Gastrointestinal Mucosal Microbiota of Young Adult and Geriatric Dogs Fed Animal- or Plant-Based Diets

The gastrointestinal microbiota are known to be important for host health and disease, but most studies rely on fecal samples that may not be an accurate indicator of populations in the gastrointestinal tract and/or those adhering to the mucosa and important for disease. Therefore, the objective of this study was to characterize the phylogeny and predicted functional capacity of microbiota residing on the gut mucosa of healthy young adult and geriatric dogs fed different diets. Twelve weanling (8 wk old) and 12 senior (11.1 yr old) beagles were randomly assigned to an animal product-based diet (APB) or plant product-based diet (PPB) and fed for 12 mo. After 12 mo, mucosal samples from the stomach, duodenum, jejunum, ileum and mid-colon were collected. DNA was extracted and the V4 region of the bacterial 16S rRNA gene was amplified for Illumina MiSeq sequencing. Data were analyzed using QIIME 1.9.1. and Statistical Analyses of Metagenomic Profiles (STAMP) software 2.1.3. Gene predictions were made using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Taxonomic assessment revealed that the mid-colon had a greater (p<0.05) species richness compared to other segments. Principal coordinates analysis (PCoA) of weighted and unweighted UniFrac distances demonstrated that mid-colon samples clustered together and away from other segments that were more variable. Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria were the predominant phyla in all five segments, but the abundances of each were unique. The stomach had the greatest (p<0.05) relative abundance of Proteobacteria, followed by the jejunum, duodenum, mid-colon, and ileum. The duodenum had a greater (p<0.05) relative abundance of Bacteroidetes than the stomach or ileum. The ileum and mid-colon had greater relative abundance of Firmicutes than the other segments. The mid-colon had a greater (p<0.05) relative abundance of Fusobacteria than other segments. Within the mid-colon, PCoA of unweighted UniFrac distances demonstrated separate clustering of young adult and geriatric dogs as well as dogs fed APB vs. PPB. Unlike the taxonomic analyses, PICRUST prediction suggested that the functional capacity of microbiota present in the stomach was different from those present in the other segments. In conclusion, the mucosal microbiota were distinct among gastrointestinal segments. In addition to segment effects, age and diet also affected the mucosal microbiota communities, especially in the mid-colon.