Using the Microbiome to Diagnose Disease

By Ross Pelton, RPh, PhD, CCN
Scientific Director, Essential Formulas

New genome sequencing technologies are enabling microbiome science to undergo swift advancement. Numerous studies have reported differences in the microbiome between healthy individuals and people with various health problems such as obesityi, metabolic syndromeii, clostridium difficile infectionsiii, and anxiety and depressioniv.

Microbiome-Based Diagnostics

Exciting new studies are being published, which report that analysis of the microbiome can accurately diagnose diseases. Although microbiome-based diagnostics is still in its infancy, the fact that several studies have utilized microbiome analysis to accurately diagnose diseases heralds an exciting new frontier for microbiome science and the practice of medicine.

Microbiome Diagnoses IBS with 80% accuracy: Irritable bowel syndrome (IBS) is an intestinal tract disorder estimated to affect 20% of the world’s populationv,vi and account for about 12% of office visits to primary care physicians and up to 40% of gastroenterologists’ referrals.vii

Researchers in a recently published study explored the associations between abdominal pain and the gut microbiome in preadolescent children diagnosed with IBS. By analyzing features of microbiome bacteria and postbiotic metabolites in IBS patients, the scientists were able to diagnose children with IBS with a remarkable 80% accuracy.viii

Microbiome in Critical Illness: Physicians are increasingly examining the microbiome’s role in patients with critical illnesses such as sepsis and acute respiratory failure. In a study published in the Journal of Critical Care, researchers evaluated 51 critical illness-microbiome studies in animals and pediatric and adult critically ill patients. The results suggested that the microbiome analysis may enable physicians to diagnose and treat acute care infections more precisely and effectively. From a longer-term perspective, the study’s authors suggested that microbiome analysis may transform critical care treatment from its current isolated focus on the patient to a more integrated personalized approach. This approach addresses how the patient’s condition and microbiome condition contribute to their critical illness.ix

Microbiome Diagnosis of Skin Health: Research into the skin microbiome is relatively new compared to the decades of research into the gut and stool microbiome. However, it is well established that the human skin microbiome plays an intimate role in skin health and skin diseases.x

In a recent study, scientists conducted a three-city (two Chinese and one American) comparison of the skin microbiome from children with atopic dermatitis with healthy pediatric controls. Atopic dermatitis is a highly inflammatory skin condition that is also known as eczema. The results revealed that a microbial index of skin health, which was based on assessing the presence of 25 types of skin bacteria, was able to diagnose atopic dermatitis with an accuracy ranging from 83 to 95% within each city, and with 86.4% accuracy when skin samples from children from all three cities were combined.xi

The Microbiome—A Revolution in Healthcare: The studies reviewed in this article indicate that the human microbiome can help diagnose some diseases. Exponential advancements in genetic sequencing technologies and microbiome science set the stage for the human microbiome to play a significant role in a revolution in healthcare and medicine. This will usher in a new era of personalized medicine and personalized healthcare because knowledge of an individual’s microbiome will help prevent, diagnose, and treat illnesses.


i Maruvada P, et al. The Human Microbiome and Obesity: Moving beyond Associations. Cell Host Microb. 2017 Nov 8;22(5):589-599.
ii Dabke K, et al. The gut microbiome and metabolic syndrome. J Clin Invest. 2019 Oct 1;129(10):4050-4057.
iii Chen LA, et al. Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile
iv Lach G, et al. Anxiety, Depression, and the Microbiome: A Role for Gut Peptides. Neurotherapeutics. 2018 Jan;15(1):36-59.
v Rasquin A, et al. Childhood functional gastrointestinal disorders: child/adolescent. Gastroenterology. 2006; 130: 1527-1537.
vi Quibley EM, et al. A global perspective on irritable bowel syndrome: a consensus statement of the World Gastroenterology Organization Summit Task Force on irritable bowel syndrome. J Clin Gastroenterol. 2012; 46: 356-366.
vii Zaman A. Irritable bowel syndrome. Clin Cornerstone. 2002;4(4):22-33.
viii Hollister EB, et al. Leveraging Human Microbiome Features to Diagnose and Stratify Children with Irritable Bowel Syndrome. J Mol Diagnostics. 2019 May 1;21(3):449-461.
ix Kitsios G, et al. Dysbiosis in the intensive care unit: Microbiome science coming to the bedside. J Crit Care. 2017 Apr;38:84-91.
x Dreno B, et al. Microbiome in healthy skin, update for dermatologists. J Eur Acad Dermatol Venerol. 2016 Dec;30(12):2038-2047.
xi Sun Z, et al. A Microbiome-Based Index for Assessing Skin Health and Treatment Effects for Atopic Dermatitis in Children. mSystems. 2019 Aug 20;4(4):e00293-19.