2025
Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms
Moreau A, Nguyen D, Hinbest A, Zamora A, Weerasekera R, Matej K, Zhou X, Sanchez S, Rodriguez Brenes I, Tai J, Nadell C, Ng W, Gordon V, Komarova N, Olson R, Li Y, Yan J. Surface remodeling and inversion of cell-matrix interactions underlie community recognition and dispersal in Vibrio cholerae biofilms. Nature Communications 2025, 16: 327. PMID: 39747177, PMCID: PMC11695861, DOI: 10.1038/s41467-024-55602-2.Peer-Reviewed Original ResearchMeSH KeywordsBacterial AdhesionBacterial ProteinsBiofilmsExtracellular MatrixPolysaccharide-LyasesPolysaccharides, BacterialVibrio choleraeConceptsCell-matrix interactionsCausative agent of choleraSurface-associated bacterial communitiesAgent of choleraV. cholerae cellsVibrio cholerae biofilmsSurface remodelingInvestigate cell-matrix interactionsBiofilm cellsBacterial communitiesVibrio choleraeBiofilm developmentBiofilmCausative agentBiofilm growthBiochemical analysisExtracellular matrixVibrioBiofilm ageCell dispersionMatrix componentsCholeraCellsRbmBShed light
2022
Bacterial Surface Detachment during Nebulization with Contaminated Reusable Home Nebulizers
Harris JC, Collins MS, Huang PH, Schramm CM, Nero T, Yan J, Murray TS. Bacterial Surface Detachment during Nebulization with Contaminated Reusable Home Nebulizers. Microbiology Spectrum 2022, 10: e02535-21. PMID: 35107362, PMCID: PMC8809330, DOI: 10.1128/spectrum.02535-21.Peer-Reviewed Original ResearchMeSH KeywordsAerosolsBacteriaBacterial AdhesionCystic FibrosisEquipment ContaminationHumansNebulizers and VaporizersConceptsAlbuterol nebulizationNebulized therapyHome nebulizersCystic fibrosisChronic respiratory diseasesAerosolized medicationsLung infectionCF patientsRespiratory diseasePathogenic bacteriaPatientsNext Generation ImpactorClinical isolatesMedicationsLungPari LCTherapyAnonymous patientsClinical bacteriaNebulizationNebulizerAerosolizationPathogenic microbesDetachmentSubset of bacteria
2021
Mechanical forces drive a reorientation cascade leading to biofilm self-patterning
Nijjer J, Li C, Zhang Q, Lu H, Zhang S, Yan J. Mechanical forces drive a reorientation cascade leading to biofilm self-patterning. Nature Communications 2021, 12: 6632. PMID: 34789754, PMCID: PMC8599862, DOI: 10.1038/s41467-021-26869-6.Peer-Reviewed Original ResearchMeSH KeywordsBacterial AdhesionBiofilmsBiomechanical PhenomenaModels, BiologicalMutationVibrio choleraeConceptsVibrio cholerae biofilmsSurface-attached aggregatesBacterial communitiesCell-surface interactionsDevelopmental processesBiofilm developmentBacterial cellsCell reorientationExtracellular matrixNonadherent mutantsDifferential growthBacterial biofilmsMechanical forcesBiofilmsBacterial growthDifferential orderingCellsGrowthMutantsLarge collectionRoadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation
Wong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O’Toole G, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Physical Biology 2021, 18: 10.1088/1478-3975/abdc0e. PMID: 33462162, PMCID: PMC8506656, DOI: 10.1088/1478-3975/abdc0e.Peer-Reviewed Original ResearchConceptsBacterial biofilmsPhysiology of microbesBiofilm microbiologyCommunities of bacteriaSingle-cell behaviorWork of physicistsAtomic physicsRecent important discoveriesNew physicsMatter physicsCellular organizationPhysical biologyPhysicsBiofilmsBiologyPhysicistsSurprising behaviorEnergy flowImportant discoveriesIntense attentionDivision of laborMicrobesMicrobiologyCommunity behaviorOpposite strategyThe Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis
