Microbial Biocatalysis within Us: The Underexplored Xenobiotic Biotransformation Potential of the Urinary Tract Microbiota.

Enzymatic biotransformation of xenobiotics by the human microbiota mediates diet-drug-microbe-host interactions and affects human health. Most research on xenobiotics has focused on the gut microbiota while neglecting other body sites, yet over two-thirds of pharmaceuticals are primarily excreted in urine. As a result, the urinary microbiota is exposed to many xenobiotics in much higher concentrations than in the gut. Microbial xenobiotic biocatalysis in the bladder has implications for urinary tract infections and the emergence of antibiotic resistance. However, we have limited knowledge of biotransformations catalyzed by the urinary microbiota. In this perspective, we investigated differences in physicochemical conditions and microbial community composition between the gut and urinary tract. We used a comparative enzyme class mining approach to profile the distribution of xenobiotic-transforming enzyme homologs in genomes of urinary bacteria. Our analysis revealed a discontinuous distribution of enzyme classes even among closely related organisms. We detected diverse amidase homologs involved in pharmaceutical and dietary additive biotransformation pathways, pinpointing microbial candidates to validate for their involvement in xenobiotic transformations in urine. Overall, we highlight the biocatalytic potential of urinary tract bacteria as a lens to study how the human microbiota may respond and adapt to xenobiotic inputs.

Legionella relative abundance in shower hose biofilms is associated with specific microbiome members.

Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with bacterial and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0-7.8%, of which only 0-0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g. Chthonomonas, Vrihiamoeba) or low (e.g. Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: (i) the colonization of a high number of real shower hoses biofilm samples; (ii) the ecological meaning of associations between Legionella and co-occurring bacterial/eukaryotic organisms; (iii) critical points and future directions of microbial-interaction-based-ecological-investigations.