Metagenomics has enabled the efficient identification of microorganisms, enzymes, and metabolic pathways that play a role in plant breakdown in the bovine rumen29. This tool has also proven to be crucial for identifying the microbiota and characterizing important traits such as methane production and feed efficiency3,8,30. This study is the first to explore rumen mobile genetic elements of Nellore cattle fed a grass diet by associating viruses and plasmids with their hosts through physical links between DNA molecules from the same genome using the Hi-C method21. We identified 31 links between bacteria and mobile genetic elements, with 14 of these links being plasmids and 17 links being viruses. Furthermore, we identified 12 genes conferring antibiotic resistance to tetracycline (6 genes), nitroimidazole (1 gene), lincosamide (1 gene), beta-lactam (1 gene), aminoglycoside (1 gene) and macrolide (1 gene). Additionally, we assembled a collection of 107 bacterial genomes, which mostly encoded pathways for central carbon and other carbohydrate metabolisms.
In this study, we identified 52 plasmid sequences, 14 of which were linked to their hosts using Hi-C. Similarly, in their evaluation of the canine fecal metagenome, Cuscó et al.23 found that six Hi-C plasmids were ligated into their bacterial hosts, including five circular plasmids and a plasmid carrying the linA resistance gene. In our investigation, we uncovered two plasmids, k141_1760976 and k141_5289202, which are associated with multiple host clusters. As previously reported by Mo et al.31 and Stewart et al.27, sequences may be shared among various bacterial species found in the rumen. Through the Hi-C approach, Stalder et al.32 found that plasmids are efficient vectors for horizontal gene transfer and that this method is useful for tracing microorganisms that harbor antibiotic-resistant genes. We identified 12 genes conferring antibiotic resistance, and among these, six genes were found to confer resistance to tetracycline: tet32, tet40, tet44, tetO, tetQ, and tetW. These findings are consistent with a previous study by Jing and Yan33, in which tetracycline resistance genes (tet44, tetQ, and tetW) were the most prevalent in rumen content samples and were the most abundant in the genome of Prevotellaceae, but Lachnospiraceae were also present. Furthermore, tetQ, tetW, and tet40 were also detected in most samples derived from the rumen of 48 beef cattle from three different taurine breeds34.
In addition to the genes that confer resistance to tetracycline, other classes of antibiotics, such as nitroimidazole nimJ, macrolide mefA, lincosamide lnuC, beta-lactam blaACI-1, and aminoglycoside aadE, were also identified. Genes that confer resistance to macrolides, lincosamide, and aminoglycosides were the most prevalent among ARGs in the study conducted by Ma et al.34, with the mefA gene being one of the most common. Genes that confer resistance to macrolides, lincosamide, and aminoglycosides were the most prevalent among ARGs in the study conducted by Ma et al.34, with the mefA gene being one of the most common. Additionally, ARGs associated with plasmids were identified, indicating that plasmids should be the focus of future investigations on antimicrobial resistance in livestock. Auffret et al.35 also found an increase in ARGs in rumen content samples from cattle fed diets with higher concentrate content, with an abundance of genes related to resistance to macrolides and beta-lactams, suggesting that this increase is associated with dysbiosis caused by more concentrated diets. The findings of this study are in agreement with those of an earlier in silico study conducted by Sabino et al.36, who analyzed the rumen resistome in 435 microbial genomes and found a high prevalence of antibiotic resistance genes (ARGs) that provide resistance to β-lactams, glycopeptides, tetracyclines, and aminoglycosides. Additionally, recent metagenomic studies have indicated that bovine rumen is a significant contributor to antibiotic resistance33.
However, advancements in bioinformatics have contributed to a deeper understanding and better characterization of the rumen virome. Yan et al.37 identified 397,180 viral operational taxonomic units (vOTUs) from 975 metagenomes of 13 ruminant species, with the majority of metagenomes derived from taurine animals. Only 23 metagenomes were from Bos indicus raised in Kenya, and none were from Brazil, supporting the significance of this research. The viral metagenomic assemblages discovered in this study were mostly assigned to unclassified genomes, which is probably because of the limited rumen virome of Bos indicus data in the ICTV phage database. This finding is consistent with those of Sato et al.38, who observed low numbers of viral operational taxonomic units shared with the RefSeq database for samples from the rumen of Japanese cattle. The assigned vMAGs belong to the families Myoviridae and Siphoviridae, which are commonly found in the rumen environment and constitute the most abundant group, along with Mimiviridae and Podoviridae 12,15,38,39.
A group of bacteria classified as UBA2868 sp003535955 (unclassified Lachnospiraceae bacterium, NCBI) was found to have the highest percentage of complete vMAGs (100%) and was characterized as high and medium quality. This genus was previously identified in a community of uncultured microorganisms from the intestines of pigs through sequencing of fecal samples40,41. Bacteria from the unclassified family Lachnospiraceae are prevalent in the ruminal environment and serve as the central microbiome in cattle9. This allowed us to infer that population-associated viruses play a crucial role in the bovine rumen, rather than populations present in low abundance, which remains a challenge20.
Friedersdorff et al.42 successfully isolated and sequenced active lytic phages belonging to the Siphoviridae family that infect Butyrivibrio fibrisolvens, which was found in both the rumen and feces of cattle and sheep. We discovered a lytic phage in Butyrivibrio sp017620235, which is commonly found in the rumen and promotes the degradation of lignocellulose and fermented carbohydrates into butyrate, formate, lactate, and acetate43–45. Two bacterial species classified as Rumen Uncultured Genomes (RUGs), (bin_16) RUG12461 sp016286115 and (bin_59) RUG191 sp002373675, were also associated with viruses having a lytic life cycle.
The study's assembly of 107 bacterial genomes achieved a high completeness (> 95%) for members of the Treponema genus, which are known as spirochetes and have been positively correlated with feed conversion in cattle3. These species are considered to be one of the main fiber degraders in the rumen of Gir cattle, along with other bacteria, such as Clostridium, Ruminococcus, Eubacterium, Butyrivibrio, Roseburia, Caldicellulosiruptor, and Rhodospirillum46. The bins identified were primarily assigned to families, such as Lachnospiraceae, Bacteroidaceae, P3, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae. These bins mainly encoded pathways related to central carbon metabolism and metabolism of various carbohydrates. One notable pathway found between these bins is the phosphate acetyltransferase-acetate kinase pathway, which is activated at high acetate concentrations, requires less ATP, and plays a role in energy metabolism 47. Additionally, the aromatic amino acid metabolism pathway with tryptophan biosynthesis was abundant among the bins in the current study. This pathway occurs only in microorganisms and plants, and tryptophan is obtained by animals via symbiosis for protein synthesis48.
The identification of CAZymes in the bacterial genomes revealed the presence of genes encoding glycoside hydrolases and polysaccharide lyase groups, with GH2, GH3, GH5, GH13, and GH43 being the most prevalent. These groups degrade xylan polysaccharides, which are heterogeneous and require different catalytic enzymes10. In a study by Wang et al.49, the same GH families, GH2, GH3, GH13, and GH43, were found to comprise the majority of CAZymes present in the rumen of dairy cows fed different proportions of roughage and concentrate. The GH3 group was particularly more abundant in the high-roughage diet, and these observations are consistent with the current study's findings for pasture-fed Nellore cows, where glycoside hydrolase groups were the most prevalent.
In summary, this study provides a thorough examination of the MGEs in the rumen of Nellore cattle, shedding new light on the connection between these elements and their microbial inhabitants. The impact and function of these MGEs in beef cattle are currently being investigated by our research group.