Menard, J., Bagheri, S., Menon, S. et al. 2023. Noninvasive sampling of the small intestinal chyme for microbiome, metabolome and antimicrobial resistance genes in dogs, a proof of concept. Animal Microbiome 5(1), 64.

Background The gastrointestinal microbiome and metabolome vary greatly throughout the different segments of the gastrointestinal tract, however current knowledge of gastrointestinal microbiome and metabolome in health and disease is limited to fecal samples due to ease of sampling. The engineered Small Intestinal MicroBiome Aspiration (SIMBATM) capsule allows specific sampling of the small intestine in humans. We aimed to determine whether administration of SIMBATM capsules to healthy beagle dogs could reliably and safely sample the small intestinal microbiome and metabolome when compared to their fecal microbiome and metabolome. Results Eleven beagle dogs were used for the study. Median transit time of capsules was 29.93 h (range: 23.83–77.88). Alpha diversity, as measured by the Simpson diversity, was significantly different (P = 0.048). Shannon diversity was not different (P = 0.114). Beta diversity results showed a significant difference between capsule and fecal samples regarding Bray–Curtis, weighted and unweighted unifrac (P = 0.002) and ANOSIM distance metric s (R = 0.59, P = 0.002). In addition to observing a statistically significant difference in the microbial composition of capsules and feces, distinct variation in the metabolite profiles was seen between the sample types. Heat map analysis showed 16 compounds that were significantly different between the 2 sampling modes (adj-P value ranged between 0.004 and 0.036) with 10 metabolites more abundant in the capsule than in the feces and 6 metabolites more abundant in the feces compared to the capsules. Conclusions The engineered Small Intestinal MicroBiome Aspiration (SIMBATM) capsule was easy and safe to administer to dogs. Microbiome and metabolome analysis from the capsule samples were significantly different than that of the fecal samples and were like previously published small intestinal microbiome and metabolome composition.