Digestive enzyme supplements are generally used to aid the breakdown of proteins, carbohydrates, and lipids, and they may help alleviate digestive issues caused by high fiber intake. Here's what the research says about their impact on the microbiome:

1. Digestive Enzyme Function and Efficacy: Digestive enzyme supplements are formulated to break down various nutrients, potentially easing symptoms like bloating and discomfort related to high fiber intake¹.

2. Impact on Gut Microbiome: A study investigating the effect of an enzyme-probiotics blend on the gut microbiome found no significant changes in the overall microbiome profile at higher taxonomic levels². This indicates that digestive enzyme supplements do not adversely affect the gut microbiome significantly.

3. Potential Positive Effects: The same study suggested there might be some positive alterations in protein digestibility, amino acid absorption, and the gut microbiome, although these findings were not statistically significant and would require confirmation through larger studies².

Overall, current evidence suggests that digestive enzyme supplements do not harm the gut microbiome significantly and might even provide some digestive benefits. However, if you have concerns, it's always a good idea to consult a healthcare professional before starting any new supplement regimen.

Footnotes

1. Gianluca Ianiro, "Digestive Enzyme Supplementation in Gastrointestinal Diseases," NCBI, 2025. ↩

2. Abhijit Rathi, "Study of amino acids absorption and gut microbiome on consumption of pea protein blended with enzymes-probiotics supplement," NCBI, 2023. ↩ ↩²