Comparison of the Fecal Microbiota of Healthy Horses and Horses with Colitis by High Throughput Sequencing of the V3-V5 Region of the 16S rRNA Gene
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{"title"=>"Comparison of the fecal microbiota of healthy horses and horses with colitis by high throughput sequencing of the V3-V5 region of the 16s rRNA gene", "type"=>"journal", "authors"=>[{"first_name"=>"Marcio C.", "last_name"=>"Costa", "scopus_author_id"=>"16554419700"}, {"first_name"=>"Luis G.", "last_name"=>"Arroyo", "scopus_author_id"=>"6701602095"}, {"first_name"=>"Emma", "last_name"=>"Allen-Vercoe", "scopus_author_id"=>"6602534706"}, {"first_name"=>"Henry R.", "last_name"=>"Stämpfli", "scopus_author_id"=>"6701808970"}, {"first_name"=>"Peter T.", "last_name"=>"Kim", "scopus_author_id"=>"35072743300"}, {"first_name"=>"Amy", "last_name"=>"Sturgeon", "scopus_author_id"=>"55324539200"}, {"first_name"=>"J. Scott", "last_name"=>"Weese", "scopus_author_id"=>"56702153300"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84864444221", "pui"=>"365351858", "doi"=>"10.1371/journal.pone.0041484", "isbn"=>"10.1371/journal.pone.0041484", "sgr"=>"84864444221", "pmid"=>"22859989"}, "id"=>"e21a46b8-d895-3727-9b7d-58a7bb526152", "abstract"=>"The intestinal tract houses one of the richest and most complex microbial populations on the planet, and plays a critical role in health and a wide range of diseases. Limited studies using new sequencing technologies in horses are available. The objective of this study was to characterize the fecal microbiome of healthy horses and to compare the fecal microbiome of healthy horses to that of horses with undifferentiated colitis. A total of 195,748 sequences obtained from 6 healthy horses and 10 horses affected by undifferentiated colitis were analyzed. Firmicutes predominated (68%) among healthy horses followed by Bacteroidetes (14%) and Proteobacteria (10%). In contrast, Bacteroidetes (40%) was the most abundant phylum among horses with colitis, followed by Firmicutes (30%) and Proteobacteria (18%). Healthy horses had a significantly higher relative abundance of Actinobacteria and Spirochaetes while horses with colitis had significantly more Fusobacteria. Members of the Clostridia class were more abundant in healthy horses. Members of the Lachnospiraceae family were the most frequently shared among healthy individuals. The species richness reported here indicates the complexity of the equine intestinal microbiome. The predominance of Clostridia demonstrates the importance of this group of bacteria in healthy horses. The marked differences in the microbiome between healthy horses and horses with colitis indicate that colitis may be a disease of gut dysbiosis, rather than one that occurs simply through overgrowth of an individual pathogen.", "link"=>"http://www.mendeley.com/research/comparison-fecal-microbiota-healthy-horses-horses-colitis-high-throughput-sequencing-v3v5-region-16s", "reader_count"=>110, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>23, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>6, "Other"=>7, "Student > Master"=>16, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>5, "Librarian"=>1, "Researcher"=>23, "Student > Doctoral Student"=>5, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>6, "Other"=>7, "Student > Master"=>16, "Student > Bachelor"=>11, "Lecturer"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>5, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Materials Science"=>1, "Agricultural and Biological Sciences"=>67, "Medicine and Dentistry"=>9, "Arts and Humanities"=>1, "Veterinary Science and Veterinary Medicine"=>13, "Chemistry"=>4, "Immunology and Microbiology"=>3}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>9}, "Chemistry"=>{"Chemistry"=>4}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>67}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Unspecified"=>{"Unspecified"=>5}, "Environmental Science"=>{"Environmental Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>13}}, "reader_count_by_country"=>{"Canada"=>1, "Sweden"=>1, "United States"=>2, "United Kingdom"=>2, "Mexico"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/599858"], "description"=>"<p>Rarefaction curves comparing the number of reads with the number of phylotypes found in the DNA from feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10).</p>", "links"=>[], "tags"=>["genetics and genomics", "Infectious diseases", "microbiology", "Gastroenterology and hepatology"], "article_id"=>270325, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Rarefaction_curves_/270325", "title"=>"Rarefaction curves.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:36:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/599984"], "description"=>"<p>Overall percentages of bacterial populations at the phylum level (Fig. A) and intra-phylum variation (Fig. B) present in feces of healthy horses and horses affected by colitis.</p>", "links"=>[], "tags"=>["bacterial"], "article_id"=>270473, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fecal_bacterial_population_/270473", "title"=>"Fecal bacterial population.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:37:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/600078"], "description"=>"<p>Phylogenetic tree demonstrating the similarity of OTUs found in feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10). Results were obtained using the Yue & Clayton measure (A) and the Jaccard index (B).