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 chromatographyV3V4Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens
Chopyk J, Chattopadhyay S, Kulkarni P, Claye E, Babik K, Reid M, Smyth E, Hittle L, Paulson J, Cruz-Cano R, Pop M, Buehler S, Clark P, Sapkota A, Mongodin E. Mentholation affects the cigarette microbiota by selecting for bacteria resistant to harsh environmental conditions and selecting against potential bacterial pathogens. Microbiome 2017, 5: 22. PMID: 28202080, PMCID: PMC5312438, DOI: 10.1186/s40168-017-0235-0.Peer-Reviewed Original ResearchConceptsQuantitative Insights Into Microbial EcologyResistant to harsh environmental conditionsBacterial pathogensHarsh environmental conditionsV3-V4 hypervariable regionIllumina MiSeq platformHuman bacterial pathogensBacterial community profilesBacterial community richnessPotential bacterial pathogensEnvironmental conditionsRRNA geneMiSeq platformAbundant generaBacterial microbiotaBacterial communitiesMicrobial ecologyGenomic DNACommunity richnessBacterial compositionHypervariable regionPCR amplificationCommunity profilesPseudomonas putidaLysis protocol
2013
Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection
Lindsay B, Pop M, Antonio M, Walker A, Mai V, Ahmed D, Oundo J, Tamboura B, Panchalingam S, Levine M, Kotloff K, Li S, Magder L, Paulson J, Liu B, Ikumapayi U, Ebruke C, Dione M, Adeyemi M, Rance R, Stares M, Ukhanova M, Barnes B, Lewis I, Ahmed F, Alam M, Amin R, Siddiqui S, Ochieng J, Ouma E, Juma J, Mailu E, Omore R, O'Reilly C, Hannis J, Manalili S, DeLeon J, Yasuda I, Blyn L, Ranken R, Li F, Housley R, Ecker D, Hossain M, Breiman R, Morris J, McDaniel T, Parkhill J, Saha D, Sampath R, Stine O, Nataro J. Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection. Journal Of Clinical Microbiology 2013, 51: 3263-3269. PMID: 23884998, PMCID: PMC3811648, DOI: 10.1128/jcm.01342-13.Peer-Reviewed Original ResearchConceptsEnteroaggregative Escherichia coliEnteropathogenic E. coliEnterotoxigenic E. coliDNA samplesShigella sppGoldenGate assaySequencing of 16S rRNA genesRRNA gene sequencesBiosensor assayCultivation-based assaysMolecular technologiesStool samplesIdentification of pathogensBacterial pathogen detectionDetect bacterial pathogensEnzyme-linked immunosorbent assay (ELISA)-based methodVirulence genesRRNA geneVirulence factorsGene sequencesBacterial pathogensDiarrheal pathogensEnteric pathogensPathogen detectionDNA