Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses

Authors

• Boxuan Yang, Foshan University
• Jianbo Yang, Foshan University
• Routing Chen, Foshan University
• Jianmin Chai, Foshan University
• Xiaoyuan Wei, University of Arkansas, Fayetteville
• Jiangchao Zhao, University of Arkansas, FayettevilleFollow
• Junxiang Zhao, Guangxi University
• Feilong Deng, Foshan University
• Ying Li, Foshan University

Document Type

Article

Publication Date

11-24-2024

Keywords

metagenome-assembled genomes; antibiotic resistance genes; viruses; pig gut

Abstract

Simple Summary

The gut microbiota of pigs plays an essential role in their health and growth. Observing the connections between antibiotic resistance genes, viruses, and their potential microbial hosts helps in comprehensively understanding the pig gut microbiota. This study aims to use metagenomic assembly and binning techniques to understand the distribution of antibiotic resistance genes and viruses in the pig gut microbiota and to identify possible microbial hosts.

Abstract

Gut microbiota plays a crucial role in the health and productivity of pigs. However, the spread of antibiotic resistance genes (ARGs) and viruses within the pig intestinal microbiota poses significant threats to animal and public health. This study utilized 181 pig samples from nine European countries and employed metagenomic assembly methods to investigate the dynamics and distribution of ARGs and viruses within the pig intestinal microbiota, aiming to observing their associations with potential bacterial hosts. We identified 4605 metagenome-assembled genomes (MAGs), corresponding to 19 bacterial phyla, 97 families, 309 genera, and a total of 449 species. Additionally, 44 MAGs were classified as archaea. Analysis of ARGs revealed 276 ARG types across 21 ARG classes, with Glycopeptide being the most abundant ARG class, followed by the class of Multidrug. Treponema D sp016293915 was identified as a primary potential bacterial host for Glycopeptide. Aligning nucleotide sequences with a viral database, we identified 1044 viruses. Among the viral genome families, Peduoviridae and Intestiviridae were the most prevalent, with CAG-914 sp000437895 being the most common potential host species for both. These findings highlight the importance of MAGs in enhancing our understanding of the gut microbiome, revealing microbial diversity, antibiotic resistance, and virus–bacteria interactions. The data analysis for the article was based on the public dataset PRJEB22062 in the European Nucleotide Archive.

Citation

Yang, B., Yang, J., Chen, R., Chai, J., Wei, X., Zhao, J., Zhao, Y., Deng, F., & Li, Y. (2024). Metagenome-Assembled Genomes of Pig Fecal Samples in Nine European Countries: Insights into Antibiotic Resistance Genes and Viruses. Microorganisms, 12(12), 2409. https://doi.org/10.3390/microorganisms12122409

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.