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Dysbiosis Decoded: Symptoms, Why You Get It, and Link to Autoimmunity, Breast Cancer, Irritable Bowel Syndrome, Plus Other Common Conditions

Dysbiosis is an imbalance in your gut flora caused by too few beneficial bacteria and an overgrowth of bad bacteria, yeast, and/or parasites. The more clinical term that relates to the problem is “Small Intestinal Bacterial Overgrowth” (SIBO), and this term refers to the gut flora that crawled backward into the small intestine from the colon, where it belongs. Over the past ten years, I’ve noticed a dramatic rise in symptoms of dysbiosis in my patients and the people that I work with online in my semi-annual detox. The symptoms of dysbiosis are vague and often go unnoticed, undiagnosed, and even worse, dismissed by your conventional health care clinicians. That needs to change! Here are the top 5 questions that I receive about dysbiosis. twitter-top

If you have 5 or more of these symptoms, there is a good chance you have dysbiosis.


Q1: How do you know if you have dysbiosis?

  • Frequent gas or bloating on most days of the week
  • Cramping, urgency, and/or mucus in your poop once per week
  • Brain fog, anxiety, or depression
  • Food sensitivities
  • Missing micronutrients
  • Chronic bad breath
  • Loose stool, diarrhea, constipation, or a combination
  • Diagnosis of Irritable Bowel Syndrome (IBS)
  • History of “stomach bugs,” gastroenteritis, and/or food poisoning
  • History of prolonged antibiotics such as for acne or sinusitis
  • Carbohydrate intolerance, particularly after eating fiber and/or beans
  • Fatigue or low energy
  • Use of anti-acids for heartburn, reflux, or hiatal hernia?
  • Autoimmunity, or an autoimmune condition such as Hashimoto’s thyroiditis, psoriasis, or multiple sclerosis
  • Sinus congestion
Scoring: While I have yet to see a validated scale, if you have five or more symptoms, there is a good chance you have dysbiosis. Read on to learn about what it is, why you should care, and what causes it. If you scored four or less symptoms, there’s a good chance that you have normal gut flora, or a mild case of dysbiosis. [caption id="attachment_21493" align="alignright" width="300"]Your top 5 questions about dysbiosis answered Your top 5 questions about dysbiosis answered[/caption]

The Functional Medicine Approach

Sydney Baker MD, one of the early practitioners of functional medicine, used to say that if you’re sitting on a tack, the solution is to find and remove the tack, not treat the pain. In conventional medicine, the tendency is to throw prescriptions at problems to try to mask symptoms rather than to treat the root cause. In functional medicine, the goal is root cause analysis so that you remove the tack and feel better. Dysbiosis is a common cause of many health problems, from dysestrogenism and breast cancer to irritable bowel syndrome. More on that in a minute. First, let’s run through the most frequently asked questions that I get in my functional medicine practice.

Q2: What does the normal gut flora do for you?

In general, your gut flora, called the microbiota, and their DNA, called your microbiome, are stable in healthy people. But a shift in the microbiota can lead to a permanent imbalance known as dysbiosis. Frankly, I don’t know many people with normal microbiota and microbiome. Maybe three people in the past 10 years, and it’s becoming alarmingly rare. Your intestinal microbiota are inherited at birth from your mother as you move through the vaginal canal (or not). Later, your diet and lifestyle become more important in their effect on the structure of your microbiota and their diversity. Overall, you microbiota consist of approximately 1014 microbes, which outnumber human cells by 10-fold, and perform several key functions:
  • synthesizing vitamin K and other essential nutrients [1]
  • preventing your gut wall from becoming leaky [2]
  • digestion of cellulose
  • promoting angiogenesis
  • supporting enteric nerve function
  • keeping your immune system healthy and recognizing self versus nonself [3]
  • preventing kidney stones [4]

Q3: What caused my dysbiosis? Or, why did the bad bugs take over?

