High Nutrient Transport and Cycling Potential Revealed in the Microbial Metagenome of Australian Sea Lion (Neophoca cinerea) Faeces
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{"title"=>"High nutrient transport and cycling potential revealed in the microbial metagenome of australian sea lion (neophoca cinerea) faeces", "type"=>"journal", "authors"=>[{"first_name"=>"Trish J.", "last_name"=>"Lavery", "scopus_author_id"=>"36894715000"}, {"first_name"=>"Ben", "last_name"=>"Roudnew", "scopus_author_id"=>"36090389900"}, {"first_name"=>"Justin", "last_name"=>"Seymour", "scopus_author_id"=>"7202401306"}, {"first_name"=>"James G.", "last_name"=>"Mitchell", "scopus_author_id"=>"7406515555"}, {"first_name"=>"Thomas", "last_name"=>"Jeffries", "scopus_author_id"=>"45161415400"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84861013406", "sgr"=>"84861013406", "pui"=>"364803061", "isbn"=>"1932-6203", "pmid"=>"22606263", "doi"=>"10.1371/journal.pone.0036478"}, "id"=>"f9b1f549-ee9e-32e3-a88a-f9302f310fd4", "abstract"=>"Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (Neophoca cinerea) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to Firmicutes (80%) were dominant, with Proteobacteria and Actinobacteria representing 8% and 2% of matches respectively. The relative proportion of Firmicutes (80%) to Bacteriodetes (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production.", "link"=>"http://www.mendeley.com/research/high-nutrient-transport-cycling-potential-revealed-microbial-metagenome-australian-sea-lion-neophoca", "reader_count"=>89, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>25, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>3, "Other"=>3, "Student > Master"=>16, "Student > Bachelor"=>11, "Professor"=>5}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>2, "Researcher"=>25, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>18, "Student > Postgraduate"=>3, "Other"=>3, "Student > Master"=>16, "Student > Bachelor"=>11, "Professor"=>5}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>8, "Biochemistry, Genetics and Molecular Biology"=>6, "Nursing and Health Professions"=>1, "Agricultural and Biological Sciences"=>60, "Medicine and Dentistry"=>3, "Veterinary Science and Veterinary Medicine"=>3, "Psychology"=>1, "Computer Science"=>1, "Immunology and Microbiology"=>2, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Psychology"=>{"Psychology"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>2}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>60}, "Computer Science"=>{"Computer Science"=>1}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>8}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>3}}, "reader_count_by_country"=>{"Belgium"=>1, "United States"=>3, "Norway"=>1, "Luxembourg"=>1, "Brazil"=>1, "United Kingdom"=>2, "Italy"=>1, "France"=>1, "Germany"=>1, "India"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330046/Figure_S1.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330099/Figure_S2.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330168/Figure_S3.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330223/Figure_S4.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330263/Figure_S5.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/330307/Figure_S6.pdf"], "description"=>"<div><p>Metagenomic analysis was used to examine the taxonomic diversity and metabolic potential of an Australian sea lion (<em>Neophoca cinerea</em>) gut microbiome. Bacteria comprised 98% of classifiable sequences and of these matches to <em>Firmicutes</em> (80%) were dominant, with <em>Proteobacteria</em> and <em>Actinobacteria</em> representing 8% and 2% of matches respectively. The relative proportion of <em>Firmicutes</em> (80%) to <em>Bacteriodetes</em> (2%) is similar to that in previous studies of obese humans and obese mice, suggesting the gut microbiome may confer a predisposition towards the excess body fat that is needed for thermoregulation within the cold oceanic habitats foraged by Australian sea lions. Core metabolic functions, including carbohydrate utilisation (14%), protein metabolism (9%) and DNA metabolism (7%) dominated the metagenome, but in comparison to human and fish gut microbiomes there was a significantly higher proportion of genes involved in phosphorus metabolism (2.4%) and iron scavenging mechanisms (1%). When sea lions defecate at sea, the relatively high nutrient metabolism potential of bacteria in their faeces may accelerate the dissolution of nutrients from faecal particles, enhancing their persistence in the euphotic zone where they are available to stimulate marine production.</p> </div>", "links"=>[], "tags"=>["cycling", "revealed", "microbial", "metagenome", "australian", "faeces"], "article_id"=>125163, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/High_Nutrient_Transport_and_Cycling_Potential_Revealed_in_the_Microbial_Metagenome_of_Australian_Sea_Lion_Neophoca_cinerea_Faeces/125163", "title"=>"High Nutrient Transport and Cycling Potential Revealed in the Microbial Metagenome of Australian Sea Lion (<em>Neophoca cinerea</em>) Faeces", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-05-11 01:26:03"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/639838/Figure_1.tif"], "description"=>"<p>A: The Australian sea lion gut microbiome was dominated by <i>Firmicutes</i> and <i>Proteobacteria</i>. The following phyla were also present in the ASL gut microbiome but had <10 sequences and thus are not shown on the graph: <i>Aquificae</i>, <i>Viridiplantae</i>, <i>Korarchaeota</i>, Bacteriophage ROSA, <i>Englenozoa</i>, <i>Lactobacillus plantarum</i> bacteriophage phiJL-1, Plasmid PCD4, Plasmid pIP404, Environmental samples, ssRNA negative strand viruses. B: <i>Firmicutes</i> were in turn dominated by <i>Clostridia</i> and <i>Bacilli</i>.