Comparative Microbiome Signatures and Short-Chain Fatty Acids in Mouse, Rat, Non-human Primate, and Human Feces

Abstract

Gut microbiome plays a fundamental role in several aspects of host health and diseases. There has been an exponential surge in the use of animal models that can mimic different phenotypes of the human intestinal ecosystem. However, data on host species-specific signatures of gut microbiome and its metabolites like short-chain fatty acids (SCFAs; i.e., acetate, propionate, and butyrate) and lactate in these models and their similarities/differences from humans remain limited, due to high variability in protocols and analyses. Here, we analyze the fecal microbiota composition and the fecal levels of SCFAs and lactate in three of the most-widely used animal models, i.e., mice, rats, and non-human primates (NHPs) and compare them with human subjects, using data generated on a single platform with same protocols. The data show several species-specific similarities and differences in the gut microbiota and fecal organic acids between these species groups. Based on β-diversity, the gut microbiota in humans seems to be closer to NHPs than to mice and rats; however, among rodents, mice microbiota appears to be closer to humans than rats. The phylum-level analyses demonstrate higher Firmicutes–Bacteroidetes ratio in humans and NHPs vs. mice and rats. Human microbiota is dominated by Bacteroides followed by Ruminococcaceae and Clostridiales. Mouse gut is predominated by members of the family S24-7 followed by those from the order Clostridiales, whereas rats and NHPs have higher abundance of Prevotella compared with mice and humans. Also, fecal levels of lactate are higher in mice and rats vs. NHPs and humans, while acetate is highest in human feces. These data of host species-specific gut microbiota signatures in some of the most widely used animal models in context to the human microbiota might reflect disparities in host factors, e.g., diets, genetic origin, gender and age, and hence call for prospective studies investigating the features of gut microbiome in such animal models by controlling for these host elements.

Household Pet Ownership and the Microbial Diversity of the Human Gut Microbiota

“…OTU 784, Akkermansia, was not present when only assessing the microbiome of cat and dog owners, though this genera has previously been identified in rodents (Nagpal et al, 2018) and reptiles (Campos et al, 2018). Akkermansia was the only differentially abundant OTU we were able to tentatively to the species level.…”

Commensal-derived metabolites govern Vibrio cholerae pathogenesis in host intestine

“…However, for our findings to be clinically relevant, it needs to be first established that the mouse gut microbiome is, to a sufficient degree, reflective of the human gut microbiome. Previous studies have reported predominantly high relative abundances of the Bacteroidetes phylum in both mouse and human gut microbiomes [43][44][45][46]. Furthermore, there is evidence that B. vulgatus isolates from human and other animal hosts are indistinguishable based on their 16S rRNA gene sequences [47], suggesting phylogenetic proximity between mouse-and human-gut resident B. vulgatus strains.…”

Microbiome-Metabolome Signature of Acute Kidney Injury

“…However, how such findings resonate with the results observed in our rat model of AKI remains unknown, as the species of Prevotella copri and Faecalibacterium prausnitzii were observed to be quantitatively reduced. Although the human gut microbiome might differ significantly from that in rat, due to differences in the relative abundance of many bacterial clades, a considerable fraction (not limited to major phyla) and many common genera are, however, extensively shared [58]. Consequently, this allows us a greater scope to extrapolate the findings from our working rat model towards a human context, with a view to dissect the potential relationship between the human microbiome and AKI/CKD progression, with proper accuracy and effect.…”