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Metaproteomics Reveals Potential Mechanisms by which Dietary Resistant Starch Supplementation Attenuates Chronic Kidney Disease Progression in Rats

View ORCID ProfileBoris L Zybailov, Galina V Glazko, Yasir Rahmatallah, Dmitri S Andreyev, View ORCID ProfileTaylor McElroy, Oleg Karaduta, Stephanie D Byrum, Lisa Orr, Alan J Tackett, Samuel G Mackintosh, Ricky D Edmondson, Dorothy A Kieffer, R J Martin, Sean H Adams, Nicolas D Vaziri, John M Arthur
doi: https://doi.org/10.1101/340513
Boris L Zybailov
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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  • ORCID record for Boris L Zybailov
  • For correspondence: blzybaylov@uams.edu JMArthur@uams.edu
Galina V Glazko
1Department of Biomedical Informatics, UAMS, Little Rock, AR;
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Yasir Rahmatallah
1Department of Biomedical Informatics, UAMS, Little Rock, AR;
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Dmitri S Andreyev
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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Taylor McElroy
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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Oleg Karaduta
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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Stephanie D Byrum
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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Lisa Orr
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
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Alan J Tackett
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
3Proteomics Core Facility, UAMS, Little Rock, AR;
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Samuel G Mackintosh
2Department of Biochemistry and Molecular Biology, UAMS, Little Rock, AR;
3Proteomics Core Facility, UAMS, Little Rock, AR;
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Ricky D Edmondson
3Proteomics Core Facility, UAMS, Little Rock, AR;
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Dorothy A Kieffer
4Department of Nutrition, University of California, Davis, CA;
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R J Martin
4Department of Nutrition, University of California, Davis, CA;
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Sean H Adams
5Arkansas Children’s Nutrition Center and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR;
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Nicolas D Vaziri
6Division of Nephrology, University of California, Irvine, CA;
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John M Arthur
7Division of Nephrology, UAMS, Little Rock, AR
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  • For correspondence: blzybaylov@uams.edu JMArthur@uams.edu
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Abstract

Background 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.

Methods 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.

Results 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.

Conclusions - 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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted June 06, 2018.
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Metaproteomics Reveals Potential Mechanisms by which Dietary Resistant Starch Supplementation Attenuates Chronic Kidney Disease Progression in Rats
Boris L Zybailov, Galina V Glazko, Yasir Rahmatallah, Dmitri S Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D Byrum, Lisa Orr, Alan J Tackett, Samuel G Mackintosh, Ricky D Edmondson, Dorothy A Kieffer, R J Martin, Sean H Adams, Nicolas D Vaziri, John M Arthur
bioRxiv 340513; doi: https://doi.org/10.1101/340513
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Metaproteomics Reveals Potential Mechanisms by which Dietary Resistant Starch Supplementation Attenuates Chronic Kidney Disease Progression in Rats
Boris L Zybailov, Galina V Glazko, Yasir Rahmatallah, Dmitri S Andreyev, Taylor McElroy, Oleg Karaduta, Stephanie D Byrum, Lisa Orr, Alan J Tackett, Samuel G Mackintosh, Ricky D Edmondson, Dorothy A Kieffer, R J Martin, Sean H Adams, Nicolas D Vaziri, John M Arthur
bioRxiv 340513; doi: https://doi.org/10.1101/340513

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