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      Genomic Sequence of Klebsiella pneumoniae IIEMP-3, a Vitamin B 12-Producing Strain from Indonesian Tempeh

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          Abstract

          Klebsiella pneumoniae strain IIEMP-3, isolated from Indonesian tempeh, is a vitamin B 12-producing strain that exhibited a different genetic profile from pathogenic isolates. Here we report the draft genome sequence of strain IIEMP-3, which may provide insights on the nature of fermentation, nutrition, and immunological function of Indonesian tempeh.

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          REAPR: a universal tool for genome assembly evaluation

          Martin Hunt, Taisei Kikuchi, Mandy Sanders … (2013)
          Methods to reliably assess the accuracy of genome sequence data are lacking. Currently completeness is only described qualitatively and mis-assemblies are overlooked. Here we present REAPR, a tool that precisely identifies errors in genome assemblies without the need for a reference sequence. We have validated REAPR on complete genomes or de novo assemblies from bacteria, malaria and Caenorhabditis elegans, and demonstrate that 86% and 82% of the human and mouse reference genomes are error-free, respectively. When applied to an ongoing genome project, REAPR provides corrected assembly statistics allowing the quantitative comparison of multiple assemblies. REAPR is available at http://www.sanger.ac.uk/resources/software/reapr/.
          Article 0 comments Cited 233 times – based on 0 reviews     Review now
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            Primary liver abscess due to Klebsiella pneumoniae in Taiwan.

            Huai-Yung Wang, Yan Chen, L Wann … (1998)
            Pyogenic liver abscess is an uncommon complication of intra-abdominal or biliary tract infection and is usually a polymicrobial infection associated with high mortality and high rates of relapse. However, over the past 15 years, we have observed a new clinical syndrome in Taiwan: liver abscesses caused by a single microorganism, Klebsiella pneumoniae. We reviewed 182 cases of pyogenic liver abscess during the period September 1990 to June 1996; 160 of these cases were caused by K. pneumoniae alone, and 22 were polymicrobial. When patients with K. pneumoniae liver abscess were compared with those who had polymicrobial liver abscess, we found higher incidences of diabetes or glucose intolerance (75% vs. 4.5%) and metastatic infections (11.9% vs. 0) and lower rates of intra-abdominal abnormalities (0.6% vs. 95.5%), mortality (11.3% vs. 41%), and relapse (4.4% vs. 41%) in the former group. Liver abscess caused by K. pneumoniae is a new clinical syndrome that has emerged as an important infectious complication in diabetic patients in Taiwan.
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              A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

              Martin Swain, Isheng J. Tsai, Samual A Assefa … (2012)
              Genome projects now produce draft assemblies within weeks owing to advanced high-throughput sequencing technologies. For milestone projects such as Escherichia coli or Homo sapiens, teams of scientists were employed to manually curate and finish these genomes to a high standard. Nowadays, this is not feasible for most projects, and the quality of genomes is generally of a much lower standard. This protocol describes software (PAGIT) that is used to improve the quality of draft genomes. It offers flexible functionality to close gaps in scaffolds, correct base errors in the consensus sequence and exploit reference genomes (if available) in order to improve scaffolding and generating annotations. The protocol is most accessible for bacterial and small eukaryotic genomes (up to 300 Mb), such as pathogenic bacteria, malaria and parasitic worms. Applying PAGIT to an E. coli assembly takes ∼24 h: it doubles the average contig size and annotates over 4,300 gene models.
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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): 25 February 2016
                Publication date Collection: Jan-Feb 2016
                Volume: 4
                Issue: 1
                Electronic Location Identifier: e01724-15
                Affiliations
                [a ]Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
                [b ]Department of Biology, Faculty of Science and Mathematics, Bogor Agricultural University, Bogor, Indonesia
                Author notes
                Address correspondence to Antonius Suwanto, antoniussuwanto@ 123456gmail.com .
                Article
                Publisher ID: genomeA01724-15
                DOI: 10.1128/genomeA.01724-15
                PMC ID: 4767921
                PubMed ID: 26950331
                SO-VID: ee7131be-44ed-4407-a06e-8e564e0a7a45
                Copyright © Copyright © 2016 Yulandi et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 16 December 2015
                Date accepted : 12 January 2016
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 11, Pages: 1, Words: 841
                Funding
                This research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date January/February 2016

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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