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

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.

Keywords: antibiotic resistance genes; metagenome-assembled genomes; pig gut; viruses.

Figure 1

Phylogenetic tree of MAGs of pigs from nine European countries. Phylogenetic tree describing the relationships among MAGs in pig fecal samples from nine European countries, with each color corresponding to a different bacterial phylum.

Figure 2

Analysis of resistance genes in MAGs of pigs from nine European countries. (a) The TPM of major ARG classes across nine countries. (b) The TPM of major ARG types across nine countries. The axes from top to bottom are 13,753; 11,003; 8252; 5501; and 2751.

Figure 3

Analysis of ARGs and their potential bacterial hosts. (a) The bubble chart shows the relationships between ARG classes and their potential bacterial hosts. The sizes of the bubbles correspond to abundance, with larger bubbles representing ARG classes. Within each large bubble, three smaller bubbles represent the three most abundant potential bacterial hosts within that ARG class. (b) Chord diagram from potential bacterial hosts to ARG types. The thickness of the chords corresponds to abundance.

Figure 4

Heatmap of ARGs clustering in different hosts of five species. CM, SP, LC, SE, and WC correspond to Catenibacterium mitsuokai, Streptococcus pasteurianus, Latilactobacillus curvatus, Salmonella enterica, and Weissella cibaria, respectively. Each species is divided into four groups: EU (the MAGs in this article), human, pig, and wild (wild animals). For Catenibacterium mitsuokai, no data for wild animals were downloaded. The y-axis represents the ARG class. The “count” indicates the number of ARGs.

Figure 5

Analysis of viral genomes in MAGs of pigs from nine European countries. (a) Bar chart. Viral genomes with only one host were categorized as the Specialist group, and those with two or more hosts were categorized as the Generalist group. The x-axis represents the number of hosts, and the y-axis represents the number of viral genome types. The pie chart shows the methods, including CAT, Demovir, Kaiju, Phagcn, BLASTn, and GeNomad. (b) A percentage stacked bar chart shows the proportion of classified and unclassified viral genome families at the phylum level. (c) Sankey diagram. The first axis represents the viral genome family. The second axis represents the genus level, illustrating the relationship between bacterial genera and families.