Shen TD, Daniel SG, Patel S, Kaplan E, Phung L, Lemelle-Thomas K, Chau L, Herman L, Trisolini C, Stonelake A, Toal E, Khungar V, Bittinger K, Reddy KR, Wu GD. The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis. Gut Microbes 2021, 13: 1987781. PMID: 34747331, PMCID: PMC8583005, DOI: 10.1080/19490976.2021.1987781.Peer-Reviewed Original ResearchConceptsAlcohol-related cirrhosisRectal swabsBacterial culture studiesAssociated gut microbiomeCross-sectional analysisHost-derived metabolitesConcentration-dependent mannerAdult patientsMucosal microenvironmentCirrhosis etiologyPatient populationDifferent etiologiesColonic mucosaCirrhosisMucosal microbiotaGut microbiotaGut microbiomeAdherent microbiotaFecal microbiotaOxidative metabolitesSwabsStoolDisease statesEase of collectionCellular proliferation
2020
c-di-GMP modulates type IV MSHA pilus retraction and surface attachment in Vibrio cholerae
Floyd KA, Lee CK, Xian W, Nametalla M, Valentine A, Crair B, Zhu S, Hughes HQ, Chlebek JL, Wu DC, Hwan Park J, Farhat AM, Lomba CJ, Ellison CK, Brun YV, Campos-Gomez J, Dalia AB, Liu J, Biais N, Wong GCL, Yildiz FH. c-di-GMP modulates type IV MSHA pilus retraction and surface attachment in Vibrio cholerae. Nature Communications 2020, 11: 1549. PMID: 32214098, PMCID: PMC7096442, DOI: 10.1038/s41467-020-15331-8.Peer-Reviewed Original Research
2019
Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion
Ahearn C, Kirkham C, Chaves L, Kong Y, Pettigrew M, Murphy T. Discovery and Contribution of Nontypeable Haemophilus influenzae NTHI1441 to Human Respiratory Epithelial Cell Invasion. Infection And Immunity 2019, 87: 10.1128/iai.00462-19. PMID: 31427451, PMCID: PMC6803334, DOI: 10.1128/iai.00462-19.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseRespiratory epithelial cellsEnzyme-linked immunosorbent assayEpithelial cellsAirways of adultsObstructive pulmonary diseaseCell invasionHuman respiratory epithelial cellsNontypeable Haemophilus influenzaeCell enzyme-linked immunosorbent assayAlveolar epithelial cellsAcute exacerbationLower airwaysPulmonary diseaseSerum IgGNTHi strainsTherapeutic interventionsHaemophilus influenzaeHuman bronchialSurface-exposed epitopesEpithelial cell invasionIsogenic knockout mutantsNTHiImmunosorbent assayIntracellular survivalNew Twists and Turns in Bacterial Locomotion and Signal Transduction
Watts KJ, Vaknin A, Fuqua C, Kazmierczak BI. New Twists and Turns in Bacterial Locomotion and Signal Transduction. Journal Of Bacteriology 2019, 201: 10.1128/jb.00439-19. PMID: 31358610, PMCID: PMC6755736, DOI: 10.1128/jb.00439-19.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaBacterial AdhesionBacterial Physiological PhenomenaBacterial ProteinsCongresses as TopicFlagellaLocomotionSignal TransductionConceptsSignal transductionTwo-component signal transduction pathwayTwo-component signal transduction systemBacterial locomotionContribution of motilityCryo-electron tomographySignal transduction systemSystems biology approachSignal transduction pathwaysIndividual bacterial cellsMulticellular organismsProkaryotic organismsBiology approachChemosensory receptorsFlagellar motorPathogenic interactionsTransduction pathwaysTransduction systemIndividual proteinsSensing pathwaysProtein labelingBehavior of thousandsComplex ecosystemsProtein spaceLiving cellsLack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality
Park K, Greenwood-Quaintance K, Cunningham S, Rajagopalan G, Chia N, Jeraldo P, Mandrekar J, Patel R. Lack of correlation of virulence gene profiles of Staphylococcus aureus bacteremia isolates with mortality. Microbial Pathogenesis 2019, 133: 103543. PMID: 31102653, DOI: 10.1016/j.micpath.2019.103543.Peer-Reviewed Original ResearchMeSH KeywordsAgedAged, 80 and overAnimalsBacteremiaBacterial AdhesionBase SequenceCell ProliferationDrug Resistance, BacterialFemaleHLA-DR3 AntigenHumansImmune EvasionMaleMethicillin-Resistant Staphylococcus aureusMiceMice, TransgenicMiddle AgedMinnesotaPolymerase Chain ReactionStaphylococcal InfectionsStaphylococcus aureusSuperantigensVirulenceVirulence FactorsConceptsMethicillin-susceptible S. aureusS. aureus bacteremiaAureus bacteremiaMedical CenterHLA-DR3 transgenic miceStaphylococcus aureus bacteremiaMinnesota Medical CenterLarge medical centerImmune evasion genesVirulence genesVirulence gene profilesNumber of deathsClinical dataClinical valueTransgenic miceClinical practiceIndividual PCR assaysWhole-genome sequencing analysisMortalitySAg genesSurvivorsLack of correlationBacteremiaWGS analysisFunctional assays
2018
Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin
Murphy TF, Brauer AL, Pettigrew MM, LaFontaine ER, Tettelin H. Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. The Journal Of Infectious Diseases 2018, 219: 1448-1455. PMID: 30496439, PMCID: PMC6467191, DOI: 10.1093/infdis/jiy680.Peer-Reviewed Original ResearchConceptsChronic obstructive pulmonary diseaseObstructive pulmonary diseaseM. catarrhalisPulmonary diseaseMoraxella catarrhalisPersistent strainsDuration of persistenceHuman airwaysCatarrhalisCessation of expressionAirwayMajor pathogenPatientsBacterial pathogensDiseaseVirulence-associated phenotypesAdultsCollected strainsMost strainsExpressionHuman cellsPathogensPathogenesisPersistenceMonthsBacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling
Yan J, Moreau A, Khodaparast S, Perazzo A, Feng J, Fei C, Mao S, Mukherjee S, Košmrlj A, Wingreen NS, Bassler BL, Stone HA. Bacterial Biofilm Material Properties Enable Removal and Transfer by Capillary Peeling. Advanced Materials 2018, 30: e1804153. PMID: 30368924, PMCID: PMC8865467, DOI: 10.1002/adma.201804153.Peer-Reviewed Original ResearchConceptsBiofilm removal strategiesMaterial propertiesBiofouling problemsInterfacial propertiesSurface foulingRheological characterizationIndustrial operationsMechanical protectionSurface analysisBiofilm-forming bacterial speciesMultiple surfacesBiofilm-dwelling cellsVibrio cholerae biofilmsSurface-attached communitiesSurfaceRemoval strategiesPropertiesFouling
2017
Structural basis of host recognition and biofilm formation by Salmonella Saf pili
Zeng L, Zhang L, Wang P, Meng G. Structural basis of host recognition and biofilm formation by Salmonella Saf pili. ELife 2017, 6: e28619. PMID: 29125121, PMCID: PMC5700814, DOI: 10.7554/elife.28619.Peer-Reviewed Original ResearchConceptsHost recognitionBiofilm formationNovel functionStructure-based mutantsSelf-association activityFunctional characterizationBiofilm formation assaysStructural basisBacterial aggregationFormation assaysCell aggregationPiliAdherence assaysColonizationSAXS characterizationAssaysMutantsSAFABacterial infectionsSAFDOligomerizationCrystal structureAggregationMechanismFormationTranscriptional Response of Respiratory Epithelium to Nontuberculous Mycobacteria
