SEGMENT-SPECIFIC ANALYSIS OF GUT MICROBIOTA IN A RAT MODEL OF CHRONIC KIDNEY DISEASE

Chronic kidney disease (CKD) significantly impairs the gut-kidney axis; however, the spatial organization of the microbiota along the colonic segments remains poorly defined. This study characterized microbial alterations in a rat model of renal dysfunction, providing a distinct analysis of the ascending, transverse, and descending colon, as well as the rectum. The experimental work presented in this thesis was conducted at the Laboratory of Gastrointestinal Physiology, directed by Prof. Laura Grasa, at the University of Zaragoza (Spain), within the framework of an Erasmus+ mobility programme. The methodology involved DNA extraction from fecal samples, followed by full-length 16S rRNA gene sequencing using the Oxford Nanopore MinION platform. Bioinformatic analysis was performed in RStudio to evaluate diversity, differential taxonomic abundance, metabolite production, and the functional potential of the intestinal microbiota. The results demonstrate that renal dysfunction induces a segment-dependent dysbiosis. In the ascending colon only species richness was altered, while the transverse, descending, and rectal segments exhibited significant reductions in α-diversity. Furthermore, β-diversity analysis confirmed a separation between control and CKD rats, with more pronounced divergences observed in the distal portions. LEfSe analysis identified a prevalence of pro-inflammatory and proteolytic taxa — such as Escherichia-Shigella and Clostridium sensu stricto 1 — predominantly in the distal colon, alongside a depletion of beneficial saccharolytic genera, including Lachnospiraceae and Roseburia. These structural shifts correlate with increased levels of uremic toxins and alterations in specific functional pathways, such as flavone biosynthesis and FoxO signaling. In conclusion, renal dysfunction disrupts the microbial structure throughout the entire intestinal tract, with an impact that intensifies from the proximal to the distal colon. These findings support the link between uremia and regional microbiota alterations and underscore the necessity of segment-specific analyses in the study of CKD.