Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections

Abstract

Background: Urinary tract infections (UTIs) affect 15 million women each year in the United States, with > 20% experiencing frequent recurrent UTIs. A recent placebo-controlled clinical trial found a 39% reduction in UTI symptoms among recurrent UTI sufferers who consumed a daily cranberry beverage for 24 weeks. Using metagenomic sequencing of stool from a subset of these trial participants, we assessed the impact of cranberry consumption on the gut microbiota, a reservoir for UTI-causing pathogens such as Escherichia coli, which causes > 80% of UTIs.

Results: The overall taxonomic composition, community diversity, carriage of functional pathways and gene families, and relative abundances of the vast majority of observed bacterial taxa, including E. coli, were not changed significantly by cranberry consumption. However, one unnamed Flavonifractor species (OTU41), which represented ≤1% of the overall metagenome, was significantly less abundant in cranberry consumers compared to placebo at trial completion. Given Flavonifractor's association with negative human health effects, we sought to determine OTU41 characteristic genes that may explain its differential abundance and/or relationship to key host functions. Using comparative genomic and metagenomic techniques, we identified genes in OTU41 related to transport and metabolism of various compounds, including tryptophan and cobalamin, which have been shown to play roles in host-microbe interactions.

Conclusion: While our results indicated that cranberry juice consumption had little impact on global measures of the microbiome, we found one unnamed Flavonifractor species differed significantly between study arms. This suggests further studies are needed to assess the role of cranberry consumption and Flavonifractor in health and wellbeing in the context of recurrent UTI.

Trial registration: Clinical trial registration number: ClinicalTrials.gov NCT01776021 .

Keywords: Cranberry; Flavonifractor; Metagenome; Microbiome; Urinary tract infection (UTI).

Fig. 1

Cranberry beverage consumption does not change the overall composition of the gut microbiome. a The cohort consisted of 70 women with a history of recurrent UTIs, who either consumed cranberry beverage or placebo daily for 6 months. The stool samples, collected before and after the 6-month study period, were subjected to 16S rRNA and whole metagenomic shotgun sequencing to infer gut microbial profiles and functions. b 16S rRNA-based taxonomic profiles displaying the phylum-level composition of the microbial population indicate that the composition did not change over time or due to cranberry consumption (Wilcoxon rank sum test, p > 0.3). The sample order was sorted by the relative abundance of Firmicutes. c The species richness, based on 16S OTUs, did not change significantly with cranberry beverage consumption (Wilcoxon rank sum test, p > 0.6). d A comparison of all samples at the 16S OTU level, using principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarities, indicated that the samples from the cranberry cohort did not cluster into a specific group, and the trajectories from week 0 to week 24 (shown by arrows) were scattered, indicating no common shift in microbial composition through time. The magnitude of the change between timepoints, when comparing the two cohorts, was also not significant (p = 0.51). The first two principal components (PCo1 and PCo2) accounted for 13.4 and 8.9% of the variability, respectively

Fig. 2

OTU41 is the only significantly different OTU between the cranberry and control cohorts. a Distribution of OTU relative abundance differences between cranberry and control cohorts. The X axis represents the difference of the log2 median fold-change of cranberry to placebo cohorts for each OTU. The Y axis is the -log₁₀ unadjusted p-value of the Wilcoxon rank sum test for each OTU. The size of the point represents the magnitude of the median change in the OTU relative abundance in the cranberry cohort, while the color indicates the direction of said change (blue = decrease, gray = no change, red = increase). Only OTU41 (shown in the top left) was significant after correction (adjusted p = 0.02). b The relative abundance of OTU41 decreased significantly in the cranberry beverage cohort. c A phylogenetic tree, based on 16S V4 regions, of OTU41 together with the other OTUs from this study assigned to the Flavonifractor genus, as well as additional sequenced strains closely related to Flavonifractor, including Flavonifractor sp. 54, Flavonifractor plautii, Lachnospiraceae bacterium, Flintibacter butyricus, Pseudoflavonifractor sp., and Pseudoflavonifractor capillosus indicated a very close relationship between OTU41 and Flavonifractor sp. 54. Relevant bootstrap values are shown. d Alignment of the 16S V4 sequence for OTU41 and Flavonifractor sp. 54, showing only one base pair difference

Fig. 3

Whole-genome comparative analysis of Flavonifractor genomes related to Flavonifractor sp. 54. Genome sequences were selected based on phylogenetic proximity to Flavonifractor sp. 54 and used to construct a whole-genome phylogeny using TBA. All bootstrap support values are 100%. Average Nucleotide Identity calculations indicated that Flavonifractor sp. 54 is in its own separate species from other references (< 95% ANI is considered a separate species)