The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia

Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism—critical for processing the lions’ high-purine diet—with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.