Digestive Diseases and Sciences

, Volume 63, Issue 12, pp 3167–3177 | Cite as

Clinician Guide to Microbiome Testing

  • Christopher StaleyEmail author
  • Thomas Kaiser
  • Alexander Khoruts
Invited Review


Recent recognition that the intestinal microbiome plays potential roles in the pathogenesis of multiple common diseases has led to a growing interest in personalized microbiome analysis among clinical investigators and patients. Permissibility of direct access testing has allowed the emergence of commercial companies offering microbiome analysis to patients seeking to gain a better understanding of their symptoms and disease conditions. In turn, physicians are often asked to help with interpretation of such tests or even requested by their patients to order them. Therefore, physicians need to have a basic understanding of the current state of microbiome science. This review examines how the perspective of microbial ecology, which is fundamental to understanding the microbiome, updates the classical version of the germ theory of disease. We provide the essential vocabulary of microbiome science and describe its current limitations. We look forward to the future when microbiome diagnostics may live up to its potential of becoming integral to clinical care that will become increasingly individualized, and microbiome analysis may become incorporated into that future paradigm. However, we caution patients and providers that the current microbiome tests, given the state of knowledge and technology, do not provide much value in clinical decisions. Considerable research remains to be carried out to make this objective a reality.


Bacteria Community Disease Dysbiosis Microbiome Next-generation sequencing 


Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of SurgeryUniversity of MinnesotaMinneapolisUSA
  2. 2.Biotechnology InstituteUniversity of MinnesotaSt. PaulUSA
  3. 3.Division of Gastroenterology, Department of MedicineUniversity of MinnesotaMinneapolisUSA

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