2025
Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus
Yang Y, Yan J, Olson R, Jiang X. Comprehensive genomic and evolutionary analysis of biofilm matrix clusters and proteins in the Vibrio genus. MSystems 2025, 10: e00060-25. PMID: 40207939, PMCID: PMC12090793, DOI: 10.1128/msystems.00060-25.Peer-Reviewed Original ResearchMeSH KeywordsBacterial ProteinsBiofilmsEvolution, MolecularGenome, BacterialGenomicsMultigene FamilyPhylogenyVibrioConceptsGene clusterVibrio speciesEvolutionary analysisBiofilm dispersalBiofilm matrix proteinsVibrio cholerae</i>Genetic modificationTail proteinsVibrio genusCholera pathogenIdentified genesGene groupsVibrio cholerae</i>.Host functionsEvolutionary patternsBiofilm diversityBiofilm formationBiofilm proteinsBiofilm matrixVibrioBiofilm developmentEngineered biofilmsGenusStructural domainsAcute diarrheal diseaseEngineering a genomically recoded organism with one stop codon
Grome M, Nguyen M, Moonan D, Mohler K, Gurara K, Wang S, Hemez C, Stenton B, Cao Y, Radford F, Kornaj M, Patel J, Prome M, Rogulina S, Sozanski D, Tordoff J, Rinehart J, Isaacs F. Engineering a genomically recoded organism with one stop codon. Nature 2025, 639: 512-521. PMID: 39910296, PMCID: PMC11903333, DOI: 10.1038/s41586-024-08501-x.Peer-Reviewed Original ResearchA new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission
Sobkowiak B, Cudahy P, Chitwood M, Clark T, Colijn C, Grandjean L, Walter K, Crudu V, Cohen T. A new method for detecting mixed Mycobacterium tuberculosis infection and reconstructing constituent strains provides insights into transmission. Genome Medicine 2025, 17: 8. PMID: 39871355, PMCID: PMC11771024, DOI: 10.1186/s13073-025-01430-y.Peer-Reviewed Original ResearchConceptsShort-read WGS dataWhole-genome sequencingStrain sequencesWGS dataMultiple strainsStrain proportionsMycobacterium tuberculosis populationMixed infectionGenome sequenceBioinformatics pipelineClustering allele frequenciesDownstream analysisAllele frequenciesEvidence of mixed infectionSequenceTuberculosis populationStrainIsolatesIn vitroTransmission clustersMixed samplesAllelesInfectionMycobacterium tuberculosis infectionPathogens
2024
Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation
Machado L, Galán J. Loss of function of metabolic traits in typhoidal Salmonella without apparent genome degradation. MBio 2024, 15: e00607-24. PMID: 38572992, PMCID: PMC11077982, DOI: 10.1128/mbio.00607-24.Peer-Reviewed Original ResearchConceptsSalmonella enterica</i> serovar TyphiAdaptive convergent evolutionFunction of metabolic pathwaysAmino acid substitutionsConvergent evolutionMetabolic pathwaysParatyphi A.Paratyphi AHuman hostTranscriptional regulationAcid substitutionsMetabolic capabilitiesPoint mutationsParatyphoid feverTranscriptional regulatory proteinsMetabolic enzymesAffecting different genesPresence of point mutationsGenome degradationTyphoidal SalmonellaGlucose-6-phosphateCoding sequenceBioinformatics approachTyphiBacterial pathogens
2022
Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity
Khoder M, Osman M, Kassem I, Rafei R, Shahin A, Fournier P, Rolain J, Hamze M. Whole Genome Analyses Accurately Identify Neisseria spp. and Limit Taxonomic Ambiguity. International Journal Of Molecular Sciences 2022, 23: 13456. PMID: 36362240, PMCID: PMC9657967, DOI: 10.3390/ijms232113456.Peer-Reviewed Original ResearchConceptsDraft genomeComplete genome sequenceWhole-genome analysisNCBI GenBank databaseMatrix-assisted laser desorptionGenomic toolsPhylogenetic relationshipsTaxonomic ambiguityBacterial taxonomyGenome sequenceGenome analysisGenomic levelTaxonomic relationshipsTaxonomic toolGenBank databaseGenome sequencingGenomeLaser desorptionSpeciesNeisseria sppWGS analysisSppNeisseriaSequencingStrainsTranscriptome of Epibiont Saccharibacteria Nanosynbacter lyticus Strain TM7x During the Establishment of Symbiosis
