Shotgun sequencing of camel milk microbiome

Camel milk is recognized as a functional food with significant nutritional value and health benefits. The consumption of raw camel milk is common despite safety concerns, with around 6 billion people globally consumes its products. The identification of camel milk microbiome to the species level using advanced technology remains limited. This study investigated the microbiome of raw camel milk employing shotgun metagenomic sequencing. Dromedary camel milk samples were collected from retail stores and farms (healthy and mastitis) in Kuwait. Shotgun sequencing revealed the presence of technologically relevant microorganisms that play a role as health-promoting bacteria, including Lactococcus lactis and Streptococcus thermophilus, key dairy starter cultures, as well as bacteriophages known to infect a broad range of pathogenic bacteria. Furthermore, pathogenic bacteria represented a significant fraction of the population detected in raw milk including Clostridium botulinum, Klebsiella pneumoniae, Acinetobacter baumannii, Streptococcus parasuis among others. The eukaryotic community was dominated by Babesia bigemina in addition to yeast and mold species. Additionally, mastitis-causing pathogens were revealed in this study, mainly Escherichia coli and Enterococcus faecalis. These findings highlighted the raw camel milk microbiome and revealed the presence of bacterial species known as the most significant industrial dairy starter and frequently utilized in probiotic formulations, along with bacteriophages useful as antibacterial agents in dairy industry. These microorganisms may enhance the quality and safety of dairy products and improve optimization processes.