GEO series

A polyphenol-rich extract recovered from an industrial byproduct regulates the intestinal microbiota and restricts enteric parasite infection

GSE328345 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2026/07/01 Platform GPL34328

At a glance

RNA-seq (gene expression) · mouse · 36 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: 36 samples: 9 × Control Diet vs 9 × Red Clover Diet vs 9 × Control Diet + H polygyrus vs 9 × Red Clover Diet + H polygyrusGroups 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.

Summary (written by the submitters)

Dietary polyphenols have shown potential in limiting inflammation during noncommunicable diseases. However, interaction of polyphenols with the immune system and gut microbiome during enteric infections are not well defined. Moreover, efficient methods to recover high-value polyphenols from industrial processes are limited. Here, we describe the recovery of a polyphenol-rich extract from a byproduct of protein-producing biorefineries.

Read the full summary ↓

The extract was modified to allow incorporation into a semi-synthetic mouse diet. During infection with the intestinal nematode Heligmosomoides polygyrus, mice fed the polyphenol-enriched diet had significantly lower parasite burdens and enhanced mast cell–related gene expression in the jejunum, potentially accelerating worm expulsion. Effects on the gut microbiome were dependent on infection status. In uninfected animals, the extract significantly reshaped the gut microbiome by expanding a broad range of short-chain fatty acid (SCFA)-producing bacteria. However, during H. polygyrus infection, its modulatory effect on the microbiome was markedly diminished concomitant with an extensive increase in the abundance of the Lactobacillaceae and Enterobacteriaceae families in infected mice. However, the extract reduced the relative abundance of Clostridiaceae during infection, suggesting a role in restoring gut homeostasis by counteracting parasite-induced expansion of potentially pathogenic bacteria. Collectively, these findings demonstrate that byproducts from the biorefining industry can be repurposed as functional food components with the potential to limit enteric infection and inflammation.

This dataset

Open GSE328345 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 GSE328345_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 PRJNA1454808 and SRA study SRP692686. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 × Control Diet vs 9 × Red Clover Diet vs 9 × Control Diet + H polygyrus vs 9 × Red Clover Diet + H polygyrus

Supports a between-group comparison across 36 samples.

How we read this: 4 replicated groups read from 36 sample titles; they account for 36 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

GSM9679610 Control Diet 1 Control Diet
GSM9679611 Control Diet 2 Control Diet
GSM9679612 Control Diet 3 Control Diet
GSM9679613 Control Diet 4 Control Diet
GSM9679614 Control Diet 5 Control Diet
GSM9679615 Control Diet 6 Control Diet
GSM9679616 Control Diet 7 Control Diet
GSM9679617 Control Diet 8 Control Diet
GSM9679618 Control Diet 9 Control Diet
GSM9679619 Red Clover Diet 1 Red Clover Diet
GSM9679620 Red Clover Diet 2 Red Clover Diet
GSM9679621 Red Clover Diet 3 Red Clover Diet
GSM9679622 Red Clover Diet 4 Red Clover Diet
GSM9679623 Red Clover Diet 5 Red Clover Diet
GSM9679624 Red Clover Diet 6 Red Clover Diet
GSM9679625 Red Clover Diet 7 Red Clover Diet
GSM9679626 Red Clover Diet 8 Red Clover Diet
GSM9679627 Red Clover Diet 9 Red Clover Diet
GSM9679628 Control Diet + H polygyrus 1 Control Diet + H polygy…
GSM9679629 Control Diet + H polygyrus 2 Control Diet + H polygy…
GSM9679630 Control Diet + H polygyrus 3 Control Diet + H polygy…
GSM9679631 Control Diet + H polygyrus 4 Control Diet + H polygy…
GSM9679632 Control Diet + H polygyrus 5 Control Diet + H polygy…
GSM9679633 Control Diet + H polygyrus 6 Control Diet + H polygy…
GSM9679634 Control Diet + H polygyrus 7 Control Diet + H polygy…
GSM9679635 Control Diet + H polygyrus 8 Control Diet + H polygy…
GSM9679636 Control Diet + H polygyrus 9 Control Diet + H polygy…
GSM9679637 Red Clover Diet + H polygyrus 1 Red Clover Diet + H pol…
GSM9679638 Red Clover Diet + H polygyrus 2 Red Clover Diet + H pol…
GSM9679639 Red Clover Diet + H polygyrus 3 Red Clover Diet + H pol…
GSM9679640 Red Clover Diet + H polygyrus 4 Red Clover Diet + H pol…
GSM9679641 Red Clover Diet + H polygyrus 5 Red Clover Diet + H pol…
GSM9679642 Red Clover Diet + H polygyrus 6 Red Clover Diet + H pol…
GSM9679643 Red Clover Diet + H polygyrus 7 Red Clover Diet + H pol…
GSM9679644 Red Clover Diet + H polygyrus 8 Red Clover Diet + H pol…
GSM9679645 Red Clover Diet + H polygyrus 9 Red Clover Diet + H pol…

Datasets on a similar topic

GSE322757 IL-17RC signaling connects intestinal microbiota and neuroimmune interactions in atherosclerosis 42 samples shares intestinal, microbiota
GSE58086 Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences [30_week_Liver] 12 samples shares intestinal, microbiota
GSE302208 Regional encoding of enteric nervous system responses to microbiota and type 2 inflammation [Neuron SmartSeq2] 169 samples shares microbiota
GSE287225 Laboratory mice engrafted with natural gut microbiota possess a wildling-like phenotype 160 samples shares microbiota
GSE216620 Gut microbiota dysbiosis rewires host mRNA m6A epitranscriptomic landscape via bile acid metabolism 102 samples shares microbiota
GSE293180 Analysis of Host and Microbiome Responses to Antibiotics Reveals Microbiota-Independent Effects on Gut Immune Response [multiabx] 97 samples shares microbiota
GSE294512 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation [RNA-seq] 92 samples shares intestinal
GSE260491 Microbiota of infants consuming secretors or non-secretors mothers milk impacts gut and immune system in mice. 83 samples shares microbiota

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.