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      Draft Genome Sequence of Streptomyces sp. Strain PBH53, Isolated from an Urban Environment

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          Abstract

          We report the draft genome sequence of Streptomyces sp. strain PBH53, a strain isolated from an urban transit station in Ottawa, Canada. The analysis of the genome using the bioinformatics tool antiSMASH showed the presence of many unique natural product biosynthetic pathways.

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          How many antibiotics are produced by the genus Streptomyces?

          M Watve, R Tickoo, M Jog … (2001)
          Streptomyces is the largest antibiotic-producing genus in the microbial world discovered so far. The number of antimicrobial compounds reported from the species of this genus per year increased almost exponentially for about two decades, followed by a steady rise to reach a peak in the 1970s, and with a substantial decline in the late 1980s and 1990s. The cumulative number shows a sigmoid curve that is much flatter than what a logistic equation would predict. We attempted to fit a mathematical model to this curve in order to estimate the number of undiscovered antimicrobials from this genus as well as to predict the trends in the near future. A model assuming that the screening efforts are encouraged by a previous year's success and that the probability of finding a new antibiotic is a function of the fraction of antibiotics undiscovered so far offered a good fit after optimizing parameters. The model estimated the total number of antimicrobial compounds that this genus is capable of producing to be of the order of a 100,000 - a tiny fraction of which has been unearthed so far. The decline in the slope appeared to be due to a decline in screening efforts rather than an exhaustion of compounds. Left to itself, the slope will become zero in the next one or two decades, but if the screening efforts are maintained constant, the rate of discovery of new compounds will not decline for several decades to come.
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            antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

            Tilmann Weber, Kai Blin, Srikanth Duddela … (2015)
            Microbial secondary metabolism constitutes a rich source of antibiotics, chemotherapeutics, insecticides and other high-value chemicals. Genome mining of gene clusters that encode the biosynthetic pathways for these metabolites has become a key methodology for novel compound discovery. In 2011, we introduced antiSMASH, a web server and stand-alone tool for the automatic genomic identification and analysis of biosynthetic gene clusters, available at http://antismash.secondarymetabolites.org. Here, we present version 3.0 of antiSMASH, which has undergone major improvements. A full integration of the recently published ClusterFinder algorithm now allows using this probabilistic algorithm to detect putative gene clusters of unknown types. Also, a new dereplication variant of the ClusterBlast module now identifies similarities of identified clusters to any of 1172 clusters with known end products. At the enzyme level, active sites of key biosynthetic enzymes are now pinpointed through a curated pattern-matching procedure and Enzyme Commission numbers are assigned to functionally classify all enzyme-coding genes. Additionally, chemical structure prediction has been improved by incorporating polyketide reduction states. Finally, in order for users to be able to organize and analyze multiple antiSMASH outputs in a private setting, a new XML output module allows offline editing of antiSMASH annotations within the Geneious software.
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              DNA fingerprinting reveals links among agricultural crops, soil properties, and the composition of soil microbial communities

              K.M. Scow, K.Y. Lee, M.J. Johnson (2003)
              Article 0 comments Cited 23 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 30 July 2015
                Publication date Collection: Jul-Aug 2015
                Volume: 3
                Issue: 4
                Electronic Location Identifier: e00859-15
                Affiliations
                [a ]Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
                [b ]Department of Biology, University of Ottawa, Ottawa, Canada
                [c ]MR DNA, Molecular Research LP, Shallowater, Texas, USA
                Author notes
                Address correspondence to Christopher N. Boddy, cboddy@ 123456uottawa.ca .
                Article
                Publisher ID: genomeA00859-15
                DOI: 10.1128/genomeA.00859-15
                PMC ID: 4520906
                PubMed ID: 26227608
                SO-VID: d7f648ed-95f0-43f3-a8d9-5d0e95a78ee2
                Copyright © Copyright © 2015 Gosse et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.

                History
                Date received : 23 June 2015
                Date accepted : 29 June 2015
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 10, Pages: 2, Words: 1085
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date July/August 2015
                access-type free

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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