Interestingly, reads assigned to Gardnerella were only identified in 3/8 urine samples, even though this genus was the 3rd most abundant group in the pooled sequence

MK-2206 order dataset for both the V1V2 and V6 regions (Figure 2A). Three other genera and a group of 5 genera were identified by reads belonging to 3 or 2 urine samples, respectively. 24 genera were only detected in 1 out of the 8 samples. Species richness and diversity estimates of the female urine microbiota Bacterial taxonomic richness and diversity varied greatly among urine samples investigated in this study. Community richness and diversity were determined using rarefaction plots, Chao1 and Shannon index estimations (Figure 3 and Table 2). Figure 3 Number of OTUs as function of the total number of sequences. A and B: Rarefaction curves of individual samples for the V1V2 (A) and the V6 datasets (B). Curves were generated at 3% genetic difference using MOTHUR v1.17.0 [39]. C and D: Rarefaction curves of the pooled dataset for both V1V2 reads (C) and V6 reads (D). OTUs with ≤3%, ≤6% and ≤10% pairwise sequence selleck products difference generated using MOTHUR v1.17.0 [39] are assumed to belong to the same species, genus and family, respectively. Rarefaction curves were generated for 3% genetic difference level (e.g., at the species level).

The number of OTUs calculated for the eight individual samples ranged from 20-504 and 63-499 OTUs for the V1V2 and V6 regions, respectively 4��8C (Figure 3A, B and Table 2). OTU numbers of the total bacterial

community in the female urine at 3% difference for the V1V2 sequence pool was calculated to 1209 OTUs and to 1435 OTUs for the V6 sequence pool (Figure 3C, D and Table 2). Furthermore, total unique OTUs for the V1V2 pooled reads were 1354 and for the V6 pooled reads 2069 (Table 2). To compare the diversity between the eight different urine samples, the Shannon diversity index was determined both with the original, and with normalized numbers of sequences (Table 2). There was no substantial difference between the two Shannon indices calculated for the same sample. Discussion In this work we sequenced two different variable regions of 16S rDNA isolated from eight culture-negative urine samples. Urine samples are at risk of contamination by the bacterial flora of the female urogenital system [82, 83], therefore sampling of mid-stream urine was performed by the clean catch method, under guidance of an experienced urotherapy nurse. To avoid further bacterial growth, which could skew the results, the samples were kept on ice and analyzed within an hour. Amplicon lengths used here exceed the typical fragment size (150-200 bp) of circulating cell-free DNA in urine [84], thus reducing the frequency of such DNA in our analyses.