Extensive novel diversity and phenotypic associations in the dromedary camel microbiome are revealed through deep metagenomics and machine learning

Abstract

The dromedary camel, also known as one-humped camel or Arabian camel, is an iconic and economically important feature of Arabian society. Its contemporary importance in commerce and transportation, along with the historical and modern use of its milk and meat products for dietary health and wellness, make it an ideal subject of scientific scrutiny. The gut microbiome has recently been associated with numerous aspects of health, diet, lifestyle, and disease in livestock and humans alike, as well as serving as an exploratory and diagnostic marker of many physical characteristics. Our initial pilot analysis of 55 camel gut microbiomes from the Fathi Camel Microbiome Project using deep metagenomic shotgun sequencing reveals substantial novel species-level microbial diversity, for which we have generated an extensive catalog of prokaryotic metagenome-assembled microorganisms (MAGs) as a foundational microbial reference database for future comparative analysis. Exploratory correlation analysis exhibits substantial correlation structure among the collected subject-level metadata, including physical characteristics. Machine learning using these novel microbial markers, as well as statistical testing, demonstrates strong predictive performance of microbes to distinguish between multiple dietary and lifestyle characteristics in dromedary camels. We derive strongly predictive models for camel age, diet (including wheat), level of captivity. These findings and resources represent substantial strides toward understanding the camel microbiome and pave the way for a deeper understanding of the camel microbiome, as well as the nuanced factors that shape camel health.