Alterations of microbiota in urine from women with interstitial cystitis

BMC Microbiology

Table 1 Sampling depth and biodiversity found by amplicon 454 pyrosequencing V1V2 and V6 region from urine

		Combined sequence pool from HF urine ¹		Combined sequence pool from IC urine ²
		V1V2	V6	V1V2	V6
*Preprocessing*
	Total reads	78346	74067	74211	98720
	Length cutoff ³	48861	45382	46272	62325
	Denoised⁴	48860	45136	46267	62173
	Cleaned⁵	48452	44760	46138	62032
*Taxonomy analysis*
	Phyla⁶	10	8	5	7
	Genera⁶	35	28	23	25
*OTU and Diversity indices*
	Cleaned⁵	48452	44760	46138	62032
	Silva 16S alignment⁷	46001	44146	44594	61170
	Unique OTUs	974	2045	514	1432
	OTUs⁸ (3%)	724	1537	344	1008
	OTUs⁸ (6%)	615	1265	292	786
	Chao1⁹ (3%)	1435	3936	357	2485
	Chao1 LCI95	1261	3521	675	2172
	Caho1 HCI95	1664	4437	1137	2883
	Shannon index¹⁰ (3%)	2.62	3.02	1.67	1.95
	Inverse Simpson index¹¹ (3%)	6.97	7.03	3.57	3.72

¹Combined sequence data from eight healthy female (HF) urine samples, sequences generated in prior study (Siddiqui et al. (2011)[16]).
²Combined sequence data from eight interstitial cystitis (IC) urine samples.
³Length cutoff at minimum 218 nt for V1V2 and 235 nt for V6 reads.
⁴Total number of sequences after processing the dataset through Pyronoise[21].
⁵The number of reads per dataset after removal of sequences that could be from the same source as those in the contamination control dataset as described in Siddiqui et al. (2011)[16].
⁶Number of phyla and genera based on taxonomic classification by MEGAN V3.4[23, 24].
⁷The number of total reads after Silva 16S alignment as recommended by MOTHUR[29].
⁸OTUs: Operational Taxonomic Units at 3% or 6% nucleotide difference.
⁹Chao1 is an estimator of the minimum richness and is based on the number of rare OTUs (singletons and doublets) within a sample.
¹⁰The Shannon index combines estimates of richness (total number of OTUs) and evenness (relative abundance).
¹¹Inverse Simpson index (1/D) is an indication of the richness a community with uniform evenness would have at the same level of diversity. It takes into account the number of OTUs present, as well as the abundance of each OTU.

ISSN: 1471-2180