Sequencing Data and Relative Abundances of Urinary Bacteria
We obtained 3,926,088 sequences, 5,802,274 reads from the 70 samples.
The
median number of reads in mild group was 77,177, and in the
moderate/severe group was 78,329 (P = 0.951). The reads were
classified into 4,415 OTUs that were used for downstream analyses. Venn
diagrams demonstrated that 1019 OTUs were shared between the two cohorts
(Figure S1). The median number of OTUs was significant increased in M/S
group (M group 177,
M/S
group 208, P = 0.043). Most of the OTUs were classified at the
genus level and these OTUs belong to 47 different Phyla from all urine
specimens. Relative abundance
of
bacteria was used to detect the composition of bacteria phyla and
families (Figure S2, Table
2).
The most common phylum in both two groups wasFirmicutes(M
group 47.7%, M/S group 37.0%), followed by Proteobacteria (M
group 28.2%, M/S group 24.7%),Actinobacteria(M group 5.1%, M/S group 12.2%) andBacteroidetes(M
group 5.0%,
M/S
group 7.8%). And phylumActinobacteriawas significantly more abundant in the moderate/severe group (P =
0.018). Bacteria from these four phyla were found in all urine specimens
at some level.
In
general, the most abundant bacterial
families
with mean abundances >2% wereLactobacillaceae ,Veillonellaceae ,Staphylococcaceae , Enterococcaceae andStreptococcaceae(Firmicutesphylum),Moraxellaceae ,Methylobacteriaceae and Sphingomonadaceae(Proteobacteriaphylum),Bifidobacteriaceae(Actinobacteria phylum),Prevotellaceae(Bacteroidetes phylum). Although these families are different
between the two groups to some extent, as shown in Table 2, only the
family Bifidobacteriaceae was found at significantly higher mean
abundances in mild cohort when compared to the moderate/severe cohort.
(P = 0.04). At the genus level, 7 genera had mean abundances
>2%. These include Lactobacillus andStreptococcus (Firmicutes phylum), Gardnerella(Actinobacteria phylum), Prevotella (Bacteroidetesphylum),Methylobacterium ,Acinetobacter and Sphingomonas (Proteobacteriaphylum).