2025
Body mass index and benign prostatic hyperplasia correlate with urinary microbiome diversity and lower urinary tract symptoms in men
Bowie K, Garzotto M, Orwoll E, Karstens L. Body mass index and benign prostatic hyperplasia correlate with urinary microbiome diversity and lower urinary tract symptoms in men. Communications Medicine 2025, 5: 159. PMID: 40328908, PMCID: PMC12056106, DOI: 10.1038/s43856-025-00866-y.Peer-Reviewed Original ResearchLower urinary tract symptomsBenign prostatic hyperplasiaUrinary tract symptomsBody mass indexUrinary microbiomeProstatic hyperplasiaMass indexAssociated with lower urinary tract symptomsLower urinary tractAbsence of infectionCohort of menOsteoporotic fracturesUrinary tractClinical characteristicsSignificant associationBackgroundSeveral studiesUrine samplesHyperplasiaSymptomsStudy designIllumina MiSeqRRNA geneAlpha diversityMenMicrobiome diversity
2022
Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways
Rafei R, Koong J, Osman M, Al Atrouni A, Hamze M, Hamidian M. Analysis of pCl107 a large plasmid carried by an ST25 Acinetobacter baumannii strain reveals a complex evolutionary history and links to multiple antibiotic resistance and metabolic pathways. FEMS Microbes 2022, 3: xtac027. PMID: 37332503, PMCID: PMC10117892, DOI: 10.1093/femsmc/xtac027.Peer-Reviewed Original ResearchComplex evolutionary historyEvolutionary historyMetabolic pathwaysHybrid assembly approachConjugative transfer systemOxford Nanopore sequencingLarge plasmidsMetabolic modulesComplete sequenceMetabolism modulesAntibiotic resistance genesAncestral structureIllumina MiSeqNanopore sequencingResistance genesPossible ancestorAntibiotic resistanceGlobal clone 2PlasmidMultiple antibiotic resistanceClone 2Important pathogenResistance islandsKb plasmidSequence typesDiversity and distribution of MHC class I and II alleles in chicken populations worldwide
Martin R, Tregaskes C, Kaufman J. Diversity and distribution of MHC class I and II alleles in chicken populations worldwide. Molecular Immunology 2022, 150: 27. DOI: 10.1016/j.molimm.2022.05.092.Peer-Reviewed Original ResearchMinimal essential MHCClass II lociPeptide binding specificityPopulation bottlenecksClass II genesFancy breedsIllumina MiSeqPopulation geneticsLinkage disequilibriumCommercial flocksLow diversityChicken populationsArtificial selectionBinding specificityFree-range local chickensExon 2Genetic associationII lociHaplotypesResponse to infectionTapasin geneII genesTranslocation specificityExpress class II genesMHC alleles
2021
Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain
Liepa R, Mann R, Osman M, Hamze M, Gunawan C, Hamidian M. Cl415, a carbapenem-resistant Acinetobacter baumannii isolate containing four AbaR4 and a new variant of AbGRI2, represents a novel global clone 2 strain. Journal Of Antimicrobial Chemotherapy 2021, 77: 345-350. PMID: 34741594, PMCID: PMC8809195, DOI: 10.1093/jac/dkab399.Peer-Reviewed Original ResearchConceptsWhole genome sequencesWide geographical distributionGene complementNovel variantsPhylogenetic analysisGenomic analysisNew lineageComplete genomeOxford NanoporeIllumina MiSeqGenetic contextResistance genesGenesAntibiotic resistance determinantsResistance phenotypeGeographical distributionCopiesAntibiotic resistance phenotypesResistance islandsGlobal distributionResistance determinantsComM geneAntibiotic resistanceSubcladesVariants
2018
Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species
Kim J, Lim H, Shin S, Cha H, Seo J, Kim S, Park S, Son G. Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species. Scientific Data 2018, 5: 180220. PMID: 30398471, PMCID: PMC6219405, DOI: 10.1038/sdata.2018.220.Peer-Reviewed Original ResearchConceptsGenome informationSarcophaga peregrinaFly speciesSequence informationS. peregrinaComprehensive transcriptome analysisPrecise sequence informationDe novo assemblyMinimal postmortem intervalImportant fly speciesPrimary sequence informationGene expression datasetsFunctional annotationGenome databaseNovo assemblyTranscriptome analysisGene OntologyKyoto EncyclopediaRaw readsRNA sequencingRNA transcriptsIllumina MiSeqExpression datasetsForensic importanceUnigenes
2017
Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions
Chopyk J, Chattopadhyay S, Kulkarni P, Smyth E, Hittle L, Paulson J, Pop M, Buehler S, Clark P, Mongodin E, Sapkota A. Temporal Variations in Cigarette Tobacco Bacterial Community Composition and Tobacco-Specific Nitrosamine Content Are Influenced by Brand and Storage Conditions. Frontiers In Microbiology 2017, 08: 358. PMID: 28326071, PMCID: PMC5339245, DOI: 10.3389/fmicb.2017.00358.Peer-Reviewed Original ResearchOperational taxonomic unitsCore bacterial operational taxonomic unitsStorage conditionsBacterial operational taxonomic unitsV3V4 hypervariable regionBacterial community compositionTaxonomic unitsDay 0Illumina MiSeqRRNA geneCommunity compositionMicrobial ecosystemBacterial communitiesHypervariable regionTobacco-specific nitrosamine contentTime series experimentsBacillus pumilusNitrosamine contentAbundanceRelative humidityStorageIlluminaMiSeqLiquid chromatographyV3V4
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