915549, DOI: 10.1098/rspb.2023.2823.Peer-Reviewed Original ResearchNew approaches for understanding the potential role of microbes in Alzheimer's disease
Whitson H, Banks W, Diaz M, Frost B, Kellis M, Lathe R, Schmader K, Spudich S, Tanzi R, Garden G. New approaches for understanding the potential role of microbes in Alzheimer's disease. Brain Behavior & Immunity - Health 2024, 36: 100743. PMID: 38435720, PMCID: PMC10906156, DOI: 10.1016/j.bbih.2024.100743.Peer-Reviewed Original ResearchAlzheimer's diseaseAD pathologyAntimicrobial protection hypothesisInfluence AD pathologyGene-environment interactionsModel organismsMicrobial organismsMicrobesPotential roleAmyloid accumulationProtection hypothesisAlzheimerImmune cell activationReview new evidencePathological processesCell activationComplex pathological processAmyloidGermOrganizationAlzheimer's Disease Research Center
2023
Five questions on how biochemistry can combat climate change
Chen K, Guo Y, How K, Acosta A, Documet D, Liang C, Arul D, Wood S, Moon K, Oliver L, Fajardo E, Kopyto M, Shine M, Neugebauer K. Five questions on how biochemistry can combat climate change. BBA Advances 2023, 4: 100111. PMID: 38075469, PMCID: PMC10709155, DOI: 10.1016/j.bbadva.2023.100111.Peer-Reviewed Original ResearchClimate changeCell biologyGreater ecosystemMolecular biophysicsEnvironmental changesEnvironmental conditionsOrganismsBiochemistryMolecular pointNew diseaseHuman activitiesDispersalMicrobesGeneticsBiologyEcosystemsPlantsGlobal warmingPathwayHigh levelsSalt concentrationBiophysicsCellsAccumulationWeather patternsConstructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes
Lou S, Yang M, Li T, Zhao W, Cevasco H, Yang Y, Gerstein M. Constructing a full, multiple-layer interactome for SARS-CoV-2 in the context of lung disease: Linking the virus with human genes and microbes. PLOS Computational Biology 2023, 19: e1011222. PMID: 37410793, PMCID: PMC10325097, DOI: 10.1371/journal.pcbi.1011222.Peer-Reviewed Original ResearchConceptsProtein-coding genesHuman protein-coding genesProtein-protein interactionsFull interactomeDirect protein-protein interactionHuman protein-protein interactionsSingle-cell sequencing dataHuman genesExogenous microbesHuman microRNAsSequencing dataInteractomeGenesPathway structureMicrobesMiRNAsNetwork propagationRothia mucilaginosaInitial linkageComprehensive understandingMicroRNAsViral infectionMillions of deathsAbundanceSimilar patternCross-feeding in the gut microbiome: Ecology and mechanisms
Culp E, Goodman A. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host & Microbe 2023, 31: 485-499. PMID: 37054671, PMCID: PMC10125260, DOI: 10.1016/j.chom.2023.03.016.Peer-Reviewed Original ResearchConceptsHost healthHost-microbe interactionsSpecies fitnessMicrobe-microbeEvolutionary implicationsMicrobial inhabitantsGut communitiesTrophic networksMicrobial communitiesTrophic levelsMammalian gutPrimary fermentersMetabolic outputDifferent microbesAmino acidsGut commensalsCooperative interactionsGut microbiomeNegative interactionsFitnessMutualismEcologyMicrobesEmergent roleCofactor
2022
A microbial transporter of the dietary antioxidant ergothioneine
