Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
VAGINAL MICROBIOME RESULT
Indication
Vaginal bacterial profile to differentiate between eubiosis/dysbiosis
Diagnosis
The community state type CST IVC1 found with a predominance of streptococci (approx. 50%), the detection of other potentially pathogenic species (Sneathia vaginalis approx. 5%) and the reduction of lactobacilli (L. jensenii approx. 3%, L. crispatus approx. 1%) indicates a dysbiotic vaginal microbiome (1,2,3,4). This imbalance is also expressed in the significantly increased bacterial species count (species richness = 52).
Results
Fundamental microbiome parameter
Measured values of the bacterial spectrum.

Microbiome diversity (Shannon): high
Resilience = 9.16
The species diversity is in the upper 25% of the analysed samples.
Shannon diversity compared to the reference population (white line = 50th percentile). The black bar/arrow shows the value for this sample. 75 % of the healthy samples fall into the green range. A minority of the reference samples have values in the yellow/red range. Shannon alpha diversity is a statistical, quantitative value that combines the number of bacterial sequences detected (richness) and the uniformity of their distribution.
Microbiome species richness: high
Species richness = 52.0
The species richness is in the upper 25% of the analysed samples.
Number of species compared to the reference population (white line = 50th percentile). The black bar/arrow shows the value for this sample. 75 % of the healthy samples fall into the green range. A minority of the reference samples have values in the yellow/red range. A high content of Lactobacillus and a low overall density indicate a healthy microbiome. Measurements of individual samples are compared with the general population.
Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Microbiome species evenness hoch
Species evenness = 0.6
The species homogenity is in the upper 25% range of the analysed samples.
Uniformity of the species compared to the population (white line = 50th percentile). The black bar/arrow shows the value for this sample. 75 % of the population falls within the green range. A minority of the samples have values in the yellow/red range. The values for the homogenity of healthy vaginal flora are low due to a high proportion of lactobacilli. The measurements of the individual samples are compared with those of the general population.

Bacterial strains associated with infections

There are only a few groups of bacteria that are associated with healthy humans, including the Phyla Firmicutes and Bacteriodetes. Under the right circumstances, almost every bacterium is potentially pathogenic. In particular, strains of Fusobacteria and Proteobacteria are associated with opportunistic infections.
Percentage of Fusobacteria in the microbiome: potential pathogenic
Fusobacteria = 4.711
The proportion of Fusobacteria is higher than 90% of the reference samples.
Percentage of Fusobacteria compared to the reference population. The black bar/arrow shows the value for this sample. Healthier samples generally have lower Fusobacteria levels. Values in the yellow/red area are higher than 75% or more of the population. The Fusobacteria strain contains several known human pathogens. Certain Fusobacteria can promote inflammation and contribute to infections and diseases. The individual measurement ranges are based on the reference population.
Fusobacteria species detected
The Fusobacteria strain contains several known human pathogens. Certain Fusobacteria can promote inflammation and contribute to infections and diseases. The individual areas are based on the reference population.
Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Bacterial strains associated with diseases
Percentage of Proteobacteria in the microbiome: potential pathogenic
Proteobacteria = 0.827
The proportion of Proteobacteria is higher than 90% of the samples tested.
Percentage of Proteobacteria compared to the reference population (white line = 50th percentile). The black bar/arrow shows the value for this sample. 75% of the population falls in the green range. A minority of the reference samples have values in the yellow/red range. The Proteobacteria strain contains several known human pathogens. High levels of Proteobacteria can promote inflammation and contribute to infections and diseases.
Proteobacteria species detected
The Proteobacteria strain contains several known human pathogens. High levels of Proteobacteria can promote inflammation and contribute to infections and diseases.
Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Species Barplot
The colour bars represent the relative proportions of the bacterial species in the microbiome.
Bar chart species

Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Most frequently detected bacterial species
Streptococcus mitis: 32.88%
Rare bacterium
The significance of Streptococcus mitis is not precisely defined. It is not considered a common pathogen.
Gemella haemolysans: 24.41%
Rare bacterium
The significance of Gemella haemolysans is not precisely defined. It is not considered a common pathogen.
Streptococcus agalactiae: 8.62%
Potential pathogenic
Although it is more commonly associated with infections in newborns, it can also lead to urinary tract infections in adults, especially in pregnant women.
Streptococcus salivarius: 7.25%
Rare Bacterium
The significance of Streptococcus salivarius is not precisely defined. It is not considered a common pathogen.
Sneathia vaginalis: 4.71%
Potential pathogenic
Low levels of Sneathia are common, but higher levels of this toxin-producing, gram-negative species have been associated with pregnancy complications and occasional infections.
Staphylococcus hominis: 3.77%
Rare bacterium
The significance of Staphylococcus hominis is not precisely defined. It is not considered a common pathogen.

'Percentage of the most common species in the sample compared to the reference population (white line = 50th percentile). The black bar/arrow shows the value for this sample. 75 % of the population falls into the green range. A minority of the reference samples have values in the yellow/red range. Note that for potential pathogens, values higher than the majority of the population in the red range indicate an over-representation of the pathogen, while values lower than the majority of the population indicate an under-representation of the pathogen.'
Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Species reference diagram - total microbiome
Sunburst diagram - The coloured discs represent the relative representation of the bacterial taxa. The centre ring is the lowest resolution (domain/kingdom), followed by phylum, class, order, family, genus, species, the last outer ring is the individual amplicon sequence variant (ASV) DNA sequences for the species. Note that strains usually have multiple ASVs. The last number in the ASV ring is the percent identity (PID) to the named species. Novel strains usually have a lower PID than known strains. Closely related strains have a PID of more than 98%.
Species sunburst diagram

Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Principal component analysis (PCA) of the sample plotted together with other samples from the reference database. The colours of the dots refer to the Shannon Diversity Microbiome Resilience. Lighter colours have higher values for microbiome resilience, darker colours have lower diversity and uniformity and therefore lower resilience. The samples with the highest diversity tend to be grouped in the centre of the diagram.
PCA reference population space diagram

Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Species Table- Total microbiome
List of all species in the smear and their relative proportion
Species Table
Dr. Martin Gencik, FA für Medizinische Genetik
Brünnlbadgasse 15, 1090 Wien
Tel: 01/95 80 164, Fax: 01/89 07 943
e-mail: mikrobiom@medgene.at, Web: mikrobiom.medgene.at
Summary and general assessment

Interpretation
Analysis of the vaginal microbiome composition with the bacteria present indicates a non-lactobacillus-dominated flora (CST IVC1), which can be associated with various health implications. Such a bacterial spectrum is an indication of a disturbed microbial balance (dysbiosis).

1.Streptococcus mitis (32.88%): Normally a commensal of the oral microbiome, Streptococcus mitis is occasionally found in vaginal samples. It is generally non-pathogenic but can cause infections in immunocompromised individuals. Over-representation in the vagina may indicate an abnormal flora possibly associated with inflammation or infection.

2.Gemella haemolysans (24.41%): Gemella haemolysans is also a common inhabitant of the upper respiratory tract and is less frequently detected in the vagina. High levels of this bacterium may be associated with dysbiosis, indicating a vaginal environment that is not dominated by protective lactobacilli.

3.Streptococcus agalactiae (8.62%): This species, also known as Group B Streptococcus, is potentially pathogenic and can lead to neonatal infections in pregnant women. In the vagina, an increase in S. agalactiae can increase the risk of infections and complications, especially during pregnancy.

4.Streptococcus salivarius (7.25%): Streptococcus salivarius is also part of the normal oral flora. Its presence in the vagina could indicate contamination or dysbiosis, as it is not common in the healthy vaginal flora.

5.Sneathia vaginalis (4.71%): This bacterial species is frequently detected in bacterial vaginosis and is an indication of a disturbance in the microbial balance. Its association with inflammation and vaginal infections makes it a potential indicator of vaginal dysbiosis.

6.Staphylococcus hominis (3.77%): These skin bacteria are not typically present in high proportions in the vagina. Their increased prevalence may indicate a disturbed flora that may have been influenced by external factors such as hygiene products or mechanical irritation.

