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
2018
Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water
Kulkarni P, Olson N, Paulson J, Pop M, Maddox C, Claye E, Goldstein R, Sharma M, Gibbs S, Mongodin E, Sapkota A. Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water. The Science Of The Total Environment 2018, 639: 1126-1137. PMID: 29929281, PMCID: PMC8290890, DOI: 10.1016/j.scitotenv.2018.05.178.Peer-Reviewed Original ResearchConceptsWastewater treatment plantsTreatment plantsWastewater treatmentSpray irrigation siteMunicipal wastewater treatment plantU.S. wastewater treatment plantsConventional wastewater treatmentReclaimed waterIrrigated sitesCommunity structureBacterial communitiesFuture treatment technologiesOpen-air storageOn-site treatmentTreatment technologiesAlpha diversity of bacterial communitiesUltraviolet treatmentOperational taxonomic unitsRRNA gene sequencesInfluentBacterial community structureSprayWastewaterPumphouseWater recycling
2017
Simplified and representative bacterial community of maize roots
Niu B, Paulson J, Zheng X, Kolter R. Simplified and representative bacterial community of maize roots. Proceedings Of The National Academy Of Sciences Of The United States Of America 2017, 114: e2450-e2459. PMID: 28275097, PMCID: PMC5373366, DOI: 10.1073/pnas.1616148114.Peer-Reviewed Original ResearchConceptsCommunity assemblyBacterial communitiesDynamics of community assemblyComposition of plant microbiomesBacterial interspecies interactionsSynthetic bacterial communityPlant-associated microbesCulture-dependent methodsRoot microbiome assemblyHost-mediated selectionFusarium verticillioides</i>Maize rootsRoot microbiotaMicrobiome assemblyPlant microbiomeRoot microbiomePlant hostsHost genotypeKeystone speciesDominant phylaAbiotic factorsInterspecies interactionsModel ecosystemsMicrobiomeMaize seedlingsTemporal 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
2016
Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection
Morris A, Paulson J, Talukder H, Tipton L, Kling H, Cui L, Fitch A, Pop M, Norris K, Ghedin E. Longitudinal analysis of the lung microbiota of cynomolgous macaques during long-term SHIV infection. Microbiome 2016, 4: 38. PMID: 27391224, PMCID: PMC4939015, DOI: 10.1186/s40168-016-0183-0.Peer-Reviewed Original ResearchConceptsDevelopment of obstructive lung diseaseObstructive lung diseaseNon-human primate modelLung microbiomeSHIV infectionLung microbiotaRibosomal RNALung diseasePrimate modelNon-obstructive groupSHIV-infected animalsResponse to immunosuppressionBronchoalveolar lavage fluid samplesCynomolgous macaquesDevelopment of obstructive diseaseLavage fluid samplesMultiple other speciesSIV-HIVOral anaerobesOral bacteriaTropheryma whippleiObstructive diseaseCommunity compositionBacterial communitiesDisease onset