Featured Publications
Bacteria surfing the elastic wave
Nijjer J, Cohen T, Yan J. Bacteria surfing the elastic wave. Nature Physics 2022, 19: 6-7. DOI: 10.1038/s41567-022-01862-y.Peer-Reviewed Original ResearchSocial evolution of shared biofilm matrix components
Tai J, Mukherjee S, Nero T, Olson R, Tithof J, Nadell C, Yan J. Social evolution of shared biofilm matrix components. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2123469119. PMID: 35771939, PMCID: PMC9271185, DOI: 10.1073/pnas.2123469119.Peer-Reviewed Original ResearchConceptsBiofilm matrix componentsCooperative public goodsMatrix componentsBiofilm formationBiofilm matrix proteinsMatrix productionSocial evolution theoryBiofilm spatial structureCell surface adhesionEvolutionary timescalesCell clustersRelatedness coefficientsBacterial communitiesBiofilm habitatAdhesion proteinsEvolutionary advantageEvolutionary stabilityMatrix proteinsAssociated analysis toolsDiffusible compoundsHost environmentSocial evolutionUbiquitous modeOutstanding questionsProteinMechanical Resilience of Biofilms toward Environmental Perturbations Mediated by Extracellular Matrix
Zhang Q, Nguyen D, Tai J, Xu X, Nijjer J, Huang X, Li Y, Yan J. Mechanical Resilience of Biofilms toward Environmental Perturbations Mediated by Extracellular Matrix. Advanced Functional Materials 2022, 32 DOI: 10.1002/adfm.202110699.Peer-Reviewed Original ResearchMechanical resilienceNonlinear viscoelastic behaviorMaterials science pointLarge shear forcesBiofilm removal strategiesMechanical behaviorViscoelastic materialsViscoelastic behaviorBiofilm mechanicsSoft materialsStructure-property relationshipsRheological regimesRheological measurementsShear forceFunctional soft materialsLarge mechanical perturbationsPhysical insightPolymeric networkRemoval strategiesDynamics simulationsMolecular dynamics simulationsMaterialsDynamic environmentMatrixMechanical perturbationsMechanical 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 ResearchConceptsVibrio cholerae biofilmsSurface-attached aggregatesBacterial communitiesCell-surface interactionsDevelopmental processesBiofilm developmentBacterial cellsCell reorientationExtracellular matrixNonadherent mutantsDifferential growthBacterial biofilmsMechanical forcesBiofilmsBacterial growthDifferential orderingCellsGrowthMutantsLarge collectionMorphogenesis and cell ordering in confined bacterial biofilms
Zhang Q, Li J, Nijjer J, Lu H, Kothari M, Alert R, Cohen T, Yan J. Morphogenesis and cell ordering in confined bacterial biofilms. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2107107118. PMID: 34330824, PMCID: PMC8346881, DOI: 10.1073/pnas.2107107118.Peer-Reviewed Original ResearchConceptsInherent developmental programsBiofilm-dwelling cellsBiofilm-forming speciesSingle-cell imagingDevelopmental programSpecific matrix componentsCell orderingBiofilm developmentSpherical biofilmsBacterial cellsCell communityExtracellular matrixBiofilm morphologyBacterial biofilmsBiophysical mechanismsMatrix componentsHost tissuesBiofilmsBiofilm growthStiff gelsCellsMorphogenesisMutagenesisSpeciesVibrio
2024
Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms
Li C, Nijjer J, Feng L, Zhang Q, Yan J, Zhang S. Agent-based modeling of stress anisotropy driven nematic ordering in growing biofilms. Soft Matter 2024, 20: 3401-3410. PMID: 38563244, PMCID: PMC11041162, DOI: 10.1039/d3sm01535a.Peer-Reviewed Original ResearchConceptsStress anisotropyShear stressShear stress relaxationHigh shear stressLow shear stressHydrostatic stressStress relaxationBiomedical applicationsTime delayComplex multicellular patternsMicroscopy imagesSpatial organization of cellsThree-dimensionalCell orderingNematic orderOrganization of cellsMulticellular patternsSpatiotemporal correlationAgarose gelBacterial biofilmsStressBiofilmStress landscapeGrowth conditionsAnisotropyLipoarabinomannan mediates localized cell wall integrity during division in mycobacteria
