Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut

While metagenomics has transformed our view of microbial ecosystems, culture-based methods remain indispensable for accessing microbial functionality and biotechnological potential. In this study, we applied a culturomics strategy to explore the diversity, abundance, and distribution of culturable aerobic and facultative anaerobic bacteria along the gastrointestinal tract of dromedary camels (Camelus dromedarius) grazing on pristine desert flora. Using six culture media-including modified YCFA formulations-we isolated 97 bacterial species across 42 genera, 31 families, and four phyla: Firmicutes, Proteobacteria, Actinomycetota, and Bacteroidota. Strikingly, 88.6% of this diversity was recovered using YCFA-based media, and four candidate novel species were identified. The rumen harbored the most diverse and Gram-positive-dominated community, whereas the small intestine was enriched with Gram-negative taxa, many with pathogenic potential. These findings highlight the camel's unique physiological adaptation to extreme arid environments, characterized by efficient fiber degradation under nutrient- and water-limited conditions and the presence of stress-tolerant gut microbes capable of resisting acidic and osmotic challenges. Overall, this study establishes a foundational understanding of the camel gut microbiota and underscores the complementary power of culture-dependent methods to metagenomics. Future integration with anaerobic culturing and multi-omics analyses will further unveil the ecological and biotechnological potential of desert-adapted microbial life.