Saliva Template Microbiome Report

Percentage of Fusobacteria in the microbiome: good

Fusobacteriea = 4.903
The proportion of fusobacteria is in the 75% of the reference population.

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 bar ranges are based on the reference population.

Detected Fusobacteria strains

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

Phyla associated with poor oral health

Percentage of Proteobacteria in the total microbiome: good

Proteobacteria = 10.466

Proteobacteria were found in the measurement range of 75 % of the total population.

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.

Detected Proteobacteria species

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

Types of bar chart

Coloured horizontal stripes represent the relative distribution of bacterial species.

Stacked bar chart of bacterial 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 gwangjuense: 53.93%

Probably commensal

Streptococcus gwangjuense is similar to S. mitis, a bacterium commonly found in the oral microbiota. It plays a role in the early formation of dental plaque and is generally considered benign, although it can be involved in the development of caries when the balance of oral bacteria is disturbed.

Neisseria sicca: 8.01%

Potentially pathogenic

It is assumed that Neisseria sicca promotes the formation and growth of biofilms in the oral cavity.

Streptococcus sanguinis: 5.53%

Probably commensal

Streptococcus sanguinis is a commensal organism in the oral cavity that can become pathogenic under certain conditions.

Streptococcus oralis: 4.12%

Probably commensal

Streptococcus oralis is a commensal organism in the oral cavity that can become pathogenic under certain conditions.

Fusobacterium nucleatum: 3.76%

Potentially pathogenic

Fusobacterium nucleatum is an important bacterial species in dental plaque and is frequently associated with periodontal disease; it can act as a bridge between early and late colonisers in dental biofilms and promote the attachment of other pathogenic bacteria; it is involved in the formation of dental plaque and plays a role in disease progression.

Streptomyces lasalocidi: 2.27%

Rare bacterium

The significance of Streptomyces lasalocidi 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/orange 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, comparatively better than most samples'

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

Target Plot - The colour 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 Target Plot

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 cluster in the centre of the diagram.

Four-dimensional principle component 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 list total microbiome

List of all species in the sample and their relative proportion in percent

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

General report information

Interpretation

In the examined microbiome, two fundamental microbiome parameters (microbiome resilience and microbiome species evenness) are outside the range of 75% of the population. Two potential pathogens among the six most abundant bacteria were detected. The dominant species is Streptococcus gwangjuense (54%), which is associated with pericoronitis.

Personalized Supportive Therapies

1. General dental therapy approaches:
Professional dental cleaning (PDC): Removes subgingival plaques and tartar to reduce the number of bacteria, especially Fusobacterium nucleatum and other biofilm formers. Scaling and Root Planing (SRP): Deep cleaning of root surfaces to remove colonies of pathogenic bacteria.

2. Antibiotic therapy
Topical antibiotics: Application of chlorhexidine gel or antibacterial rinses in periodontal pockets to combat anaerobic bacteria like Fusobacterium nucleatum. Systemic antibiotics: In severe cases, especially if Fusobacterium nucleatum or other highly inflammatory species are involved, amoxicillin in combination with metronidazole or doxycycline may be prescribed.

3. Specific bacteria management approaches
Streptococcus gwangjuense (53.93%): Such a high relative abundance of Streptococcus gwangjuense indicates possible dysbiosis. However, specific scientific studies describing the role of this bacterium in the oral microbiome are lacking. A microbial imbalance with the dominance of a single bacterium can increase the risk of oral diseases. Therapy should aim to promote the diversity of the oral microbiome. This can be achieved through the regular use of probiotic toothpastes containing Lactobacillus and Bifidobacterium. In addition, consistent mechanical cleaning of teeth and tongue is necessary to limit the overgrowth of this bacterium.

Neisseria sicca (8.01%): Neisseria sicca is an opportunistic bacterium that can develop pathogenic properties under dysbiotic conditions. It is often associated with mild inflammatory processes in the oral cavity. Treatment should include antibacterial mouthwashes with agents such as chlorhexidine or cetylpyridinium chloride to reduce bacterial load.

Fusobacterium nucleatum (3.76%): Fusobacterium nucleatum is a key organism that plays a significant role in periodontitis. It contributes to biofilm formation and is known for its involvement in inflammatory processes. Therapy can include systemic antibiotics such as metronidazole to reduce bacterial burden. Complementary laser therapy can specifically reduce anaerobic bacteria and sustainably alleviate inflammation.

