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Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal...

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Autores principales: Swanson, Kelly S, Dowd, Scot E, Suchodolski, Jan S, Middelbos, Ingmar S, Vester, Brittany M, Barry, Kathleen A, Nelson, Karen E, Torralba, Manolito, Henrissat, Bernard, Coutinho, Pedro M, Cann, Isaac KO, White, Bryan A, Fahey, George C
Formato: Texto
Lenguaje:English
Publicado: Nature Publishing Group 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105739/
https://www.ncbi.nlm.nih.gov/pubmed/20962874
http://dx.doi.org/10.1038/ismej.2010.162
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author Swanson, Kelly S
Dowd, Scot E
Suchodolski, Jan S
Middelbos, Ingmar S
Vester, Brittany M
Barry, Kathleen A
Nelson, Karen E
Torralba, Manolito
Henrissat, Bernard
Coutinho, Pedro M
Cann, Isaac KO
White, Bryan A
Fahey, George C
author_facet Swanson, Kelly S
Dowd, Scot E
Suchodolski, Jan S
Middelbos, Ingmar S
Vester, Brittany M
Barry, Kathleen A
Nelson, Karen E
Torralba, Manolito
Henrissat, Bernard
Coutinho, Pedro M
Cann, Isaac KO
White, Bryan A
Fahey, George C
author_sort Swanson, Kelly S
collection PubMed
description This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.
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spelling pubmed-31057392012-04-01 Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice Swanson, Kelly S Dowd, Scot E Suchodolski, Jan S Middelbos, Ingmar S Vester, Brittany M Barry, Kathleen A Nelson, Karen E Torralba, Manolito Henrissat, Bernard Coutinho, Pedro M Cann, Isaac KO White, Bryan A Fahey, George C ISME J Original Article This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503 280 (K9C) and 505 061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease. Nature Publishing Group 2011-04 2010-10-21 /pmc/articles/PMC3105739/ /pubmed/20962874 http://dx.doi.org/10.1038/ismej.2010.162 Text en Copyright © 2011 International Society for Microbial Ecology
spellingShingle Original Article
Swanson, Kelly S
Dowd, Scot E
Suchodolski, Jan S
Middelbos, Ingmar S
Vester, Brittany M
Barry, Kathleen A
Nelson, Karen E
Torralba, Manolito
Henrissat, Bernard
Coutinho, Pedro M
Cann, Isaac KO
White, Bryan A
Fahey, George C
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title_full Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title_fullStr Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title_full_unstemmed Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title_short Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
title_sort phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105739/
https://www.ncbi.nlm.nih.gov/pubmed/20962874
http://dx.doi.org/10.1038/ismej.2010.162
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