Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans

Abstract

The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.

Fig. 1

The general concept of the large-scale One Health Project and sample site locations. (A) Global strategy to study the relationship between human and animal health and the transfer of microbial species (pathogens and non-pathogens) between these systems. (B) Five geographic regions in which samples were collected in Brazil.

Fig. 2

Quality determination of metagenome-assembled genomes (MAGs). (A) Completeness and (B) contamination were estimated by the identification of individual marker genes. (C) Genome size was calculated by the sum of bases present in all contigs of each MAG. (D) Number of contigs.

Fig. 3

Taxonomy and host-distribution of MAGs. (A) Circus plot demonstrating the abundance of phyla in each host microbiome. The external track indicates the relative number (%) of phyla or host. The internal track shows the absolute number of MAGs generalized by phyla or host, (B) Number of potential novel lineages for each host microbiome, and (C) Absolute number of shared MAGs assigned to the genus level between host-associated microbiomes (human, swine, cattle, and poultry).