A novel lineage of Chilomastix mesnili in wild Moroccan Barbary macaques (Macaca sylvanus)

Chilomastix spp. are flagellated protists found in the intestines of a broad range of hosts. They are generally non-pathogenic and have been little studied, especially using molecular techniques, and significant taxonomic uncertainty regarding the host specificity of lineages remains. As part of a study of intestinal microbial communities of wild Barbary macaques (Macaca sylvanus) from Morocco, we mined 50 faecal metagenomic sequence libraries and found 11 rRNA sequences matching Chilomastix. Compared to published 18S rRNA sequences, the Barbary macaque Chilomastix sequences formed a well-supported clade distinct from human-derived C. mesnili ST1 from Indonesia. The macaque Chilomastix sequences cluster with a single pig-derived isolate and two sequences from Japanese macaques (Macaca fuscata). This indicates that M. sylvanus harbours a lineage of Chilomastix distinct from the common human strain of C. mesnili and geographically widespread. We were also able to reconstruct the complete rDNA operon from this lineage.