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      Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216 T

      case-report

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          Abstract

          Bacillus smithii is a facultatively anaerobic, thermophilic bacterium able to use a variety of sugars that can be derived from lignocellulosic feedstocks. Being genetically accessible, it is a potential new host for biotechnological production of green chemicals from renewable resources. We determined the complete genomic sequence of the B. smithii type strain DSM 4216 T, which consists of a 3,368,778 bp chromosome (GenBank accession number CP012024.1) and a 12,514 bp plasmid (GenBank accession number CP012025.1), together encoding 3880 genes. Genome annotation via RAST was complemented by a protein domain analysis. Some unique features of B. smithii central metabolism in comparison to related organisms included the lack of a standard acetate production pathway with no apparent pyruvate formate lyase, phosphotransacetylase, and acetate kinase genes, while acetate was the second fermentation product.

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          Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

          C Woese, O Kandler, M L Wheelis (1990)
          Molecular structures and sequences are generally more revealing of evolutionary relationships than are classical phenotypes (particularly so among microorganisms). Consequently, the basis for the definition of taxa has progressively shifted from the organismal to the cellular to the molecular level. Molecular comparisons show that life on this planet divides into three primary groupings, commonly known as the eubacteria, the archaebacteria, and the eukaryotes. The three are very dissimilar, the differences that separate them being of a more profound nature than the differences that separate typical kingdoms, such as animals and plants. Unfortunately, neither of the conventionally accepted views of the natural relationships among living systems--i.e., the five-kingdom taxonomy or the eukaryote-prokaryote dichotomy--reflects this primary tripartite division of the living world. To remedy this situation we propose that a formal system of organisms be established in which above the level of kingdom there exists a new taxon called a "domain." Life on this planet would then be seen as comprising three domains, the Bacteria, the Archaea, and the Eucarya, each containing two or more kingdoms. (The Eucarya, for example, contain Animalia, Plantae, Fungi, and a number of others yet to be defined). Although taxonomic structure within the Bacteria and Eucarya is not treated herein, Archaea is formally subdivided into the two kingdoms Euryarchaeota (encompassing the methanogens and their phenotypically diverse relatives) and Crenarchaeota (comprising the relatively tight clustering of extremely thermophilic archaebacteria, whose general phenotype appears to resemble most the ancestral phenotype of the Archaea.
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            The minimum information about a genome sequence (MIGS) specification.

            Dawn Field, George Garrity, Tanya Gray … (2008)
            With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases.
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              Toward almost closed genomes with GapFiller

              Marten Boetzer, Walter Pirovano (2012)
              De novo assembly is a commonly used application of next-generation sequencing experiments. The ultimate goal is to puzzle millions of reads into one complete genome, although draft assemblies usually result in a number of gapped scaffold sequences. In this paper we propose an automated strategy, called GapFiller, to reliably close gaps within scaffolds using paired reads. The method shows good results on both bacterial and eukaryotic datasets, allowing only few errors. As a consequence, the amount of additional wetlab work needed to close a genome is drastically reduced. The software is available at http://www.baseclear.com/bioinformatics-tools/.
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                Author and article information

                Contributors
                Richard van Kranenburg:
                ORCID: http://orcid.org/0000-0001-5856-1546
                richard.van.kranenburg@corbion.com
                Journal
                Journal ID (nlm-ta): Stand Genomic Sci
                Journal ID (iso-abbrev): Stand Genomic Sci
                Title: Standards in Genomic Sciences
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1944-3277
                Publication date (Electronic): 24 August 2016
                Publication date PMC-release: 24 August 2016
                Publication date Collection: 2016
                Volume: 11
                Issue: 1
                Electronic Location Identifier: 52
                Affiliations
                [1 ]Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
                [2 ]Present address: The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Kgs. Lyngby, 2800 Denmark
                [3 ]Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
                [4 ]CMBI, NCMLS, Geert-Grooteplein Zuid 26-28, 6525 GA Nijmegen, The Netherlands
                [5 ]Corbion, Arkelsedijk 46, 4206 AC Gorinchem, The Netherlands
                Author information
                http://orcid.org/0000-0001-5856-1546
                Article
                Publisher ID: 172
                DOI: 10.1186/s40793-016-0172-8
                PMC ID: 4995803
                PubMed ID: 27559429
                SO-VID: 3e578484-dae7-4198-8c88-b68a3a5467bf
                Copyright © © The Author(s). 2016
                License:

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                Date received : 21 August 2015
                Date accepted : 9 August 2016
                Funding
                Funded by: Corbion
                Categories
                Subject: Extended Genome Report
                Custom metadata
                issue-copyright-statement © The Author(s) 2016

                ScienceOpen disciplines: Genetics
                Keywords: bacillus smithii,genome sequence,lactic acid,thermophile,thermophilic bacillus,biotechnology
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: bacillus smithii, genome sequence, lactic acid, thermophile, thermophilic bacillus, biotechnology

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