These numbers for richness are considerably lower than found in HF urine (Table 1 and Figure 3A). The number of OTUs at 3% difference for the individual samples for both IC and HF
are indicated in https://www.selleckchem.com/products/tpca-1.html box plots (Figure 3B) for both V1V2 and V6 analysis. In general, fewer number of OTU clusters were observed for IC individuals than that for HF individuals. Ecological diversity measured by Shannon and inverse Simpson indices also indicate lower diversity in IC urine in comparison to what was seen in urine from HF (Figure 3C and D). Specifically, a significant (p < 0.05) decrease in inverse Simpson index in IC patients compared to HF was found for the V6 analysis. Taken together, the results for both V1V2 and V6 support each other and confirm that the urine community is less diverse in IC patients than in HF individuals. However, the compound screening assay single IC outlier with high richness and diversity (Figure 3B-D) also clustered outside the IC group in the clustering analysis done using taxonomy data (Figure 2) showing that there is also potential for variation within the IC community. Figure 3 Comparison of richness and diversity estimations of urine from interstitial cystitis (IC) patients and healthy females (HF). A: Rarefaction curves depicting number of OTUs (at 3% genetic difference) as function of the total number of
sequences for the combined sequence pool datasets for IC urine V1V2 and V6 (red and orange) and HF urine V1V2 and V6 (dark and light blue). The curves show a decreased estimate of species richness in the IC urine microbiome compared to the HF urine microbiome. B, C, and D: Box plots showing richness and diversity of 16S rDNA sequences. Boxes contain 50% of Casein kinase 1 the data and have lines
at the lower quartile (red), median and upper quartile (green) values. Ends of the whiskers mark the lowest and highest value. The plots show the results of a combined assessment of the eight urine samples in each HF and IC microbiome and with normalized numbers of sequences for OTU and Shannon index values (B and C). B: Observed OTU counts (at 3% genetic difference) of all urine samples taken from HF and IC, for both V1V2 and V6 datasets. C and D: Shannon index and inverse Simpson index at 3% sequence dissimilarity calculated to estimate diversity for both V1V2 and V6 datasets. Asterisks (*) indicate significant differences (Wilcox rank sum test: * p < 0.05). Note that a single sample (P2) in the IC community is the only outlier with the highest values for both richness and diversity (for both V1V2 and V6 analysis). The IC and HF urine also showed a degree of community similarity at 3% sequence dissimilarity level – about 12% and 9.5% of the total OTUs for V1V2 and V6, respectively, were present in both groups (Additional file 4: Figure S1).