Investigating the effect of mycoprotein-based products on microbial diversity in the human gut using a colonic in vitro fermentation experiment and shotgun metagenomics sequencing

Mycoprotein is a fungal-derived ingredient used for meat alternative products, characterised by its fungal cell walls rich in dietary fibre which define its structure. While consuming mycoprotein-products has been linked to health benefits, the impact of mycoprotein fermentation on the gut microbiota is yet to be understood. This study aims to identify changes in microbiome composition and microbial metabolites during colonic fermentation of mycoprotein following simulated upper gastrointestinal digestion. This experiment is performed using three substrates: mycoprotein, a plant-based (oat) and animal-based (chicken) controls. For each substrate, parallel fermentations (duplicates) were performed in anaerobic vessels with the media and a faecal slurry produced from the stools of six donors. A sample was taken at 0, 4, 8, 24 and 72 hours for DNA extraction and metagenomics shotgun sequencing.