Deep Metagenomics Uncovers Functional Adaptations and Pathogenic Risks in the Gut Microbiome of Antarctic Fur Seals (Arctocephalus gazella)

The Antarctic fur seal (Arctocephalus gazella) plays a key role in the Antarctic marine ecosystem by regulating krill, fish, and cephalopod populations through selective foraging, promoting Southern Ocean productivity via excretion, and influencing coastal island ecosystems during breeding season. Despite the importance of the gut microbiota in reflecting diet, health, and environmental adaptation, the gut microbiome of the Antarctic fur seal remains underexplored. This study employed shotgun metagenomics and 16S rRNA amplicon sequencing to analyze the gut microbiota of Antarctic fur seals, using fresh fecal samples directly collected from four individuals at King George Island, Western Antarctica. Despite inter-individual variation, both approaches identified Bacillota as the dominant phylum but showed genus-level discrepancies, with Fusobacterium prevailing in metagenomes and Clostridium in 16S amplicons. Viral communities constituted up to 5.3% of the microbiome, including immunodeficiency-associated Lentivirus. Core microbiome analysis identified 31 (16S rRNA) and 1,522 (metagenomics) shared genera, with functional enrichment in carbohydrate, amino acid, and lipid metabolism pathways. Chitin-degrading enzymes, crucial for krill digestion, were ubiquitous. Additionally, a total of 16 antibiotic resistance gene types were detected, with bacitracin, polymyxin, and multidrug resistance dominating the resistome. Metagenome-assembled genomes revealed phylogenetic diversity, with Angelakisella, Massillimalia and Faecousia encoding chitinase, while Helicobacter, especially abundant in S62, implied pathogenic potential. These findings provide an in-depth elucidation of the microbial community composition, functional potential, and ecological adaptation of seal gut microbiota, also offering valuable scientific data and methodological insights for the conservation of polar marine mammals.