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Marker Guide

Oral species

What this marker measures

The presence of oral-origin bacteria detected within the gut microbiome. These species are normal residents of the mouth but elevated levels in the gut may indicate increased oral-to-gut transfer and colonisation. This pattern has been associated with intestinal inflammation, proton pump inhibitor use, poor oral or periodontal health, and reduced microbial load1–7.

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Clinical associations

Consider this marker when your patient presents with:

Oral or periodontal concerns
Known or suspected periodontitis, gingivitis, dental plaque burden, or poor oral hygiene
Medication use
Current or recent proton pump inhibitor (PPI) use
Gut inflammation
Intestinal inflammation, IBD-type context, or persistent GI symptoms where oral-to-gut transfer may be relevant.

Interpreting the result

All results are compared to Microba's healthy cohort to determine whether they fall within or outside the expected range.

LOW
Oral-origin species detected at lower  than expected
This result does not suggest elevated oral-to-gut microbial transfer via this marker.No intervention needed for this marker.
Within Range
Oral-origin species detected is within expected parameters
Interpret alongside dental health, PPI use, symptoms, and inflammatory context.
HIGH
Oral-origin species detected at higher  than expected
May suggest increased oral-to-gut microbial transfer or persistence and may be relevant in the context of intestinal inflammation, PPI use, or oral health concerns.Action: see patient management insights below.

Patient management insights

Reduce oral species colonisation of the gut through dental and dietary intervention.

Dental health
If gum disease is present, periodontal treatment by a dental professional may help reduce oral species in the gut.8,9GRADE C 
Dietary strategies
Increasing intake of fermentable dietary fibre may support increased faecal microbial load.10
GRADE D
Lifestyle factors
A combination of high DHA fish oil and probiotic strains B. animalis ssp lactis 420 and L. rhamnosus HN001 may decrease oral-origin species in pregnant women with BMI ≥2511.
GRADE D

Tips for patients discussion

Your report shows higher-than-expected levels of bacteria in the gut that usually live in the mouth. This may relate to oral health, gum inflammation, reduced stomach acidity, or gut environment changes. Addressing oral health and supporting a fibre-rich diet are key steps.

The community

Oral-origin species are defined by the Human Oral Microbiome Database. Here are some of the most commonly-detected specie, howeverthis list is not exhaustive.

  • Dialister invisus
  • Fusobacterium animalis
  • Haemophilus_D parainfluenzae
  • Haemophilus_D parainfluenzae_K
  • Haemophilus_D parainfluenzae_L
  • Haemophilus_D parainfluenzae_M
  • Haemophilus_D sp001679485
  • Haemophilus_D sp001815355
  • Pauljensenia bouchesdurhonensis
  • Pauljensenia sp000278725
  • Pauljensenia sp000466265
  • Streptococcus anginosus
  • Streptococcus anginosus_C
  • Streptococcus MIC7033
  • Streptococcus mutans
  • Streptococcus parasanguinis_B
  • Streptococcus salivarius
  • Streptococcus sp000479315
  • Streptococcus sp001556435
  • Streptococcus sp001587175
  • Veillonella atypica
  • Veillonella dispar_A
  • Veillonella parvula_A
  • UBA1417 sp003531055

How results are calculated

All microbiome marker results are compared against the Microba Healthy Cohort — a purpose-built reference group of more than 450 healthy individuals, collected and analysed using the same workflow as patient samples.

Each marker is scored by comparing the patient's relative abundance against the cohort average. The distance from this average is expressed as standard deviations, and determines whether a result is classified as Low, Borderline, or High.

How the result scale works
▲ AVG (Healthy Cohort average)
The patient's relative abundance is compared to the Healthy Cohort average. A negative distance from average means the microbial group is less abundant than the Healthy Cohort. A positive distance means it is more abundant. Results falling outside the expected range are classified as borderline or high/low  (borderline high/low:+/-0.68,andhigh/low:+/-1.28).
Evidence grading for patient management insights
The letter grades shown next to each patient management insight show the quality of the research behind it. Every insight provided has been through a rigorous review of the scientific literature and graded using the NHMRC Levels of Evidence, so you can see exactly how strong the evidence is before applying it in practice.

Source references for all clinical associations, interpretation definitions, and patient management insights on this card.

1. Peter Rimmer et al. The Gut Microbiome at the Onset of Inflammatory Bowel Disease: A Systematic Review and Unified Bioinformatic Synthesis. Gastroenterology 170, 539–556 (2026).
2. Nishijima, S. et al. Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations. Cell 188, 222-236.e15 (2025).
3. Xiao, X. et al. Proton pump inhibitors alter gut microbiota by promoting oral microbiota translocation: a prospective interventional study. https://doi.org/10.1136/gutjnl-2023-330883 (2024) doi:10.1136/gutjnl-2023-330883.
4. Kageyama, S. et al. High-Resolution Detection of Translocation of Oral Bacteria to the Gut. J Dent Res 102, 752–758 (2023).
5. Bao, J. et al. Periodontitis may induce gut microbiota dysbiosis via salivary microbiota. Int J Oral Sci 14, 1–11 (2022).
6. Imhann, F. et al. Proton pump inhibitors affect the gut microbiome. Gut 65, 740–748 (2016).
7. Zhernakova, A. et al. Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science 352, 565–569 (2016).
8. Baima, G. et al. Effect of Periodontitis and Periodontal Therapy on Oral and Gut Microbiota. J Dent Res 103, 359–368 (2024).
9. Bajaj, J. S. et al. Periodontal therapy favorably modulates the oral-gut-hepatic axis in cirrhosis. American Journal of Physiology-Gastrointestinal and Liver Physiology 315, G824–G837 (2018).
10. Ghetti, F. D. F. et al. Effects of Dietary Intervention on Gut Microbiota and Metabolic-Nutritional Profile of Outpatients with Non-Alcoholic Steatohepatitis: a Randomized Clinical Trial. J Gastrointestin Liver Dis 28, 279–287 (2019).
11. Mokkala, K. et al. Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial. https://doi.org/10.1136/gutjnl-2020-321643 (2021) doi:10.1136/gutjnl-2020-321643.

© Copyright 2025 Microba Life Sciences
THESE PRODUCTS ARE ONLY AVAILABLE FOR PURCHASE THROUGH A HEALTHCARE PROFESSIONAL.
1.The quantitative faecal occult blood, polymerase chain reaction (qPCR) and enzyme-linked immunosorbent assays (ELISA) used in the Microbiome Explorer range are diagnostic and are approved for clinical use.
2.The faeces pH assay used in the Microbiome Explorer range is for research use only and not to be used as a basis for diagnosis. The metagenomic assays used in the Microbiome Explorer range are to determine the microbiome populations and associated functional pathways in a faecal sample. The application is for research use only and not to be used as a basis for diagnosis. Learn more about the journey we are on to validate this gold-standard technology for clinical diagnosis and application.
3. The Microbiome Explorer range is intended for adults 18 years or older only.

Disclaimer:
The information provided on this site is for the use of qualified healthcare professionals. The information contained on this website is in no way to be taken as prescriptive or to replace the healthcare professionals duty of care and personalised care practices.