Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira hyodysenteriae Reveals Adaptations to Its Lifestyle in the Porcine Large Intestine
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{"title"=>"Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine", "type"=>"journal", "authors"=>[{"first_name"=>"Matthew I.", "last_name"=>"Bellgard", "scopus_author_id"=>"6701705865"}, {"first_name"=>"Phatthanaphong", "last_name"=>"Wanchanthuek", "scopus_author_id"=>"26322108000"}, {"first_name"=>"Tom", "last_name"=>"La", "scopus_author_id"=>"6603556837"}, {"first_name"=>"Karon", "last_name"=>"Ryan", "scopus_author_id"=>"54396121900"}, {"first_name"=>"Paula", "last_name"=>"Moolhuijzen", "scopus_author_id"=>"14525407700"}, {"first_name"=>"Zayed", "last_name"=>"Albertyn", "scopus_author_id"=>"26321323700"}, {"first_name"=>"Babak", "last_name"=>"Shaban", "scopus_author_id"=>"26321952400"}, {"first_name"=>"Yair", "last_name"=>"Motro", "scopus_author_id"=>"14014035400"}, {"first_name"=>"David S.", "last_name"=>"Dunn", "scopus_author_id"=>"25824235900"}, {"first_name"=>"David", "last_name"=>"Schibeci", "scopus_author_id"=>"8428264500"}, {"first_name"=>"Adam", "last_name"=>"Hunter", "scopus_author_id"=>"8674053800"}, {"first_name"=>"Roberto", "last_name"=>"Barrero", "scopus_author_id"=>"8880390500"}, {"first_name"=>"Nyree D.", "last_name"=>"Phillips", "scopus_author_id"=>"7201973191"}, {"first_name"=>"David J.", "last_name"=>"Hampson", "scopus_author_id"=>"34975078700"}], "year"=>2009, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-61849108691", "pui"=>"354278578", "doi"=>"10.1371/journal.pone.0004641", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"61849108691", "pmid"=>"19262690"}, "id"=>"5f001cbc-a6ce-3dac-9e7d-6f61d359038a", "abstract"=>"Brachyspira hyodysenteriae is an anaerobic intestinal spirochete that colonizes the large intestine of pigs and causes swine dysentery, a disease of significant economic importance. The genome sequence of B. hyodysenteriae strain WA1 was determined, making it the first representative of the genus Brachyspira to be sequenced, and the seventeenth spirochete genome to be reported. The genome consisted of a circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular plasmid that has not previously been described. The spirochete had 2,122 protein-coding sequences. Of the predicted proteins, more had similarities to proteins of the enteric Escherichia coli and Clostridium species than they did to proteins of other spirochetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine. A reconstruction of central metabolic pathways identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non-oxidative pentose phosphate pathway, nucleotide metabolism, lipooligosaccharide biosynthesis, and a respiratory electron transport chain. A notable finding was the presence on the plasmid of the genes involved in rhamnose biosynthesis. Potential virulence genes included those for 15 proteases and six hemolysins. Other adaptations to an enteric lifestyle included the presence of large numbers of genes associated with chemotaxis and motility. B. hyodysenteriae has diverged from other spirochetes in the process of accommodating to its habitat in the porcine large intestine.", "link"=>"http://www.mendeley.com/research/genome-sequence-pathogenic-intestinal-spirochete-brachyspira-hyodysenteriae-reveals-adaptations-life", "reader_count"=>44, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>3, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>11, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>13, "Student > Postgraduate"=>2, "Student > Master"=>5, "Other"=>3, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Biochemistry, Genetics and Molecular Biology"=>1, "Materials Science"=>1, "Agricultural and Biological Sciences"=>31, "Medicine and Dentistry"=>3, "Veterinary Science and Veterinary Medicine"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>31}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>5}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"Canada"=>1, "Belgium"=>1, "Switzerland"=>1}, "group_count"=>3}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/905893"], "description"=>"<p>COG analysis of <i>Clostridium</i>-like and <i>Escherichia</i>-like genes identified in <i>B. hyodysenteriae</i> WA1.