PXD048985-1

PXD048985 is an original dataset announced via ProteomeXchange.

Title	impacts of resistant starch fermentation in ex vivo microbiomes of pediatric IBD patients
Description	Interindividual variability in responses to prebiotic fibers is an obstacle to improving health via microbiome modulation. Recent advances in ex vivo screening have enabled the personalized selection of prebiotics. This approach, when integrated with meta-omic analyses, hold the potential to unveil microbial factors underlying interindividual variability. Furthermore, most prebiotic-based therapies target butyrate production, a process which is dysregulated in conditions like inflammatory bowel disease (IBD). Other metabolites and functional pathways are rarely considered as targets of microbiome modulation. We conducted high-throughput microbiome culturing using stool samples obtained from 15 pediatric IBD patients with a panel of 9 different resistant starches. After an 18 h culture, we performed meta-omic analyses (16S metagenomics, semi-targeted metabolomics, and shotgun metaproteomics) to examine changes to the microbiomes. Parallel group-level and individual-level analyses revealed starch- and individual-specific changes in fermentation, taxonomic diversity, and functional output. Microbiome responses principally differed by proteins involved in amino acid and nucleic acid metabolism, the metabolite uridine, and Clostridia. We also highlight individualized resistant starch-driven increases in reportedly anti-inflammatory metabolites, such as alpha-ketoglutaric acid, and preferential production of acetate over butyrate. Our ex vivo findings reinforce recent calls to individualize prebiotic therapies, particularly in clinically relevant populations. We present evidence to reconceptualize the beneficial properties of prebiotics to include fermentation by-products beyond butyrate.
HostingRepository	PRIDE
AnnounceDate	2026-09-07
AnnouncementXML	Submission_2026-09-06_16:55:58.642.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhibin Ning
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	acetylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-01-29 11:17:48	ID requested
⏵ 1	2026-09-06 16:55:59	announced

10.1038/s41522-026-01003-w;

Dobranowski P, Duan H, Butcher J, Mayne J, Figeys D, Mack DR, Stintzi A, Individual variability shapes ex vivo responses to resistant starch in inflammatory bowel disease derived microbiomes. NPJ Biofilms Microbiomes, 12(1):(2026) [pubmed]

submitter keyword: IBD,resistant starch, microbiomes

Daniel Figeys
contact affiliation	School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa
contact email	dfigeys@uottawa.ca
lab head
Zhibin Ning
contact affiliation	research associate
contact email	ningzhibin@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD048985
     1. Label: PRIDE project
     2. Name: impacts of resistant starch fermentation in ex vivo microbiomes of pediatric IBD patients