Featured Publications
Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants
Paulson J, Williams B, Hehnly C, Mishra N, Sinnar S, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge D, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell L, Burgoine K, Couto-Rodriguez M, Ericson J, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs A, Kaaya B, Kangere S, Kulkarni A, Kumbakumba E, Li X, Limbrick D, Magombe J, Morton S, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson M, Roy F, Sheldon K, Townsend R, Weeks A, Whalen A, Quackenbush J, Ssenyonga P, Galperin M, Almeida M, Atkins H, Warf B, Lipkin W, Broach J, Schiff S. Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Science Translational Medicine 2020, 12 PMID: 32998967, PMCID: PMC7774825, DOI: 10.1126/scitranslmed.aba0565.Peer-Reviewed Original ResearchConceptsPostinfectious hydrocephalusCSF samplesPIH casesPotential causative organismsCerebrospinal fluid accumulationCytomegalovirus coinfectionUgandan infantsNeonatal sepsisSurgical palliationNeonatal infectionInfant casesOptimal treatmentInfant cohortCommon causeCausative organismPediatric hydrocephalusFluid accumulationHydrocephalusAnaerobic bacterial isolatesControl casesInfectionFacultative anaerobic bacterial isolatesInfantsParasitic DNADiseaseDifferential abundance analysis for microbial marker-gene surveys
Paulson J, Stine O, Bravo H, Pop M. Differential abundance analysis for microbial marker-gene surveys. Nature Methods 2013, 10: 1200-1202. PMID: 24076764, PMCID: PMC4010126, DOI: 10.1038/nmeth.2658.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsArea Under CurveCluster AnalysisComputer SimulationDatabases, GeneticGene Expression ProfilingGenetic MarkersGenetic VariationHumansIntestinesMetagenomicsMiceMicrobiotaModels, GeneticModels, StatisticalNormal DistributionPhenotypeRNA, Ribosomal, 16SSequence Analysis, DNASoftware
2022
Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus
Hehnly C, Shi A, Ssentongo P, Zhang L, Isaacs A, Morton S, Streck N, Erdmann-Gilmore P, Tolstoy I, Townsend R, Limbrick D, Paulson J, Ericson J, Galperin M, Schiff S, Broach J. Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. MBio 2022, 13: e02688-22. PMID: 36374038, PMCID: PMC9765702, DOI: 10.1128/mbio.02688-22.Peer-Reviewed Original ResearchConceptsPostinfectious hydrocephalusClinical isolatesVirulence factorsCritical virulence factorPotential virulence factorsPoor long-term outcomesPrevention of hydrocephalusLong-term outcomesBacterial pathogensDevastating sequelaeNeonatal sepsisMiddle-income countriesNeonatal infectionSurgical interventionReference strainsNovel bacterial pathogensAfrican cohortBeta-lactamase genesChildhood mortalityHydrocephalusTherapeutic targetInfectionVirulent strainDevastating diseaseWhole-genome sequencing
2017
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat
Damgaard M, Pærregaard S, Søgaard I, Agerholm M, Paulson J, Treebak J, Sina C, Holm J, Kristiansen K, Jensen B. Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. The Journal Of Nutritional Biochemistry 2017, 54: 66-76. PMID: 29268121, DOI: 10.1016/j.jnutbio.2017.09.026.Peer-Reviewed Original ResearchConceptsGlucose homeostasisGut microbial alterationsGene amplicon sequencingInfluence of dietary fat sourceLow-fat dietAmplicon sequencingFatty acidsGut microbiotaResponse to insulinDietary fat sourceMicrobial alterationsAssessed glucose homeostasisMetabolic homeostasisDietary fatGlucose clearanceGlucose regulationLFD-fed miceFat sourcesHomeostasisFish oilGroups of miceInsulin tolerance testWeek 8 to weekSoybean oilSevere nonalcoholic steatohepatitis
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
2015
Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine
Carrillo J, He Y, Luo J, Menendez K, Tablante N, Zhao K, Paulson J, Li B, Song J. Methylome Analysis in Chickens Immunized with Infectious Laryngotracheitis Vaccine. PLOS ONE 2015, 10: e0100476. PMID: 26107953, PMCID: PMC4481310, DOI: 10.1371/journal.pone.0100476.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsChickensCpG IslandsDNA MethylationEukaryotic Initiation Factor-2Gene Regulatory NetworksGenomeHerpesvirus 1, GallidImmune System DiseasesInflammationRibosomal Protein S6 Kinases, 70-kDaRNA Processing, Post-TranscriptionalSignal TransductionTOR Serine-Threonine KinasesTranscription Initiation SiteVaccinesConceptsTranscription start siteMethyl-CpG binding domain protein-enriched genome sequencingDNA methylationProtein-enriched genome sequencingRNA post-transcriptional modificationsIdentified canonical pathwaysRegulation of eIF4Post-transcriptional modificationsDifferentially expressed genesAxonal guidance signalingGlobal DNA methylationHypermethylated DMRsP70S6K signalingGenome sequenceStart siteMethylome analysisCpG islandsGene networksMethyl-CpGEIF2 signalingCanonical pathwaysK signalingGenesMTOR signalingInfectious laryngotracheitis
2014
Reply to: "A fair comparison"
Paulson J, Bravo H, Pop M. Reply to: "A fair comparison". Nature Methods 2014, 11: 359-360. PMID: 24681718, DOI: 10.1038/nmeth.2898.Peer-Reviewed Original Research