Is there a medical test that can detect the health of gut flora?

No, microbiota research is still far too preliminary to be able to predictably define what healthy gut microbiota entails. OTOH, presence of certain microbes in gut microflora usually signals sign of ill-health. Illustrative examples are superbugs and Clostridium difficile. Gut microflora disturbances can also be indirectly gauged using tests for increased intestinal permeability and through breath tests. Such tests are still only suggestive, not confirmatory.


Colloquially called ‘superbugs’, presence in the GI tract of multi-drug resistant microbes (Antimicrobial resistance – Wikipedia) such as KPC (Klebsiella pneumoniae carbapenemase-producing K. pneumoniae) (1) and Vancomycin-resistant Enterococcus – Wikipedia (2) could signal ill-health. Not foolproof though since healthy immune systems can keep such microbes at bay. However, they become a problem during immunodeficiency, in the elderly, and the like.

Clostridium difficile (bacteria) – Wikipedia

Apart from its propensity to cause infection, Clostridium difficile infection – Wikipedia (CDI), presence of Clostridium difficile in human gut flora is usually a sign of something having gone awry. Rather than a normal gut flora inhabitant, C. difficile is opportunistic (3, 4) and usually establishes residence when gut microbiota niches become depleted or vacant. This can happen after antibiotics which indiscriminately wipe out various components of the normal gut microflora, leaving vacant niches that are then exploited by opportunists like C.difficile.

In fact, CDI risk correlates with recent antibiotic Rx, especially Clindamycin – Wikipedia and third generation Cephalosporin – Wikipedia (5, 6). In contrast, healthy gut microflora manifest Colonization resistance – Wikipedia, which prevents colonization by harmful microbes (7, 8).

Serum Zonulin Levels : Test For Increased Intestinal Permeability

Assessing GI tract permeability indirectly assesses its health. The healthy intestinal epithelium functions as an effective physical barrier keeping pathogens out. When this functionality is impaired, it can be read out in the form of increased blood concentration of certain protein components involved in maintaining intestinal permeability. One of the best studied examples is Zonulin – Wikipedia, whose increased presence in serum correlates with increased intestinal permeability (9, 10, 11, 12, 13).

Breath test – Wikipedia (BT)

BTs are a very convenient, non-invasive approach to test for GI tract disturbances such as SIBO (Small intestinal bacterial overgrowth – Wikipedia). A typical BT measures hydrogen in the breath, the rationale being that colon-resident anaerobes are the usual hydrogen producers in the GI tract. Thus, disproportionate hydrogen in the breath signals presence of colonic bacteria in the small intestine, i.e., SIBO. Breath methane levels correlate with degree of constipation (14) and may be useful for IBS (Irritable bowel syndrome – Wikipedia) diagnosis (15).

Problem with BTs is lack of standardization and false positives are all too common. For example, a systematic review (16) of 13 Case-control study – Wikipedia found they ‘used 13 different methodologies to conduct the breath test or interpret the results‘ (17).


1. Tirumalai Kamala’s answer to Are infections frequent during routine surgeries?

2. Ubeda, Carles, et al. “Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans.” The Journal of clinical investigation 120.12 (2010): 4332-4341. JCI – Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

3. Wilson, Kenneth H. “The microecology of Clostridium difficile.” Clinical Infectious Diseases 16.Supplement 4 (1993): S214-S218.…

4. Karen C, Carroll, and Bartlett John G. “Biology of Clostridium difficile: implications for epidemiology and diagnosis.” Annual review of microbiology 65 (2011): 501-521.

5. Garey, K. W., et al. “Meta-analysis to assess risk factors for recurrent Clostridium difficile infection.” Journal of Hospital infection 70.4 (2008): 298-304.

6. Slimings, Claudia, and Thomas V. Riley. “Antibiotics and hospital-acquired Clostridium difficile infection: update of systematic review and meta-analysis.” Journal of Antimicrobial Chemotherapy 69.4 (2014): 881-891.…

7. Wells, C. L., et al. “Role of intestinal anaerobic bacteria in colonization resistance.” European Journal of Clinical Microbiology & Infectious Diseases 7.1 (1988): 107-113.

8. Buffie, Charlie G., and Eric G. Pamer. “Microbiota-mediated colonization resistance against intestinal pathogens.” Nature Reviews Immunology 13.11 (2013): 790-801.…

9. Sapone, Anna, et al. “Zonulin upregulation is associated with increased gut permeability in subjects with type 1 diabetes and their relatives.” Diabetes 55.5 (2006): 1443-1449.…

10. Moreno-Navarrete, José María, et al. “Circulating zonulin, a marker of intestinal permeability, is increased in association with obesity-associated insulin resistance.” PloS one 7.5 (2012): e37160.…

11. Żak-Gołąb, Agnieszka, et al. “Gut microbiota, microinflammation, metabolic profile, and zonulin concentration in obese and normal weight subjects.” International journal of endocrinology 2013 (2013).…

12. Jayashree, B., et al. “Increased circulatory levels of lipopolysaccharide (LPS) and zonulin signify novel biomarkers of proinflammation in patients with type 2 diabetes.” Molecular and cellular biochemistry 388.1-2 (2014): 203-210.

13. Mokkala, Kati, et al. “Gut microbiota richness and composition and dietary intake of overweight pregnant women are related to serum zonulin concentration, a marker for intestinal permeability.” The Journal of nutrition 146.9 (2016): 1694-1700.

14. Chatterjee, Soumya, et al. “The degree of breath methane production in IBS correlates with the severity of constipation.” The American journal of gastroenterology 102.4 (2007): 837-841.

15. Hwang, Laura, et al. “Evaluating breath methane as a diagnostic test for constipation-predominant IBS.” Digestive diseases and sciences 55.2 (2010): 398-403.

16. Khoshini, Reza, et al. “A systematic review of diagnostic tests for small intestinal bacterial overgrowth.” Digestive diseases and sciences 53.6 (2008): 1443-1454.

17. Rezaie, Ali, et al. “Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus.” The American Journal of Gastroenterology (2017).…


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