Gut and microbiome tests: metrics, methodology & scientific basis
A microbiome test analyzes the composition of intestinal bacteria from a stool sample—for example, their diversity, the ratio of different bacterial groups, and indications of dysbiosis. It describes the current state of the intestinal environment but does not provide a diagnosis. “Leaky gut” is a scientifically discussed concept, not an established independent finding. Abnormal results should be medically evaluated.
What gut/microbiome tests are scientifically about
The gut microbiome is the totality of the trillions of microorganisms in the intestine. The Human Microbiome Project showed that the composition varies considerably among healthy people and that there is no single “normal” microbiome [1]. A microbiome test determines which bacterial groups are present and in what proportions, and derives metrics such as bacterial diversity or indications of an imbalance (dysbiosis) from this.
Research links the composition of the microbiome to diet, metabolism, and immune function [2]. For example, bacteria produce short-chain fatty acids such as butyrate from dietary fiber, which are important for the intestinal lining [4]. Such relationships are predominantly associative—they show patterns, but rarely establish clear cause-and-effect chains for individuals.
This page explains which metrics a microbiome test provides, which studies its classification is based on, how the stool sample is processed, and—equally important—where the limitations lie. Professional medical societies have so far taken a cautious view of the clinical significance of such tests [6].
Analyzed metrics at a glance
| Metric | What it describes | Why it matters | Classification (probabilistic) | Source |
|---|---|---|---|---|
| Bacterial diversity (diversity) | How many different bacterial species are present and how evenly balanced they are. | Higher diversity is often linked in studies to stability of the intestinal environment. | An orientation value, not a health score; “more” is not automatically “better.” | HMP 2012 [1] |
| Enterotype | Classification according to dominant bacterial groups. | Describes broad microbiome patterns across populations. | Enterotypes are tendencies rather than sharply defined categories. | Arumugam 2011 [3] |
| Dysbiosis | Ratio of bacteria that are considered more protective to those considered more burdensome. | An imbalance has been associated with various symptoms. | Associative, not diagnostic; a pattern, not evidence of disease. | Valdes 2018 [2] |
| Short-chain fatty acids (SCFA producers) | Proportion of bacteria that, for example, produce butyrate from dietary fiber. | SCFAs are relevant to providing energy for the intestinal lining. | Derived from the bacterial composition; no direct SCFA measurement. | Koh 2016 [4] |
| Intestinal Mucosa & Barrier | Marker bacteria associated with mucosal/barrier function. | Related to the scientifically debated topic of intestinal permeability. | The test measures composition, not the permeability of the barrier directly. | Fasano 2011 [5] |
| FODMAP & Metabolism Indices | Functional inferences related to utilization and the intestinal environment. | Intended to provide guidance for dietary adjustments. | Computational interpretations; should be reviewed individually with qualified professionals. | Valdes 2018 [2] |
According to the provider, the Complete test detects over 1,500 bacterial species and several functional areas. All metrics are statistical classifications based on microbiome research and are not individual diagnoses.
The Metrics in Detail
Bacterial Diversity
Diversity describes how many bacterial species are present and how evenly they are distributed. The Human Microbiome Project showed that healthy people have very different but functionally similar microbiomes [1]. Low diversity is linked to unfavorable patterns in some studies—however, a single diversity value is not a health assessment.
Enterotypes
Arumugam and colleagues described how microbiomes can be broadly grouped according to dominant genera (enterotypes) [3]. This classification helps categorize patterns, but is not a rigid pigeonhole system: transitions are fluid and influenced by diet and lifestyle.
Dysbiosis
Dysbiosis refers to an imbalance between relatively beneficial and relatively unfavorable bacterial groups. Reviews associate dysbiosis patterns with diet and various symptom profiles [2]. Important: Such a pattern is an association, not evidence of disease and not an indication for treatment.
Short-Chain Fatty Acids (SCFAs) and Energy Metabolism
Gut bacteria produce short-chain fatty acids (SCFAs) such as butyrate, acetate, and propionate from dietary fiber. Butyrate is an important energy source for intestinal lining cells [4]. The test estimates the potential based on the SCFA-producing bacteria present; it does not measure the fatty acids directly.
Intestinal Barrier and “Leaky Gut”
The term “Leaky Gut” (increased intestinal permeability) describes increased permeability of the intestinal barrier. The concept and the possible messenger molecule zonulin are scientifically debated [5], but have not been conclusively recognized as an independent disease. The microbiome test assesses the composition of bacteria associated with barrier function—it does not measure permeability directly.
Privacy, Methodology & Quality
Data protection & data processing: Protecting your data is our top priority. Under the General Data Protection Regulation (GDPR), health data belongs to the specially protected categories of personal data (Article 9 GDPR). At mybody®, it is processed for a specific purpose—solely to perform and analyze your test—and on the basis of your consent. It is not processed further for other purposes without your consent.
