We cover the gut microbiome and its impact on overall health

leaky gut word cloud

The Microbiome's Impact on Intestinal Permeability, aka leaky gut

Intestinal permeability, aka leaky gut, describes a state where the lining of the gastrointestinal tract is impaired, allowing increased entry of dietary and microbial antigens into the body, which may contribute to inflammatory states. The integrity of the gut lining involves many components. The first is a mucus layer and the second is the gut cells themselves, called epithelial cells. Epithelial cells create a barrier by interlocking with proteins called tight junctions. The immune system, the nervous system, and the microbiome are all involved in maintaining a healthy barrier.

A healthy gut barrier is an important component to overall health. Research suggests that increased intestinal permeability may be involved in several conditions such as obesity, fatty liver disease, inflammatory bowel disease, type 1 diabetes, irritable bowel syndrome, celiac disease, autism, eczema, psoriasis, fibromyalgia, depression, chronic fatigue syndrome, multiple sclerosis, rheumatoid arthritis and more.1,2 More research is needed to fully understand the role of intestinal permeability and disease. In some instances, intestinal permeability may drive the development of disease and in other instances, it may be a side effect of the disease that simply worsens the underlying pathology. Regardless, it is clear that having a healthy intestinal barrier can only be positive for your health.

Intestinal permeability can happen in a variety of ways. First, the tight junctions may fail, creating small gaps between cells. This is referred to as the paracellular pathway. The second type of intestinal permeability is through the epithelial cell itself, called the transcellular pathway. Intestinal permeability can also happen when epithelial cells are dying (apoptosis) or there is a hole in the lining (ulceration). Intestinal permeability can happen anywhere along the digestive tract—the stomach, small intestine, and large intestine, with the small intestine being the most common site. 

Testing for Intestinal Permeability

Lactulose/Mannitol Test

Testing for intestinal permeability is easier said than done. The most common test in clinical practice is the lactulose/mannitol test. This involves drinking a solution of the two sugars and collecting urine for a period of time to be analyzed for the sugars. With a normal gut barrier, lactulose should not be absorbed, so if it is showing up in the urine, that may indicate intestinal permeability. Lactulose is thought to indicate paracellular permeability. Since lactulose is fermented in the large intestine, it is assessing small intestine permeability only. In the research, different substrates can be used to assess the permeability of the stomach or the large intestine, but these tests are not available in clinical practice.2,3 However, the research has not fully validated the lactulose/mannitol test. Reference ranges and standardized test procedures have not been fully established, so data from these tests should be interpreted with caution.3 


Zonulin is a protein that interacts with the tight junctions, increasing intestinal permeability. Zonulin is made primarily by the liver, and also gut cells, fat cells, and organs like the brain, heart, lungs, kidneys, and skin.4 In the research and clinical practice, zonulin levels can be measured in the blood or urine. However, the research has been very inconsistent on the use of these tests in clinical practice.

While increased zonulin in the blood has been associated with a disease states such as autoimmune diseases and metabolic diseases4, research studies have not found increased serum zonulin to correlate with intestinal permeability on lactulose/mannitol testing5. Zonulin in the blood may be coming from non-gut tissues and non-gut sources of zonulin may not act on the tight junctions in the gut. In fact, studies have found high zonulin to be associated with markers of metabolic disease such as high BMI, high insulin, and high blood sugar, but not associated with digestive symptoms or conditions.4,6 Furthermore, research has not fully elucidated normal vs abnormal levels of zonulin in the blood. So at this point, we cannot confidently make assumptions about intestinal permeability based on serum zonulin.

Likewise, the research does not demonstrate consistent results with stool zonulin testing. One study compared the lactulose/mannitol test to stool zonulin and found no associations.7 Another study found that fecal zonulin correlated with the lactulose/mannitol test in patients with higher BMI only.8 Studies in patients with inflammatory bowel disease indicate fecal zonulin may be elevated during an active flare, as defined by elevated calprotectin (inflammatory marker of IBD).9 Fecal zonulin may only be elevated at certain stages of the disease process, so it may have a limited testing window. 

Other Markers

Researchers are currently investigating other potential markers, like lipopolysaccharide binding protein.8 The currently available tests for leaky gut have many challenges, limiting their utility in clinical practice. At this point in time, it is best to wait for more research before testing leaky gut in clinical practice. Additional research may be able to strengthen the lactulose/mannitol test or zonulin testing, or it may uncover new clinical markers. 

