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Dietary fiber inulin enables intestinal microbiome to clear fructose and protect the host

GSE268945 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2025/06/03 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
24 samples: 5 conditions, mostly with about 5 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper
Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosisNature metabolism · 2025
Summary (written by the submitters)
Excessive consumption of fructose leads to various cardiometabolic diseases. However, inulin, dietary fiber composed of numerous fructose molecules, exerts health-beneficial effects. Here we report that inulin shifts fructose catabolism from the host organs to gut microbiome, reversing fructose-induced hyperlipidemia, hepatic steatosis and systemic glucose intolerance.
Read the full summary ↓
Both simultaneous and delayed inulin intake enhances fructose clearance by the small intestinal microbiome, effectively reducing fructose dose reaching the liver and colon and thus suppressing hepatic lipogenesis. Inulin also activates the hepatic de novo serine synthesis pathway and cystine uptake to augment glutathione production and reduce oxidative stress. This dual effect of inulin is blocked by antibiotics and transmittable by fecal transplantation. Moreover, inulin-enriched Bacteroides acidifaciens is protective against HFCS-induced lipogenesis. Our data provide mechanistic insights into how fructose-polymer fiber inulin rewires gut microbial fructose catabolism and protects the host from excessive fructose exposure, paving the way to mitigate fructose-induced metabolic disease.
Published in
Dietary fibre-adapted gut microbiome clears dietary fructose and reverses hepatic steatosis
Jung S, Bae H, Song WS et al. · Nature metabolism 2025 · PMID 40954286 · doi:10.1038/s42255-025-01356-0
This dataset
Open GSE268945 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE268945_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1119487 and SRA study SRP511447. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40954286) ↗
Study design
5 conditions, mostly with about 5 replicates each
CW ×5 IW ×5 CF ×5 IF ×5 CIF ×4

Supports a between-group comparison across 24 samples.

How we read this: 5 replicated groups read from 24 sample titles; they account for 24 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.