Supplementation of direct-fed microbials into ruminants' nutrition has shown great potential in manipulating rumen fermentation and enhancing productive animal performance. However, little is known about rumen microbial composition and diversity of Damara and Meatmaster sheep, breeds indigenous to South Africa. The study aimed at exploring and comparing the rumen microbiomes of two breeds with different feeding treatments as follows: no antibiotic, no probiotics (T1), only potential probiotic (T2), only potential probiotic (T3), the combination of potential probiotics (T4), antibiotic (T5); using a metagenomic approach. The results showed that based on the Shannon index, the microbial diversity of Damara was higher (p < 0.05) than Meatmaster, while treatment T4 was higher than treatment T1 (p < 0.05). The principal coordinate analysis showed no significant difference among treatments, while there were significant dissimilarities between sheep breeds and sample-day (p < 0.05). Canonical correspondence analysis (CCA) displayed the dispersion of microbial communities among treatments, where negative control (T1) was distinct from other treatments. Bacteroidetes and Firmicutes were the most abundant microbial phyla across treatments for both breeds. Negative control and the combination of potential probiotics showed lower proportions of Proteobacteria compared to other treatments. At the genus level, Prevotella and Clostridium were abundant across all treatments, while Pseudomonas was abundant only in T2, T3, and T5. In all treatments, Fibrobacter was detected after the feeding trials, while it was not detected in most treatments before trials. The results revealed that the rumen microbiome's structure and abundance were slightly altered by administering lactic acid as a putative probiotic.

Background: The gut microbiome is very signi cant in the stability of the rumen ecosystem, also in the maintenance of the host's health.The gut ora in uences the nutritional, physiological, immunological, and directly or indirectly affects the host's well-being. A synergy between the rumen microbiota and the host genetics creates a symbiotic relationship, bene cial to the host's health. In this study, the association between the host genetics and rumen microbiome of Damara and Meatmaster sheep was investigated. The composition of rumen microbiota was estimated through the analysis of the V3-V4 region of the 16S rRNA gene, while the sheep blood DNA was genotyped with Illumina OvineSNP50 BeadChip and the genome-wide association (GWA) was analyzed.Results: Sixty signi cant SNPs dispersed in 21 regions across the Ovis aries genome were found to be associated with the relative abundance of seven genera: Acinetobacter, Bacillus, Clostridium, Flavobacterium, Prevotella, Pseudomonas and Streptobacillus. A total of eighty-four candidate genes were identi ed, and their functional annotations were mainly associated with immunity responses and function, metabolism, and signal transduction. Conclusion:We are of the opinion, as evident from our results that candidate genes identi ed may be modulating the composition of rumen microbiota and, thus further indicate the signi cance of comprehending the interactions between the host and rumen microbiota to gain better insight into the health of sheep. We conclude that host genetics is important in modulating microbial composition; though various factors may alter the rumen microbiota. More studies are necessary to help determine genetic combinations favorable for the propagation of bene cial microbiota and provide excellent intestinal health.

Background: The gut microbiome is very significant in the stability of the rumen ecosystem, also in the maintenance of the host’s health. The gut flora influences the nutritional, physiological, immunological, and directly or indirectly affects the host’s well-being. A synergy between the rumen microbiota and the host genetics creates a symbiotic relationship, beneficial to the host’s health. In this study, the association between the host genetics and rumen microbiome of Damara and Meatmaster sheep was investigated. The composition of rumen microbiota was estimated through the analysis of the V3-V4 region of the 16S rRNA gene, while the sheep blood DNA was genotyped with Illumina OvineSNP50 BeadChip and the genome-wide association (GWA) was analyzed. Results: Sixty significant SNPs dispersed in 21 regions across the Ovis aries genome were found to be associated with the relative abundance of seven genera: Acinetobacter, Bacillus, Clostridium, Flavobacterium, Prevotella, Pseudomonas and Streptobacillus. A total of eighty-four candidate genes were identified, and their functional annotations were mainly associated with immunity responses and function, metabolism, and signal transduction. Conclusion: We are of the opinion, as evident from our results that candidate genes identified may be modulating the composition of rumen microbiota and, thus further indicate the significance of comprehending the interactions between the host and rumen microbiota to gain better insight into the health of sheep. We conclude that host genetics is important in modulating microbial composition; though various factors may alter the rumen microbiota. More studies are necessary to help determine genetic combinations favorable for the propagation of beneficial microbiota and provide excellent intestinal health.