Microbiome Testing

What about microbiome testing like Biomesight? Can that tell us anything about leaky gut? The short answer is no—16S rRNA sequencing does not provide a direct assessment of the health of the intestinal barrier. However, since the microbiome helps to regulate the intestinal barrier, microbiome testing can help us identify potential risks to the intestinal barrier.

It is important to note that 16S rRNA sequencing is only assessing the large intestine. The majority of increased intestinal permeability is most likely happening in the small intestine due to the thinner mucus layer in the small intestine. No stool tests can provide information about the small intestine microbiome. In clinical practice, the majority of patients with suspected leaky gut have small intestine bacterial overgrowth (SIBO). The microbiome alterations in SIBO are the cause of leaky gut. Many patients are treated for leaky gut using supplements or elimination diets and SIBO is ignored. This usually results in only mild improvements in symptoms and quick relapses when treatments are discontinued. When SIBO is successfully treated, we see resolution of more than 90% of digestive symptoms without restrictive diets or ongoing supplementation. 

The Microbiome & Intestinal Barrier Health

Microbes and their metabolites are involved in regulating mucus production and tight junctions, thus playing a key role in the health of the intestinal barrier. 16S rRNA stool testing can provide insights into how the microbiome may be impacting the large intestine gut barrier.

The mucus layer is the first line of protection for the intestinal barrier. Since certain bacteria can degrade the mucus, microbial composition is important to a healthy mucus layer. Akkermansia is an important mucus degrader that actually promotes a thicker, healthier mucus layer.10 So maintaining healthy levels of Akkermansia may be important for a healthy gut barrier. Strategies to promote Akkermansia include fasting for 16 hours11, decreasing saturated fat and alcohol consumption12, fructooligosaccharides12, glucommanan13, and polyphenols13.

Certain Bacteroides species can degrade mucus when there is a lack of dietary fiber.14 In the long run, this can damage the intestinal barrier14, so maintaining healthy Bacteroides levels by eating adequate fiber and reducing consumption of fat and protein may be beneficial.

Butyrate producers and butyrate are also very important to a healthy gut barrier. Faecalibacterium is associated with more goblet cells (cells that produce mucus) and upregulating genes involved in making mucus.15 Butyrate is also involved in regulating the tight junctions in a variety of ways.15 So bolstering butyrate producers like Faecalibacterium, Blautia and Roseburia may help to maintain a healthy gut barrier. Resistant starch, inulin, xylooligosaccharides, and arabinogalactan can increase butyrate producers.16

Lipopolysaccharide (LPS), a toxin produced by certain microbes, also influences the gut barrier. LPS triggers changes in the immune system of the gut that promotes increased intestinal permeability.17 The immune system alterations involve M1 polarization of macrophages. LPS activates TLR4, up regulating NF-KB signaling and resulting in the expression of inflammatory cytokines like TNF-a and IL-6 in the gut.17 These inflammatory cytokines alter the tight junctions resulting in leaky gut.18 LPS from Proteobacteria is the specific type of LPS involved in this pathway, so maintaining healthy levels of Proteobacteria may be important for a healthy gut barrier. For an in depth discussion about Proteobacteria, see Managing Proteobacteria Overgrowth. 

Please be sure to talk to your health care provider before making any changes to your diet or supplements.