Hendrickson EL, Bor B, Kerns KA, Lamont EI, Chang Y, Liu J, Cen L, Schulte F, Hardt M, Shi W, He X, McLean JS. Transcriptome of Epibiont Saccharibacteria Nanosynbacter lyticus Strain TM7x During the Establishment of Symbiosis. Journal Of Bacteriology 2022, 204: e00112-22. PMID: 35975994, PMCID: PMC9487520, DOI: 10.1128/jb.00112-22.Peer-Reviewed Original ResearchConceptsCandidate Phyla RadiationEstablishment of symbiosisStable symbiosisStress-related genesGene expressionReduced genomePeptidoglycan biosynthesisHost bacteriaHuman microbiomeBiosynthesis gene expressionMonophyletic radiationCell sizeEffector genesPartitioning genesObligate parasitesUnique organismsBiosynthetic pathwayHigher gene expressionCell shapeTransporter geneCell wallObligate epibiontsLow expressionSymbiosisCell cycleMachine-learning approaches prevent post-treatment resistance-gaining bacterial recurrences
Osman M, Mahieu R, Eveillard M. Machine-learning approaches prevent post-treatment resistance-gaining bacterial recurrences. Trends In Microbiology 2022, 30: 612-614. PMID: 35599112, DOI: 10.1016/j.tim.2022.05.006.Peer-Reviewed Original ResearchMetagenome assembly of high-fidelity long reads with hifiasm-meta
Feng X, Cheng H, Portik D, Li H. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods 2022, 19: 671-674. PMID: 35534630, PMCID: PMC9343089, DOI: 10.1038/s41592-022-01478-3.Peer-Reviewed Original ResearchMeSH KeywordsGenome, BacterialHigh-Throughput Nucleotide SequencingMetagenomeMicrobiotaSequence Analysis, DNASoftware
2020
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing
Knight JR, Dunne EM, Mulholland EK, Saha S, Satzke C, Tothpal A, Weinberger DM. Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing. Microbial Genomics 2020, 7: mgen000494. PMID: 33355528, PMCID: PMC8115901, DOI: 10.1099/mgen.0.000494.Peer-Reviewed Original ResearchDrug-Resistant Tuberculosis A Glance at Progress and Global Challenges
Dousa K, Kurz S, Bark C, Bonomo R, Furin J. Drug-Resistant Tuberculosis A Glance at Progress and Global Challenges. Infectious Disease Clinics Of North America 2020, 34: 863-886. PMID: 33011048, DOI: 10.1016/j.idc.2020.06.001.Peer-Reviewed Original ResearchConceptsSecond-line medicationsMultidrug-resistant Mycobacterium tuberculosisDrug susceptibility predictionOral formulationMultinational trialDrug resistancePublic health threatEconomic burdenDiagnostic techniquesTuberculosisAdequate clinical resourcesClinical resourcesHealth threatLaboratory services
2019
Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome
Carrión V, Perez-Jaramillo J, Cordovez V, Tracanna V, de Hollander M, Ruiz-Buck D, Mendes L, van Ijcken W, Gomez-Exposito R, Elsayed S, Mohanraju P, Arifah A, van der Oost J, Paulson J, Mendes R, van Wezel G, Medema M, Raaijmakers J. Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science 2019, 366: 606-612. PMID: 31672892, DOI: 10.1126/science.aaw9285.Peer-Reviewed Original ResearchMeSH KeywordsBacteriaBacterial Physiological PhenomenaBacteroidetesBeta vulgarisBiodiversityChitinasesDisease ResistanceEndophytesFlavobacteriumGenes, BacterialGenome, BacterialMetagenomeMicrobiotaMutagenesis, Site-DirectedPeptide SynthasesPlant DiseasesPlant RootsPolyketide SynthasesRhizoctoniaSoil MicrobiologyConceptsEndophytic root microbiomeNonribosomal peptide synthetasesGene clusterPolyketide synthaseRoot microbiomeBiosynthetic gene clusterInfection of plant rootsFungal root diseasesSite-directed mutagenesisPromote plant growthGenome reconstructionPeptide synthetasesRoot endosphereFunctional traitsNRPS-PKSFunctional diversityChitinase geneEndophytic consortiaFungal infectionsDisease suppressionRoot diseasePlant growthNetwork inferenceDisease-suppressive functionsPlant rootsDiscovery 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 survivalMapping human microbiome drug metabolism by gut bacteria and their genes
Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL. Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature 2019, 570: 462-467. PMID: 31158845, PMCID: PMC6597290, DOI: 10.1038/s41586-019-1291-3.Peer-Reviewed Original ResearchConceptsHuman gut bacteriaGut bacteriaHigh-throughput genetic analysisMicrobial gene productsDiverse cladeGene contentGenomic contentGene productsGenetic analysisMolecular mechanismsDrug metabolismBacteriaMultiple disease indicationsMetabolic activityDrug-metabolizing activityGut microbiomeMicrobiomeMetabolismDrug developmentMedical therapyTreatment delayMass spectrometryCladeDisease indicationsAdverse effects
2018
BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections
Allicock O, Guo C, Uhlemann A, Whittier S, Chauhan L, Garcia J, Price A, Morse S, Mishra N, Briese T, Lipkin W. BacCapSeq: a Platform for Diagnosis and Characterization of Bacterial Infections. MBio 2018, 9: 10.1128/mbio.02007-18. PMID: 30352937, PMCID: PMC6199491, DOI: 10.1128/mbio.02007-18.Peer-Reviewed Original ResearchConceptsHigh-throughput sequencingVirulence Factor DatabaseComprehensive Antibiotic Resistance DatabaseBacterial infectionsResistance genesAntimicrobial resistance genesHealth care costsHuman pathogenic speciesUnbiased high-throughput sequencingAntimicrobial sensitivity profileCharacterization of bacteriaDifferential diagnosisReal-time PCRBlood samplesCare costsCenter databaseTotal readsInappropriate useBacterial readsCapture sequencingBacterial speciesAntimicrobial resistanceVirulence determinantsVirulence factorsFactor databaseAn Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila
Shapiro L, Paulson J, Arnold B, Scully E, Zhaxybayeva O, Pierce N, Rocha J, Klepac-Ceraj V, Holton K, Kolter R. An Introduced Crop Plant Is Driving Diversification of the Virulent Bacterial Pathogen Erwinia tracheiphila. MBio 2018, 9: 10.1128/mbio.01307-18. PMID: 30279283, PMCID: PMC6168856, DOI: 10.1128/mbio.01307-18.Peer-Reviewed Original ResearchConceptsTemperate eastern North AmericaEastern North AmericaErwinia tracheiphila</i>,Host plant speciesPlant speciesCrop plantsCausal agent of bacterial wiltAgent of bacterial wiltVirulence gene repertoireLow genetic heterogeneityLarge-scale sequencingSusceptible to isolatesNorth AmericaDriving diversificationPhylogenomic analysisPopulation bottlenecksGenetic clustersEcological traitsIsolate collectionGene repertoirePopulation expansionGeographic rangeEvolutionary trajectoriesGenetic heterogeneityCausal agentGenomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Frontiers In Cellular And Infection Microbiology 2018, 8: 193. PMID: 29971217, PMCID: PMC6018220, DOI: 10.3389/fcimb.2018.00193.Peer-Reviewed Original ResearchConceptsSerovar CopenhageniPublic health relevanceSevere casesSerogroup IcterohaemorrhagiaeSerovar IcterohaemorrhagiaeWorldwide zoonosisHealth relevanceIcterohaemorrhagiaeCopenhageniVirulent strainHigh discriminatory powerSerovarsGlobal isolatesFrameshift mutationDiscriminatory powerFirst studyPathogenic speciesIsolatesSubcellular Organization: A Critical Feature of Bacterial Cell Replication
