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

peer-reviewed · PLOS ONE · 2019

peer-reviewed · PLOS ONE · 2019. Boris Zybailov et al. Background Resistant starch is a prebiotic metabolized by the gut bacteria. It has been shown to attenuate…
Date 2019-01-30
Type peer-reviewed
Venue PLOS ONE
Publisher Public Library of Science (PLoS)
Contribution downstream-application
DOI 10.1371/journal.pone.0199274
Citations (OpenAlex) 34

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.

Authors

  1. Boris Zybailov · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  2. Galina Glazko · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  3. Yasir Rahmatallah · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  4. Dmitri S. Andreyev · University of Arkansas for Medical Sciences
  5. Taylor McElroy · University of Arkansas for Medical Sciences
  6. Oleg Karaduta · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  7. Stephanie D. Byrum · University of Arkansas for Medical Sciences
  8. Lisa Orr · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  9. Alan Tackett · Arkansas Children’s Research Institute, University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  10. Samuel Mackintosh · University of Arkansas Medical Center, University of Arkansas for Medical Sciences
  11. Ricky D. Edmondson · University of Arkansas for Medical Sciences
  12. Dorothy A. Kieffer · University of California, Davis
  13. R. J. Martin · University of California, Davis
  14. Sean H. Adams · Arkansas Children’s Nutrition Center, University of Arkansas for Medical Sciences
  15. Nosratola D. Vaziri · University of California, Irvine
  16. John Arthur · University of Arkansas Medical Center, University of Arkansas for Medical Sciences

Methods and tools

Methods it uses

  • PEAKS: Commercial DP-based de novo
  • SPIDER: Protein identification from sequence tags while accounting for de novo sequencing error.

Data deposited

  • Metaproteomics of the Resistant Starch-fed Chronic Kidney Disease Rats — as deposited · PXD008845

Cites (2)

Cited by (1)

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