2024
An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms
Hart T, Sonnert N, Tang X, Chaurasia R, Allen P, Hunt J, Read C, Johnson E, Arora G, Dai Y, Cui Y, Chuang Y, Yu Q, Rahman M, Mendes M, Rolandelli A, Singh P, Tripathi A, Ben Mamoun C, Caimano M, Radolf J, Lin Y, Fingerle V, Margos G, Pal U, Johnson R, Pedra J, Azad A, Salje J, Dimopoulos G, Vinetz J, Carlyon J, Palm N, Fikrig E, Ring A. An atlas of human vector-borne microbe interactions reveals pathogenicity mechanisms. Cell 2024, 187: 4113-4127.e13. PMID: 38876107, PMCID: PMC11959484, DOI: 10.1016/j.cell.2024.05.023.Peer-Reviewed Original ResearchCell invasionHost-microbe interactionsArthropod-borne pathogensHost sensingMicrobe interactionsTranscriptional regulationLyme disease spirocheteMicrobial interactionsExtracellular proteinsMicrobial pathogenesisEpidermal growth factorTissue colonizationEnvironmental cuesBacterial selectivityIntracellular pathogensPutative interactionsNext-generation therapeuticsPathogensFunctional investigationsInteractomeVector-borne diseasesImmune evasionPathogenic mechanismsStrainUnmet medical need
2023
Cross-feeding in the gut microbiome: Ecology and mechanisms
Culp E, Goodman A. Cross-feeding in the gut microbiome: Ecology and mechanisms. Cell Host & Microbe 2023, 31: 485-499. PMID: 37054671, PMCID: PMC10125260, DOI: 10.1016/j.chom.2023.03.016.Peer-Reviewed Original ResearchConceptsHost healthHost-microbe interactionsSpecies fitnessMicrobe-microbeEvolutionary implicationsMicrobial inhabitantsGut communitiesTrophic networksMicrobial communitiesTrophic levelsMammalian gutPrimary fermentersMetabolic outputDifferent microbesAmino acidsGut commensalsCooperative interactionsGut microbiomeNegative interactionsFitnessMutualismEcologyMicrobesEmergent roleCofactorActivity‐based Tools for Interrogating Host Biology During Infection
Ramanathan R, Hatzios S. Activity‐based Tools for Interrogating Host Biology During Infection. Israel Journal Of Chemistry 2023, 63 PMID: 37744997, PMCID: PMC10512441, DOI: 10.1002/ijch.202200095.Peer-Reviewed Original ResearchActivity-based protein profilingPost-translational modificationsHost post-translational modificationsHost-microbe interactionsHost biologyCells senseCell signalingMicrobial mechanismsEnzyme functionProtein profilingProtein structureSide-chain reactivityChemical probesInfected cellsHost-directed therapiesPotential targetRapid modulationHost responseSignalingBiologyInfectionEnzymeProfilingPathwayPathogens
2018
Microbial nitrogen limitation in the mammalian large intestine
Reese A, Pereira F, Schintlmeister A, Berry D, Wagner M, Hale L, Wu A, Jiang S, Durand H, Zhou X, Premont R, Diehl A, O’Connell T, Alberts S, Kartzinel T, Pringle R, Dunn R, Wright J, David L. Microbial nitrogen limitation in the mammalian large intestine. Nature Microbiology 2018, 3: 1441-1450. PMID: 30374168, PMCID: PMC6264799, DOI: 10.1038/s41564-018-0267-7.Peer-Reviewed Original ResearchConceptsNitrogen limitationMicrobial nitrogen limitationHost-microbe interactionsGut microbial ecosystemMicrobial symbiontsHost useEcological communitiesMicrobial communitiesMammal speciesCommensal taxaPhylum BacteroidetesNitrogen availabilityDietary nutrientsMammalian large intestineResource limitationsNitrogen supplyTotal nitrogen supplyProtein levelsResource supplyCommensal microbiotaMicrobiomeLarge intestineGerm-free miceExcess dietary proteinHost
2016