Sparks I, Kado T, Prithviraj M, Nijjer J, Yan J, Morita Y. Lipoarabinomannan mediates localized cell wall integrity during division in mycobacteria. Nature Communications 2024, 15: 2191. PMID: 38467648, PMCID: PMC10928101, DOI: 10.1038/s41467-024-46565-5.Peer-Reviewed Original ResearchConceptsCell wall integrityWall integrityRod cell shapeCell envelope integrityHost-pathogen interactionsCell envelope componentsClinically relevant pathogensAssociated with divisionBiosynthetic mutantsEnvelope integritySubcellular locationMycobacterium smegmatisOld poleMulti-septateCell shapeMutantsBacterial modelRelevant pathogensSeptal placementPhysiological functionsMycobacterium tuberculosisEnvelope componentsMycobacteriaLipoarabinomannanDiderm
2023
Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization
Huang X, Nero T, Weerasekera R, Matej K, Hinbest A, Jiang Z, Lee R, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng W, Malaker S, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nature Communications 2023, 14: 2104. PMID: 37055389, PMCID: PMC10102183, DOI: 10.1038/s41467-023-37660-0.Peer-Reviewed Original ResearchConceptsBiofilm matrix exopolysaccharideFacilitate host colonizationVibrio cholerae biofilmsΒ-propeller domainMatrix exopolysaccharideModular domainsHost colonizationRedundant rolesDistinct functionsAbiotic surfacesAdhesive proteinsHost surfaceHuman pathogensVibrio choleraeAdhesinsBacterial biofilmsHost tissuesColonization modelColonizationBAP1BiofilmsPathogensAntibiotic resistanceRBMCDomainNew Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology
Tai J, Ferrell M, Yan J, Waters C. New Insights into Vibrio cholerae Biofilms from Molecular Biophysics to Microbial Ecology. Advances In Experimental Medicine And Biology 2023, 1404: 17-39. PMID: 36792869, PMCID: PMC10726288, DOI: 10.1007/978-3-031-22997-8_2.Peer-Reviewed Original ResearchConceptsV. cholerae biofilmsBacterial signal transduction networkSignal transduction networksBiofilm formationVibrio cholerae biofilmsKey model systemV. choleraeEcological roleMicrobial ecologyTransduction networksBiofilm maturationEnvironmental survivalCholera pathogenesisMolecular biophysicsRegulatory systemVibrio choleraeEl Tor biotypeBacterial surface attachmentRecent insightsModel systemBiofilmsLife cycleSurface attachmentCholeraeCentral functionMechanical Characterization and Single‐Cell Imaging of Bacterial Biofilms
Moreau A, Mukherjee S, Yan J. Mechanical Characterization and Single‐Cell Imaging of Bacterial Biofilms. Israel Journal Of Chemistry 2023, 63 DOI: 10.1002/ijch.202200075.Peer-Reviewed Original Research
2022
Interfacial cavitation
Henzel T, Nijjer J, Chockalingam S, Wahdat H, Crosby A, Yan J, Cohen T. Interfacial cavitation. PNAS Nexus 2022, 1: pgac217. PMID: 36714841, PMCID: PMC9802248, DOI: 10.1093/pnasnexus/pgac217.Peer-Reviewed Original ResearchInterfacial failureInterfacial cavitationAdditive manufacturing methodCritical applied loadIndependent material propertiesMultimaterial compositesConstitutive modelDuctile metalsUnstable propagationApplied loadManufacturing methodsMaterial propertiesCavitation limitCavitation modeElastic responseUltimate failureCavitationModern materialsCritical pressureDominant mechanismSuch interfacesInterfaceMaterialsHomogeneous mediumExperimental systemMolecular Mechanism of Vibrio cholerae biofilm adhesion
Weerasekera R, Hinbest A, Nero T, Huang X, Yan J, Olson R. Molecular Mechanism of Vibrio cholerae biofilm adhesion. The FASEB Journal 2022, 36 DOI: 10.1096/fasebj.2022.36.s1.l7499.Peer-Reviewed Original ResearchΒ-prism domainV. cholerae biofilmsBiofilm matrixAbiotic surfacesCommunity of microorganismsComplex N-glycansΒ-propeller domainHost colonizationSequence identityAdhesion proteinsDistinct functionsMolecular mechanismsN-glycansBacterial cellsFunctional assaysHost surfaceVirulence factorsVibrio choleraeProteinMain proteinsV. choleraeSpecific adhesion moleculesBiofilmsBAP1CholeraeImpact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement
