2022
Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome
Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 2022, 185: 1487-1505.e14. PMID: 35366417, PMCID: PMC10619838, DOI: 10.1016/j.cell.2022.03.008.Peer-Reviewed Original ResearchConceptsSynthetic genetic elementsGenetic elementsBiosynthetic gene clusterCross-species expressionCross-species interactionsDiverse organismsGene clusterBiosynthetic machineryHeterologous expressionRegulatory regionsTRNA synthetasesBiosynthetic pathwayNative contextTranslational activityBiosynthetic capacityHuman microbiomeMetabolic capacityPositive bacteriaSmall moleculesExpressionPathwayValuable compoundsLactobacillus inersEukaryotesSynthetases
2021
Escherichia coli small molecule metabolism at the host–microorganism interface
Gatsios A, Kim CS, Crawford JM. Escherichia coli small molecule metabolism at the host–microorganism interface. Nature Chemical Biology 2021, 17: 1016-1026. PMID: 34552219, PMCID: PMC8675634, DOI: 10.1038/s41589-021-00807-5.Peer-Reviewed Original ResearchConceptsSmall molecule metabolismE. coliHost-bacteria interfaceModel organismsHost-bacterial interactionsChemical arsenalMolecule metabolismEscherichia coliHuman microbiotaColiSmall molecule chemistryMetabolismCommon componentSignalingOrganismsBiologyDisease modulationCommensalEscherichiaHostPathogenic roleRoleMicrobiotaMembersMolecules from the Microbiome
Shine EE, Crawford JM. Molecules from the Microbiome. Annual Review Of Biochemistry 2021, 90: 1-27. PMID: 33770448, DOI: 10.1146/annurev-biochem-080320-115307.Peer-Reviewed Original ResearchConceptsHuman microbiomeSpecific microbial moleculesSmall moleculesSecond genomeEcological nichesSpecies compositionGenetic capacityInteraction networksMicrobial moleculesMicrobiome editingBiochemical complexitySynthetic biologyMolecular mechanismsHuman cellsImmune system developmentChemical biologyFunctional interactionMicrobiomeDetailed mechanistic studiesBiologyHost responseMechanistic studiesGenomeMoleculesMicrobes
2019
Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior
Lozano GL, Bravo JI, Diago M, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. MBio 2019, 10: 10.1128/mbio.02846-18. PMID: 30837345, PMCID: PMC6401489, DOI: 10.1128/mbio.02846-18.Peer-Reviewed Original ResearchConceptsGenetic dissectionModel communitiesCommunity-level interactionsMicrobial community behaviorRhizosphere microbiomeModel microbiomeMicrobiome assemblyEmergent propertiesHistory of biologyMicrobial communitiesMammalian gutRobust biofilmsDominant phylaGene expressionBiochemical toolsRhizosphereCommunity interactionsNovel familyHitchhikersMicrobiomeFlavobacteriumModel systemCommunity behaviorPseudomonasAgricultural productivity
2018
Discovering antibiotics from the global microbiome
Lam YC, Crawford JM. Discovering antibiotics from the global microbiome. Nature Microbiology 2018, 3: 392-393. PMID: 29588534, DOI: 10.1038/s41564-018-0135-5.Peer-Reviewed Original Research
2017
Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior
Fischer C, Trautman EP, Crawford JM, Stabb EV, Handelsman J, Broderick NA. Metabolite exchange between microbiome members produces compounds that influence Drosophila behavior. ELife 2017, 6: e18855. PMID: 28068220, PMCID: PMC5222558, DOI: 10.7554/elife.18855.Peer-Reviewed Original ResearchConceptsMicrobial communitiesContext-dependent fitness benefitsMulti-species microbial communitiesMicrobial community influencesMicrobe-microbe interactionsEgg-laying preferenceInter-species interactionsEgg-laying behaviorHost-microbiome interactionsDistinct volatile profileMicrobiome membersFitness benefitsMetabolite exchangePopulation declineDrosophila behaviorMolecular mechanismsOlfactory receptorsMetabolic derivativesEthanol catabolismAnimal behaviorCurrent understandingMicrobiomeOr42bIndividual membersDrosophila
2016
Linking Biosynthetic Gene Clusters to their Metabolites via Pathway-Targeted Molecular Networking
Trautman EP, Crawford JM. Linking Biosynthetic Gene Clusters to their Metabolites via Pathway-Targeted Molecular Networking. Current Topics In Medicinal Chemistry 2016, 16: 1705-1716. PMID: 26456470, PMCID: PMC5055756, DOI: 10.2174/1568026616666151012111046.Peer-Reviewed Original ResearchConceptsBiosynthetic gene clusterGene clusterMicrobial biosynthetic gene clustersMetabolic pathwaysGenome sequence informationSecondary metabolic pathwaysMolecular networkingHuman-microbe interactionsNew metabolic pathwaysComplex metabolomeSmall moleculesBiosynthetic logicActive small moleculesFunctional characterizationBioinformatics predictionSequence informationSmall molecule metabolitesHuman microbiomeExperimental structural characterizationGut bacteriaPathwayNatural productsMetabolitesPharmacological potentialAvailable databases