Regional Gut Microbiota Is Distinct from Fecal Microbiota in Murine Ischemic AKI

Background: Fecal microbiota analyses have been widely used to examine the gut microbiota but may not truly reflect the significant regional heterogeneity existing throughout the gastrointestinal tract. We hypothesized that the regional microbiota of the intestine is distinct from the fecal microbiota in acute kidney injury (AKI) Methods: Wild-type C57BL/6 (n=3/group) mice underwent bilateral ischemia-reperfusion injury (IRI). Mice were sacrificed three days post IRI and samples were collected from: small intestine-proximal (SI-P), small intestine-distal (SI-D), ascending colon (AC), and stool samples, from control and ischemic AKI mice. Samples were subjected to 16S (V4) sequencing and analyzed using the QIIME 2 package for taxonomic assignment and diversity analysis. A taxonomic bar plot was created to visualize the relative abundance of different taxa across samples at the species level. To identify regional microbial shifts, we performed linear discriminant analysis (LEfSe and MaAsLin 2) Results: Alpha diversity analysis using dominance and Simpson's evenness showed reduced species richness in SI-P and stool of AKI mice, while Bray-Curtis β diversity confirmed distinct microbial shifts. In control mice, the gut microbiota in the SI-P and SI-D regions was enriched with species including Allobaculum, Lactobacillus, Pseudolongum, Turicibacter, and Ruminococcus gnavus. In AKI mice, Enterococcus constituted up to 60% of the total microbial population in the SI-P region post-AKI, gradually declining in the subsequent intestinal regions. Staphylococcus emerged as the most abundant genus in the AKI group, particularly in the SI-D region, which reached 50%. Furthermore, Akkermansia muciniphila was more prevalent in the AC region and showed a higher abundance in stool samples in the AKI group Conclusion: Control mice have regional heterogeneity in the intestinal microbiota, andAKI further accentuates this heterogeneity. Enterococcus dominated the SI-P region while Staphylococcus was more prevalent in the SI-D. Akkermansia muciniphila increased in the AC and stool post-AKI. The homeostatic and pathophysiologic effects of the microbiota on the kidney can be better understood by elucidation of the regional gut microbiota compared to fecal microbiota. Funding: NIDDK Support