Abnormal shifts in your gut flora occur with use of antibiotics, illness, stress, aging, lousy dietary habits (sugar, processed foods, eating foods you’re intolerant toward), and other lifestyle issues. [5] [caption id="attachment_21494" align="alignright" width="194"]Is that bread giving you dybiosis? And the booze? Is that bread giving you dybiosis? And the booze?[/caption]

Q4: What’s so bad about dysbiosis? (Or, why should you care?)

Dysbiosis sets up a sequence of events leading to inflammation, followed by a multitude of vague symptoms (as mentioned at the beginning of this article), and ultimately to problems such as:
  • breast cancer [6]
  • colorectal cancer [7]
  • irritable bowel syndrome [8]
  • inflammatory bowel disease [9]
  • autoimmunity [10]
  • metabolic diseases such as obesity, [11] diabetes, [12] and gestational diabetes [13]
  • autism [14]
  • other neurological conditions such as Parkinson’s disease [15]
  • how effectively you detoxify endocrine disruptors or xenobiotics [16]
  • plus many other conditions and diseases with linkage still emerging, such as chronic venous insufficiency [17]

Q5: Is dysbiosis linked to misfiring hormones?

As my 15-year-old daughter is fond of saying: “Hells yes!” I’m a hormone expert, which makes me especially concerned about the role of dysbiosis in potentially causing your hormones to become imbalanced. Here are just a few examples of the problems tied to dysbiosis:
  • Creates the type of inflammation that may suppress the control system for making hormones, called the Hypothalamic-Pituitary-Adrenal-Thyroid-Gonadal axis.
  • Changes the subset of the microbiome involved in estrogen metabolism, called by Martin Blaser the estrobolome.[18] The estrobolome is one of the levers in the body for your estrogen load.
  • Raises beta-glucuronidase activity in the body, which reverses the important estrogen inactivation system in the liver—that means estrogens get recirculated over and over in your body, like bad karma, and raising estrogen levels and thereby estrogenic load. Ultimately, high estrogenic load may increase your risk of estrogen-related conditions, such as diabetes, obesity, breast and prostate cancer. Read more in the next blog post! [caption id="attachment_21495" align="alignright" width="200"]Dysbiosis suppresses the control system for your adrenals called the Hypothalamic-Pituitary-Adrenal-Thyroid-Gonadal axis Dysbiosis suppresses the control system for your adrenals called the Hypothalamic-Pituitary-Adrenal-Thyroid-Gonadal axis[/caption]

How do I fix dysbiosis?

Alas, the solution is not quick or simple. You’d think that perhaps a quick shift in the microbiome might cure you of dysbiosis. But biology is rarely that easy or charitable. [19] Dysbiosis can be tricky to diagnose and even harder to correct, and your rehab program will depend on the state of your gut and how committed you are to make changes. I’ll write more next time about how to test for and treat dysbiosis. Additionally, you can join my free upcoming webinar where I go into more detail about gut health, leaky gut, and, how to rebuild your digestive system. Remember, eat your probiotic-rich food such as cultured vegetables, sauerkraut, and kimchi--it's a great way to jump start gut health repair.  


