2020
Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water
Kulkarni P, Olson N, Bui A, Bradshaw R, Del Collo L, Hittle L, Handy E, Paulson J, Ghurye J, Nasko D, East C, Van Kessel J, Kniel K, Chiu P, Mongodin E, Pop M, Sharma M, Sapkota A. Zero-Valent Iron Sand Filtration Can Reduce Human and Plant Pathogenic Bacteria While Increasing Plant Growth Promoting Bacteria in Reclaimed Water. Frontiers In Environmental Science 2020, 8: 541921. DOI: 10.3389/fenvs.2020.541921.Peer-Reviewed Original ResearchProportion of open reading framesNitrogen-fixing bacterial generaZVI-sand filtrationPlant pathogenic genusPlant growth-promoting bacteriaPlant pathogenic bacteriaRRNA gene sequencesOpen reading frameMetagenomic shotgun sequencingExploratory functional analysisAntimicrobial susceptibility testingGrowth-promoting bacteriaBacterial community structureTetracycline-resistant E. coliReclaimed waterOxidative stress responseShotgun sequencingReading frameZVI-sandGene sequencesBacterial generaPathogenic generaBacterial communitiesIron-rich environmentsPromoting bacteria
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
2014
Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition
Pop M, Walker A, Paulson J, Lindsay B, Antonio M, Hossain M, Oundo J, Tamboura B, Mai V, Astrovskaya I, Bravo H, Rance R, Stares M, Levine M, Panchalingam S, Kotloff K, Ikumapayi U, Ebruke C, Adeyemi M, Ahmed D, Ahmed F, Alam M, Amin R, Siddiqui S, Ochieng J, Ouma E, Juma J, Mailu E, Omore R, Morris J, Breiman R, Saha D, Parkhill J, Nataro J, Stine O. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome Biology 2014, 15: r76. PMID: 24995464, PMCID: PMC4072981, DOI: 10.1186/gb-2014-15-6-r76.Peer-Reviewed Original ResearchConceptsMicrobiota compositionAnaerobic lineagesRRNA gene sequencesGut microbiota compositionLevels of PrevotellaDiarrhea-causing pathogensSevere diarrheal diseaseIntestinal microbiota compositionFecal microbiota compositionGene sequencesDiarrheal pathogensDiarrhea pathogensMolecular techniquesPathogensDiarrhea-free controlsGranulicatella speciesEscherichia/ShigellaDiarrheal diseaseLineagesMSD casesYears of ageBackgroundDiarrheal diseasesYoung childrenAssociated with MSDLow-income countries
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