Dumitrescu D, Gordon E, Kovalyova Y, Seminara A, Duncan-Lowey B, Forster E, Zhou W, Booth C, Shen A, Kranzusch P, Hatzios S. A microbial transporter of the dietary antioxidant ergothioneine. Cell 2022, 185: 4526-4540.e18. PMID: 36347253, PMCID: PMC9691600, DOI: 10.1016/j.cell.2022.10.008.Peer-Reviewed Original ResearchConceptsInter-kingdom competitionHost-associated microbesIntracellular redox homeostasisGastric pathogen Helicobacter pyloriPathogen Helicobacter pyloriRedox regulationSmall molecule antioxidantsRedox homeostasisBiosynthetic pathwayColonization advantageUnappreciated mechanismLMW thiolsHost environmentHuman faecal bacteriaWeight thiolsCertain microorganismsAntioxidant ergothioneineGastrointestinal microbesMetabolite trimethylamine N-oxideMicrobesMillimolar levelsHuman tissuesErgothioneineTrimethylamine N-oxideFecal bacteriaA previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond
Medley BJ, Leclaire L, Thompson N, Mahoney KE, Pluvinage B, Parson MAH, Burke JE, Malaker S, Wakarchuk W, Boraston AB. A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond. Journal Of Biological Chemistry 2022, 298: 102439. PMID: 36049519, PMCID: PMC9513282, DOI: 10.1016/j.jbc.2022.102439.Peer-Reviewed Original ResearchConceptsUncharacterized proteinsCarbohydrate-binding moduleHuman gut microbiotaHost adaptationSubstrate recognitionCatalytic motifN-terminalHost healthGut environmentPeptidase activityHost mucinsNutrient sourceAkkermansia muciniphilaEnzymeKey membersPeptide bondProteinBacteriumActive siteGut microbiotaTn antigenPeptide backboneGenesMicrobesMetabolic interactions between disease-transmitting vectors and their microbiota
Song X, Zhong Z, Gao L, Weiss BL, Wang J. Metabolic interactions between disease-transmitting vectors and their microbiota. Trends In Parasitology 2022, 38: 697-708. PMID: 35643853, DOI: 10.1016/j.pt.2022.05.002.Peer-Reviewed Original ResearchConceptsDisease-transmitting vectorsSymbiotic microbesPathogen defenseHost biologyHematophagous arthropodsBacterial metabolic activitySand fliesArthropod vectorsImportant vectorAnimals/humansMetabolic interactionsEndogenous microbiotaTsetse fliesFliesRecent discoveryVector-borne diseasesBiologyMetabolic activityMosquitoesMicrobiotaDifferent arthropod vectorsArthropodsMicrobesOrganismsTicksThe metabolism and biotransformation of AFB1: Key enzymes and pathways
Wang L, Huang Q, Wu J, Wu W, Jiang J, Yan H, Huang J, Sun Y, Deng Y. The metabolism and biotransformation of AFB1: Key enzymes and pathways. Biochemical Pharmacology 2022, 199: 115005. PMID: 35318037, DOI: 10.1016/j.bcp.2022.115005.Peer-Reviewed Original ResearchConceptsAflatoxin aldehyde reductaseAspergillus parasiticusAspergillus flavusAflatoxin B<sub>1</sub>Glutathione-S-transferaseCytochrome P450sAspergillusDetoxification strategiesFood safetyMetabolismEnzymeBiotransformation of AFB1Metabolic fateDetoxificationHealth of humansEnvironmental-friendly approachDevelopment of protective strategiesNon-toxic productsParasiticusFlavusMicrobesBiotransformationAnimalsReductaseCytochrome
2021
Multivariate log‐contrast regression with sub‐compositional predictors: Testing the association between preterm infants' gut microbiome and neurobehavioral outcomes
Liu X, Cong X, Li G, Maas K, Chen K. Multivariate log‐contrast regression with sub‐compositional predictors: Testing the association between preterm infants' gut microbiome and neurobehavioral outcomes. Statistics In Medicine 2021, 41: 580-594. PMID: 34897772, DOI: 10.1002/sim.9273.Peer-Reviewed Original ResearchConceptsLinear log-contrast modelLog-contrast modelGut microbiomeGut microbiome of preterm infantsHypothesis testing procedureInfant gut microbiomeLinear constraintsCompositional covariatesInference proceduresMultivariate responsePenalization approachSimulation studyGroup structureMicrobiome dataIdentified microbesMicrobiome analysisTaxonomic hierarchyInference methodsPreterm infant studyTest procedureMicrobiomeMicrobesBiological understandingCovariatesFeature matrix
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