  1. Odenwald MA, Turner JR. Intestinal permeability defects: Is it time to treat? Clin Gastroenterol Hepatol. 2013;11(9):1075-1083. doi:10.1016/j.cgh.2013.07.001
  2. Schoultz I, Keita ÅV. The Intestinal Barrier and Current Techniques for the Assessment of Gut Permeability. Cells. 2020;9(8):1909. doi:10.3390/cells9081909
  3. Camilleri M. The Leaky Gut: Mechanisms, Measurement and Clinical Implications in Humans. Gut. 2019;68(8):1516-1526. doi:10.1136/gutjnl-2019-318427
  4. Ohlsson B, Orho-Melander M, Nilsson PM. Higher Levels of Serum Zonulin May Rather Be Associated with Increased Risk of Obesity and Hyperlipidemia, Than with Gastrointestinal Symptoms or Disease Manifestations. Int J Mol Sci. 2017;18(3):582. doi:10.3390/ijms18030582
  5. Power N, Turpin W, Espin-Garcia O, Smith MI, The CCC GEM Project Research Consortium, Croitoru K. Serum Zonulin Measured by Commercial Kit Fails to Correlate With Physiologic Measures of Altered Gut Permeability in First Degree Relatives of Crohn’s Disease Patients. Frontiers in Physiology. 2021;12. Accessed March 2, 2023. https://www.frontiersin.org/articles/10.3389/fphys.2021.645303
  6. Moreno-Navarrete JM, Sabater M, Ortega F, Ricart W, Fernández-Real JM. Circulating Zonulin, a Marker of Intestinal Permeability, Is Increased in Association with Obesity-Associated Insulin Resistance. PLOS ONE. 2012;7(5):e37160. doi:10.1371/journal.pone.0037160
  7. Hałasa M, Maciejewska D, Ryterska K, Baśkiewicz-Hałasa M, Safranow K, Stachowska E. Assessing the Association of Elevated Zonulin Concentration in Stool with Increased Intestinal Permeability in Active Professional Athletes. Medicina (Kaunas). 2019;55(10):710. doi:10.3390/medicina55100710
  8. Seethaler B, Basrai M, Neyrinck AM, et al. Biomarkers for assessment of intestinal permeability in clinical practice. American Journal of Physiology-Gastrointestinal and Liver Physiology. 2021;321(1):G11-G17. doi:10.1152/ajpgi.00113.2021
  9. Szymanska E, Wierzbicka A, Dadalski M, Kierkus J. Fecal Zonulin as a Noninvasive Biomarker of Intestinal Permeability in Pediatric Patients with Inflammatory Bowel Diseases—Correlation with Disease Activity and Fecal Calprotectin. Journal of Clinical Medicine. 2021;10(17). doi:10.3390/jcm10173905
  10. Zhang T, Li Q, Cheng L, Buch H, Zhang F. Akkermansia muciniphila is a promising probiotic. Microb Biotechnol. 2019;12(6):1109-1125. doi:10.1111/1751-7915.13410
  11. Su J, Braat H, Verhaar A, Peppelenbosch M. Commentary: Intermittent Fasting and Akkermansia Muciniphila Potentiate the Antitumor Efficacy of FOLFOX in Colon Cancer. Front Pharmacol. 2022;13:843133. doi:10.3389/fphar.2022.843133
  12. Zhou K. Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies. J Funct Foods. 2017;33:194-201. doi:10.1016/j.jff.2017.03.045
  13. Yue C, Chu C, Zhao J, Zhang H, Chen W, Zhai Q. Dietary strategies to promote the abundance of intestinal Akkermansia muciniphila, a focus on the effect of plant extracts. Journal of Functional Foods. 2022;93:105093. doi:10.1016/j.jff.2022.105093
  14. Chikina A, Matic Vignjevic D. At the right time in the right place: How do luminal gradients position the microbiota along the gut? Cells & Development. 2021;168:203712. doi:10.1016/j.cdev.2021.203712
  15. Singh V, Lee G, Son H, et al. Butyrate producers, “The Sentinel of Gut”: Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Frontiers in Microbiology. 2023;13. Accessed February 13, 2023. https://www.frontiersin.org/articles/10.3389/fmicb.2022.1103836
  16. Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Front Microbiol. 2016;7:979. doi:10.3389/fmicb.2016.00979
  17. Candelli M, Franza L, Pignataro G, et al. Interaction between Lipopolysaccharide and Gut Microbiota in Inflammatory Bowel Diseases. Int J Mol Sci. 2021;22(12):6242. doi:10.3390/ijms22126242
  18. Al-Sadi R, Guo S, Ye D, Rawat M, Ma TY. TNF-α Modulation of Intestinal Tight Junction Permeability Is Mediated by NIK/IKK-α Axis Activation of the Canonical NF-κB Pathway. Am J Pathol. 2016;186(5):1151-1165. doi:10.1016/j.ajpath.2015.12.016
DISCLAIMER This service has not been evaluated by the Food and Drug Administration or other healthcare authorities. Our platform and related products and services are not intended to diagnose, treat, cure or prevent any disease. Ranges apply to over 18s only.