Analyses of intestinal microbiome – commercially available, but to be used with caution in hospitals

02.2026
Author Dr. Martin Claßen, Bremen

We have learnt more and more in recent years about the huge importance of the microbiome in terms of health and risks of disease – not just for bowel diseases but also for psychic, metabolic and immunological disorders. New methods of analysing the microbiome without cultures have helped to increase our knowledge, with gene analyses of the gut bacteria which have been enabled by enhanced data processing capacities. On that basis, it would seem obvious to integrate these methods into everyday patient care.

However, a recent consensus paper published in the renowned magazine “The Lancet” by an international group of researchers has shown that these analyses should only be carried out under certain circumstances.

The paper addressed five areas:

  1. General principles and minimum requirements for diagnostic testing
  2. Procedural steps before testing
  3. Conducting microbiome analysis
  4. Characteristics of reports
  5. Relevance of microbiome testing in clinical practice

I think the following recommendations are particularly important:

  • No testing merely by patient request without a medical reason.
  • Contamination should be avoided when collecting and sending samples.
  • Amplicon sequencing or whole genome sequencing should be the preferred methods, and not methods based on cultures or PCR.
  • The results should include data on diversity and comparisons with healthy cohorts.
  • An analysis of the microbial metabolites (“metabolome”) and indication of a dysbiosis index are not recommended.
  • The laboratory should not make any direct treatment recommendations based on the findings.
  • Microbiome analyses are not a necessary part of routine patient care.

For details, see the paper.

Comment: Intestinal microbiome analyses are very exciting from a scientific point of view, and there is no doubt that they will play a key role in future in enhancing our understanding of various diseases. Intervention studies with faecal microbiota transfer (FMT) will also contribute to this. However, in terms of diagnosing dysbiosis or disorders of the intestinal microbiome, the ability to translate this theoretical knowledge into clinical practice has not yet been sufficiently demonstrated. The consensus paper presented here explains this in detail and warns against requesting this kind of analysis without a clear clinical indication. In addition, the lack of standard values for different age and population groups means there are no reference values against which to compare findings. It is relatively expensive to use commercial laboratories. I would currently recommend exercising the same caution reflected in this consensus paper if parents have questions about this.

The best summary of the problems with using microbiome analyses comes from this sentence in the paper: 

“Despite this enthusiasm, the application of gut microbiome research in clinical practice remains minimal because of a number of factors, including the complexity of the microbiota and associated sequencing datasets, the difficulties in disentangling correlation from causation, the reliance on pre-clinical models with low generalisability to humans, the limited knowledge most clinicians have about this field, the absence of any validated test to enable therapeutic follow-up, and the absence of established regulations and framework for the clinical translation of this research.”

However, it is an exciting area, and this assessment will probably be revised in five years’ time.

Reference:
Porcari S, Mullish BH, Asnicar F et al. International consensus statement on microbiome testing in clinical practice. Lancet Gastroenterol Hepatol. 2025 Feb;10(2):154-167. Epub 2024 Dec 5. PMID: 39647502; PMCID: PMC12343204. DOI: 10.1016/S2468-1253(24)00311-X