An Optimised Faecal microRNA Sequencing Pipeline Reveals Fibrosis in Trichuris muris Infection

The intestine is a site of diverse functions including digestion, nutrient absorption, immune surveillance, and microbial symbiosis. As such, intestinal homeostasis is vital for overall wellbeing. Faecal microRNAs (miRNAs) offer valuable non-invasive insights into the transcriptional state of the intestine. However, typical faecal miRNA yields and profiles remain incompletely characterised. Here, we develop an optimised protocol for faecal miRNA detection, and describe a reproducible murine faecal miRNA profile across several studies by performing a meta-analysis. By examining faecal miRNA changes during chronic infection with the gastrointestinal helminth, Trichuris muris, we identify the altered expression of miRNAs associated with fibrosis, barrier integrity and wound healing. Fibrosis was confirmed in vivo, suggesting a role for these miRNAs in regulating wound healing during chronic infection where the production of classical wound healing Th2 cytokines are low. Further implementations of this technique can identify novel hypotheses and therapeutic strategies in diverse disease contexts. 7 mice were gavaged with a low dose of Trichuris muris (mouse whipworm) eggs. 5 mice were gavaged with water as a control. Faecal samples were collected for small RNA sequencing at 21 and 35 days post-treatment for all mice. An additional collection was taken from the infected mice immediately prior to gavage with eggs / infection (I0).