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.

中文翻译：

---

来自非洲牛瘤胃的 1200 个高质量宏基因组组装基因组及其在次优喂养背景下的相关性

背景 Boran ( Bos indicus ) 是来自撒哈拉以南非洲的本土瘤牛品种，非常适合恶劣的热带环境。由于财政限制和低质量草料，非洲牲畜很少以 100% 维持能量需求 (MER) 喂养，并且次优限制喂养对非洲瘤牛瘤胃微生物群的影响在很大程度上仍未得到探索。我们从六头以次优和最优 MER 水平喂养的 Boran 牛收集了 24 份瘤胃液样本，并通过执行鸟枪宏基因组学和宏基因组组装基因组 (MAG) 的从头组装来表征它们的瘤胃微生物组成。这些 MAG 被用作参考数据库，以研究饮食限制对非洲牛瘤胃微生物组的组成和功能潜力的影响。结果 我们报告了 1200 个新发现的来自 Boran 牛瘤胃的 MAG。总共有 850 个被去复制，它们的独特性通过非洲 MAG 和瘤胃中其他公开可用基因组之间的成对比较（基于 Mash 距离）得到证实。对次优饮食的以基因组为中心的调查强调了对瘤胃微生物丰度曲线的统计学显着影响，以及之前未观察到的功能潜力的整个微生物组变化与代谢途径中分类群水平关联之间的关系。结论 本研究首次鉴定了 1200 种高质量的非洲瘤胃特异性 MAG，并进一步深入了解了食物短缺的恶劣环境中的瘤胃功能。