title: Sequencing rare marine actinomycete genomes reveals high density of unique natural product biosynthetic gene clusters.
abstract: Traditional natural product discovery methods have nearly exhausted the accessible diversity of microbial chemicals, making new sources and techniques paramount in the search for new molecules. Marine actinomycete bacteria have recently come into the spotlight as fruitful producers of structurally diverse secondary metabolites, and remain relatively untapped. In this study, we sequenced 21 marine-derived actinomycete strains, rarely studied for their secondary metabolite potential and under-represented in current genomic databases. We found that genome size and phylogeny were good predictors of biosynthetic gene cluster diversity, with larger genomes rivalling the well-known marine producers in the Streptomyces and Salinispora genera. Genomes in the Micrococcineae suborder, however, had consistently the lowest number of biosynthetic gene clusters. By networking individual gene clusters into gene cluster families, we were able to computationally estimate the degree of novelty each genus contributed to the current sequence databases. Based on the similarity measures between all actinobacteria in the Joint Genome Institute's Atlas of Biosynthetic gene Clusters database, rare marine genera show a high degree of novelty and diversity, with Corynebacterium, Gordonia, Nocardiopsis, Saccharomonospora and Pseudonocardia genera representing the highest gene cluster diversity. This research validates that rare marine actinomycetes are important candidates for exploration, as they are relatively unstudied, and their relatives are historically rich in secondary metabolites.
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
authors.forename: Michelle A
authors.initials: MA
authors.lastname: Schorn
authors.affiliation: German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany.
authors.forename: Mohammad M
authors.initials: MM
authors.lastname: Alanjary
authors.affiliation: Thermo Fisher Scientific, Carlsbad, CA, USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Aguinaldo
authors.affiliation: Center for Algorithmic Biotechnology, St. Petersburg State University, St. Petersburg, Russia.|Department of Statistical Modeling, St. Petersburg State University, St. Petersburg, Russia.
authors.forename: Anton
authors.initials: A
authors.lastname: Korobeynikov
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
authors.forename: Sheila
authors.initials: S
authors.lastname: Podell
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
authors.forename: Nastassia
authors.initials: N
authors.lastname: Patin
authors.affiliation: Thermo Fisher Scientific, Carlsbad, CA, USA.
authors.forename: Tommie
authors.initials: T
authors.lastname: Lincecum
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.|Center for Microbiome Innovation, University of California, San Diego, USA.
authors.forename: Paul R
authors.initials: PR
authors.lastname: Jensen
authors.affiliation: German Centre for Infection Research (DZIF), Interfaculty Institute for Microbiology and Infection Medicine Tuebingen (IMIT), University of Tuebingen, Tuebingen, Germany.
authors.forename: Nadine
authors.initials: N
authors.lastname: Ziemert
authors.affiliation: Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.|Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, USA.|Center for Microbiome Innovation, University of California, San Diego, USA.
authors.forename: Bradley S
authors.initials: BS
authors.lastname: Moore
mesh_terms: D039903:Actinobacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001688:Biological Products / Q000378:metabolism*; D016680:Genome, Bacterial; D010802:Phylogeny; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D001688:Biological Products