Shifts in ruminant fermentation during inhibition of methanogenesis are reflected in the isotope compositions of volatile fatty acids

ABSTRACT Ruminant animals are a major source of the potent greenhouse gas methane, but they are also a tractable target for climate solutions. Several strategies have been developed to lower methane emissions from ruminants, including feed additives that inhibit methanogenic archaea. Sustainable solutions must eliminate methane emissions without hampering the microbial fermentation of plant material, which the animal host relies on for nutrients. However, current tools cannot directly quantify or characterize the metabolic pathways of in vivo ruminant fermentation. To fill this gap, we developed an electrospray (ESI) Orbitrap mass spectrometry technique to measure the stable isotope ratios ( 13 C/ 12 C and 2 H/ 1 H) of volatile fatty acids (VFAs) at their natural isotopic abundances directly from rumen fluid. We tested this technique on in vitro incubations of rumen fluid fed three different substrates with and without the methanogen-inhibiting additive Asparagopsis taxiformis . We found that the isotope composition of VFAs changed and reflected a remodeling of microbial fermentation pathways. Specifically, acetate’s δ 13 C value increased when methanogens were inhibited, suggesting a lower relative rate of acetate synthesis and a lack of acetogenic activity. Furthermore, the δ 2 H value of propionate decreased, which may indicate a change in the balance between the two pathways of propionate synthesis toward the less energetic acrylate pathway. Both signals were consistent across feed types. Taken together, our results provide evidence that under the conditions of our study, fermentative metabolism is remodeled during methanogenesis inhibition. More broadly, this study demonstrates the utility of ESI-Orbitrap-based isotopic analysis for studying fermentation pathways in the rumen. IMPORTANCE Slowing methane production from ruminant animals (e.g., cows) is a major target for the mitigation of anthropogenic climate change. While strategies that inhibit microorganisms producing methane have been successful, they have cascading impacts on the microbial ecology of the rumen, possibly affecting animal health and productivity. Of particular importance is microbial fermentation, which generates easily digested volatile fatty acids (VFAs) from hard-to-breakdown plant matter. To better understand how fermentation responds to methane mitigation strategies, we measured the isotope composition of VFAs in cow rumen. Our results indicate that fermentation changes pathways when methane production is inhibited under our conditions. As methane mitigation strategies are developed in the coming decade, isotopic analysis of VFAs may be a useful and accessible contribution to our understanding of rumen microbiology.