2024
Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies
Sumboh J, Agyenkwa-Mawuli K, Schwinger E, Donkor I, Akorli J, Dwomoh D, Ashong Y, Osabutey D, Ababio F, Nusbaum O, Humphries D, Cappello M, Koram K, Kwofie S, Wilson M. Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies. American Journal Of Tropical Medicine And Hygiene 2024, 112: 561-570. PMID: 39813691, PMCID: PMC11884298, DOI: 10.4269/ajtmh.24-0384.Peer-Reviewed Original ResearchConceptsEffective cation exchange capacityCation exchange capacitySandy-loam soilDominant helminth speciesSoil samplesClay contentSoil parametersExchange capacityHelminth larvaeAnalysis of DNA sequencesGPS trackingSoilParastrongyloides trichosuriAssociated with exposureLarvaeChemical propertiesPotential sourcesMovement dataSpeciesPredominant speciesHelminth speciesLarval countsMetagenomic technologiesDNA sequencesMetagenomic analysisMetagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice
Chen H, Huang S, Zhao Y, Sun R, Wang J, Yao S, Huang J, Yu Z. Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice. Microbiology Spectrum 2024, 12: e03735-23. PMID: 38441977, PMCID: PMC10986500, DOI: 10.1128/spectrum.03735-23.Peer-Reviewed Original ResearchConceptsTaxonomic compositionGut microbiomeIntestinal microbiomeFunctional genesKEGG OrthologyMetagenomic analysisIntestinal microbiotaRegulatory mechanismsFunction of gut microbiomeComposition of gut microbiotaAbundance of functional genesMetagenomic sequencingGene functionGut microbiotaPotential regulatory mechanismSpecies levelIntervention of probioticsBacillus amyloliquefaciensMicrobiomeGenesMicrobiotaHost immune responseProbiotic interventionMetabolic reactionsSchistosoma japonicum</i>
2023
New insight into the granule formation in the reactor for enhanced biological phosphorus removal
Pelevina A, Gruzdev E, Berestovskaya Y, Dorofeev A, Nikolaev Y, Kallistova A, Beletsky A, Ravin N, Pimenov N, Mardanov A. New insight into the granule formation in the reactor for enhanced biological phosphorus removal. Frontiers In Microbiology 2023, 14: 1297694. PMID: 38163067, PMCID: PMC10755871, DOI: 10.3389/fmicb.2023.1297694.Peer-Reviewed Original ResearchPhosphate-accumulating organismsSequencing batch reactorBiological phosphorus removalGlycogen accumulating organismsPhosphorus removalLaboratory sequencing batch reactorEfficiency of phosphorus removalProcess of granule formationActivated sludge flocsSludge flocsBatch reactorAggregate typeHigh efficiencyGranule formationReactorMicrobial taxonomic compositionPhysicochemical processesTaxonomic compositionMorphotype IIMetagenomic analysisSuccession of communitiesMorphotype IMicrobial communitiesBacterial cellsEBPR
2022
Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection
Cen L, Chang Y, Bedree JK, Ma Y, Zhong Q, Utter DR, Dong PT, Lux R, Bor B, Liu J, McLean JS, Le S, He X. Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection. Journal Of Virology 2022, 96: e01063-22. PMID: 36000841, PMCID: PMC9472602, DOI: 10.1128/jvi.01063-22.Peer-Reviewed Original ResearchConceptsLytic transglycosylaseLytic phagesPhage receptorsOral phageRemarkable host specificityHuman oral microbiomeSimilar expression levelsPeptidoglycan remodelingWhole-genome sequencingMutant backgroundBacterial physiologyHost specificityMicrobial communitiesSurface-grown cellsPhage populationsSensitive phenotypeBacterial hostsOral microbiomePeptidoglycan structureWild typeMetagenomic analysisMutantsSpontaneous mutantsXH001Frameshift mutationMicrobial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival
Nikolaev Y, Yushina Y, Mardanov A, Gruzdev E, Tikhonova E, El-Registan G, Beletskiy A, Semenova A, Zaiko E, Bataeva D, Polishchuk E. Microbial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival. Microorganisms 2022, 10: 1583. PMID: 36014001, PMCID: PMC9415349, DOI: 10.3390/microorganisms10081583.Peer-Reviewed Original ResearchMeat processing plantsSurfaces of technological equipmentSimilarity of cellsHeterogeneity of cellsTaxonomic compositionFood productsMetagenomic analysisFood qualityAnimal pathogensMorphological similarityBacteria survivalBiofilm bacteriaRuthenium red stainingBiofilmMicrobial biofilmsUnique familyStructural organizationFoodCutting tableBacterial infectionsPlantsBacteriaRaw materialsDiversityElectron microscopic studiesNew Insight Into the Interspecies Shift of Anammox Bacteria Ca. “Brocadia” and Ca. “Jettenia” in Reactors Fed With Formate and Folate
Kallistova A, Nikolaev Y, Grachev V, Beletsky A, Gruzdev E, Kadnikov V, Dorofeev A, Berestovskaya J, Pelevina A, Zekker I, Ravin N, Pimenov N, Mardanov A. New Insight Into the Interspecies Shift of Anammox Bacteria Ca. “Brocadia” and Ca. “Jettenia” in Reactors Fed With Formate and Folate. Frontiers In Microbiology 2022, 12: 802201. PMID: 35185828, PMCID: PMC8851195, DOI: 10.3389/fmicb.2021.802201.Peer-Reviewed Original ResearchAnammox bacteriaNitrogen removal rateAnaerobic ammonium oxidationAnammox bacteria CaAnammox processBatch reactorAnammox speciesRemoval rateAnammoxAmmonium loadingEffect of formationAmmonium oxidationReactorComparative genome analysisRRNA gene profilingBacteria CaDissimilatory nitrate reductionGenomic analysisLow temperaturesMetagenomic analysisMicrobial communitiesEnvironmental fluctuationsGene profilesJetteniaBacteria
2016
Privacy-preserving microbiome analysis using secure computation
Wagner J, Paulson J, Wang X, Bhattacharjee B, Corrada Bravo H. Privacy-preserving microbiome analysis using secure computation. Bioinformatics 2016, 32: 1873-1879. PMID: 26873931, PMCID: PMC4908319, DOI: 10.1093/bioinformatics/btw073.Peer-Reviewed Original ResearchConceptsDNA of micro-organismsMicrobiome research communityPrivacy concernsSensitive attributesResearch participant dataFeature countsSharing dataSupplementary dataMetagenomic analysisResearch datasetsMicrobiome sequencingSequencing studiesMicrobial DNAHuman DNAResearch communityMicrobiome analysisMicrobiomeDNAAnalysis toolsDatasetComputerMicro-organismsBioinformaticsImplementationIndividual collections
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