Identification of mobile genetic elements in the rumen microbiome of Nellore cattle

Author(s)

Camila Aparecida Faleiros

• Document type: Master's Dissertation
• Press: Pirassununga.
• Institution: Universidade de São Paulo (USP). Faculdade de Zootecnica e Engenharia de Alimentos (FZE/BT)
• Defense date: 2024-04-11

Examining board members

Heidge Fukumasu; Pâmela Almeida Alexandre; Luciano Lopes Queiroz

• Advisor: Heidge Fukumasu

Abstract

With the advent of metagenomics, it became possible to understand the importance of the dynamics between the ruminal microbiome and phenotypes of interest in animal production. Among the applications of this technique, the prospecting of mobile genetic elements (MGEs) stands out, which act as agents allowing the movement of DNA between genomes, generally carrying accessory genes that provide advantages to their hosts, in addition to acting in population control through lytic bacteriophages, maintaining the environmental balance. The objective of the present study was to identify MGEs associated with ruminal bacteria through physical chromosomal links using the Hi-C method, aiming to establish the relationship between viruses and bacteria in the ruminal environment. Shotgun metagenomic sequencing and the ProxiMeta proximity linkage method were used to analyze DNA obtained from rumen content samples from four Nellore cows, obtaining 1,713,111,307 bp, which gave rise to 107 bacterial genomes attributed mainly to the Lachnospiraceae, Bacteroidaceae, Ruminococcaceae, Saccharofermentanaceae, and Treponemataceae family. Most bacterial genomes encoded pathways that included steps in the central pathway of carbon metabolism and the metabolism of other carbohydrates. Enzymes active in carbohydrate (CAZymes) were identified, among which the glycosidic hydrolases GH2, GH3, GH5, GH13 and GH43 stand out. A total of 31 associations between host bacteria and MGE were detected, of which 17 were linked to viruses and 14 were linked to plasmids, in addition to coinfection events, in which a host harbored more than one MGEs or the same MGEs possessed more than one host. The viral genomes have been assigned to the Myoviridae and Siphoviridae families, but the most could not be classified. In addition, 12 antibiotic resistance genes were found, among them, seven conferred resistance to tetracycline by tet32, tet40, tet44, tetO, tetQ and tetW, and the others conferred resistance to the nitroimidazole classes nimJ, macrolide mefA, lincosamide lnuC, beta- lactam blaACI-1, and aminoglycoside aadE. To our knowledge, this is the first study in Brazilian cattle that connects MGEs with their microbial hosts, identifying MGEs present in the rumen of pasture-raised Nellore cattle, offering insights into biotechnological advancement related to food digestion and improved animal performance ruminants in production systems. (AU)

• FAPESP's process: 22/05541-9 - Prospecting for viruses and ruminal mobile elements in Nellore cattle associated with feed efficiency
• Grantee: Camila Aparecida Faleiros
• Support Opportunities: Scholarships in Brazil - Master