PXD008845

PXD008845 is an original dataset announced via ProteomeXchange.

Title	Metaproteomics of the Resistant Starch-fed Chronic Kidney Disease Rats
Description	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. 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.
HostingRepository	PRIDE
AnnounceDate	2019-12-13
AnnouncementXML	Submission_2019-12-13_07:36:35.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD008845
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Boris Zybailov
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	Met->Hse; Dethiomethyl; Amidated; Diethyl; Hex; Lys->AminoadipicAcid; Pro->pyro-Glu; Ethanolyl; Propionamide; Phospho; Propargylamine; Deamidated; Methylpyrroline; Acetyl; Trp->Oxolactone; Methylamine; CHDH; HexNAc(1)dHex(1); Nitro; Cation:K; Methylthio; dichlorination; Carboxymethyl; HexNAc; Carbamidomethyl; Cation:Ca[II]; Gln->pyro-Glu; Met->Hsl; Guanidinyl; Glu->pyro-Glu; DAET; MercaptoEthanol; Hydroxymethyl; Delta:H(2)C(2); Fluoro; Ethyl; Ammonia-loss; Cation:Fe[II]; Methyl; ISD_z+2_ion; Oxidation; AEC-MAEC; Carboxy; Ethanedithiol; Quinone; Didehydro; Cation:Na; Trp->Kynurenin; Pro->Pyrrolidinone; Sulfo; SMA; Deoxy; Iodo; Malonyl; Methyl+Deamidated; Formyl; Carbamyl; Lys->Allysine; Amidine; Sulfide; Amino; Ammonium; Dehydrated; Dimethyl; Dioxidation; Ethyl+Deamidated; glycidamide
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2018-02-03 04:16:12	ID requested
1	2018-12-18 11:01:30	announced
⏵ 2	2019-12-13 07:36:37	announced	2019-12-13: Updated publication reference for PubMed record(s): 30699108.

Zybailov BL, Glazko GV, Rahmatallah Y, Andreyev DS, McElroy T, Karaduta O, Byrum SD, Orr L, Tackett AJ, Mackintosh SG, Edmondson RD, Kieffer DA, Martin RJ, Adams SH, Vaziri ND, Arthur JM, Metaproteomics reveals potential mechanisms by which dietary resistant starch supplementation attenuates chronic kidney disease progression in rats. PLoS One, 14(1):e0199274(2019) [pubmed]

curator keyword: Metaproteomics

submitter keyword: Rat, gut microbiome, metaproteomics, chronic kidney disease, resistant starch

Boris Zybaylov
contact affiliation	Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
contact email	BLZybaylov@uams.edu
lab head
Boris Zybailov
contact affiliation	Biochemistry and Molecular Biology
contact email	boriszybailov@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008845
     1. Label: PRIDE project
     2. Name: Metaproteomics of the Resistant Starch-fed Chronic Kidney Disease Rats