Abstract
Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 4374 metagenome assembled genomes (MAGs) from gut samples of 180 predominantly wild animal species representing 5 classes. Combined with existing datasets, we produced 5596 non-redundant, quality MAGs and 1522 species-level genome bins (SGBs). Most SGBs were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse and largely novel biosynthetic gene clusters. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to life within a living host.
Competing Interest Statement
The authors have declared no competing interest.
