Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species

Abstract

Ruminant livestock like cattle, sheep, goat, and camel, have a unique digestive system with complex microbiota communities that facilitate feed conversion and production of various secondary metabolites including greenhouse gases, which are significant in livestock-vector and livestock environment interactions. However, there is limited understanding of the diversity of rumen microbes and secondary metabolites that have advantageous traits to livestock physiology, productivity, climate, and defense across different ruminant species. In this study using metagenomics and metabolomics data from four evolutionary distinct livestock species, we show that there are signature microbes and secondary metabolites for each species. For instance, camels host a unique anaerobic fungus(F) called Oontomyces, cattle harbor more unique microbes like Psychrobacter (F) and three unique bacteria genera Anaeromyces, Cyllamyces, and Orpinomyces. Goats have Cleistothelebolus (F), while sheep host Liebetanzomyces (F). This phenomenon may indicate that there are species-specific microbes that requires host rumen-microbes environment balance. Additionally, there are conserved core bacterial microbes present and in equal abundance regardless of the host genetics, indicating their essential role in maintaining crucial functions. The studied livestock fed on diverse plant materials, including grass, shrubs to acacia trees. Regarding secondary metabolites camel rumen is rich in organic acids, goat with alcohols, and hydrocarbons, sheep with indoles and cattle with sesquiterpenes. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry. IMPORTANCERumen fermentation that depends on feed component and rumen microbes plays a crucial role in feed conversion and production of various metabolites, important for physiological functions, health and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has signature microbe(s) and secondary metabolites. These findings may contribute towards understanding rumen ecosystem, microbiome and metabolite networks, that mayprovide a gateway to manipulate rumen ecosystem pathways towards making livestock production, efficient, sustainable and environmentally friendly.