Evidence for participation of neutrophil gelatinase‐associated lipocalin/matrix metalloproteinase‐9 (NGAL•MMP‐9) complex in the inflammatory response to infection in pregnancies complicated by preterm birth
Rood KM, Buhimschi IA, Rodewald Millen K, Bahtiyar MO, Thung S, Summerfield T, Zhao G, Ackerman W, Shellhaas C, Samuels P, Buhimschi CS. Evidence for participation of neutrophil gelatinase‐associated lipocalin/matrix metalloproteinase‐9 (NGAL•MMP‐9) complex in the inflammatory response to infection in pregnancies complicated by preterm birth. American Journal Of Reproductive Immunology 2016, 76: 108-117. PMID: 27251223, PMCID: PMC4942349, DOI: 10.1111/aji.12523.Peer-Reviewed Original ResearchConceptsIntra-amniotic infection/inflammationNeutrophil Gelatinase-Associated LipocalinMatrix metalloproteinase-9Preterm birthNGAL mRNA expressionGelatinase-Associated LipocalinNormal pregnancy outcomeAmniotic fluid levelsInfection/inflammationPlacental villous trophoblastNGAL levelsPregnancy outcomesInflammatory conditionsInflammatory responseMetalloproteinase-9Villous trophoblastFluid levelsInnate immunityCollagenolytic effectMRNA expressionGelatinolytic activityPregnancyHost-microbe interactionsQRT-PCRAmniochorion
2015
The colibactin warhead crosslinks DNA
Vizcaino MI, Crawford JM. The colibactin warhead crosslinks DNA. Nature Chemistry 2015, 7: 411-417. PMID: 25901819, PMCID: PMC4499846, DOI: 10.1038/nchem.2221.Peer-Reviewed Original ResearchConceptsDNA-damaging activityHost-microbe interactionsUncharacterized familyColibactin biosynthesisSmall moleculesHybrid pathwayCancer formationMode of actionDuplex DNACrosslinks DNAMicrobial metabolitesUnexpected modelHuman microbiotaSelect strainsMetabolomic analysisDNAPathwayEscherichia coli presentHuman colonLabeling studiesDisease statesDirect experimental evidenceHuman healthBiosynthesisColibactin
2013
Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut
Dantas G, Sommer MO, Degnan PH, Goodman AL. Experimental Approaches for Defining Functional Roles of Microbes in the Human Gut. Annual Review Of Microbiology 2013, 67: 459-475. PMID: 24024637, PMCID: PMC4718711, DOI: 10.1146/annurev-micro-092412-155642.Peer-Reviewed Original ResearchConceptsMicrobial communitiesFree-living microbial communitiesHigh-throughput DNA sequencingCulture-independent surveysGenome sequence projectHuman gutHost-microbe interactionsGut microbial communityMicrobial genomesGene contentMicrobial genesModel organismsHost-microbiota relationshipFunctional roleDNA sequencingFunction strategyModel systemExperimental approachUnderlying mechanismGenomeGutGenesMicrobesOrganismsSpecies
2012
Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Philip Schumm L, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D’Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, Silverberg M, Annese V, Hakonarson H, Brant S, Radford-Smith G, Mathew C, Rioux J, Schadt E, Daly M, Franke A, Parkes M, Vermeire S, Barrett J, Cho J. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012, 491: 119-124. PMID: 23128233, PMCID: PMC3491803, DOI: 10.1038/nature11582.Peer-Reviewed Original ResearchMeSH KeywordsColitis, UlcerativeCrohn DiseaseGenetic Predisposition to DiseaseGenome-Wide Association StudyGenome, HumanHaplotypesHost-Pathogen InteractionsHumansInflammatory Bowel DiseasesMycobacteriumMycobacterium InfectionsMycobacterium tuberculosisPhenotypePolymorphism, Single NucleotideReproducibility of Results
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