2018
Meta-analysis of the lung microbiota in pulmonary tuberculosis
Hong B, Paulson J, Stine O, Weinstock G, Cervantes J. Meta-analysis of the lung microbiota in pulmonary tuberculosis. Tuberculosis 2018, 109: 102-108. PMID: 29559113, DOI: 10.1016/j.tube.2018.02.006.Peer-Reviewed Original ResearchConceptsSpecies signatureNext generation sequencing dataLung microbiotaGeneration sequencing dataClustering of microbiotaMycobacterium tuberculosisCaulobacter henriciiLung microbiota compositionSequence dataBody nichesR. mucilaginosaMicrobiota compositionSputum microbiotaActinomyces graevenitziiBioinformatics analysisMicrobiotaRothia mucilaginosaTB patientsHealthy controlsTB casesAssociated with pulmonary TBHaemophilus parahaemolyticusMeta-analysisLower respiratory tractBody sites
2016
Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
Pop M, Paulson J, Chakraborty S, Astrovskaya I, Lindsay B, Li S, Bravo H, Harro C, Parkhill J, Walker A, Walker R, Sack D, Stine O. Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment. BMC Genomics 2016, 17: 440. PMID: 27277524, PMCID: PMC4898365, DOI: 10.1186/s12864-016-2777-0.Peer-Reviewed Original ResearchConceptsGene sequencesBackgroundEnterotoxigenic Escherichia coliHuman gut microbiotaRRNA gene sequencesEnterotoxigenic Escherichia coliHuman intestinal microbiotaFecal E. coliCiprofloxacin treatmentETEC infectionETEC diarrheaRibosomal RNAGut microbiotaFecal microbiotaIntestinal microbiotaE. coliMicrobiotaMonthly follow-up visitsCompared to variationsETECFollow-up visitQuantitative PCRHuman challenge studiesCiprofloxacinQuantitative culturesSequence
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