Metagenomic shotgun sequencing of endocervical, vaginal and rectal samples among Fijian women with and without Chlamydia trachomatis

Chlamydia trachomatis (Ct) is the primary cause of bacterial sexually transmitted infections worldwide with a disturbing increase in annual rates. While there is a plethora of data on healthy and pathogenic vaginal microbiomes-defining microbial profiles and associations with STIs-far fewer studies have similarly examined the endocervix or rectum. Further, vulnerable populations such as Pacific Islanders remain under-represented in research. We investigated the microbial composition, structure and function of these anatomic microbiomes using metagenomic shotgun sequencing among a Fijian cohort. We found, primarily among Ct-infected women, unique microbial profiles in endocervical, vaginal and rectal microbiomes with an increased diversity and more complex microbial pathways in endocervical compared to vaginal microbiomes. Similarities in microbiome composition across sites for some women suggested intra-genitorectal transmission. These novel insights into genitorectal microbiomes and their purported function require prospective studies to better define Pacific Islander microbiomes and microbial/microbiome interactions that promote Ct infection.