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Microbiome diagnostics: a new approach to understanding health through bacteria
Microbiome diagnostics has become one of the most important areas of modern laboratory medicine. This method allows us to look into the world of microorganisms that live inside us and understand how they affect our health. Today, doctors are increasingly talking about the microbiome as a «"second genome"» person is the key to an individual approach to treatment, prevention, and nutrition.
What is microbiome diagnostics and how does it work?
Microbiome diagnostics is a laboratory study that determines the composition of microorganisms that inhabit various parts of the human body: the intestines, skin, oral cavity, and genitourinary system.
Unlike classic stool analysis, which detects only a small fraction of bacteria, this method uses genetic technologies — 16S rRNA sequencing or metagenomic sequencing (WGS).
According to Dr. Olena Hnatiuk, gastroenterologist of the highest category,
“Microbiome diagnostics make it possible to see not only what bacteria are present, but also how they function. It is not just an analysis, but a true «gut health map.»
Research stages:
Sample collection — usually feces, sometimes saliva or a swab.
DNA isolation from the bacteria in the sample.
Sequencing — reading unique sections of the 16S gene that differ in different types of microorganisms.
Bioinformatic analysis — computer comparison of data with international databases.
Report generation — the doctor receives a detailed map of the patient's microbiome.
What does microbiome diagnostics show?
General microflora balance: the ratio of beneficial, opportunistic, and pathogenic bacteria.
Availability bacteria that affect immunity, metabolism, digestion.
Potential ability to synthesize vitamins (B, K) and short-chain fatty acids.
Signs dysbiosis, inflammation, or decreased microbial diversity.
Level microbiota diversity (Shannon, Simpson indices).
According to Mayo Clinic (2024), a change in bacterial balance can be an early marker of conditions such as:
irritable bowel syndrome (IBS);
adiposity;
depression;
autoimmune diseases (celiac disease, Crohn's disease, rheumatoid arthritis).
Doctors' opinion on the role of the microbiome
Dr. Andriy Lozynsky, immunologist:
“The microbiome controls up to 70% of the immune system’s activity. When the balance of bacteria is disrupted, it paves the way for chronic inflammation, allergies, and even cancer.”
Dr. Marina Koval, nutritionist:
“Microbiome diagnostics help personalize nutrition. We can see which bacteria are responsible for carbohydrate or fat metabolism, and we can adjust the diet to activate the ‘beneficial’ colonies.”
Comparison with traditional stool analysis
| Criterion | Microbiome diagnostics | Classic stool culture |
|---|---|---|
| Number of species detected | 300–500 | 10–15 |
| Method | Genetic sequencing (DNA analysis) | Sowing on nutrient media |
| Precision | High, including uncultivated bacteria | Limited |
| Duration | 7–10 days | 5–7 days |
| Information about the functions of bacteria | Yes | No |
| Use in science | Active in clinical trials | Limited |
Dr. Serhiy Ivanenko, microbiologist:
“Traditional culture shows only the ‘tip of the iceberg.’ 90% microorganisms do not grow in laboratory conditions, so we simply do not see them. Genetic diagnostics has opened the door to a new dimension of medicine.”
Who is recommended to undergo microbiome testing?
Patients with digestive disorders (bloating, diarrhea, constipation).
To those who accepted antibiotics or hormonal drugs.
People from skin, autoimmune or allergic diseases.
Patients with metabolic syndrome, diabetes, obesity.
For prevention - for everyone who wants monitor the state of microflora.
Dr. Natalia Chernova, gastroenterologist:
“We see that after courses of antibiotics, the microbiome can recover for months. Diagnostics allows us to assess the extent of changes and choose the right probiotics or diet.”
Development prospects
According to the forecast WHO (2024), by 2030, microbiome diagnostics will become the standard of preventive examinations in developed countries. Already today, it is used in clinics in the USA and the EU microbiome profiling for choosing treatment for diabetes, irritable bowel syndrome, allergies and even depressive conditions.
The FDA has approved the first clinical microbiome monitoring programs as an adjunct method in assessing a patient's response to antibiotics and chemotherapy.
What the research says
Mayo Clinic (2024): people with a more diverse microflora have a lower risk of obesity and chronic inflammation.
Harvard Health Review (2023): restoration of the microbiome after antibiotics through probiotics or fermented foods reduces the risk of intestinal disorders by 40%.
WHO: Microbiome analysis allows for personalized treatment, instead of universal regimens.
Microbiome as part of personalized medicine
Microbiome diagnostics already allows us to create «"individual health profiles"», taking into account genetics, eating habits and microflora.
The doctor can see which bacteria predominate in the patient, how they affect metabolism, and what needs to be changed — diet, lifestyle, probiotic support.
As he says Dr. Hnatiuk,
“Microbiome — it’s not just bacteria. It’s an intelligent system that responds to our emotions, nutrition, and stress. And microbiome diagnostics is a mirror of our internal state.”
Sources
World Health Organization (WHO). Human Microbiome and Precision Health Report, 2024.
Mayo Clinic. Microbiome Diagnostics and Personalized Medicine Overview, 2024.
FDA. Genomic and Metagenomic Diagnostics in Clinical Practice, 2023.
Harvard Health Review. Gut Microbiota and Modern Health, 2023.