</p>", "links"=>[], "tags"=>["trees", "otus"], "article_id"=>270561, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_trees_8211_OTUs_approach_/270561", "title"=>"Phylogenetic trees – OTUs approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:37:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/600202"], "description"=>"<p>PCoA (Fig. A and B) and MNDS (Fig. C and D) showing the representation of vectorial analysis of sequences found in feces of healthy horses (blue dots) and horses affected by colitis (red dots). Results were obtained using the Yue & Clayton measure (Fig. A and C), the Jaccard index (Fig. B and D).</p>", "links"=>[], "tags"=>["genetics and genomics", "Infectious diseases", "microbiology", "Gastroenterology and hepatology"], "article_id"=>270688, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PCoA_and_NMDS_/270688", "title"=>"PCoA and NMDS.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:38:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/600359"], "description"=>"<p>Phylogenetic tree demonstrating the similarity of Phylotypes found in feces of healthy horses (Healthy 1–6) and horses affected by colitis (Colitis 1–10). Results were obtained using the Yue & Clayton measure (A) and the Jaccard index (B).</p>", "links"=>[], "tags"=>["trees", "phylotypes"], "article_id"=>270846, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_trees_8211_Phylotypes_approach_/270846", "title"=>"Phylogenetic trees – Phylotypes approach.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-20 01:39:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/600445"], "description"=>"*<p>Phylotypes.</p>", "links"=>[], "tags"=>["phylotypes", "inverted", "simpson"], "article_id"=>270930, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.t005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Total_number_of_sequences_coverage_number_of_Phylotypes_and_inverted_Simpson_with_lower_and_upper_confidence_interval_limits_/270930", "title"=>"Total number of sequences, coverage, number of Phylotypes and inverted Simpson with lower and upper confidence interval limits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:39:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/600498"], "description"=>"<p>Total number of sequences, coverage, number of OTUs and inverted Simpson with lower and upper confidence interval limits.</p>", "links"=>[], "tags"=>["otus", "inverted", "simpson"], "article_id"=>270978, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.t004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Total_number_of_sequences_coverage_number_of_OTUs_and_inverted_Simpson_with_lower_and_upper_confidence_interval_limits_/270978", "title"=>"Total number of sequences, coverage, number of OTUs and inverted Simpson with lower and upper confidence interval limits.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:39:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/600545"], "description"=>"<p>Total number of sequences, number of base pairs and the mean length of sequences (bp) present in the original fasta file before and after MG-RAST standard quality control filters. Means and standard deviations (±SD) among healthy horses and horses with colitis are also presented.</p>", "links"=>[], "tags"=>["metrics", "mg-rast"], "article_id"=>271031, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pyrosequencing_metrics_from_raw_data_before_and_after_standard_MG_RAST_quality_control_QC_filters_/271031", "title"=>"Pyrosequencing metrics from raw data before and after standard MG-RAST quality control (QC) filters.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:40:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/600606"], "description"=>"<p>Classification of the intestinal bacteria of healthy horses and horses affected by colitis (in percentages) at the phylum level, total number of bacterial reads and species richness after data cleaning (pyrosequencing noise and chimera removal) and filtering (e-value of 30, minimum identity of 97% and minimum alignment of 75bp on MG-RAST).</p>", "links"=>[], "tags"=>["richness", "fecal", "horses", "affected"], "article_id"=>271081, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.t003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_and_species_richness_of_the_fecal_bacteria_of_healthy_horses_and_horses_affected_by_colitis_/271081", "title"=>"Classification and species richness of the fecal bacteria of healthy horses and horses affected by colitis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:40:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/600648"], "description"=>"<p>Total number of reads after data cleaning (pyrosequencing noise and chimera removal), after filtering (e-value of 30, minimum identity of 97% and minimum alignment of 75bp on MG-RAST), and percentage of reads classified by MG-RAST using the SSU databank as Bacteria, Eukaryota, Archaea, unclassified bacteria and sequences unassigned to any Kingdom. Means and standard deviations (±SD) among healthy horses and horses with colitis are also presented.</p>", "links"=>[], "tags"=>["metrics", "cleaned"], "article_id"=>271133, "categories"=>["Microbiology", "Chemistry", "Genetics", "Infectious Diseases"], "users"=>["Marcio C. Costa", "Luis G. Arroyo", "Emma Allen-Vercoe", "Henry R. Stämpfli", "Peter T. Kim", "Amy Sturgeon", "J. Scott Weese"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041484.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pyrosequencing_metrics_of_the_cleaned_data_and_its_distribution_at_the_Kingdom_level_/271133", "title"=>"Pyrosequencing metrics of the cleaned data and its distribution at the Kingdom level.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-20 01:40:34"}

PMC Usage Stats | Further Information

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Relative Metric

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