Information security is organized according to ISO/IEC 27001, the internationally recognized standard for information security management systems. Your data is transmitted and stored in encrypted form. You have the data subject rights under the GDPR, particularly the rights to access, rectify, and erase your data. Details concerning storage duration, processing, and your rights are set out in the privacy policy.
The sample is collected at home as a stool sample. Bacterial DNA is extracted from the sample and analyzed by DNA sequencing; the composition and derived metrics are then calculated. Microbiome profiles of this kind are generally based on sequencing the bacterial 16S rRNA gene.
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Collecting the stool sample
At home using the test kit and return envelope.
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Return shipping
Free return shipping to the analysis laboratory.
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DNA sequencing
DNA extraction and sequencing of the bacterial DNA.
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Bioinformatics
Analysis and comparison with reference data.
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Result
Report preparation; 5–10 business days after receipt of the sample.
Laboratory & accreditation: The analysis is performed at the medical laboratory MVZ GANZIMMUN GmbH (Mainz) using DNA sequencing; the laboratory is accredited according to DIN EN ISO 15189:2024 (DAkkS registration number D-ML-13151-01-00) [8]. It participates in external proficiency testing programs, including INSTAND e.V., Referenzinstitut für Bioanalytik/RfB, UK NEQAS, and ERNDIM. The term accredited (technical and professional competence assessment according to DIN EN ISO 15189 by DAkkS) must be distinguished from certified (management system, e.g. ISO/IEC 27001) [7].
What these tests cannot do
- Not a diagnosis. A microbiome test describes a composition; it does not identify a disease and does not replace medical diagnosis.
- High variability. The microbiome changes with diet, medication, and time. Results are a snapshot and reproducibility varies depending on the method.
- “Leaky gut syndrome” is not an established diagnosis. The concept is being researched; a composition-based test cannot prove increased intestinal permeability.
- Cautious professional assessment. International professional bodies currently consider the clinical use of microbiome tests to be limited [6]; recommendations based on them should be interpreted cautiously.
- When medical evaluation is necessary. Blood in the stool, unintentional weight loss, or persistent or severe symptoms should be evaluated by a doctor—not with a self-test.
Frequently asked questions
Do I need to do anything before collecting the stool sample?
For a meaningful result, the sample should be collected according to the instructions. Recent antibiotic use, acute diarrhea, or a significantly changed diet can temporarily alter the microbiome. It is best to note such circumstances and take them into account when interpreting the report.
What is dysbiosis?
Dysbiosis refers to an imbalance between bacterial groups considered more beneficial and those considered less beneficial in the gut. Such patterns have been associated with diet and symptoms in studies. An indication of dysbiosis is an association, not evidence of a disease.
Can a microbiome test diagnose diseases?
No. The test describes the composition of the gut microbiome but does not provide a diagnosis. Intestinal diseases are evaluated by a doctor, for example through medical history, blood, stool, or endoscopic examinations. At most, the test can provide points of reference for a discussion.
What does “leaky gut” mean—and does the test measure it?
“Leaky gut” refers to increased permeability of the intestinal barrier. The concept is scientifically debated but is not recognized as an independent disease. The microbiome test assesses the bacterial composition associated with the barrier; it does not directly measure permeability itself.
How reliable and reproducible are stool microbiome tests?
The results depend on sample collection, timing, diet, and the analysis method and may vary. Professional societies have so far taken a cautious view of the clinical significance of direct-to-consumer tests. At present, they are only of limited suitability for a reliable medical assessment.
What are enterotypes?
Enterotypes are a broad classification of microbiomes based on the dominant bacterial groups. They help describe patterns across populations. The boundaries between types are fluid and are influenced by diet and lifestyle.
How is the sample collected, and how long does it take?
The stool sample is collected at home using the test kit and sent back to the laboratory free of charge. After the sample arrives, analysis usually takes 5–10 business days; the report is then made available in the online portal. The exact timeframe is stated on the product page.
How is my data protected?
Processing is GDPR-compliant; the information security management system is established in accordance with ISO/IEC 27001. Health data is encrypted during transmission and storage. Details are governed by the provider’s privacy policy.
Sources
- Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486:207–214. PubMed
- Valdes AM, Walter J, Segal E, Spector TD. Role of the gut microbiota in nutrition and health. BMJ 2018;361:k2179. PMC
- Arumugam M et al. Enterotypes of the human gut microbiome. Nature 2011;473:174–180. Nature
- Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 2016;165(6):1332–1345. PubMed
- Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev 2011;91(1):151–175. Physiological Reviews
- Cammarota G et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol 2024. PMC
- DAkkS – Medical laboratories / DIN EN ISO 15189 (accreditation explanation). dakks.de
- MVZ GANZIMMUN GmbH. Quality management – accreditation according to DIN EN ISO 15189:2024 (DAkkS D-ML-13151-01-00). ganzimmun.de
Suitable gut & microbiome tests
From the compact basic gut flora check to the comprehensive Complete analysis.
Would you like to learn more about our tests? Feel free to contact us :)!
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