</p>", "links"=>[], "tags"=>["genes"], "article_id"=>576336, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.t004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_COG_analysis_of_Clostridium_like_and_Escherichia_like_genes_identified_in_B_hyodysenteriae_WA1_/576336", "title"=>"COG analysis of <i>Clostridium</i>-like and <i>Escherichia</i>-like genes identified in <i>B. hyodysenteriae</i> WA1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-03-05 01:45:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/905452"], "description"=>"<p>A, Chromosome (CI); B , Plasmid (PI). Circles range from 1 (outer circle) to 6 (inner circle) for CI and I (outer circle) to IV (inner circle) for PI. Circles 1/I and 2/II, genes and forward and reverse strand; circle 3, tRNA genes; circle 4, rRNA genes, circle 5/III, GC bias/skew ((G-C)/(G+C); red indicates values >0; green indicates values <0); circles 6/IV, A+T percentage content. All genes are color-coded according to Cluster of Orthologous Group (COG) functions: violet for translation, ribosomal structure and biogenesis; plum for RNA processing and modification; pink for transcription; deep pink for DNA replication, recombination and repair; hot pink for chromatin structure and dynamics; wheat for cell division and chromosome partitioning; light salmon for nuclear structure; yellow for defence mechanisms; gold for signal transduction mechanisms; pale green for cell envelope biogenesis, outer membrane; spring green for cell motility and secretion; lawn green for cytoskeleton; yellow green for extracellular structures; aquamarine for intracellular trafficking, secretion, and vesicular transport; medium aquamarine for posttranslational modification, protein turnover, chaperones; cyan for energy production and conversion; deep sky blue for carbohydrate transport and metabolism; sky blue for amino acid transport and metabolism; light slate blue for nucleotide transport and metabolism; orchid for coenzyme metabolism; medium orchid for lipid metabolism; dark orchid for inorganic ion transport and metabolism; blue violet for secondary metabolites biosynthesis, transport and catabolism; slate grey for general function prediction only; grey for function unknown; gray for not in COGS; black for tRNA.</p>", "links"=>[], "tags"=>["wa1", "annotated"], "article_id"=>575898, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Circular_representation_of_the_B_hyodysenteriae_WA1_genome_with_annotated_genes_/575898", "title"=>"Circular representation of the <i>B. hyodysenteriae</i> WA1 genome, with annotated genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-05 01:38:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/448370", "https://ndownloader.figshare.com/files/448434"], "description"=>"<div><p><em>Brachyspira hyodysenteriae</em> is an anaerobic intestinal spirochete that colonizes the large intestine of pigs and causes swine dysentery, a disease of significant economic importance. The genome sequence of <em>B. hyodysenteriae</em> strain WA1 was determined, making it the first representative of the genus <em>Brachyspira</em> to be sequenced, and the seventeenth spirochete genome to be reported. The genome consisted of a circular 3,000,694 base pair (bp) chromosome, and a 35,940 bp circular plasmid that has not previously been described. The spirochete had 2,122 protein-coding sequences. Of the predicted proteins, more had similarities to proteins of the enteric <em>Escherichia coli</em> and <em>Clostridium</em> species than they did to proteins of other spirochetes. Many of these genes were associated with transport and metabolism, and they may have been gradually acquired through horizontal gene transfer in the environment of the large intestine. A reconstruction of central metabolic pathways identified a complete set of coding sequences for glycolysis, gluconeogenesis, a non-oxidative pentose phosphate pathway, nucleotide metabolism, lipooligosaccharide biosynthesis, and a respiratory electron transport chain. A notable finding was the presence on the plasmid of the genes involved in rhamnose biosynthesis. Potential virulence genes included those for 15 proteases and six hemolysins. Other adaptations to an enteric lifestyle included the presence of large numbers of genes associated with chemotaxis and motility. <em>B. hyodysenteriae</em> has diverged from other spirochetes in the process of accommodating to its habitat in the porcine large intestine.