</p>", "links"=>[], "tags"=>["australian"], "article_id"=>310329, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Taxonomic_Diversity_of_Australian_Sea_Lion_Gut_Microbiome_/310329", "title"=>"Taxonomic Diversity of Australian Sea Lion Gut Microbiome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:05:29"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/639915/Figure_2.tif"], "description"=>"<p>A: The metabolic potential of the Australian sea lion gut microbiome is dominated by clustering-based subsystems and carbohydrates. Protein metabolism and DNA metabolism are also highly represented. Sequences coding for prophage, secondary metabolism, macromolecular synthesis and dormancy and sporulation were also present but were represented by <10 sequences each and hence are not shown here. B: The metabolic potential of the clustering based subsystems in the Australian sea lion gut microbiome are dominated by clustering based subsystems, cell division and protein export. The following metabolic functions were also present but had <10 sequences and are not shown here: hypothetical associated with RecF, carotenoid biosynthesis, tricarboxylate transporter, probably organic hydroperoxide resistance related hypothetical, protein, pigment biosynthesis, related to N-acetylglucosamine utilization subsystem, TldD cluster, tRNA sulfuration, chemotaxis, response regulators, cluster of unknown function, DNA polymerase III episolon cluster, lipoprotein B cluster, putrescine/GABA utilization cluster, D-tyrosyl-tRNA (Tyr) deacylase (EC′3.1.-.-) cluster, metaylamine utilisation, putative GGDEF doman protein related to agglutinin secretion, and siderophore biosynthesis. C: The clustering-based subsystems were further dominated by clustering-based systems (hierarchical level 3), di- and oligosaccharides, central carbohydrate metabolism, monosaccharides.</p>", "links"=>[], "tags"=>["australian"], "article_id"=>310410, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Metabolic_Potential_of_Australian_Sea_Lion_Gut_Microbiome_/310410", "title"=>"Metabolic Potential of Australian Sea Lion Gut Microbiome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:06:50"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/639988/Figure_3.tif"], "description"=>"<p>Metabolic potential of the Australian sea lion gut microbiome is compared to publicly available seawater samples (Antarctic, North Pacific, South Pacific and Indian Oceans), gut microbiomes (human, fish, cow and chicken), and whale fall microbiomes from the MG-RAST server.</p>", "links"=>[], "tags"=>["scaling", "comparing", "australian", "microbiome", "metabolic", "seawater"], "article_id"=>310473, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Multi_Dimensional_Scaling_Plot_Comparing_Australian_Sea_Lion_Microbiome_Metabolic_Potential_with_several_other_Gut_Seawater_and_Whale_Fall_Microbiomes_/310473", "title"=>"Multi-Dimensional Scaling Plot Comparing Australian Sea Lion Microbiome Metabolic Potential with several other Gut, Seawater and Whale Fall Microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:07:53"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/640153/Figure_4.tif"], "description"=>"<p>A: The metabolic subsystems that are over-represented in the Australian sea lion faecal microbiome compared to Human A and Fish A gut microbiomes. B: The metabolic subsystems that are under-represented in the Australian sea lion faecal microbiome compared to Human A and Fish A gut microbiomes.</p>", "links"=>[], "tags"=>["subsystems", "over-represented", "under-represented", "australian", "faecal", "microbiome", "compared"], "article_id"=>310638, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Metabolic_Subsystems_Over_represented_and_Under_represented_in_the_Australian_Sea_Lion_Faecal_Microbiome_compared_to_both_Human_A_and_Fish_A_Gut_Microbiomes_/310638", "title"=>"Metabolic Subsystems Over-represented and Under-represented in the Australian Sea Lion Faecal Microbiome compared to both Human A and Fish A Gut Microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:10:38"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/640259/Figure_5.tif"], "description"=>"<p>A: The metabolic subsystems that are over-represented in the Australian sea lion faecal microbiome compared to two Antarctic seawater microbiomes. B: The metabolic subsystems that are under-represented in the Australian sea lion faecal microbiome compared to two Antarctic seawater microbiomes.</p>", "links"=>[], "tags"=>["subsystems", "over-represented", "under-represented", "australian", "faecal", "microbiome", "compared", "antarctic", "seawater"], "article_id"=>310743, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Metabolic_Subsystems_Over_represented_and_Under_represented_in_the_Australian_Sea_Lion_Faecal_Microbiome_compared_to_two_Antarctic_Seawater_Microbiomes_/310743", "title"=>"Metabolic Subsystems Over-represented and Under-represented in the Australian Sea Lion Faecal Microbiome compared to two Antarctic Seawater Microbiomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-05-11 00:12:23"}
  • {"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/640346/Table_1.xls"], "description"=>"<p>Publically Available Metagenomes used for Comparison with the Australian Sea Lion Gut Microbiome. Number of hits determined with BLASTX E value of 10<sup>−5</sup>, no minimum base pair alignment length.</p>", "links"=>[], "tags"=>["metagenomes", "australian", "hits", "blastx", "alignment"], "article_id"=>310832, "categories"=>["Physiology", "Inorganic Chemistry", "Ecology", "Microbiology"], "users"=>["Trish J. Lavery", "Ben Roudnew", "Justin Seymour", "James G. Mitchell", "Thomas Jeffries"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0036478.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Publically_Available_Metagenomes_used_for_Comparison_with_the_Australian_Sea_Lion_Gut_Microbiome_Number_of_hits_determined_with_BLASTX_E_value_of_10_8722_5_no_minimum_base_pair_alignment_length_/310832", "title"=>"Publically Available Metagenomes used for Comparison with the Australian Sea Lion Gut Microbiome. Number of hits determined with BLASTX E value of 10<sup>−5</sup>, no minimum base pair alignment length.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-05-11 00:13:52"}

PMC Usage Stats | Further Information

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Relative Metric

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