Table 2. Cervicovaginal microbiome structures and community state types across five ethnic groups.
| Cervicovaginal microbiome structure | Cluster description, relative abundances of taxa (%) | Assigned CST | AA | AC | AI | AK | CG |
|---|---|---|---|---|---|---|---|
| L. crispatus predominant, RA > 50% | L. crispatus—dominant > 98.9% | I | 5 | 1 | 2 | 4 | |
| L. crispatus—dominant > 97%, Prevotella bivia > 0.5% | I | 2 | |||||
| L. crispatus—dominant > 97%, G. vaginalis > 2.0% | I | 1 | |||||
| L. crispatus—dominant > 92%, L. iners > 0.5% | I | 5 | 2 | 1 | |||
| L. crispatus—dominant > 66%, L. iners > 30% | I | 1 | |||||
| L. crispatus—dominant ≥ 55%, L. iners 40%, heterogenous bacteria | I | 1 | |||||
| L. crispatus—dominant > 90%, L. iners > 4%, Corynebacterium 1 > 1.0% | I | 1 | |||||
| L. crispatus—dominant > 57%, Atopobium >20%, G. vaginalis >14% | I | 2 | |||||
| L. crispatus—dominant > 86%, G. vaginalis > 5.0%, Streptococcus agalactiae > 2.5%, Staphylococcus > 1.6% | I | 1 | |||||
| L. crispatus—dominant > 86%, L. iners > 3.0%, heterogenous bacteria | I | 1 | |||||
| L. crispatus—dominant > 80%, Bifidobacterium breve > 6.3%, Enterococcus > 5.2% | I | 1 | |||||
| L. crispatus—dominant > 80%, Bifidobacterium breve > 6.3%, Streptococcus > 3.1% | I | 1 | |||||
| L. crispatus—dominant ≥ 80%, G. vaginalis > 8.0%, heterogenous bacteria | I | 1 | |||||
| Number/percentage of samples CST-I | 14 (50%) | 2 (11%) | 7 (19%) | 3 (9.7%) | 7 (18%) | ||
| L. gasseri predominant, RA > 50% | |||||||
| L. gasseri—dominant 52%, L. iners 43% | II | 1 | |||||
| Number/percentage of samples CST- II | 0 | 0 | 1 (2.8%) | 0 | 0 | ||
|
L. iners
predominant, RA > 50% |
|||||||
| L. iners—dominant ≥ 98% | III | 2 | 2 | 1 | 6 | 1 | |
| L. iners—dominant > 90%, L. crispatus > 1.5% | III | 3 | 1 | 1 | |||
| L. iners—dominant 60–75%, L. crispatus > 24% | III | 2 | |||||
| L. iners—dominant > 80%, L. gasseri 2.8–17% | III | 4 | |||||
| L. iners—dominant ≥ 80%, heterogenous bacteria | III | 3 | 1 | ||||
| L. iners—dominant 72%, unassigned bacteria 25%, heterogenous bacteria | III | 1 | |||||
| L. iners—dominant > 80%, G. vaginalis 4.0%— ≥ 10% | III | 1 | 4 | ||||
| L. iners—dominant >55G. vaginalis > 25% Atopobium | III | 2 | 1 | ||||
| L. iners > 50% THPP = Staphylococcus, Streptococcus, Enterococcus | III | 1 | 1 | ||||
| Number/percentage of samples CST- III | 13 (46%) | 3 (17%) | 5 (14%) | 8 (26%) | 9 (24%) | ||
| Polymicrobial microbiome with G. vaginalis most dominant but with a RA < 50% | |||||||
| Heterogenous bacteria, G. vaginalis 44%, Atopobium 32%, Veillonella montpellierensis 11% | IV-A | 1 | |||||
| Heterogenous bacteria, G. vaginalis 28–32% and Prevotella bivia 11–15% | IV-A | 2 | 1 | ||||
| Heterogenous bacteria, G. vaginalis 34% Prevotella amnii 6.4% | IV-A | 1 | |||||
| Heterogenous bacteria, G. vaginalis 36% Prevotella amnii 25–34%, Atopobium 17–23% | IV-A | 2 | |||||
| Heterogenous bacteria, G. vaginalis 25–45% L. iners 37–44% | IV-A | 1 | 1 | 4 | |||
| Heterogenous bacteria, G. vaginalis > Prevotella, Atopobium, Streptococcus, Veillonella, Anaerococcus | IV-A | 4 | 2 | ||||
| Heterogenous bacteria, G. vaginalis > Prevotella, Shuttleworthia, Megasphaera, Sneathia, L. iners | IV-A | 1 | 4 | ||||
| Number/percentage of samples CST- IV-A | 0 | 0 | 4 (11%) | 10 (32%) | 10 (26%) | ||
| Polymicrobial microbiome with Prevotella species most dominant but with a RA < 50% | |||||||
| Heterogenous bacteria, Prevotella 18%, low abundance Lactobacilli | IV-B | 3 | |||||
| Heterogenous bacteria, Prevotella > 36%, No Gardnerella | IV-B | 2 | |||||
| Heterogenous bacteria, Prevotella 16–46% | IV-B | 1 | 2 | ||||
| Heterogenous bacteria, Prevotella > G. vaginalis, Shuttleworthia, Megasphaera, Sneathia amnii, L. iners | IV-B | 2 | 6 | ||||
| Heterogenous bacteria, Prevotella > G. vaginalis, Gemella, Megasphaera, Sneathia amnii, L. iners, M. hominis | IV-B | 2 | 4 | ||||
