First trimester "clean catch" urine and vaginal swab sample distinct microbiological niches

The Urinary, Vaginal, and Perineal Microbiome: Commonalities and Differences

INTRODUCTION AND HYPOTHESIS

The relationship of adjacent pelvic microbiomes in women has not been well characterized. This study aimed to compare the microbiomes of catheterized urine, vagina, and perineum from well-characterized women undergoing urogynecologic surgery.

METHODS

Clinical data was extracted from the electronic medical record. Participants contributed three samples (catheterized urine, vaginal swab, perineal swab) that were subjected to DNA sequencing following amplification of hyper-variable region 4 (V4) of the bacterial 16S rRNA gene. The sequences were processed, annotated, and decontaminated. Only participants with sequence-positive samples from all three samples were included in the analytic cohort. Alpha (within-sample) and beta (between-sample) diversity indices were computed, and the microbiome compositions within each participant and across all participants were compared.

RESULTS

The mean age of the 104 participants was 60.5 years old (range 35-89) with a mean BMI of 28.2 kg/m2; most (89%) were White. Lactobacillus was the most common genus detected, with a mean relative abundance of 64.8% in the bladder, 67.4% in the vagina, and 42.6% in the perineum. Across these niches, alpha diversity differed significantly, whereas beta diversity was similar. Within an individual, the three microbiomes were very similar to each other, with the bladder and vagina considerably more similar to each other than to the perineum. Taxonomic diversity tended to increase with age and was highest in overweight participants.

CONCLUSION

The microbiomes of the bladder, vagina, and perineum of women are very similar to each other.

Urine microbiome in individuals with an impaired immune system

With the advent of next generation sequencing, it is now appreciated that human urine is not sterile. Recent investigations of the urinary microbiome (urobiome) have provided insights into several urological diseases. Urobiome dysbiosis, defined as non-optimal urine microbiome composition, has been observed in many disorders; however, it is not clear whether this dysbiosis is the cause of urinary tract disorders or a consequence. In addition, immunologically altered disorders are associated with higher rates of urinary tract infections. These disorders include immunoproliferative and immunodeficiency diseases, cancer, and immunosuppressant therapy in transplant recipients. In this review, we examine the current state of knowledge of the urobiome in immunologically altered diseases, its composition and metabolomic consequences. We conclude that more data are required to describe the urobiome in immune altered states, knowledge that could facilitate understanding the role of the urobiome and its pathophysiological effects on urinary tract infections and other disorders of the urinary tract.