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The genome sequencing and analysis pipeline was modified to enable sampling of the microbiome from the small intestines of dogs, and the sequencing was performed by Illumina in the same manner as for human stool samples. Sequencing data were analyzed by QIIME  and transferred to the Human Oral Microbiome Database . The microbial composition of seven canine fecal samples was analyzed at two timepoints, three months apart, and compared with human samples obtained from two cohorts, one in Boston and one in Helsinki. These human cohorts, as with the mouse and pig cohorts, have been completely different in all aspects other than the employment of a different sequencing platform: The human samples were sequenced as part of the Human Microbiome Project (HMP) using the Roche 454 platform, while dog samples were sequenced as part of a separate project using Illumina. Following quality control filtering, samples were clustered using a weighted UniFrac measure of beta diversity, and visualized using non-metric multidimensional scaling (nMDS). The dog fecal samples cluster together (Fig. 2), further supporting the notion that dogs, like humans, harbor a distinct fecal microbiota and that, like humans, changes in diet have a significant impact on the composition of the gut microbiome in dogs.
We found that the dog catalog size was smaller than that of the human (3,345,817 vs. 3,974,380 genes), the mouse (4,681,937 vs. 6,837,095), and the pig (9,780,814 vs. 10,999,300). This trend can be explained by the lower sampling depth of the dog samples, as reflected in the rarefaction curve (Additional file 7: Figure S5).
We also observed a greater fraction of genes in the dog gut that are associated with disease- and metabolism-related pathways, such as the metabolism of cofactors and vitamins, lipid metabolism, and amino acid metabolism, as well as more general terms such as immune response, intracellular trafficking, and cell growth and death, when compared to the human, mouse and pig catalogs. Finally, dog gut genes are more closely related to human genes than are those of the other three host-associated microbiomes, based on the distribution of mutual KEGG Orthology terms. These differences in the host-associated microbiomes of dogs and pigs thus suggest that these organisms can be used as model systems to study the effect of diet on the microbiome.
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