| Number/percentage of samples CST- IV-B | 0 | 7 (39%) | 5 (14%) | 0 | 10 (26%) | ||
| Polymicrobial microbiome with genera other than Gardnerella or Prevotella most dominant but with a RA < 50% | |||||||
| Heterogenous bacteria, L. iners 25–45% | 3 | ||||||
| Heterogenous bacteria, Corynebacterium 1 27% | IV-C | 1 | |||||
| Heterogenous bacteria, Bifidobacterium 47%, Scardovia wiggsiae 49% | IV-C | 1 | |||||
| Heterogenous bacteria, Streptococcus agalactiae -dominant 46%, L. iners 13%, Sneathia spp. 10% | IV-C | 2 | |||||
| Heterogenous bacteria, Ureaplasma parvum 36%, Escherichia 33%, Staphylococcus 16% | IV-C | 1 | |||||
| Heterogenous bacteria, Clostridiales bacterium 34%, Shuttleworthia 16%, Veillonella 6.6% | IV-C | 1 | |||||
| Heterogenous bacteria, Peptostreptococcus 28%, Prevotella 25%, L. iners 13% | IV-C | 1 | |||||
| Number/percentage of samples CST- IV-C | 1 (4.0%) | 0 | 6 (17%) | 2 (6.4%) | 1 (2.6%) | ||
| L. jensenii predominant, RA > 50% | |||||||
| L. jensenii—dominant > 50% | V | 0 | 0 | 0 | 0 | 0 | |
| Number/percentage of samples CST- V | 0 | 0 | 0 | 0 | 0 | ||
| G. vaginalis predominant, RA > 50% | |||||||
| G. vaginalis—dominant > 53%, L. iners 47% | VI | 1 | 1 | ||||
| G. vaginalis—dominant >60%, Sneathia spp., Shuttleworthia, Megasphaera, Atopobium, Aerococcus | VI | 1 | 1 | ||||
| G. vaginalis—dominant 54%, Streptococcus agalactiae 45% | VI | 1 | |||||
| G. vaginalis—dominant 68%, L. gasseri 22% | VI | 1 | |||||
| Number/percentage of samples CST- VI | 0 | 2 (11%) | 2 (5.6%) | 2 (6.4%) | 0 | ||
| Prevotella species dominant, RA > 50% | |||||||
| Prevotella sp.—dominant > 70%, heterogenous bacteria | VII | 1 | |||||
| Number/percentage of samples CST- VII | 0 | 1 (5%) | 0 | 0 | 0 | ||
| THPP predominant, RA > 50% | |||||||
| Streptococcus—dominant 60%, Sneathia sanguinegens 23%, G. vaginalis 9.0%, heterogenous bacteria | VIII | 1 | |||||
| Streptococcus agalactiae-dominant > 85%, heterogenous bacteria | VIII | 2 | |||||
| Peptostreptococcus 54%, heterogenous bacteria | VIII | 1 | |||||
| Enterococcus—dominant >80%, Bacilli 15% | VIII | 1 | |||||
| Staphylococcus—dominant 65–86%, low abundance L. iners, Escherichia | VIII | 2 | |||||
| Escherichia-Shigella—dominant 88%, low abundance L. iners 5%, Anaerococcus | VIII | 1 | 1 | ||||
| Number/percentage of samples CST- VIII | 0 | 0 | 5 (14%) | 4 (13%) | 0 | ||
| Genera other than Lactobacillus, Gardnerella, Prevotella and THPP that are predominant, RA > 50% | Finegoldia—dominant 71%, heterogenous bacteria | IX | 1 | ||||
| Anaerococcus vaginalis -dominant 93%, Howardella 5% | IX | 1 | |||||
| Anaerococcus—dominant 62%, G. vaginalis 26%, Veillonella montpellierensis 4.7%, Prevotella bivia 2.0% | IX | 1 | |||||
| Shuttleworthia—dominant ≥80%, G. vaginalis 2–6.2%, heterogenous bacteria | IX | 2 | |||||
| Ralstonia—dominant > 51%, Corynebacterium 1 9.0%, some THPP | IX | 1 | |||||
| Bifidobacterium breve—dominant > 98% | IX | 1 | |||||
| Number/percentage of samples CST- IX | 0 | 3 (17%) | 1 (2.8%) | 2 (6.5%) | 1 (2.6%) | ||
| Number of samples in ethnic group (Total No. of samples 151) | 28 | 18 | 36 | 31 | 38 |
Note:
AA, African American; AC, Afro-Caribbean; AI, Asian Indonesian; AK, African Kenyan; CG, Caucasian German; CST = Community State Type. Heterogenous bacteria = low abundance (<7.0%) of various bacteria such as Sneathia amnii, Sneathia sanguinegens, Megasphaera, Atopobium, Clostridiales bacterium, Dialister, Parvimonas, M. hominis, U. parvum, Finegoldia, Peptoniphilus, Mobiluncus, Corynebacterium, Howardella, Porphyromonas, Acinetobacter, Fusobacterium among other rare taxa. THPP = Campylobacter, Enterococcus, Haemophilus, Escherichia, Mycoplasma, Streptococcus, Staphylococcus, Ureaplasma; RA = Relative abundance; Shuttleworthia = BVAB1 = Candidatus Lachnocurva vaginae (Holm et al., 2020). Numbers and percentages shown in bold represent the total number and percentage of an identified CST in a given ethnic group.