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Variation of the microbiota and metabolome along the canine gastrointestinal tract



The fecal microbiota are relevant to the health and disease of many species. The importance of the fecal metabolome has more recently been appreciated, but our knowledge of the microbiota and metabolome at other sites along the gastrointestinal tract remains deficient.


To analyze the gastrointestinal microbiota and metabolome of healthy domestic dogs at four anatomical sites.


Samples of the duodenal, ileal, colonic, and rectal contents were collected from six adult dogs after humane euthanasia for an unrelated study. The microbiota were characterized using Illumina sequencing of 16S rRNA genes. The metabolome was characterized by mass spectrometry-based methods.


Prevalent phyla throughout the samples were Proteobacteria, Firmicutes, Fusobacteria, and Bacteroidetes, consistent with previous findings in dogs and other species. A total of 530 unique metabolites were detected; 199 of these were identified as previously named compounds, but 141 of them had at least one significantly different site-pair comparison. Noteworthy examples include relative concentrations of amino acids, which decreased from the small to large intestine; pyruvate, which peaked in the ileum; and several phenol-containing carboxylic acid compounds that increased in the large intestine.


The microbiota and metabolome vary significantly at different sites along the canine gastrointestinal tract.

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Correspondence to Jan S. Suchodolski.

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The authors declare no conflict of interest.

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All applicable international, national, and institutional guidelines for the care and use of animals were followed. All procedures performed in studies involving animals were in accordance with the ethical standards of the institution at which the studies were conducted.

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Honneffer, J.B., Steiner, J.M., Lidbury, J.A. et al. Variation of the microbiota and metabolome along the canine gastrointestinal tract. Metabolomics 13, 26 (2017).

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  • Microbiota
  • Canine
  • Metabolome
  • Inter-omic
  • Gastrointestinal