Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event
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{"title"=>"Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event", "type"=>"journal", "authors"=>[{"first_name"=>"Stephanie M.", "last_name"=>"Rosales", "scopus_author_id"=>"56979143200"}, {"first_name"=>"Rebecca Vega", "last_name"=>"Thurber", "scopus_author_id"=>"23986487200"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"607884000", "doi"=>"10.1371/journal.pone.0143944", "sgr"=>"84955593545", "scopus"=>"2-s2.0-84955593545", "pmid"=>"26630132"}, "id"=>"60a47821-d51a-3b71-8187-e02eb5ba5b1e", "abstract"=>"Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have applied this technique in marine systems. In 2009 seven harbor seals, Phoca vitulina, stranded along the California coast from a similar brain disease of unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified Burkholderia and Coxiella burnetii as important pathogens associated with this stranding event. Burkholderia were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while C. burnetii was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, C. burnetii showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that Burkholderia taxa and C. burnetii are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.", "link"=>"http://www.mendeley.com/research/brain-metatranscriptomics-harbor-seals-infer-role-microbiome-virome-stranding-event", "reader_count"=>17, "reader_count_by_academic_status"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1, "Student > Doctoral Student"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Researcher"=>2, "Student > Ph. D. Student"=>1, "Student > Postgraduate"=>1, "Other"=>1, "Student > Master"=>2, "Student > Bachelor"=>6, "Lecturer"=>1, "Professor"=>1, "Student > Doctoral Student"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>3, "Agricultural and Biological Sciences"=>8, "Medicine and Dentistry"=>2, "Chemistry"=>1, "Social Sciences"=>1, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>3}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Brazil"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2597580"], "description"=>"<p>Absolute sequence counts of assignments to viral genera from comparative (com) and unknown cause of death (UCD) harbor seals.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616673, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Viral_genera_associated_with_stranded_harbor_seal_brain_tissues_/1616673", "title"=>"Viral genera associated with stranded harbor seal brain tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597581"], "description"=>"<p>(A) Relative abundance of bacterial phyla with > 1.5% relative abundance samples and (B) bacterial phyla with > 10 absolute sequence counts from comparative (com) and unknown cause of death (UCD).</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616674, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microbial_phyla_associated_with_stranded_harbor_seal_brain_tissues_/1616674", "title"=>"Microbial phyla associated with stranded harbor seal brain tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597582"], "description"=>"<p>Relative abundance of bacterial orders with > 2% relative abundance from comparative (com) and unknown cause of death (UCD) harbor seals.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616675, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microbial_orders_associated_with_stranded_harbor_seal_brain_tissues_/1616675", "title"=>"Microbial orders associated with stranded harbor seal brain tissues.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597585"], "description"=>"<p>Heatmap hierarchical clustering of the 50 bacterial genera with the highest variance.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616678, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g004", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microbial_genera_community_analysis_of_brain_tissues_from_comparative_com_and_unknown_cause_of_death_UCD_harbor_seals_/1616678", "title"=>"Microbial genera community analysis of brain tissues from comparative (com) and unknown cause of death (UCD) harbor seals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597586"], "description"=>"<p>(A) Relative abundance of sequences similar to the genera of <i>Burkholderia</i> and (B) Relative abundance of sequences similar to <i>Burkholderia</i> virulence factors in comparative (com) and unknown cause of death (UCD) harbor seal samples.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616679, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Burkholderia_and_Burkholderia_virulence_factors_across_samples_/1616679", "title"=>"<i>Burkholderia</i> and <i>Burkholderia</i> virulence factors across samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597590"], "description"=>"<p>Scatter plot of change in coverage of each base pair position of RNA sequences from sample UCD6 that aligned to (A) <i>Coxiella burnetii</i> RSA 493 chromosome and (B) <i>Coxiella burnetii</i> RSA 493 plasmid pQpH1. (C) 16S RNA gene maximum likelihood tree with 1000 bootstrap values generated from the following bacterial gene sequences and their corresponding NCBI accession numbers: <i>Rickettsia conorii</i> strain Malish 7 (NR_074480.1), <i>Rickettsia montanensis</i> str. OSU 85–930 (NR_074472.1), <i>Legionella sp.</i> L-29 gene (AB856218.1) <i>Legionella hackeliae</i> strain Lancing 2 (NR_104894.1), <i>Coxiella burnetii</i> RSA 493(AE016828.2), <i>Coxiella sp.