The Induction of Oxalate Metabolism In Vivo Is More Effective with Functional Microbial Communities than with Functional Microbial Species

Abstract

For mammals, oxalate enters the body through the diet or is endogenously produced by the liver; it is removed by microbial oxalate metabolism in the gut and/or excretion in feces or urine. Deficiencies in any one of the these pathways can lead to complications, such as calcium oxalate urinary stones. While considerable research has been conducted on individual oxalate-degrading bacterial isolates, interactions between oxalate and the gut microbiota as a whole are unknown. We examined the reduction in oxalate excretion in a rat model following oral administration of fecal microbes from a mammalian herbivore adapted to a high oxalate diet or to fecal transplants consisting of two different formulations of mixed oxalate-degrading isolates. While all transplants elicited a significant reduction in oxalate excretion initially, the greatest effect was seen with fecal microbial transplants, which persisted even in the absence of dietary oxalate. The reduction in oxalate excretion in animals given fecal transplants corresponded with the establishment of diverse bacteria, including known oxalate-degrading bacteria and a cohesive network of bacteria centered on oxalate-degrading specialists from the Oxalobacteraceae family. Results suggested that the administration of a complete community of bacteria facilitates a cohesive balance in terms of microbial interactions. Our work offers important insights into the development of targeted bacteriotherapies intended to reduce urinary oxalate excretion in patients at risk for recurrent calcium oxalate stones as well as bacteriotherapies targeting other toxins for elimination. IMPORTANCE Oxalate is a central component in 80% of kidney stones. While mammals do not possess the enzymes to degrade oxalate, many gastrointestinal bacteria are efficient oxalate degraders. We examined the role of cohesive microbial networks for oxalate metabolism, using Sprague-Dawley rats as a model host. While the transplantation of oxalate-degrading bacteria alone to the Sprague-Dawley hosts did increase oxalate metabolism, fecal transplants from a wild mammalian herbivore, Neotoma albigula, had a significantly greater effect. Furthermore, the boost for oxalate metabolism persisted only in animals that received fecal transplants. Animals receiving fecal transplants had a more diverse and cohesive network of bacteria associated with the Oxalobacteraceae, a family known to consist of specialist oxalate-degrading bacteria, than did animals that received oxalate-degrading bacteria alone. Our results indicate that fecal transplants are more effective at transferring specific functions than are microbial specialists alone, which has broad implications for the development of bacteriotherapies.

Keywords: fecal transplant; gut microbiota; oxalate; probiotics; woodrat.

FIG 1

Oxalate metrics over the course of the experiment. Significant treatment differences among groups were determined via a repeated-measures ANOVA, for which the P values and degrees of freedom (in parentheses) for effect and error, respectively, were as follows: for oxalate degradation, treatment (3, 18), P < 0.001; time (2, 48), P < 0.001; treatment × time (8, 66), P < 0.001; for urinary oxalate, treatment (3, 18), P = 0.002; time (2, 48), P < 0.001; treatment × time (8, 66), P = 0.693; for fecal oxalate, treatment (3, 18), P ≤ 0.001; time (2, 48), P < 0.001; treatment × time (8, 66), P ≤ 0.001. Treatment differences are indicated by letters in the legend. Letters above columns indicate significant differences between treatments within a time point, as assessed by a post hoc, Holm’s-corrected Tukey’s analysis. The black lines indicates N. albigula degradation and excretion. Animals were consuming 1.5% oxalate at each of the time points shown.

FIG 2

PCoA plots of the β-diversity (unweighted UniFrac analysis) by time point. Statistical differences between SDR treatment groups across the whole trial were determined by using ANOSIM (P = 0.001, R = 0.39). Animals consumed 1.5% oxalate at each of the time points shown.

FIG 3

γ-Diversity, reflecting the total number of overlapping and nonoverlapping OTUs between the control, NA feces, and N. albigula treatment groups. Time points: T1, before transplant (1.5% oxalate); T3, after transplant (1.5% oxalate); T4, no-oxalate period (0% oxalate), T5, after no-oxalate period (1.5% oxalate). Circles represent specific groups, and numbers reflect the number of OTUs. In panel D, the small circle outside the overlapping circles contains the numbers of taxa shared between N. albigula and the NA feces treatment group at T5 but not at T3.

FIG 4

Oxalobacteraceae found in each group before transplant, after transplant, and after no oxalate exposure. Significance between groups was determined with a repeated-measures ANOVA. Letters next to groups indicate significantly different treatments across the experiment as assessed by a post hoc, Holm’s-corrected Tukey’s analysis. For each panel, the degrees of freedom (in parentheses) for effect and error, respectively, were as follows. (A) Number of unique Oxalobacteraceae. Treatment (4, 24), P < 0.001; time (2, 60), P = 0.008; treatment × time (14, 84), P = 0.002. (B) Relative abundance of Oxalobacteraceae. Treatment (4, 24), P < 0.001; time (2, 60), P = 0.006; treatment × time (14, 84), P = 0.002. Animals were consuming 1.5% oxalate at each of the time points shown.

FIG 5

Multilayered cooccurrence network analysis of OTUs that exhibited a significant positive Spearman’s correlation with oxalate consumption at the end of the diet trial. Nodes, which have been minimized to enable clear viewing of entire networks, represent individual OTUs, and edges represent a significant interaction between two OTUs. Dashes represent isolated interactions of a few OTUs. Animals were consuming 1.5% oxalate at the time of sampling.

FIG 6

A comparison of techniques to identify the bacteria associated with oxalate metabolism, correlating specific OTUs to either oxalate consumption (black) or to cooccurrence with Oxalobacteraceae (gray). The shared taxa between the two techniques are shown at the level of OTU (A) and family (B).