Pseudoprevotella muciniphila (1.01%): The role of Pseudoprevotella muciniphila in the oral cavity is not well-researched. However, there is evidence that it may be associated with inflammatory processes. Promoting a healthy oral microbiome is important to support probiotic bacteria that can displace potentially pathogenic species such as Pseudoprevotella muciniphila. This can be achieved through the use of probiotic oral care products and balanced oral hygiene.

4. Probiotics and oral microbiome rebalancing
Probiotic bacteria such as Lactobacillus reuteri and Bifidobacterium play a significant role in restoring a healthy oral microbiota. Studies show that they inhibit the colonization of pathogenic bacteria while promoting the growth of beneficial bacteria. This can be particularly helpful for individuals with dysbiosis in the oral microbiome. In addition, a prebiotic toothpaste can be used to specifically support the growth of beneficial bacteria and promote long-term oral health.

5. Diet and lifestyle
Reduction in sugar intake: A significant reduction in sugar consumption inhibits the growth of cariogenic bacteria such as Streptococcus sanguinis and Streptococcus oralis. Sugar serves as a substrate for these bacteria to produce acid, which promotes the development of cavities. Increase in fiber intake: Fiber not only promotes gastrointestinal health but also helps support a stable and healthy oral microbiota. Its prebiotic effects promote the growth of beneficial bacteria in both the mouth and the gut.

6. Specific methods for oral hygiene
Toothpaste with fluoride and antibacterial additives: Toothpaste containing fluoride and antimicrobial agents such as stannous fluoride has been shown to effectively reduce pathogenic bacteria, including Streptococcus sanguinis and other streptococci.
Antimicrobial mouthwashes: Mouthwashes containing antimicrobial agents, such as essential oils or stannous fluoride, have proven effective in reducing bacterial loads in the oral cavity and mitigating inflammation.

Summary
The goal is to restore microbial balance in the oral cavity by controlling inflammation-promoting bacteria such as Fusobacterium nucleatum and promoting beneficial bacteria. Alongside regular dental care, targeted measures such as the use of probiotic preparations, dietary control, and the application of antimicrobial oral care products are essential.

Material

OMNIGENE Oral OMR-110
Localisation: Dental pocket
Description: Dental microbiome sample

Methods

The swab sample was stabilised with DNA/RNA Shield liquid for transport to the laboratory. 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

Basic Literature References

Literature used for the preparation of the report and conclusions.

1. Morrison, A. G., Sarkar, S., Umar, S., Lee, S. T. M. & Thomas, S. M. The Contribution of the Human Oral Microbiome to Oral Disease: A Review. Microorganisms 11, 1–17 (2023).
2. Zhang, X. et al. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment. Nat. Med. 21, 895–905 (2015).
3. Dhotre, S. et al. Assessment of periodontitis and its role in viridans streptococcal bacteremia and infective endocarditis. Indian Heart J. 70, 225–232 (2018).
4. Maki, K. A. et al. The role of the oral microbiome in smoking-related cardiovascular risk: a review of the literature exploring mechanisms and pathways. J. Transl. Med. 20, 1–26 (2022).
5. Pathak, J. L., Yan, Y., Zhang, Q., Wang, L. & Ge, L. The role of oral microbiome in respiratory health and diseases. Respir. Med. 185, 106475 (2021).
6. Imai, J., Kitamoto, S. & Kamada, N. The pathogenic oral–gut–liver axis: new understandings and clinical implications. Expert Rev. Clin. Immunol. 17, 727–736 (2021).
7. Ahn, J., Chen, C. Y. & Hayes, R. B. Oral microbiome and oral and gastrointestinal cancer risk. Cancer Causes Control 23, 399–404 (2012).
8. Teles, F. R. F., Alawi, F., Castilho, R. M. & Wang, Y. Association or Causation? Exploring the Oral Microbiome and Cancer Links. J. Dent. Res. 99, 1411–1424 (2020).
9. Park et al. 2019, Streptococcus gwangjuense sp. nov., Isolated from human pericoronitis, Curr Microbiol 76, 799-803. https://doi.org/10.1007/s00284-019-01687-8 10. Figuero, E., et al. 2020. Effect of probiotics in periodontal diseases: A systematic review. Journal of Clinical Periodontology, 47(5), 641-661.

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