</i> SL 1 (GU797243.1), <i>Coxiella endosymbiont of Haemaphysalis lagrangei</i> isolate TSD16 (KC170756.1), and <i>Coxiella burnetii</i> Harbor Seal (KT894209).</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616683, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.g006", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Scatter_plot_of_change_in_coverage_of_each_base_pair_position_of_RNA_sequences_from_sample_UCD6_that_aligned_to_A_Coxiella_burnetii_RSA_493_chromosome_and_B_Coxiella_burnetii_RSA_493_plasmid_pQpH1_C_16S_RNA_gene_maximum_likelihood_tree_with_1000_bootstra/1616683", "title"=>"Scatter plot of change in coverage of each base pair position of RNA sequences from sample UCD6 that aligned to (A) <i>Coxiella burnetii</i> RSA 493 chromosome and (B) <i>Coxiella burnetii</i> RSA 493 plasmid pQpH1. (C) 16S RNA gene maximum likelihood tree with 1000 bootstrap values generated from the following bacterial gene sequences and their corresponding NCBI accession numbers: <i>Rickettsia conorii</i> strain Malish 7 (NR_074480.1), <i>Rickettsia montanensis</i> str. OSU 85–930 (NR_074472.1), <i>Legionella sp.</i> L-29 gene (AB856218.1) <i>Legionella hackeliae</i> strain Lancing 2 (NR_104894.1), <i>Coxiella burnetii</i> RSA 493(AE016828.2), <i>Coxiella sp.</i> SL 1 (GU797243.1), <i>Coxiella endosymbiont of Haemaphysalis lagrangei</i> isolate TSD16 (KC170756.1), and <i>Coxiella burnetii</i> Harbor Seal (KT894209).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597592"], "description"=>"<p>PhV-1 = Phocine herpes virus -1. Age range is as follows: Pup < 1month, weaner 1–12 months, and adult > 3 years.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616685, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.t001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_necropsy_reports_and_tissue_types_from_harbor_seals_/1616685", "title"=>"Summary of necropsy reports and tissue types from harbor seals.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597593"], "description"=>"<p>List of the highest coverage regions in <i>Coxiella burnetii</i> RSA 493 chromosome and <i>Coxiella burnetii</i> RSA 493 plasmid pQpH1 found in sample UCD6.</p>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616686, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143944.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_the_highest_coverage_regions_in_Coxiella_burnetii_RSA_493_chromosome_and_Coxiella_burnetii_RSA_493_plasmid_pQpH1_found_in_sample_UCD6_/1616686", "title"=>"List of the highest coverage regions in <i>Coxiella burnetii</i> RSA 493 chromosome and <i>Coxiella burnetii</i> RSA 493 plasmid pQpH1 found in sample UCD6.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-12-02 03:48:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/2597613", "https://ndownloader.figshare.com/files/2597614", "https://ndownloader.figshare.com/files/2597615", "https://ndownloader.figshare.com/files/2597616", "https://ndownloader.figshare.com/files/2597617"], "description"=>"<div><p>Marine diseases are becoming more frequent, and tools for identifying pathogens and disease reservoirs are needed to help prevent and mitigate epizootics. Meta-transcriptomics provides insights into disease etiology by cataloguing and comparing sequences from suspected pathogens. This method is a powerful approach to simultaneously evaluate both the viral and bacterial communities, but few studies have applied this technique in marine systems. In 2009 seven harbor seals, <i>Phoca vitulina</i>, stranded along the California coast from a similar brain disease of unknown cause of death (UCD). We evaluated the differences between the virome and microbiome of UCDs and harbor seals with known causes of death. Here we determined that UCD stranded animals had no viruses in their brain tissue. However, in the bacterial community, we identified <i>Burkholderia</i> and <i>Coxiella burnetii</i> as important pathogens associated with this stranding event. <i>Burkholderia</i> were 100% prevalent and ~2.8 log2 fold more abundant in the UCD animals. Further, while <i>C</i>. <i>burnetii</i> was found in only 35.7% of all samples, it was highly abundant (~94% of the total microbial community) in a single individual. In this harbor seal, <i>C</i>. <i>burnetii</i> showed high transcription rates of invading and translation genes, implicating it in the pathogenesis of this animal. Based on these data we propose that <i>Burkholderia</i> taxa and <i>C</i>. <i>burnetii</i> are potentially important opportunistic neurotropic pathogens in UCD stranded harbor seals.</p></div>", "links"=>[], "tags"=>["Stranding Event Marine diseases", "harbor seals", "pathogen", "burnetii", "ucd", "burkholderia"], "article_id"=>1616701, "categories"=>["Biological Sciences"], "users"=>["Stephanie M. Rosales", "Rebecca Vega Thurber"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0143944.s001", "https://dx.doi.org/10.1371/journal.pone.0143944.s002", "https://dx.doi.org/10.1371/journal.pone.0143944.s003", "https://dx.doi.org/10.1371/journal.pone.0143944.s004", "https://dx.doi.org/10.1371/journal.pone.0143944.s005"], "stats"=>{"downloads"=>3, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Brain_Meta_Transcriptomics_from_Harbor_Seals_to_Infer_the_Role_of_the_Microbiome_and_Virome_in_a_Stranding_Event_/1616701", "title"=>"Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-12-02 03:48:48"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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