850/1200 High Quality Metagenome-Assembled Genomes from the Rumen of African Cattle. Feed-Restricted Rumen

Background: The Boran (Bos indicus), indigenous Zebu cattle breed from Sub-Saharan Africa, is remarkably well-adapted to harsh tropical environments. Boran cattle are known to commonly survive on low-quality vegetation and are resistant to local parasites and diseases. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% sub-maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle in relation to animal productivity remains a largely unexplored area. We collected rumen fluid samples from six Boran cattle fed at sub-optimal MER levels (40%, 60%, 80%) and at 100% MER. In order to characterise the rumen microbial composition of Boran cattle, we performed shotgun metagenomics and de-novo assembly of metagenome-assembled genomes (MAGs).Results: We report 1200 newly discovered MAGs from the rumen of Boran cattle. 850 were further identified as unique (<99% average nucleotide identity). Pairwise MASH comparisons of African MAGs with other publicly available genomes from the rumen further confirmed their uniqueness, with only 29 African MAGs showing greater than 90% similarity to any other genome.Conclusions: This study is the first to identify 850 unique African rumen-specific MAGs and provides further insight into the rumen function in harsh environments with food scarcity. The genomic information from the rumen microbiome of an indigenous African cattle breed will further shed light on the microbiome contribution to rumen functionality in African cattle species and will provide a vital resource in addressing food security in developing countries.