Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia

Environmental disturbances can be monitored using sentinel species. We present 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of the South American sea lion (Otaria flavescens) to further understanding of whether variations in the gut microbiome composition and gene content might reflect environmental disturbances from salmon farming.