Investigating Microbiome Dynamics in Chronic Kidney Disease and Post-Transplantation in Continuous Culture

The oral microbiome is subject to environmental factors that are likely to affect composition and activity in chronic kidney disease (CKD) and following kidney transplantation. These may have implications for health and recovery. A major driver of oral microbiome perturbation is the accumulation of urea in saliva. We have modelled increased salivary urea concentrations associated with CKD, and subsequent reductions that may occur post-transplantation. Oral microbiota were established in constant-depth film fermenters by inoculation with saliva. Duplicate validation runs were maintained using with artificial saliva with baseline urea concentrations (0.205 mg/ml) for 21 d. Using saliva, triplicate treatment runs were then done with baseline urea for 10 d (healthy phase) before urea was increased for 10 d to reflect CKD concentrations (0.92 mg/ml) (CKD phase). This was followed by reversion to baseline urea concentrations (post-transplant phase). Biofilms in primary validation runs reached dynamic stability within 5 days according to viable counting. DNA sequence data indicated minimal taxonomic variation over time and between low and high urea treatments, despite background noise indicating changes in bacteria belonging to the family Gemellaceae and the genera TG5 and Leptotrichia. Significant differences in alpha and beta diversity occurred between low and high urea states, but not following reversion to a low urea environment. Increased abundance of the TG5 was detected in late model phases, despite apparent count stability, and independent of changes in urea concentrations.