Overall, this microbiome composition shows a significant deviation from the protective, lactobacillus-dominated vaginal flora, which could be associated with a higher risk of infection and inflammation. Further clinical evaluation may be advisable, particularly in relation to the potential role of Sneathia vaginalis and Streptococcus agalactiae. It would also be useful to consider measures to promote a healthy vaginal microbiota, including the use of probiotics or other therapeutic approaches (5-22).
.

Personalised supportive therapies
Based on the analysed composition of the vaginal microbiome and the identified bacteria, targeted probiotic therapies could help to restore the microbial balance and inhibit the growth of pathogenic or dysbiotic bacteria. Specific probiotic approaches tailored to the identified bacteria are proposed below:

1.Promotion of lactobacilli to inhibit Streptococci and Gemella spp. Since Lactobacillus species should dominate in a healthy vaginal microbiota, probiotic preparations containing Lactobacillus crispatus or Lactobacillus gasseri can help to restore the microbial balance. Studies show that these Lactobacilli species can acidify the vaginal environment and thus inhibit the growth of streptococci such as Streptococcus mitis and Streptococcus agalactiae as well as Gemella haemolysans. Regular use of probiotics, e.g. in the form of vaginal suppositories or oral preparations, could help to restore lactobacilli dominance and suppress pathogenic bacteria (Mei and Li 2022).

2.Sneathia vaginalis ist häufig mit bakterieller Vaginose (BV) assoziiert. Therapy should aim to eliminate the conditions that favour the growth of Sneathia. Probiotics containing Lactobacillus reuteri and Lactobacillus rhamnosus have been shown to be effective in the treatment of BV by promoting microbial balance and displacing pathogenic organisms.
Oral ingestion of products such as Lactobacillus reuteri RC-14 and Lactobacillus rhamnosus GR-1 can help restore a healthy vaginal microbiota and alleviate BV symptoms. Several clinical studies have shown that these strains can reduce the recurrence of BV and stabilise vaginal health in the long term (Reid et al., 2018).

3.As Staphylococcus hominis is typically a skin bacterium, the increased presence in the vagina could indicate external contamination or a weakening of the vaginal barrier function. To reduce the growth of S. hominis, probiotics aimed at promoting the natural vaginal microflora, such as Lactobacillus crispatus, could be useful.
Studies have shown that Lactobacillus crispatus is able to both strengthen the immune system of the vaginal mucosa and inhibit the growth of unwanted microorganisms (Ravel et al., 2011).

4.General approach to supporting vaginal health

In addition to specific probiotics, the general use of multi-Lactobacilli preparations may be recommended to stabilise the vaginal microbiota. Preparations containing Lactobacillus acidophilus, Lactobacillus plantarum and Bifidobacterium bifidum may be helpful as they have been shown to improve vaginal health, support the immune system and promote the formation of a healthy biofilm.
Summary of recommended probiotics:
• Lactobacillus crispatus and Lactobacillus gasseri to inhibit Streptococci and Gemella spp.
• Lactobacillus reuteri and Lactobacillus rhamnosus to inhibit Sneathia vaginalis.
• Lactobacillus crispatus for the reduction of Staphylococcus hominis.
• Multi-lactobacilli preparations for the general promotion of vaginal health.

The targeted use of these probiotics could significantly improve the chances of restoring healthy vaginal microflora and reducing the risk of infections and dysbiosis.
.

Material
OMNIgene•VAGINAL OMR130
Localization: Vagina
Description: Microbiom Abstrichprobe

Methoden

The swab sample was stabilised for transport to the laboratory using the OMNIgene VAGINAL OMR130 collection set. DNA isolation was performed with ZymoBIOMICS DNA Miniprep, Cat: D4300. DNA barcoding and library preparation were performed using the Intus Biosciences StrainID kit (Intus Biosciences) and the LSK-114 kit (Oxford Nanopore). The 2.5 kb base pair PCR products were sequenced with a MinION MK1C on a flow cell 10.4.1 (Oxford Nanopore) and analysed with the Titan Bioinformatics Pipeline (Intus Biosciences).

