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

Abstract

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.

Figure 1

Rumen metagenome of Nellore cattle. (A) Completeness of metagenome-assembled genomes (MAGs), (B) Taxonomic classification of bins: graph on the left genus and right graph family.

Figure 2

Potential biogeochemical cycling processes by rumen bacteria. Bins are color-coded in each step within the (A) Carbon, (B) sulfur, (C) nitrogen, and (D) iron cycles. Each arrow in the figure represents a single transformation step within a cycle.

Figure 3

Central processes of metabolism and CAZymes present in the rumen microbiome of Nellore cattle. (A) Characterization of the metabolic potential of bins found in the rumen, (B) Identification and abundance of enzymes encoded by rumen microorganisms. The size of each circle corresponds to the number of hits for the respective gene.

Figure 4

Mobile genetic elements of bovine rumen. (A) Each circle represents number of sequences identified as plasmids, integrated and non-host-integrated plasmids and plasmids associated with their hosts by the Hi-C method. (B) Each circle represents the number of identified viral sequences, viral sequences integrated into the host genome (Prophages), binned viral contigs, metagenome-assembled viral genomes (MAGs) and vMAGs associated with hosts by proximity linkage (Hi-C).

Figure 5

Antimicrobial resistance genes—ARGs. The information is presented hierarchically, starting from the center to the edges, beginning with the classes of antibiotics, followed by subclasses, and finally the resistance gene symbols.

Figure 6

Taxonomic assignment of rumen viruses. Network of viral clusters assigned by vCONTACT2. Nodes with the same color have the same viral cluster, diamonds are clusters with known taxonomy and the nodes linked to them have the same viral cluster and can be assigned the same taxonomy, lilac nodes represent vMAGs that have not been assigned to clusters known.

Figure 7

Association between bacterial hosts and their Hi-C-linked mobile genetic elements. Ellipses represent bacterial hosts, hexagons represent bacteriophages, and rectangles represent plasmids.