Shared taxa but distinct communities: within-individual comparisons of oral, nasal, and urinary microbiomes in asymptomatic “healthy” females

Although microbial community compositions vary throughout the healthy human body, some taxa can be found to reside in multiple anatomical sites. Moreover, some microbiota that have been found to be interconnected, e.g., the gastrointestinal tract and the oral cavity, the female urinary tract and the vagina, the nose (specifically the nares) and the skin. Previously, the urinary microbiome has only been compared to proximal sites; however, several species that inhabit the asymptomatic female urinary tract are also found in distant communities, e.g., <i>Streptococcus mitis</i>, also found in the oral cavity, and <i>Staphylococcus epidermidis</i>, also found in the nares. This prompted our investigation of communities of the oral cavity, nares, and urinary tract, collected from the same individual. In this study, we profiled the oral, nasal, and urinary microbiomes of 26 self-identified "healthy" female participants using 16S rRNA amplicon sequencing. The urinary microbiome was found to be distinct from the oral and nasal communities. Nevertheless, <i>Actinomyces</i>, <i>Corynebacterium</i>, <i>Escherichia</i> + <i>Shigella</i>, <i>Lawsonella</i>, <i>Staphylococcus</i>, and <i>Streptococcus</i> were found to be present within communities of all three anatomical sites. Genera predominant within the oral and nasal communities were often low-abundant taxa within the urinary microbiome. To date, comparisons of the urinary microbiome to microbiomes of other anatomical sites is limited. The distinction between the urinary microbiome and that of the more distant oral and nasal site highlights the role that the environment plays in shaping these communities.