Exploration of mobile genetic elements in the ruminal microbiome of Nellore cattle.

Metagenomics has made it feasible to elucidate the intricacies of the ruminal microbiome and its role in the differentiation of animal production phenotypes of significance. The search for mobile genetic elements (MGEs) has taken on great importance, as they play a critical role in the transfer of genetic material between organisms. Furthermore, these elements serve a dual purpose by controlling populations through lytic bacteriophages, thereby maintaining ecological equilibrium and driving the evolutionary progress of host microorganisms. In this study, we aimed to identify the association between ruminal bacteria and their MGEs in Nellore cattle using physical chromosomal links through the Hi-C method. Shotgun metagenomic sequencing and the proximity ligation method ProxiMeta were used to analyze DNA, getting 1,713,111,307 bp, which gave rise to 107 metagenome-assembled genomes from rumen samples of four Nellore cows maintained on pasture. Taxonomic analysis revealed that most of the bacterial genomes belonged to the families Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae and mostly encoded pathways for central carbon and other carbohydrate metabolisms. A total of 31 associations between host bacteria and MGE were identified, including 17 links to viruses and 14 links to plasmids. Additionally, we found 12 antibiotic resistance genes. To our knowledge, this is the first study in Brazilian cattle that connect MGEs with their microbial hosts. It identifies MGEs present in the rumen of pasture-raised Nellore cattle, offering insights that could advance biotechnology for food digestion and improve ruminant performance in production systems.

Use of tannin extract as a strategy to reduce methane in Nellore and Holstein cattle and its effect on intake, digestibility, microbial efficiency and ruminal fermentation.

This study was carried out to evaluate the use of tannin extract from Acacia mearnsii as a strategy to reduce methane (CH4 ) in two distinct cattle genotypes and its effect on intake, digestibility, microbial efficiency and ruminal fermentation. Four Nellore (Bos indicus) and four Holstein (Bos taurus) dry cows fitted with rumen cannula were assigned to two 4 × 4 Latin square design, in a 2 × 4 factorial arrangement, where each genotype represented a square receiving four tannin levels (commercial extract of A. mearnsii) in the diet (0%, 0.5%, 1.0% and 1.5% of dry matter). Tannin levels used did not cause a reduction in feed intake or rumen passage rate for both genotypes (p > 0.05), although there was a linear reduction in the degradation rate and ruminal disappearance of diet (p < 0.05). The increase in tannin levels reduced the amount of entodiniomorph protozoa in the Nellore cattle (p < 0.05). There was no change in N retention or microbial efficiency (p > 0.05), despite the linear reduction of nutrient digestibility and the synthesis of microbial nitrogen (p < 0.05). The ruminal CH4 production was reduced (p < 0.05) without reducing the short-chain fatty acid production. The threshold of 0.72% of tannin in the diet was estimated as the starting point for the reduction of ruminal CH4 production with long-term efficacy. Therefore, the use of low levels of tannin extract from A. mearnsii is a potential option to manipulate rumen fermentation in Nellore and Holstein cattle and needs to be further investigated.