title: Old meets new: using interspecies interactions to detect secondary metabolite production in actinomycetes.
abstract: Actinomycetes, a group of filamentous, Gram-positive bacteria, have long been a remarkable source of useful therapeutics. Recent genome sequencing and transcriptomic studies have shown that these bacteria, responsible for half of the clinically used antibiotics, also harbor a large reservoir of gene clusters, which have the potential to produce novel secreted small molecules. Yet, many of these clusters are not expressed under common culture conditions. One reason why these clusters have not been linked to a secreted small molecule lies in the way that actinomycetes have typically been studied: as pure cultures in nutrient-rich media that do not mimic the complex environments in which these bacteria evolved. New methods based on multispecies culture conditions provide an alternative approach to investigating the products of these gene clusters. We have recently implemented binary interspecies interaction assays to mine for new secondary metabolites and to study the underlying biology of interactinomycete interactions. Here, we describe the detailed biological and chemical methods comprising these studies.
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Mohammad R
authors.initials: MR
authors.lastname: Seyedsayamdost
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Matthew F
authors.initials: MF
authors.lastname: Traxler
authors.affiliation: Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Jon
authors.initials: J
authors.lastname: Clardy
authors.affiliation: Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Roberto
authors.initials: R
authors.lastname: Kolter
mesh_terms: D039903:Actinobacteria / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D000900:Anti-Bacterial Agents / Q000096:biosynthesis / Q000302:isolation & purification / Q000494:pharmacology; D001681:Biological Assay / Q000379:methods; D003470:Culture Media / Q000378:metabolism; D005285:Fermentation; D020869:Gene Expression Profiling / Q000379:methods; D005798:Genes, Bacterial; D007501:Iron / Q000378:metabolism; D055442:Metabolome; D056265:Microbial Interactions; D005810:Multigene Family; D010641:Phenotype; D017262:Siderophores / Q000096:biosynthesis* / Q000302:isolation & purification / Q000494:pharmacology; D012988:Soil Microbiology; D013171:Spores, Bacterial / Q000254:growth & development / Q000378:metabolism
chemical_list: D000900:Anti-Bacterial Agents; D003470:Culture Media; D017262:Siderophores; D007501:Iron