Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats

Abstract

BackgroundResistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate chronic kidney disease (CKD) progression in rats. Previous studies employed taxonomic analysis using 16S rRNA sequencing and untargeted metabolomics profiling. Here we expand these studies by metaproteomics, gaining new insight into the host-microbiome interaction.MethodsDifferences between cecum contents in CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins.Results5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information derived from metaproteomics data surpassed previous 16S RNA analysis, and reached species resolutions for moderately abundant taxonomic groups. In particular, the Ruminococcaceae family becomes well resolved–with butyrate producers and amylolytic species such as R. bromii clearly visible and significantly higher while fibrolytic species such as R. flavefaciens are significantly lower with resistant starch feeding. The observed changes in protein patterns are consistent with fiber-associated improvement in CKD phenotype. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Data are available via ProteomeXchange with identifier PXD008845.ConclusionsMetaproteomics analysis of cecum contents of CKD rats with and without resistant starch supplementation reveals changes within gut microbiota at unprecedented resolution, providing both functional and taxonomic information. Proteins and organisms differentially abundant with RS supplementation point toward a shift from mucin degraders to butyrate producers.

Gut microbiota composition and frailty in elderly patients with Chronic Kidney Disease

“…It is noteworthy that although no apparent differences in macronutrients and fiber intake were found between F-CKD, NF-CKD and Controls through dietary diary analyses, 24 patients in the CKD cohort (13 F-CKD and 11 NF-CKD) were prescribed aproteic food, that may have influenced this finding since it is enriched with fibers and inulin, potentially acting as prebiotics and supporting the growth of lactobacilli [39,40].…”

Microbiome-Metabolome Signature of Acute Kidney Injury

“…The relationships between disease onset and progression with gut microflora have recently been reported, with ever-increasing clarity and importance. In humans, decreased levels of Prevotella copri and Faecalibacterium prausnitzii populations were observed in severe forms of chronic kidney disease (CKD), which also negatively correlate with the presence of important diagnostic markers, such as C-reactive protein and cystatin C levels [49][50][51]. Similarly, Prevotella copri and Faecalibacterium prausnitzii were significantly depleted in humans with diabetic nephropathy [43,52].…”

Vegetable-Based Diets for Chronic Kidney Disease? It Is Time to Reconsider

“…Among the compounds associated with vegetarian diets that have demonstrated salutary effects on the intestinal flora, several studies have shown the favorable effects of amylose, a vegetable unabsorbable complex carbohydrate that has been described to promote changes in the flora beneficial to the host both in CKD animal models [26] and end-stage renal disease (ESRD) patients [27] through the restoration of colonic epithelial barrier and attenuation of oxidative stress and inflammation [28], improvement of microbial dysbiosis in ESRD patients and retarding CKD progression. These compounds also improve the gut microbial dysbiosis and metabolomic profile [29] in CKD rats.…”