202 Metagenomic characterization of novel candidate lipid utilizers from the rumen of beef steers reveals microbial adaptations to high-lipid diets.

Abstract Beef production in intensive systems requires optimal nutritional conditions to thrive and maximize economic gains. High starch diets are commonly used for optimizing growth in feedlot cattle, because they provide easily available energy. Higher inclusion of triglycerides represents another attractive solution, as these lipids contain twice as much energy per weight as polysaccharides. However, while both of these energy sources can negatively impact rumen physiology and health, greater attention has been given to understanding the mechanisms involved in response to high-starch diets compared to high-lipid diets. To gain insight on the effects of higher inclusion of triglycerides on the rumen microbiome of beef cattle, we used a previously published study that tested their effects using a 5×5 Latin square design experiment. Treatments consisted of the addition of saturated fats (tallow) at 4% (4S) or 8% (8S), and unsaturated fats (linseed oil) at 4% (4U) or 8% (8U), compared to a non-supplemented starch-based diet control (CON). Bacterial composition analysis of rumen samples using an operational taxonomic unit (OTU)-based approach was performed by 16S rRNA gene sequencing through PCR amplification of the V1–V3 regions from microbial DNA. Adaptation to a high-lipid environment resulted in changes in microbial profiling, with eight OTUs identified as most abundant throughout the experiment. To further understand the biological mechanisms underlying the microbial response to unsaturated lipids, we employed shotgun sequencing (Illumina MiSeq 2×250) and bioinformatics tools for the assembly of metagenomes from three 8U diet samples. A total of 2041 contigs were generated, with a cumulative length of 23.08 Mbp. Samples from the 8U diets were selected to focus on two OTUs that were deemed of particular interest: Bt-0095 and Bt-01367. Gene annotation of assembled contigs revealed that these OTUs were predicted to assimilate and utilize starch as their primary energy source, and encoded lipases for triglycerides degradation. Additionally, they possessed genes potentially involved in ethanolamine assimilation (EUT A, EUT B, and EUT C), a common byproduct of triglycerides catabolism from plant oils. Intriguingly, we also found that these high-lipid associated OTUs could partially or completely synthesize vitamin B12. In this context, we hypothesize that these OTUs can use vitamin B12 as a cofactor in ethanolamine metabolism, which could provide an adaptive advantage in high-lipid environments. To our knowledge, this study is the first to identify uncharacterized rumen bacteria capable of completely or partially synthesizing vitamin B12 through metagenomics. Further investigation is needed to understand the various mechanisms modulated by this vitamin, and their potential in driving microbiota adaptation to challenging conditions such as high-lipid environments, potentially through promoting nutrient-dependent relationships among bacterial consortia in the rumen.