Matsuyama M, Martins A, Shallom S, Kamenyeva O, Kashyap A, Sampaio E, Kabat J, Olivier K, Zelazny A, Tsang J, Holland S. Transcriptional Response of Respiratory Epithelium to Nontuberculous Mycobacteria. American Journal Of Respiratory Cell And Molecular Biology 2017, 58: 241-252. PMID: 28915071, PMCID: PMC5806000, DOI: 10.1165/rcmb.2017-0218oc.Peer-Reviewed Original ResearchConceptsCholesterol biosynthesisUpregulation of genesRespiratory epitheliumGene expression signaturesCiliary genesTranscriptional responseRNA sequencingEpithelial cell infectionResponse genesInflammatory response genesHost responseCytokine/chemokine productionRespiratory epithelial cell culturesEpithelial cell culturesPulmonary nontuberculous mycobacteria (NTM) diseaseExpression signaturesMajor host responsesCytokines/chemokinesGenesRespiratory epithelial cellsCiliary functionNontuberculous mycobacteria diseaseCell infectionMultiplicity of infectionBiosynthesis
2016
Dynamic metabolic exchange governs a marine algal-bacterial interaction
Segev E, Wyche T, Kim K, Petersen J, Ellebrandt C, Vlamakis H, Barteneva N, Paulson J, Chai L, Clardy J, Kolter R. Dynamic metabolic exchange governs a marine algal-bacterial interaction. ELife 2016, 5: e17473. PMID: 27855786, PMCID: PMC5148602, DOI: 10.7554/elife.17473.Peer-Reviewed Original ResearchMeSH KeywordsAquatic OrganismsBacterial AdhesionCell SurvivalHaptophytaIndoleacetic AcidsRhodobacteraceaeTryptophanConceptsIndole-3-acetic acidAlgal cellsBacterial production of indole-3-acetic acidProduction of indole-3-acetic acidPhytohormone indole-3-acetic acidProgrammed Cell DeathPromote algal growthRoseobacter groupAlgal hostOxidative stress responseCoccolithophore physiologyMicro-algaeBacterial productionAlgal deathLaboratory model systemsCell deathAlgalAlgal growthMetabolic exchangeStress responsePopulation dynamicsBacteriaGrowth enhancementModel systemRoseobacterThe BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation
Schulte T, Mikaelsson C, Beaussart A, Kikhney A, Deshmukh M, Wolniak S, Pathak A, Ebel C, Löfling J, Fogolari F, Henriques-Normark B, Dufrêne YF, Svergun D, Nygren PÅ, Achour A. The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation. Scientific Reports 2016, 6: 32371. PMID: 27582320, PMCID: PMC5007671, DOI: 10.1038/srep32371.Peer-Reviewed Original ResearchConceptsPneumococcal biofilm formationBiofilm formationExtracellular DNAPneumococcal serine-rich repeat proteinRich repeat proteinElectrophoretic mobility shift assaysHuman pathogen Streptococcus pneumoniaeAdhesive matrix moleculesMobility shift assaysMicrobial surface componentsMajor human pathogen Streptococcus pneumoniaeN-terminal regionNon-globular structuresSerine-rich repeat proteinPathogen Streptococcus pneumoniaeHelical DNA structureRepeat proteinsHeterologous expressionCircular dichroism studiesBR domainShift assaysStructural insightsBiofilm matrixIntermolecular β-sheetsBacterial aggregationVibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging
Yan J, Sharo AG, Stone HA, Wingreen NS, Bassler BL. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: e5337-e5343. PMID: 27555592, PMCID: PMC5018804, DOI: 10.1073/pnas.1611494113.Peer-Reviewed Original ResearchMeSH KeywordsBacterial AdhesionBacterial ProteinsBiofilmsCell ProliferationHumansSingle-Cell AnalysisVibrio choleraeConceptsV. cholerae biofilmsSingle-cell live imagingSurface-associated bacterial communitiesVibrio cholerae biofilmsSingle-cell technologiesSingle founder cellRod-shaped bacteriaFounder cellsSingle geneBacterial communitiesLive imagingBiofilm architectureBiofilm componentsBiofilm structureCell heterogeneityIndividual cellsMatrix labelingMature biofilmsArt microscopy techniquesCompetition analysisBiofilmsSingle-cell resolution imagingGenesGrowth programCellsNeisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms
