Rumen-protected methionine and lysine supplementation to the low protein diet improves animal growth through modulating colonic microbiome in lambs

Abstract Background Dietary protein level and amino acid (AA) balance are crucial determinants of animal health and productivity. Supplementing rumen-protected AAs in low-protein diets was considered as an efficient strategy to improve the growth performance of ruminants. The colon serves as a crucial conduit for nutrient metabolism during rumen-protected methionine (RPMet) and rumen-protected lysine (RPLys) supplementation, however, it has been challenging to clarify which specific microbiota and their metabolites play a pivotal role in this process. Here, we applied metagenomic and metabolomic approaches to compare the characteristic microbiome and metabolic strategies in the colon of lambs fed a control diet (CON), a low-protein diet (LP) or a LP diet supplemented with RPMet and RPLys (LR). Results The LP treatment decreased the average daily weight gain (ADG) in lambs, while the LR treatment tended to elicit a remission in ADG. The butyrate molar concentration was greater ( P < 0.05), while acetate molar concentration ( P < 0.05) was lower for lambs fed the LP and LR diets compared to those fed the CON diet. Moreover, the LP treatment remarkably decreased total AA concentration ( P < 0.05), while LR treatment showed an improvement in the concentrations of methionine, lysine, leucine, glutamate, and tryptophan. Metagenomic insights proved that the microbial metabolic potentials referring to biosynthesis of volatile fatty acids (VFAs) and AAs in the colon were remarkably altered by three dietary treatments. Metagenomic binning identified distinct microbial markers for the CON group ( Alistipes spp., Phocaeicola spp., and Ruminococcus spp.), LP group ( Fibrobacter spp., Prevotella spp., Ruminococcus spp., and Escherichia coli ), and LR group ( Akkermansia muciniphila and RUG099 spp.). Conclusions Our findings suggest that RPMet and RPLys supplementation to the low-protein diet could enhance the microbial biosynthesis of butyrate and amino acids, enriche the beneficial bacteria in the colon, and thereby improve the growth performance of lambs.