Diversity and Community Composition of Methanogenic Archaea in the Rumen of Scottish Upland Sheep Assessed by Different Methods
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{"title"=>"Diversity and community composition of methanogenic archaea in the rumen of scottish upland sheep assessed by different methods", "type"=>"journal", "authors"=>[{"first_name"=>"Timothy J.", "last_name"=>"Snelling", "scopus_author_id"=>"35727177000"}, {"first_name"=>"Buʇra", "last_name"=>"Genç", "scopus_author_id"=>"9846362800"}, {"first_name"=>"Nest", "last_name"=>"McKain", "scopus_author_id"=>"6602694996"}, {"first_name"=>"Mick", "last_name"=>"Watson", "scopus_author_id"=>"55493517200"}, {"first_name"=>"Sinéad M.", "last_name"=>"Waters", "scopus_author_id"=>"9247164900"}, {"first_name"=>"Christopher J.", "last_name"=>"Creevey", "scopus_author_id"=>"6507448487"}, {"first_name"=>"R. John", "last_name"=>"Wallace", "scopus_author_id"=>"7401496291"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"25250654", "sgr"=>"84907450566", "doi"=>"10.1371/journal.pone.0106491", "scopus"=>"2-s2.0-84907450566", "pui"=>"600067890", "isbn"=>"1932-6203", "issn"=>"19326203"}, "id"=>"0781dd77-6314-357b-980c-34f022e2b51b", "abstract"=>"Ruminal archaeomes of two mature sheep grazing in the Scottish uplands were analysed by different sequencing and analysis methods in order to compare the apparent archaeal communities. All methods revealed that the majority of methanogens belonged to the Methanobacteriales order containing the Methanobrevibacter, Methanosphaera and Methanobacteria genera. Sanger sequenced 1.3 kb 16S rRNA gene amplicons identified the main species of Methanobrevibacter present to be a SGMT Clade member Mbb. millerae ($91% of OTUs); Methanosphaera comprised the remainder of the OTUs. The primers did not amplify ruminal Thermoplasmatales-related 16S rRNA genes. Illumina sequenced V6–V8 16S rRNA gene amplicons identified similar Methanobrevibacter spp. and Methanosphaera clades and also identified the Thermoplasmatales-related order as 13% of total archaea. Unusually, both methods concluded that Mbb. ruminantium and relatives from the same clade (RO) were almost absent. Sequences mapping to rumen 16S rRNA and mcrA gene references were extracted from Illumina metagenome data. Mapping of the metagenome data to16S rRNA gene references produced taxonomic identification to Order level including 2–3% Thermoplasmatales, but was unable to discriminate to species level. Mapping of the metagenome data to mcrA gene references resolved 69% to unclassified Methanobacteriales. Only 30% of sequences were assigned to species level clades: of the sequences assigned to Methanobrevibacter, most mapped to SGMT (16%) and RO (10%) clades. The Sanger 16S amplicon and Illumina metagenome mcrA analyses showed similar species richness (Chao1 Index 19–35), while Illumina metagenome and amplicon 16S rRNA analysis gave lower richness estimates (10–18). The values of the Shannon Index were low in all methods, indicating low richness and uneven species distribution. Thus, although much information may be extracted from the other methods, Illumina amplicon sequencing of the V6–V8 16S rRNA gene would be the method of choice for studying rumen archaeal communities.", "link"=>"http://www.mendeley.com/research/diversity-community-composition-methanogenic-archaea-rumen-scottish-upland-sheep-assessed-different", "reader_count"=>41, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>7, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>13, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>15, "Student > Postgraduate"=>1, "Student > Master"=>7, "Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>27, "Computer Science"=>1, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>27}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>2}}, "reader_count_by_country"=>{"New Zealand"=>1, "United States"=>2, "United Kingdom"=>1, "South Africa"=>1, "Italy"=>1, "Australia"=>1}, "group_count"=>3}