[1] Zhang, Y. J., et al. "Impacts of Gut Bacteria on Human Health and Diseases." International Journal of Molecular Sciences 16, no. 4 (2015): 7493-7519. [2] Ulluwishewa, D., et al. "Regulation of tight junction permeability by intestinal bacteria and dietary components." The Journal of Nutrition 141, no. 5 (2011): 769-776. [3] Hill, D. A., et al. "Intestinal bacteria and the regulation of immune cell homeostasis." Annual Review of Immunology 28 (2009): 623-667. [4] Jalanka-Tuovinen, J., et al. "Intestinal microbiota in healthy adults: temporal analysis reveals individual and common core and relation to intestinal symptoms." PloS One 6, no. 7 (2011): e23035. [5] Gerritsen, J., et al. "Intestinal microbiota in human health and disease: the impact of probiotics." Genes & Nutrition 6, no. 3 (2011): 209-240; Woodmansey, E. J. "Intestinal bacteria and ageing." Journal of Applied Microbiology 102, no. 5 (2007): 1178-1186; Wu, G. D., et al. "Linking long-term dietary patterns with gut microbial enterotypes." Science 334, no. 6052 (2011): 105-108; Lakshminarayanan, B. C., et al. "Compositional dynamics of the human intestinal microbiota with aging: Implications for health." The Journal of Nutrition, Health & Aging 18, no. 9 (2014): 773-786; Keeney, K.M., et al. "Effects of antibiotics on human microbiota and subsequent disease."nAnnual review of microbiology 68 (2014): 217-235; Forsyth, C.B., et al. "Circadian rhythms, alcohol and gut interactions." Alcohol (2014). [6] Shapira, I., et al. "Evolving Concepts: How Diet and the Intestinal Microbiome Act as Modulators of Breast Malignancy." ISRN Oncology 2013 (2013). [7] Sears, C. L., et al. "Microbes, microbiota, and colon cancer." Cell Host & Microbe 15, no. 3 (2014): 317-328; Keku, T.O., et al. "The Gastrointestinal Microbiota and Colorectal Cancer." American Journal of Physiology-Gastrointestinal and Liver Physiology (2014): ajpgi-00360; Rowland, I. R., "The role of the gastrointestinal microbiota in colorectal cancer." Current Pharmaceutical Design 15, no. 13 (2009): 1524-1527. [8] Bennet, S. M., et al. “Gut microbiota as potential orchestrators of irritable bowel syndrome.” Gut and Liver 23, no. 9 (2015): 318-31; Manichanh, C., et al. “The gut microbiota in IBD.” Nature Reviews Gastroenterology and Hepatology 9, no. 10 (2012):599-608. [9] Macfarlane, S. et al. "Intestinal bacteria and inflammatory bowel disease." Critical Reviews in Clinical Laboratory Sciences 46, no. 1 (2009): 25-54; Wu, G.D., et al. "Diet, the human gut microbiota, and IBD." Anaerobe 24 (2013): 117-120. [10] McLean, M. H., et al. "Does the microbiota play a role in the pathogenesis of autoimmune diseases?." Gut (2014): gutjnl-2014. [11] Gritz, E. C., et al. "The human neonatal gut microbiome: a brief review." Frontiers in Pediatrics 3 (2015); Stenvinkel, P. "Obesity—a disease with many aetiologies disguised in the same oversized phenotype: has the overeating theory failed?." Nephrology Dialysis Transplantation (2014): gfu338. [12] He, C., et al. "Targeting gut microbiota as a possible therapy for diabetes." Nutrition Research (2015); Esteve, E., et al. "Gut microbiota interactions with obesity, insulin resistance and type 2 diabetes: did gut microbiote co-evolve with insulin resistance?" Current Opinion in Clinical Nutrition & Metabolic Care 14, no. 5 (2011): 483-490. [13] Isolauri, E., et al. "Role of probiotics in reducing the risk of gestational diabetes." Diabetes, Obesity and Metabolism (2015). [14] Rosenfeld, C. S., "Microbiome Disturbances and Autism Spectrum Disorders." Drug Metabolism and Disposition (2015): dmd-115; Mayer, E. A., et al.. "Altered brain‐gut axis in autism: Comorbidity or causative mechanisms?." Bioessays 36, no. 10 (2014): 933-939. [15] Charlett, A., et al. “Blood profile holds clues to role of infection in a premonitory state for idiopathic parkinsonism and of gastrointestinal infection in established disease.” Gut Pathogens 1, no. 1 (2009): 20. [16] Guarner, F. et al. "Gut flora in health and disease." The Lancet 361, no. 9356 (2003): 512-519; Tralau, T. et al. "Insights on the human microbiome and its xenobiotic metabolism: what is known about its effects on human physiology?." Expert Opinion on Drug Metabolism & Toxicology 0 (2014): 1-15. [17] Cordts, P. R., et al. “Could gut-liver function derangements cause chronic venous insufficiency?” Journal of Vascular Surgery 35, no. 2 (2001): 107-14. [18] Plottel, C. S., et al. “Microbiome and malignancy. “ Cell Host and Microbe 10, no. 4 (2011): 324-35. [19] Ed Yong, “There Is No ‘Healthy’ Microbiome,” New York Times, accessed May 28, 2015. 


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