</p></div>", "links"=>[], "tags"=>["genome", "pathogenic", "intestinal", "spirochete", "reveals", "adaptations", "porcine", "intestine"], "article_id"=>148341, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0004641.s001", "https://dx.doi.org/10.1371/journal.pone.0004641.s002"], "stats"=>{"downloads"=>21, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Sequence_of_the_Pathogenic_Intestinal_Spirochete_Brachyspira_hyodysenteriae_Reveals_Adaptations_to_Its_Lifestyle_in_the_Porcine_Large_Intestine/148341", "title"=>"Genome Sequence of the Pathogenic Intestinal Spirochete <em>Brachyspira hyodysenteriae</em> Reveals Adaptations to Its Lifestyle in the Porcine Large Intestine", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-03-05 02:19:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/905751"], "description"=>"*<p>Genomes were downloaded from NCBI (27 November 2008) and analysed by BLASTP. Orthologs were identified using the reciprocal best hit method and candidates were selected from the top five alignments with an expected value <1e-05, percent identity >25% and sequence coverage >75%. Genomes that had >1% best protein matches <i>to B. hyodysenteriae</i> WA1 are summarized. To verify this analysis, CDS with a best match within the top five best matches also were analysed.</p>", "links"=>[], "tags"=>["proteins", "716", "microbial"], "article_id"=>576195, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Similarities_of_predicted_B_hyodysenteriae_proteins_to_those_from_716_complete_microbial_genomes_/576195", "title"=>"Similarities of predicted <i>B. hyodysenteriae</i> proteins to those from 716 complete microbial genomes<sup>*</sup>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-03-05 01:43:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/905704"], "description"=>"<p>General genomic features predicted for <i>B. hyodysenteriae</i> WA1.</p>", "links"=>[], "tags"=>["genomic"], "article_id"=>576144, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.t001", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_General_genomic_features_predicted_for_B_hyodysenteriae_WA1_/576144", "title"=>"General genomic features predicted for <i>B. hyodysenteriae</i> WA1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-03-05 01:42:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/905795"], "description"=>"*<p>BH: <i>Brachyspira hyodysenteriae</i>; BA: <i>Borrelia afzelii</i> PKo; BB: <i>Borrelia burgdorferi</i>; BG: <i>Borrelia garinii</i> PBi; TP: <i>Treponema pallidum</i>; TD: <i>Treponema denticola</i>; LB: <i>Leptospira biflexa</i> serovar Patoc Patoc 1 Paris; LC: <i>Leptospira interrogans</i> serovar Copenhageni; LL: <i>Leptospira interrogans</i> serovar Lai; LJB: <i>Leptospira borgpetersenii</i> serovar Hardjo-bovis JB197; LL5: <i>Leptospira borgpetersenii</i> serovar Hardjo-bovis L550.</p>", "links"=>[], "tags"=>["orthologous", "genes", "categories", "wa1"], "article_id"=>576238, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Cluster_of_Orthologous_Genes_categories_in_B_hyodysenteriae_WA1_and_other_spirochetes_/576238", "title"=>"Distribution of Cluster of Orthologous Genes categories in <i>B. hyodysenteriae</i> WA1 and other spirochetes.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-03-05 01:43:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/905846"], "description"=>"<p>Virulence categories were determined based on sequence similarity to the COG and KEGG datasets with an expected value <1e-05, percent identity >25% and sequence coverage >75%.</p>", "links"=>[], "tags"=>["pathogenesis", "virulence"], "article_id"=>576289, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.t005", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_with_potential_roles_in_pathogenesis_and_virulence_in_B_hyodysenteriae_/576289", "title"=>"Genes with potential roles in pathogenesis and virulence in <i>B. hyodysenteriae</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-03-05 01:44:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/905609"], "description"=>"<p>Central metabolic pathway construction for <i>B. hyodysenteriae</i> WA1.</p>", "links"=>[], "tags"=>["metabolic", "pathway"], "article_id"=>576050, "categories"=>["Microbiology", "Genetics"], "users"=>["Matthew I. Bellgard", "Phatthanaphong Wanchanthuek", "Tom La", "Karon Ryan", "Paula Moolhuijzen", "Zayed Albertyn", "Babak Shaban", "Yair Motro", "David S. Dunn", "David Schibeci", "Adam Hunter", "Roberto Barrero", "Nyree D. Phillips", "David J. Hampson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0004641.g002", "stats"=>{"downloads"=>2, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Central_metabolic_pathway_construction_for_B_hyodysenteriae_WA1_/576050", "title"=>"Central metabolic pathway construction for <i>B. hyodysenteriae</i> WA1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-03-05 01:40:50"}

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Relative Metric

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