Literature

Subdivision of the vaginal microbiome

(for details see: Rosca, A. S., Castro, J., Sousa, L. G., & Cerca, N. (2020). Gardnerella and vaginal health: the truth is out there. FEMS microbiology reviews, 44(1), 73-105.)
Bacteria play an essential role in vaginal health. Scientists have found that healthy people can have different groups of bacteria, known as community state types, and that the prevalence of CST groups can vary between different ethnic groups, cultures and behaviours.

Lactobacillus groups (CST I, II, III und V):
Lactobacilli are the most common and important bacteria in the vaginal community, typical species are L. crispatus, L. gasseri, L. iners and L. jensenii. They help maintain a balanced environment by producing lactic acid, which keeps the vaginal pH below 4.5, and bacteriocins, which limit the types of bacteria that can colonise the environment.

CST IV group:
About 30% of women do not have significant amounts of Lactobacillus; instead, the vaginal environment contains a mixture of other bacteria. Some of these bacteria can survive in a variety of different conditions. These include Gardnerella, Atopobium, Prevotella, Mobiluncus, Sneathia, Eggerthella, Finegoldia, Megasphaera, Peptoniphilus, Corynebacterium, Streptococcus and Aerococcus.

Basic literature
Literature used to prepare the report and the conclusions.

1. France, M., Alizadeh, M., Brown, S., Ma, B., & Ravel, J. (2022). Towards a deeper understanding of the vaginal microbiota. Nature Microbiology, 7(3), 367-378.
2. Holm, J. B., Carter, K. A., Ravel, J., & Brotman, R. M. (2023). Lactobacillus iners and genital health: molecular clues to an enigmatic vaginal species. Current infectious disease reports, 25(4), 67-75.
3. Zheng, N., Guo, R., Wang, J., Zhou, W., & Ling, Z. (2021). Contribution of Lactobacillus iners to vaginal health and diseases: A systematic review. Frontiers in cellular and infection microbiology, 1177.
4. Ottinger, S., Robertson, C. M., Branthoover, H., & Patras, K. A. (2024). The human vaginal microbiota: from clinical medicine to models to mechanisms. Current Opinion in Microbiology, 77, 102422.
5. van de Wijgert, J. H., & Verwijs, M. C. (2020). Lactobacilli‐containing vaginal probiotics to cure or prevent bacterial or fungal vaginal dysbiosis: a systematic review and recommendations for future trial designs. BJOG: An International Journal of Obstetrics & Gynaecology, 127(2), 287-299.
6. Gudnadottir, U., Debelius, J. W., Du, J., Hugerth, L. W., Danielsson, H., Schuppe-Koistinen, I., ... & Brusselaers, N. (2022). The vaginal microbiome and the risk of preterm birth: a systematic review and network meta-analysis. Scientific reports, 12(1), 7926.
7. Pendharkar, S., Skafte-Holm, A., Simsek, G., & Haahr, T. (2023). Lactobacilli and Their Probiotic Effects in the Vagina of Reproductive Age Women. Microorganisms, 11(3), 636.
7. Das, S., Bhattacharjee, M. J., Mukherjee, A. K., & Khan, M. R. (2023). Recent advances in understanding of multifaceted changes in the vaginal microenvironment: Implications in vaginal health and therapeutics. Critical Reviews in Microbiology, 49(2), 256-282.
8. Wei, W., Xie, L. Z., Xia, Q., Fu, Y., Liu, F. Y., Ding, D. N., & Han, F. J. (2022). The role of vaginal microecology in the cervical cancer. Journal of Obstetrics and Gynaecology Research, 48(9), 2237-2254.
9. Oliveira, N. S. D., Lima, A. B. F. D., Brito, J. C. R. D., Sarmento, A. C. A., Gonçalves, A. K. S., & Eleutério Jr, J. (2022). Postmenopausal Vaginal Microbiome and Microbiota. Frontiers in Reproductive Health, 3, 780931.
