Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes

Abstract

In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.

Effects of Dietary Protein Levels on Sheep Gut Metabolite Profiles during the Lactating Stage

“…Dietary protein is a major nutrient that provides amino acids for several metabolic pathways involved in tissue synthesis, regulation of metabolic processes, and immune as well as redox strengthening, which ultimately improves the growth performance of the ruminants [ 19 , 20 ]. In our recently published work, we evaluated how dietary protein levels (same diets as used in this experiment) change the fecal bacterial composition and found that changes in dietary protein contents altered rumen microbiota composition [ 17 ] and consequently influenced the growth performance, milk production, and blood biochemical indices [ 18 ] of the nursing ewes. Further, it is well established that dietary protein levels influence growth performance by altering the microbial and enzymatic function of sheep and cattle [ 5 , 21 ].…”

“…In our study, aspartic acid, phenylethylamine, tyrosine, tryptophan, and methionine sulfoxide showed significant differences between the different groups, and notably, all these metabolites showed a clear increasing trend with increasing dietary protein levels. The difference between groups can be associated with the differences in dietary protein levels as it is well known that dietary protein contents provide nitrogen bases as well as amino acids for metabolism [ 17 ]. Regarding the amino-acid compounds, it is established that there are correlations with the dietary protein levels as followed by the nursing ewes in the current experiment.…”

“…The feed formulations and their chemical compositions on a dry basis are detailed in Table 1 and Table 2 , respectively. The animal husbandry practices, strategic feeding, and fecal sample collection timing, protocols, and storage were detailed in our previous publications [ 17 , 18 ]. Briefly, On the 136th day of pregnancy, the individually housed ewes were fed on dietary treatments with twice-a-day feeding frequency (8:30 a.m. and 4:00 p.m. feeding times).…”

“…In summary, microbiome and metabolomic studies have been widely used in animal nutrition, but there is a lack of reports on the interaction between rumen microbiota and metabolites in lactating Yunnan semi-fine-wool ewes using different dietary protein levels. Yunnan semi-fine-wool sheep are contributing to the income of local farmers in Yunnan province by providing milk, meat, and high-quality wool [ 17 ]. Moreover, they are disease-resistant, have excellent adaptation to harsh environmental conditions, and have the ability to thrive on low-quality forage [ 18 ].…”