Surovtsev IV, Jacobs-Wagner C. Subcellular Organization: A Critical Feature of Bacterial Cell Replication. Cell 2018, 172: 1271-1293. PMID: 29522747, PMCID: PMC5870143, DOI: 10.1016/j.cell.2018.01.014.Peer-Reviewed Original ResearchConceptsSelf-replicating entitiesCellular lifeStructured genomesDynamic spatial patternsChallenge cellsIntracellular organellesCellular replicationCytoskeletal filamentsBacterial cellsUnique biological propertiesComplex internal organizationSpatial organizationSmall formsCell replicationActive transportLiving systemsBacteriaReplicationGenomeBiological propertiesCellsSpatial patternsOrganellesPowerful meansHallmarkLvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira
Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z, Santos L, Bisht V, Diggle P, Murray G, Adler B, Lopez F, Townsend JP, Groisman E, Picardeau M, Buschiazzo A, Ko AI. Lvr, a Signaling System That Controls Global Gene Regulation and Virulence in Pathogenic Leptospira. Frontiers In Cellular And Infection Microbiology 2018, 8: 45. PMID: 29600195, PMCID: PMC5863495, DOI: 10.3389/fcimb.2018.00045.Peer-Reviewed Original ResearchConceptsResponse regulatorTwo-component system proteinsDNA-binding response regulatorGlobal transcriptional regulationHybrid histidine kinaseGlobal gene regulationNovel signal pathwayComprehensive genomic analysisPhosphotransfer assaysTCS genesHistidine kinaseGene duplicationTranscriptional regulationGene regulationCorresponding genesPhylogenetic analysisGenomic analysisMolecular basisMutant strainSystem proteinsSignaling systemInfection processGenesBranched pathwayVirulence
2017
Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon
Zaki N, Salloum T, Osman M, Rafei R, Hamze M, Tokajian S. Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon. FEMS Microbiology Letters 2017, 364: fnx199. PMID: 28961704, DOI: 10.1093/femsle/fnx199.Peer-Reviewed Original ResearchConceptsGenome analysisLateral gene transferComparative genome analysisDraft genome sequencingWhole-genome single nucleotide polymorphism (SNP) analysisB. melitensisZoonotic disease brucellosisDepth genomic characterizationMultiple virulence determinantsSingle nucleotide polymorphism analysisNucleotide polymorphism analysisSequence divergenceGenome comparisonGenomic islandsSingle nucleotide polymorphismsGenetic variationGenomic characterizationDisease brucellosisGene transferMobile elementsGenomic insights into the ancient spread of Lyme disease across North America
Walter KS, Carpi G, Caccone A, Diuk-Wasser MA. Genomic insights into the ancient spread of Lyme disease across North America. Nature Ecology & Evolution 2017, 1: 1569-1576. PMID: 29185509, PMCID: PMC6431794, DOI: 10.1038/s41559-017-0282-8.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsArachnid VectorsBorrelia burgdorferiCanadaEvolution, MolecularGenetic VariationGenome, BacterialIxodesLyme DiseaseUnited StatesConceptsHistory of spreadEvolutionary historyNorth AmericaLyme disease epidemicLast Glacial MaximumAncient spreadLyme disease bacteriaComplex evolutionary historyPast centuryGlacial MaximumHistoryGenomic insightsEvolutionary changeAmericaUndocumented levelB. burgdorferi s.Large collectionSensu strictoBurgdorferi s.Vector-borne diseasesSouthern CanadaLand use changeBorrelia burgdorferi sensu strictoCenturyDisease bacteria
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