Comparative urine microbiome structure and diversity in kidney stone disease

Kidney stone disease (KSD) is a urological condition contributed by several factors including diet, metabolism, genetic factors and microbial infection. However, the role of microbial colonization and the complex microbiota structure of the urinary tract in KSD has gained. Here, we report the urinary microbiome structure of patients with different kidney stone types compared to an age and sex matched control cohort to understand the possible link between KSD and urine microbiome (UMB). The UMB structure was studied from the urine samples of the KSD and healthy (HLT) subjects through 16S rRNA gene amplicon sequencing. Different bioinformatics tools such as PICRUSt software were used to infer the metabolic capabilities of the bacterial community. The mean age of the KSD cohort was 46.3 years. The patients represented four stone types namely, calcium oxalate, struvite, uric acid and mixed composition. Among KSD group, positive stone and urine cultures were seen in 16 (39.02%) and 15 (36.5%) subjects, respectively. However, in the HLT cohort, only 12 (29.2%) of urine samples showed bacterial presence by culture-based analyses. A significant difference between HLT and KSD cohorts (p<0.05) was observed in the total community composition of the urine microbiome. A few bacterial groups were strongly associated with the stone types and metabolic reconstructions of the UMB revealed the significant abundance of many functional categories that may have influence on stone formation. The results show that UMB may play a key role in KSD and alterations in the UMB may be a risk factor for KSD or its recurrence. It is vital to identify the keystone species that may provide protection against KSD or reduce the recurrence, while strategies to maintain healthy UMB composition may possibly reduce the nucleation or growth of urinary crystals and reduce the KSD complications. To establish this fact, thorough studies across geographical regions and diverse populations is essential.