Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle

Abstract

In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.

Megasphaera elsdenii: Its Role in Ruminant Nutrition and Its Potential Industrial Application for Organic Acid Biosynthesis

“…While the interactions described above appear to be a sound model for lactate consumption patterns in the rumen, it is wise to recall that the rumen contains many bacterial species whose characteristics and functions remain to be elucidated. In this regard, two lactate-utilizing candidate species that are phylogenetically related to Butyrivibrio fibrisolvens and Anaerococcus prevotii have recently been identified from metagenomic analysis of ruminal lactate enrichment cultures [ 98 ]. The isolation, characterization, and quantification of these species in ruminal contents—along with the elucidation of their interactions with conventional lactate utilizers such as M. elsdenii —will ultimately improve our understanding of ruminal lactate metabolism.…”

Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures

“…In addition, most Megasphaera strains ferment lactate to greater molar amounts of propionate than of butyrate ( Cabral and Weimer, 2023 ), while increases in propionate paralleling decrease in lactate were not observed in this study. Recently, two bacterial operational taxonomic units with the genetic capacity to produce butyrate, phylogenetically close to Butyrivibrio fibrisolvens and Anaerococcus prevotii , were identified in rumen cultures growing on lactate ( Bandarupalli and St-Pierre, 2023 ). Butyrivibrio spp.…”