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

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...

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Published in:	PloS one Vol. 7; no. 7; p. e41484
Main Authors:	Costa, Marcio C., Arroyo, Luis G., Allen-Vercoe, Emma, Stämpfli, Henry R., Kim, Peter T., Sturgeon, Amy, Weese, J. Scott
Format:	Journal Article
Language:	English
Published:	United States Public Library of Science 31.07.2012 Public Library of Science (PLoS)
Subjects:	Analysis Animals Bacteria Bacteroidetes Biology Clostridium difficile Clostridium perfringens Colitis Colitis - microbiology Colitis - veterinary Complexity Diarrhea Dysbacteriosis Fecal microflora Feces Feces - microbiology Firmicutes Fusobacteria Fusobacterium Fusobacterium nucleatum Gene sequencing Genomes High-Throughput Nucleotide Sequencing Horse Diseases - microbiology Horses Housing Inflammatory bowel disease Intestine Medicine Metagenome Microbiota Microbiota (Symbiotic organisms) Microorganisms Models, Genetic Next-generation sequencing Phylogeny Principal Component Analysis Proteobacteria Quality control Relative abundance Residential areas RNA RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Salmonella Sequence Analysis, DNA Species richness Transplants & implants Veterinary colleges Veterinary Science Canada Guelph Ontario Canada
ISSN:	1932-6203, 1932-6203
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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.
AbstractList	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. 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.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.
Audience	Academic
Author	Arroyo, Luis G. Stämpfli, Henry R. Kim, Peter T. Sturgeon, Amy Weese, J. Scott Costa, Marcio C. Allen-Vercoe, Emma
AuthorAffiliation	2 Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada University of Aberdeen, United Kingdom 1 Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada 3 Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada 4 Department of Mathematics and Statistics, College of Physical and Engineering Science, University of Guelph, Guelph, Ontario, Canada
AuthorAffiliation_xml	– name: 1 Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada – name: 2 Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada – name: 3 Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada – name: 4 Department of Mathematics and Statistics, College of Physical and Engineering Science, University of Guelph, Guelph, Ontario, Canada – name: University of Aberdeen, United Kingdom
Author_xml	– sequence: 1 givenname: Marcio C. surname: Costa fullname: Costa, Marcio C. – sequence: 2 givenname: Luis G. surname: Arroyo fullname: Arroyo, Luis G. – sequence: 3 givenname: Emma surname: Allen-Vercoe fullname: Allen-Vercoe, Emma – sequence: 4 givenname: Henry R. surname: Stämpfli fullname: Stämpfli, Henry R. – sequence: 5 givenname: Peter T. surname: Kim fullname: Kim, Peter T. – sequence: 6 givenname: Amy surname: Sturgeon fullname: Sturgeon, Amy – sequence: 7 givenname: J. Scott surname: Weese fullname: Weese, J. Scott
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/22859989$$D View this record in MEDLINE/PubMed
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ContentType	Journal Article
Copyright	COPYRIGHT 2012 Public Library of Science Costa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2012 Costa et al 2012 Costa et al
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 ObjectType-Article-2 ObjectType-Feature-1 content type line 23 Competing Interests: The authors have declared that no competing interests exist. Conceived and designed the experiments: MCC EAV HRS JSW. Performed the experiments: MCC LGA AS. Analyzed the data: MCC PTK JSW. Contributed reagents/materials/analysis tools: LGA JSW. Wrote the paper: MCC. Critically reviewed the manuscript: MCC LGA EAV HRS AS PTK JSW.
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SubjectTerms	Analysis Animals Bacteria Bacteroidetes Biology Clostridium difficile Clostridium perfringens Colitis Colitis - microbiology Colitis - veterinary Complexity Diarrhea Dysbacteriosis Fecal microflora Feces Feces - microbiology Firmicutes Fusobacteria Fusobacterium Fusobacterium nucleatum Gene sequencing Genomes High-Throughput Nucleotide Sequencing Horse Diseases - microbiology Horses Housing Inflammatory bowel disease Intestine Medicine Metagenome Microbiota Microbiota (Symbiotic organisms) Microorganisms Models, Genetic Next-generation sequencing Phylogeny Principal Component Analysis Proteobacteria Quality control Relative abundance Residential areas RNA RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Salmonella Sequence Analysis, DNA Species richness Transplants & implants Veterinary colleges Veterinary Science
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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
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