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

Authors: ZYBAYLOV, BORIS - University Arkansas For Medical Sciences (UAMS); GLAZKO, GALINA - University Arkansas For Medical Sciences (UAMS); RAHMATALLAH, YASIR - University Arkansas For Medical Sciences (UAMS); ANDREYEV, DMITRI - University Arkansas For Medical Sciences (UAMS); MCELROY, TAYLOR - University Arkansas For Medical Sciences (UAMS); KARADUTA, OLEG - University Arkansas For Medical Sciences (UAMS); BYRUM, STEPHANIE - University Arkansas For Medical Sciences (UAMS); ORR, LISA - University Arkansas For Medical Sciences (UAMS); TACKETT, ALAN - University Arkansas For Medical Sciences (UAMS); MACKINTOSH, SAMUEL - University Arkansas For Medical Sciences (UAMS); EDMONDSON, RICKY - University Arkansas For Medical Sciences (UAMS); KIEFFER, DOROTHY - Uc Davis Medical Center; MARTIN, R - Uc Davis Medical Center; Ferruzzi, Mario; VAZIRI, NICOLAS - University Of California; ARTHUR, JOHN - University Arkansas For Medical Sciences (UAMS)

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/13/2018
Publication Date: 1/30/2019
Citation: Zybaylov, B.L., Glazko, G.V., Rahmatallah, Y., Andreyev, D.S., McElroy, T., Karaduta, O., Byrum, S.D., Orr, L., Tackett, A.J., Mackintosh, S.G., Edmondson, R.D., Kieffer, D.A., Martin, R.J., Adams, S.H., Vaziri, N.D., Arthur, J.M. 2019. Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats. PLoS One. 14(1):e0199274. https://doi.org/10.1371/journal.pone.0199274.
DOI: https://doi.org/10.1371/journal.pone.0199274

Interpretive Summary: The bacteria that normally are present in the gut (collectively referred to as microbiota) are important to overall health and help shape the body's physiological function. Foods and dietary components rapidly and profoundly alter the microbiota: e.g., resistant starch is a prebiotic fiber metabolized by the gut bacteria. What is less clear is identification of the mechanisms by which gut microbiota signal to or impact the body's systems, and even the specific bacteria that confer a positive influence on health remain to be fully elaborated. New technical methods are being applied and validated to determine which bacteria are present in the gut, and how these respond to diet. One such method is "metaproteomics," which refers to the identification of hundreds to thousands of proteins in the gut contents, to help identify which bacteria are present and to determine how these microbes shift with diet, and how they change their protein production with changes in diet. The metaproteomics method was tested in a unique rat kidney function model that is known to have a major shift in microbiota that associates with kidney dysfunction. Resistant starch has been shown to attenuate chronic kidney disease (CKD) progression in these rats. Differences between proteins in cecum (large intestine) contents from CKD rats fed a diet containing resistant starch with those fed a diet containing digestible starch were examined by comparative metaproteomics analysis. Taxonomic information (a.k.a. definition of bacteria types) was obtained using unique protein sequences. Our methodology results in quantitative data covering both host and bacterial proteins. From this analysis, 5,834 proteins were quantified, with 947 proteins originating from the host organism. Taxonomic information surpassed previous types of RNA-based 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 kidney function. Several known host CKD-associated proteins and biomarkers of impaired kidney function were significantly reduced with resistant starch supplementation. Metaproteomics analysis of cecum contents has great promise as a method to fully evaluate both the types of gut microbiota present and the proteins they produce. Such a method can be applied to studies from human clinical samples or animal models, with the promise of defining how better nutrition drives health-promoting effects in the gut.

Technical Abstract: 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 fibe-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.