Wörmann ME, Horien CL, Johnson E, Liu G, Aho E, Tang CM, Exley RM. Neisseria cinerea isolates can adhere to human epithelial cells by type IV pilus-independent mechanisms. Microbiology 2016, 162: 487-502. PMID: 26813911, PMCID: PMC4891991, DOI: 10.1099/mic.0.000248.Peer-Reviewed Original ResearchMeSH KeywordsAdhesins, BacterialBacterial AdhesionCell LineEpithelial CellsFimbriae ProteinsGene DeletionHumansNeisseria cinereaNeisseria meningitidisConceptsHuman epithelial cellsN. cinereaFunction of piliEpithelial cellsType IV piliPathogen Neisseria meningitidisHost-pathogen interactionsClose taxonomic relationshipFormation of microcoloniesPilus-pilus interactionsGenome analysisTaxonomic relationshipsMajor pilinTfp expressionPilin expressionSpecies sharesPilin genePathogenic NeisseriaNon-pathogenic Neisseria speciesCell surfaceNeisseria cinereaCinereaRole of TFPGenesNon-pathogenic Neisseria
2013
Phylogeny and phenotypes of clinical and environmental Shiga toxin‐producing Escherichia coli O174
Zhang W, Nadirk J, Kossow A, Bielaszewska M, Leopold S, Witten A, Fruth A, Karch H, Ammon A, Mellmann A. Phylogeny and phenotypes of clinical and environmental Shiga toxin‐producing Escherichia coli O174. Environmental Microbiology 2013, 16: 963-976. PMID: 24034719, DOI: 10.1111/1462-2920.12234.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAnti-Bacterial AgentsBacterial AdhesionCattleCell LineChlorocebus aethiopsDrug Resistance, Multiple, BacterialEscherichia coli ProteinsGenotypeHumansIntestinal MucosaMolecular Sequence DataMultilocus Sequence TypingPhenotypePhylogenyShiga ToxinShiga-Toxigenic Escherichia coliVero CellsConceptsDifferent clinical outcomesHaemolytic uremic syndromeMultilocus sequence typingClinical outcomesUremic syndromeStx genotypesH antigensShiga toxinO174Animal reservoirsSequence typingIntimin geneDifferent serotypesVirulence factorsAdherence capacitySerotypesNegative STECSTECSequence typesPhenotypic heterogeneityNon-motile isolatesToxinIsolate originVirulence lociDifferent genotypes
2012
The GTPase Activity of FlhF Is Dispensable for Flagellar Localization, but Not Motility, in Pseudomonas aeruginosa
Schniederberend M, Abdurachim K, Murray TS, Kazmierczak BI. The GTPase Activity of FlhF Is Dispensable for Flagellar Localization, but Not Motility, in Pseudomonas aeruginosa. Journal Of Bacteriology 2012, 195: 1051-1060. PMID: 23264582, PMCID: PMC3571332, DOI: 10.1128/jb.02013-12.Peer-Reviewed Original ResearchConceptsFlagellar functionGTPase activityOpportunistic human pathogen Pseudomonas aeruginosaHuman pathogen Pseudomonas aeruginosaSignal recognition particlePathogen Pseudomonas aeruginosaSingle-cell assaysFlhF proteinFlagellar localizationFlagellar assemblyRecognition particleAbiotic environmentProtein dimerizationFlagellar rotationNucleotide bindingFlhFPoint mutantsSurface organellesSwimming motilityBacterial motilityP. aeruginosaBacillus subtilisPseudomonas aeruginosaEnzymatic activityHydrolytic activityThe heterogeneous motility of the Lyme disease spirochete in gelatin mimics dissemination through tissue
Harman MW, Dunham-Ems SM, Caimano MJ, Belperron AA, Bockenstedt LK, Fu HC, Radolf JD, Wolgemuth CW. The heterogeneous motility of the Lyme disease spirochete in gelatin mimics dissemination through tissue. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 3059-3064. PMID: 22315410, PMCID: PMC3286914, DOI: 10.1073/pnas.1114362109.Peer-Reviewed Original Research
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