Journal Article

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

Glazko, Galina V., Andreyev, Dmitri S., Rahmatallah, Yasir, McElroy, Taylor, Orr, Lisa, Martin, R. J., Arthur, John M., Karaduta, Oleg, Kieffer, Dorothy A., Edmondson, Ricky D., Byrum, Stephanie D., Tackett, Alan J., Adams, Sean H., Mackintosh, Samuel G., Vaziri, Nosratola D., Zybailov, Boris L.

2019

Overview

Resistant 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. Differences 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. 5,834 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. Metaproteomics 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.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Animals / Bacteria / Bacterial proteins / Bacterial Proteins - analysis / Biochemistry / Biological markers / Biology and Life Sciences / Biomarkers / Carbohydrate metabolism / Cecum / Cecum - microbiology / Chronic kidney failure / Computer and Information Sciences / Criminal investigation / Diabetes / Diet / Dietary supplements / Disease Progression / Enzymes / Esters / Gastrointestinal Microbiome / Gene expression / Health aspects / Hemodialysis / Inflammation / Informatics / Intestinal microflora / Kidney diseases / Kidneys / Male / Medicine and Health Sciences / Metabolism / Metabolomics / Microbiomes / Microbiota / Microbiota (Symbiotic organisms) / Molecular biology / Mucin / Nephrology / Nutrition / Phenotypes / Phosphorylation / Physical Sciences / Proteins / Proteome - analysis / Proteomics / Rats / Rats, Sprague-Dawley / Renal Insufficiency, Chronic - chemically induced / Renal Insufficiency, Chronic - microbiology / Research and Analysis Methods / Ribonucleic acid / RNA / rRNA 16S / Ruminococcus - classification / Ruminococcus - growth & development / Species / Starch / Starch - adverse effects / Starch - pharmacology