Scopus | Further Information

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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1688777"], "description"=>"<p>Relative distribution of methanogenic archaeal clades for different sequencing and analysis methods: A. SA <i>rrn</i>. B. IM <i>rrn</i>. C. IM <i>mcrA</i>. D. IA <i>rrn.</i></p>", "links"=>[], "tags"=>["Methanosphaera", "1.3 kb 16 S rRNA gene amplicons", "mcrA gene references", "rumen 16 S rRNA", "Methanobrevibacter", "ro", "richness", "Sanger 16 S amplicon", "amplicon 16 S rRNA analysis", "Scottish Upland Sheep Assessed", "16S rRNA gene references", "SGMT Clade member Mbb", "method", "Illumina amplicon sequencing", "rumen archaeal communities", "Illumina metagenome data", "Different Methods Ruminal archaeomes", "metagenome data", "Illumina metagenome mcrA analyses", "species level clades", "otu"], "article_id"=>1180601, "categories"=>["Uncategorised"], "users"=>["Timothy J. Snelling", "Buğra Genç", "Nest McKain", "Mick Watson", "Sinéad M. Waters", "Christopher J. Creevey", "R. John Wallace"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106491.g002", "stats"=>{"downloads"=>5, "page_views"=>41, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Relative_distribution_of_methanogenic_archaeal_clades_for_different_sequencing_and_analysis_methods_A_SA_rrn_B_IM_rrn_C_IM_mcrA_D_IA_rrn_/1180601", "title"=>"Relative distribution of methanogenic archaeal clades for different sequencing and analysis methods: A. SA <i>rrn</i>. B. IM <i>rrn</i>. C. IM <i>mcrA</i>. D. IA <i>rrn.</i>", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-24 03:03:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1688770"], "description"=>"<p>Observed number of OTUs for different sequencing and analysis methods: A. SA <i>rrn</i>. B. IM <i>rrn</i>. C. IM <i>mcrA</i>. D. IA <i>rrn.</i></p>", "links"=>[], "tags"=>["Methanosphaera", "1.3 kb 16 S rRNA gene amplicons", "mcrA gene references", "rumen 16 S rRNA", "Methanobrevibacter", "ro", "richness", "Sanger 16 S amplicon", "amplicon 16 S rRNA analysis", "Scottish Upland Sheep Assessed", "16S rRNA gene references", "SGMT Clade member Mbb", "method", "Illumina amplicon sequencing", "rumen archaeal communities", "Illumina metagenome data", "Different Methods Ruminal archaeomes", "metagenome data", "Illumina metagenome mcrA analyses", "species level clades", "otu"], "article_id"=>1180594, "categories"=>["Uncategorised"], "users"=>["Timothy J. Snelling", "Buğra Genç", "Nest McKain", "Mick Watson", "Sinéad M. Waters", "Christopher J. Creevey", "R. John Wallace"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106491.g001", "stats"=>{"downloads"=>0, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_rarefaction_collectors_curves_/1180594", "title"=>"Multiple rarefaction collectors curves.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-24 03:03:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1688793"], "description"=>"<p>Placement of representative sequences of the present study in clades indicated with additional reference sequences obtained from GenBank. A sequence related to the Crenarchaeota phylum (Acc. No. AF418935) was used as an outgroup. Full multiple alignment using ClustalW and a consensus tree was constructed using the Neighbor-Joining method with the Jukes-Cantor substitution model. The trees were bootstrap resampled 1000 times with branch values ≥50% shown. Scale shows 0.05 nucleotide substitutions per nucleotide position.</p>", "links"=>[], "tags"=>["Methanosphaera", "1.3 kb 16 S rRNA gene amplicons", "mcrA gene references", "rumen 16 S rRNA", "Methanobrevibacter", "ro", "richness", "Sanger 16 S amplicon", "amplicon 16 S rRNA analysis", "Scottish Upland Sheep Assessed", "16S rRNA gene references", "SGMT Clade member Mbb", "method", "Illumina amplicon sequencing", "rumen archaeal communities", "Illumina metagenome data", "Different Methods Ruminal archaeomes", "metagenome data", "Illumina metagenome mcrA analyses", "species level clades", "otu"], "article_id"=>1180615, "categories"=>["Uncategorised"], "users"=>["Timothy J. Snelling", "Buğra Genç", "Nest McKain", "Mick Watson", "Sinéad M. Waters", "Christopher J. Creevey", "R. John Wallace"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0106491.g003", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_analysis_of_SA_rrn_OTUs_RINH01_RINH21_and_IA_rrn_OTUs_T01_T10_/1180615", "title"=>"Phylogenetic analysis of SA <i>rrn</i> OTUs (RINH01–RINH21) and IA <i>rrn</i> OTUs (T01–T10).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-09-24 03:03:39"}

PMC Usage Stats | Further Information

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Relative Metric

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