10. Wu, S., Hugerth, L. W., Schuppe-Koistinen, I., & Du, J. (2022). The right bug in the right place: opportunities for bacterial vaginosis treatment. npj Biofilms and Microbiomes, 8(1), 34.
11. Lehtoranta, L., Ala-Jaakkola, R., Laitila, A., & Maukonen, J. (2022). Healthy vaginal microbiota and influence of probiotics across the female life span. Frontiers in Microbiology, 13, 819958.
12. Rosca, A. S., Castro, J., Sousa, L. G., & Cerca, N. (2020). Gardnerella and vaginal health: the truth is out there. FEMS microbiology reviews, 44(1), 73-105.
13. Das, S., Bhattacharjee, M. J., Mukherjee, A. K., & Khan, M. R. (2023). Recent advances in understanding of multifaceted changes in the vaginal microenvironment: Implications in vaginal health and therapeutics. Critical Reviews in Microbiology, 49(2), 256-282.
14. Gaziano, R., Sabbatini, S., & Monari, C. (2023). The Interplay between Candida albicans, Vaginal Mucosa, Host Immunity and Resident Microbiota in Health and Disease: An Overview and Future Perspectives. Microorganisms, 11(5), 1211. 15. Maduta, C. S., Tuffs, S. W., McCormick, J. K., & Dufresne, K. (2024). Interplay between Stap
hylococcus aureus and the vaginal microbiota. Trends in Microbiology.
16. Theis, K. R., Florova, V., Romero, R., Borisov, A. B., Winters, A. D., Galaz, J., & Gomez-Lopez, N. (2021). Sneathia: an emerging pathogen in female reproductive disease and adverse perinatal outcomes. Critical reviews in microbiology, 47(4), 517-542.
17. Brokaw, A., Furuta, A., Dacanay, M., Rajagopal, L., & Adams Waldorf, K. M. (2021). Bacterial and host determinants of group B streptococcal vaginal colonization and ascending infection in pregnancy. Frontiers in cellular and infection microbiology, 11, 720789.
18. Redelinghuys, M. J., Geldenhuys, J., Jung, H., & Kock, M. M. (2020). Bacterial vaginosis: current diagnostic avenues and future opportunities. Frontiers in cellular and infection microbiology, 10, 354.
19. Ravel, J., Moreno, I., & Simón, C. (2021). Bacterial vaginosis and its association with infertility, endometritis, and pelvic inflammatory disease. American journal of obstetrics and gynecology, 224(3), 251-257.
20. Klein, R. D., & Hultgren, S. J. (2020). Urinary tract infections: microbial pathogenesis, host–pathogen interactions and new treatment strategies. Nature Reviews Microbiology, 18(4), 211-226.
21. Schwebke, J. R., Muzny, C. A., & Josey, W. E. (2014). Role of Gardnerella vaginalis in the pathogenesis of bacterial vaginosis: a conceptual model. The Journal of infectious diseases, 210(3), 338-343.
22. Diop, K., Dufour, J. C., Levasseur, A., & Fenollar, F. (2019). Exhaustive repertoire of human vaginal microbiota. Human microbiome journal, 11, 100051.
Quellen Personalisierte Unterstützende Therapien: Mei and Li 2022, The role of probiotics in vaginal health. Front Cell Infect Microbiol12, 963868; https://doi.org/10.3389/fcimb.2022.963868 Liu et al 2023, Use of probiotic lactobacilli in the treatment of vaginal infections: In vitro and in vivo investigations, Front Cell Infect Microbiol 13, 1153894; https://doi.org/10.3389/fcimb.2023.1153894
Dong et al 2024, Characteristics of vaginal microbiota of women of reproductive age with infections, Microorganisms 12,1030; https://doi.org/10.3390/microorganisms12051030

Note: We would like to point out that the results of molecular genetic tests should always be considered and interpreted in a clinical context.

Dr. med. Martin Gencik Dr. phil. Alfred Schöller Vivien Horvath MSc

Specialist in Medical Genetics Biologist Nutrition scientist