Monitoring dynamics of urinary microbial communities

A decade ago, when the Human Microbiome Project was starting, urinary tract(UT) was not included because the bladder and urine were considered to besterile. Today, we are presented with evidence that healthy UT possesses nativemicrobiota and any major event disrupting its “equilibrium” can impact the hostalso. This impact often leads to cystitis symptoms, which is the most frequentlower urinary tract complaint, especially among women. This makes it one of themost common causes of antimicrobial drugs prescriptions in primary andsecondary care and an important contributor to the problem of antimicrobialresistance. Despite its importance, we still have trouble distinguishing whetherthe primary cause of majority of cystitis cases is a single pathogen overgrowth,or a systemic disorder affecting entire UT microbiota. There are relatively fewstudies monitoring changes and dynamics of UT microbiota in cystitis patients,making this field of research still an unknown. In this study variations to the UTmicrobiota of cystitis patients were identified and microbial dynamics has beenmodeled. The microbial genetic profile of urine samples from 28 patients wasanalyzed by 16S rDNA sequencing and bioinformatics analysis. One patient withbacterial cystitis symptoms was prescribed therapy based on national guidelinerecommendations on antibacterial treatment of urinary tract infections and UTmicrobiota change was monitored by 16S rDNA sequencing on 24 h basis duringthe entire therapy duration. The results of sequencing showed that a particularclass of bacteria contributed to majority of cystitis cases in this study. Thecontributing role of this class of bacteria – Gammaproteobacteria, was furtherconfirmed by generalized Lotka-Volterra modeling. Longitudinal microbiotainsight obtained from a single patient under prescribed antimicrobial therapyrevealed rapid and extensive changes in microbial composition and emphasizedthe need for current guidelines change in regards to therapy duration. In bothcases, gLVM indicated protective role of native microbiota, especiallyBacteroidetes class, which appeared to actively suppress pathogen overgrowthsin both models.