1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding.

Background: The Boran (Bos indicus), indigenous Zebu cattle breed from sub-Saharan Africa, is remarkably well adapted to harsh tropical environments. Due to financial constraints and low-quality forage, African livestock are rarely fed at 100% maintenance energy requirements (MER) and the effect of sub-optimal restricted feeding on the rumen microbiome of African Zebu cattle remains largely unexplored. We collected 24 rumen fluid samples from six Boran cattle fed at sub-optimal and optimal MER levels and characterised their rumen microbial composition by performing shotgun metagenomics and de novo assembly of metagenome-assembled genomes (MAGs). These MAGs were used as reference database to investigate the effect of diet restriction on the composition and functional potential of the rumen microbiome of African cattle.

Results: We report 1200 newly discovered MAGs from the rumen of Boran cattle. A total of 850 were dereplicated, and their uniqueness confirmed with pairwise comparisons (based on Mash distances) between African MAGs and other publicly available genomes from the rumen. A genome-centric investigation into sub-optimal diets highlighted a statistically significant effect on rumen microbial abundance profiles and a previously unobserved relationship between whole microbiome shifts in functional potential and taxon-level associations in metabolic pathways.

Conclusions: This study is the first to identify 1200 high-quality 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 sheds light on the microbiome contribution to rumen functionality and constitutes a vital resource in addressing food security in developing countries.