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 () such as KPC (Klebsiella pneumoniae carbapenemase-producing K. pneumoniae) ( ) and ( ) 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.
Apart from its propensity to cause infection,(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 ( , 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, especiallyand third generation (5, ). In contrast, healthy gut microflora manifest , which prevents colonization by harmful microbes (7, ).
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, whose increased presence in serum correlates with increased intestinal permeability ( , , , 12, 13).
BTs are a very convenient, non-invasive approach to test for GI tract disturbances such as SIBO (). 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 ( ) diagnosis (15).
Problem with BTs is lack of standardization and false positives are all too common. For example, a systematic review (16) of 13found they ‘used 13 different methodologies to conduct the breath test or interpret the results‘ ( ).
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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).