article · mSystems
Ruminant livestock rely on specialised microbial communities in the rumen to convert forage into energy and essential metabolites. Through metataxonomics and metabolomics, this study evaluated the rumen biology of four distinct livestock species feeding on varied vegetation such as grass, shrubs, and acacia. Each animal species showed distinct microbial and chemical profiles: camels uniquely carried the anaerobic fungus Oontomyces and had rumens rich in organic acids, while cattle exhibited higher levels of Psychrobacter, fungal taxa, sesquiterpenes, and valencene. Goats displayed distinct alcohols, hydrocarbons, and Cleistothelebolus, whereas sheep hosted Liebetanzomyces and specific compounds including indoles, linalool propionate, and terpinolene. Alongside these species-specific profiles, a shared core microbiome of organisms including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces was identified across all species regardless of diet, highlighting critical conserved functions.
Understanding how different livestock species digest varied vegetation and produce specific metabolites is critical for addressing agricultural challenges. By revealing both shared and species-specific rumen biology, these insights can help scientists design targeted nutritional strategies to improve animal productivity and resilience while reducing the greenhouse gas footprint associated with ruminant farming.
This work is early-stage fundamental research that could eventually inform the development of targeted feed additives, probiotics, or microbiome-manipulation treatments for livestock producers and animal health companies. Such tools would aim to boost productivity and reduce greenhouse gas emissions, though practical application remains distant until specific metabolic interventions are formulated and tested in field trials.
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Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called <i>Oontomyces</i> in camels, while cattle exhibited a higher prevalence of unique microbes like <i>Psychrobacter</i>, <i>Anaeromyces</i>, <i>Cyllamyces</i>, and <i>Orpinomyces</i>. Goats hosted <i>Cleistothelebolus</i>, and <i>Liebetanzomyces</i> was unique to sheep. Furthermore, we identified a set of conserved core microbes, including <i>Prevotella</i>, <i>Rickenellaceae</i>, <i>Cladosporium</i>, and <i>Pecoramyces,</i> present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. 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, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the 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 a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.
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DOI: 10.1128/msystems.01228-23
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