BACKGROUND: Previous work has shown that the mostly beneficial modulation of intestinal microbiota generally found with legume-based diets is likely to be due, at least in part, to their constituent protein components. OBJECTIVES: The faecal microbiota composition was studied in rats fed diets differing only in their constituent proteins. METHODS: Rats ( RESULTS: Significant differences among the three groups in bacteria composition and functionality were found by both qPCR and Illumina sequencing analysis. Significant ( CONCLUSIONS: Based on the results obtained, LPI is likely to beneficially modulate the intestinal microbiota composition in rats. Additionally, LA-based diet was associated to a healthier microbiota composition than CAS, although the CAS diet also modulated the intestinal microbiota to a composition compatible with improved bowel movement frequency and lipid metabolism.