Barrasso K, Chac D, Debela M, Geigel C, Steenhaut A, Seda A, Dunmire C, Harris J, Larocque R, Midani F, Qadri F, Yan J, Weil A, Ng W. Impact of a human gut microbe on Vibrio cholerae host colonization through biofilm enhancement. ELife 2022, 11: e73010. PMID: 35343438, PMCID: PMC8993218, DOI: 10.7554/elife.73010.Peer-Reviewed Original ResearchConceptsGut microbesOutcome of infectionHuman intestinal microbiotaMurine small intestineUninfected personsEnteric infectionsDisease outcomeIntestinal microbiotaSmall intestineHuman gut microbesCommensal bacteriumEtiological agentOutcomesDiarrheal disease choleraInfectionDisease choleraRecent studiesAir-liquid interfaceBacterium altersBiofilm enhancementStoolIntestineBacterial 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 ResearchConceptsAlbuterol nebulizationNebulized therapyHome nebulizersCystic fibrosisChronic respiratory diseasesAerosolized medicationsLung infectionCF patientsRespiratory diseasePathogenic bacteriaPatientsNext Generation ImpactorClinical isolatesMedicationsLungPari LCTherapyAnonymous patientsClinical bacteriaNebulizationNebulizerAerosolizationPathogenic microbesDetachmentSubset of bacteriaNonlinear inclusion theory with application to the growth and morphogenesis of a confined body
Li J, Kothari M, Chockalingam S, Henzel T, Zhang Q, Li X, Yan J, Cohen T. Nonlinear inclusion theory with application to the growth and morphogenesis of a confined body. Journal Of The Mechanics And Physics Of Solids 2022, 159: 104709. DOI: 10.1016/j.jmps.2021.104709.Peer-Reviewed Original ResearchApproximate equilibrium solutionsMinimal analytical modelFinite element computationsJ.D. EshelbyInclusion theoryEquilibrium solutionNonlinear material responseOnset of damageCelebrated contributionsElement computationsTheoretical difficultiesTransformation of shapePhase transitionHomogenization methodFracture mechanicsExperimental observationsMechanical behaviorMaterial responseLarge deformationAnalytical modelMaterial systemElastic stressesTransformation strainMechanicsTheoretical model
2021
Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces
Jiang Z, Nero T, Mukherjee S, Olson R, Yan J. Searching for the Secret of Stickiness: How Biofilms Adhere to Surfaces. Frontiers In Microbiology 2021, 12: 686793. PMID: 34305846, PMCID: PMC8295476, DOI: 10.3389/fmicb.2021.686793.Peer-Reviewed Original ResearchActive phase separation by turning towards regions of higher density
Zhang J, Alert R, Yan J, Wingreen N, Granick S. Active phase separation by turning towards regions of higher density. Nature Physics 2021, 17: 961-967. DOI: 10.1038/s41567-021-01238-8.Peer-Reviewed Original ResearchCO 2 -Driven diffusiophoresis for maintaining a bacteria-free surface
Shim S, Khodaparast S, Lai CY, Yan J, Ault JT, Rallabandi B, Shardt O, Stone HA. CO 2 -Driven diffusiophoresis for maintaining a bacteria-free surface. Soft Matter 2021, 17: 2568-2576. PMID: 33514979, DOI: 10.1039/d0sm02023k.Peer-Reviewed Original ResearchConceptsWild-type V. choleraeCell shapeBacterial cellsDirectional migrationV. choleraeCO2 gradientNonzero surface chargeP. aeruginosaCellsCO2 sourcesFlagellaCO2 concentration gradientBacteriaCholeraeDirectional responseBacteria-free surfaceGram stainMotilityAnti-biofouling surfacesConcentration gradientGradientAeruginosa
2020
Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates
Fei C, Mao S, Yan J, Alert R, Stone H, Bassler B, Wingreen N, Košmrlj A. Nonuniform growth and surface friction determine bacterial biofilm morphology on soft substrates. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 7622-7632. PMID: 32193350, PMCID: PMC7148565, DOI: 10.1073/pnas.1919607117.Peer-Reviewed Original ResearchConceptsBiofilm matrix productionBiofilm morphologyBacterial biofilmsAvailability of nutrientsDistinct spatiotemporal patternsImportant physiological consequencesAgar substrateMatrix productionMechanistic insightsPhysiological consequencesBiofilmsSoft substratesSimilar morphologyDiffusion of nutrientsPattern formation processNutrientsBasic mechanismsAgar concentrationEukaryotesMorphological patternsMorphogenesisFundamental determinantsOrganismsGrowthVibrio
2019
Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial Biofilms
Yan J, Bassler B. Surviving as a Community: Antibiotic Tolerance and Persistence in Bacterial Biofilms. Cell Host & Microbe 2019, 26: 15-21. PMID: 31295420, PMCID: PMC6629468, DOI: 10.1016/j.chom.2019.06.002.Peer-Reviewed Original ResearchConceptsSurface-associated bacterial communitiesSingle-cell resolutionBiofilm formation processBiofilm resilienceBacterial communitiesPersister cellsAntibiotic toleranceBacterial toleranceBacterial biofilmsBiofilmsBacterial recurrenceToleranceAntibiotic resistanceRecent progressPersistencePhenotypeBiofilm eradicationNew strategyCommunityCellsHarmful role