The composition of vaginal microbiota composition in the healthy controls and women with COVID-19
Alpha diversity was evaluated by using Shannon and Simpson Index. In the COVID-19 group, the Shannon index was significantly elevated, compared to those of the healthy controls (1.09 vs. 0.75; P=0.007), and the Simpson index was significantly lower in the COVID-19 group than those of healthy controls (0.4 vs. 0.61; P=0.006) (Figure 2A). In pregnant women with asymptomatic/mild and moderate/severe disease, the Shannon index was found to be significantly higher than those of the healthy controls (1.06 and 1.16 vs. 0.75; P<0.05), whereas the Simpson index was significantly decreased, compared to the healthy controls (0.42 and 0.49 respectively, vs. 0.61; P<0.05) (Figure 2A). Beta diversity (Bray-Curtis) results indicated that there were no compositional differences between COVID-19 status and healthy controls (P=0.49) (Figure 2B).
There were no statistically significant differences in the alpha diversity of vaginal microbiota between the second and third trimesters of healthy controls according to Shannon index and Simpson index (0.41 vs. 0.5; P= 0.22 and, 0.8 vs. 0.75; P= 0.08, respectively).
The vaginal microbiota composition and relative abundances of the bacterial phylum, genera and species for two groups were summarized in Figure 3. The three phyla; Firmicutes (86.02%), Actinobacteria (12.12%) and Bacteriodata (Bacteroidetes) (0.54%) accounted for 99.8% of the bacterial species in COVID-19 group. In a comparison of COVID-19 group with healthy controls, Firmicutes significantly decreased (85.9% vs. 96.11, P=0.049) while the amounts of Bacteroidetes significantly increased (0.53% vs. 0.44%; P=0.024) (Figure 3A).
At the genus level, Lactobacillus sp. significantly decreased in the COVID-19 group compared to the healthy controls (80.6% vs. 93.98%; P=0.019).  Particularly, Lactobacillus delbrueckii (L. delbrueckii) was not detected in the COVID-19 group, although its amount was 1.5% in the healthy controls (P=0.046) (Figure 3B).
Lactobacillus iners (L.iners) , Lactobacillus crispatus (L. crispatus) , and Lactobacillus jensenii (L. jensenii) showed trends towards a decline in COVID-19 group (26.5%, 3.2%, and 7.1%, respectively) when compared to the healthy controls (32.8%, 3.9%, and 7.5%, respectively) but the differences were not statistically significant (P>0.05) (Figure 3C).
In the COVID-19 group, among anaerobe taxa, particularlyPrevotella timonensis (0.04%) and Dialister propionicifaciens (0.02%) were identified but none of these were detected in the healthy controls. In addition to these, the COVID-19-infected group showed a higher abundance of Gardnerellavaginalis (6.4% vs. 1.98%; P=0.213). Also, Ureaplasma(0.69% vs. 0.04%; P=0.054) was found to be higher in the COVID-19 group compared to the healthy controls.