BackgroundCamels, known as the enduring 'ships of the desert,' host a complex gut microbiota that plays a crucial role in their survival in extreme environments. However, amidst the fascinating discoveries about the camel gut microbiota, concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations. Indeed, the continued use of antibiotics in veterinary medicine have led to the widespread emergence of antibiotic-resistant bacteria, a situation that has continued to worsen through gene transfers. MethodologyThis study delves deep into this pressing issue, harnessing the potent tools of metagenomics to explore the intricate interplay between the camel (Camelus ferus) gut microbiota and antibiotic resistance. ResultsSamples from camels yielded varying amounts of raw and clean data, generating scaftigs and open reading frames. The camel fecal microbiome was dominated by bacteria (mainly Bacillota and Bacteriodota), followed by viruses, archaea, and eukaryota. The most abundant genera included Bacteroides, Ruminococcus, and Clostridium. Functional annotation revealed enriched pathways in metabolism, genetic information processing, and cellular processes, with key pathways involving carbohydrate transport and metabolism, replication, and amino acid transport. CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases. Antibiotic resistance gene analysis identified Bacillota and Bacteroidota as main reservoirs, with vancomycin resistance genes being most prevalent. The study identified three major resistance mechanisms: antibiotic target alteration, antibiotic target protection, and antibiotic efflux. ConclusionThe findings contribute to a broader comprehension of antibiotic resistance within animal microbiomes and lay the foundation for further investigation into strategies for managing and mitigating antibiotic resistance.