Although the effect of carbohydrates on the composition of the gut microbiota has been extensively studied, the impact of dietary proteins, particularly those found in whey, remains largely unexplored.

Recent studies suggest that bioactive peptides generated during digestion may positively modulate the microbiota and stimulate the production of metabolites such as short-chain fatty acids.

To enhance these effects, the use of enzymatic hydrolysis prior to digestion has been proposed, with the aim of obtaining peptides with specific sequences, characterised by improved digestibility and a potential reduction in allergenicity. Therefore, this study evaluated the effect of whey protein hydrolysates on the composition of the gut microbiota and on the production of metabolites via in vitro colonic fermentation.

The hydrolysates (WPH) were obtained by hydrolysis with Alcalase or Protamex for increasing durations (10, 30, 120 min), followed by digestion according to the INFOGEST protocol and colonic fermentation.

The results demonstrate that hydrolysis promotes the release of essential amino acids, such as proline and asparagine, whilst maintaining unchanged levels of branched-chain amino acids, which are important for muscle synthesis. Metagenomic analysis shows that WPHs obtained from Protamex are capable of promoting the growth of beneficial bacteria and reducing pro-inflammatory species.