Addressing patient issues that may surprisingly lead to the microbiome
THE INTESTINES ARE AN ECOSYSTEM. You have 2-6 pounds of microorganisms in your intestines (according to the National Institutes of Health). There are more bacterial cells in the colon than there are cells in your entire body (bacteria cells are much smaller than your other cells).
When describing this system, the word microbiome is frequently used. Chemical byproducts from intestinal bacteria have a powerful effect on health. Plus, over 70% of the immune system is associated with the GI tract.
Your patients’ chemical factory
Bacteria are like little chemical factories, with good flora producing vitamins, healing the intestinal lining, breaking down toxins and suppressing bad flora. Bad flora produce toxins, irritate the intestinal lining and suppress good flora.
But that is an oversimplification. We all have some bad flora, which is normal. It is offset by a large and diverse population of good flora. It isn’t always necessary to kill the bad flora (although in some cases of SIBO or IBS, that is a good strategy).
The cells of the intestines are meant to be packed tightly together, forming a barrier that keeps bacteria and undigested food out of the blood stream. Drug therapies, poor digestion (e.g., inadequate stomach HCl or pancreatic enzymes), poor diet or the presence of the wrong kind of flora can break down this barrier. This is known as increased intestinal permeability or “leaky gut.”
Leaky gut allows things into the body that should be kept out. This material, which can include bacteria, partially digested protein and toxins, will interact with the immune system and begin to create chronic health problems. Treating imbalances in the bowel flora has been shown to improve leaky gut.9
Disease and the microbiome
The key to many chronic health problems is to address the microbiome and to improve the integrity of the intestinal lining (addressing “leaky gut”).
It is fairly obvious that GI symptoms would be caused by bowel flora imbalance. Studies have shown this to be true.13,14,15 Addressing the microbiome can also be helpful in liver disease.16,17
More than just GI symptoms
Bacterial byproducts are linked to toxicity, nutrient status, the immune system and general biochemistry. The makeup of the bowel flora can affect organs and systems beyond the GI tract. Also, the GI symptoms may not be severe or obvious in patients with bowel flora imbalance or leaky gut.
Type 2 diabetes, obesity and metabolic syndrome — Several studies link insulin insensitivity and diabetes to the makeup of the bowel flora.1,2,3,4 It is also linked to obesity.5,6 Overweight people generally have different bowel flora than skinny people.
Berberine and its benefit to insulin insensitivity and type 2 diabetes has been extensively studied. Berberine also kills certain microbes and affects the bowel flora. Studies have shown that this may be the reason berberine is beneficial to diabetics.7,8
Cardiovascular — There are a few studies that show cardiovascular benefit by addressing the microbiome.18,19 High cholesterol has been linked to an imbalance of the bowel flora.47,48
The brain and nervous system — Research has shown that gut bacteria can affect the brain.20 Bowel flora may also be involved with neurodegenerative diseases, like Parkinson’s.21
Depression — New research is showing a strong connection between bowel ecology and depression.22,23,24,25 There is a lot of excitement about this; addressing the makeup of bowel flora and the accompanying inflammation may be the way to help severely depressed individuals.
Since so much of the immune system is associated with the GI tract, problems with bowel flora and leaky gut have a strong effect. The makeup of the microbiome has a profound effect on the immune system in general. There are also studies that show GI involvement with allergies and with autoimmune diseases.
General immunity — The makeup of the microbiome can affect your resistance to viral and bacterial infection. Several studies support this. Most of them show that probiotic supplementation (good flora) can support the immune system.10,11,12
Allergies — Both leaky gut and bowel flora imbalance are linked to allergies.32,33,34,35,36 The microbiome is also an issue for these patients.31 One interesting way that allergy/microbiome connection has been tested is with fecal transplant. Fecal transplant, which is moving the bowel flora from one individual to another, is one way to see if bowel flora have an effect on allergies. There are a few studies where fecal transplant improved atopic dermatitis37,38 (this is just research; I am not suggesting it as a treatment).
Something as simple as taking probiotics has benefited allergy patients.39 One study even found bifidobacterial supplementation for mothers and newborns reduced the incidence of allergy.5
There is other evidence that taking probiotics during pregnancy affects the microbiome of the newborn.46 It may give us a way to prevent asthma. Infants with delayed development of the microbiome are prone to asthma, and that issue can be addressed with probiotic supplementation.49
Autoimmune disease — Addressing the microbiome and leaky gut may be the best way to help patients with autoimmune diseases. According to studies, there is a connection between the severity of the disease and the makeup of the microbiome and the integrity of the intestinal lining.
Patients with psoriasis and psoriatic arthritis have a distinct bowel flora makeup, according to studies.41,42 In rheumatoid arthritis, changes in the microbiome can reduce symptoms.43,44 Interestingly, the changes in the microbiome and the symptomatic improvements were brought about by changes in the diet. There may be a link between inflammatory bowel disease and autoimmune disease.50 Inflammatory bowel disease seems to have both immune and autoimmune components.51
SIBO and IBS — It is appropriate to discuss SIBO (small intestine bacterial overgrowth) and IBS (irritable bowel syndrome) at the same time. For one thing, SIBO is likely to be responsible for most cases of IBS.51,52 Even if that is not the case, bacteria and the makeup of the microbiome is strongly linked to irritable bowel syndrome.53,54,55,56,57,58,59,60,61,62 Fecal transplant has been used to successfully treat IBS.59 That, combined with the fact that many cases of IBS begin as a gastrointestinal infection,60 indicate involvement of the microbiome with IBS.
IBD (inflammatory bowel disease) — IBD includes Crohn’s disease and ulcerative colitis. There is much evidence that the microbiota plays a role in these diseases. Fecal transplant has consistently helped ulcerative colitis patients to go into remission63,64,65 (there are many more studies, we have just listed a few). One study even identified problem bacteria.64
Fecal transplant in patients with Crohn’s disease has also been successful in some studies. Success is less pronounced than it is for ulcerative colitis. This makes sense because Crohn’s disease occurs mainly in the small intestine, and bacteria do not belong there. Specific bacteria have been identified and linked to symptoms of Crohn’s disease.
Saccharomyces boulardii is a yeast that displaces other flora. It is used to get rid of undesirable bowel flora. Studies have shown it to be an effective treatment for inflammatory bowel disease.66,67 Once you stop taking Saccharomyces boulardii, it goes away.
The microbiome may play a role in Crohn’s disease. Enteral feeding will produce remission in 80-90% of patients. The authors of one study believe the improvement is due to changes in the microbiome69 and a reduction in bacterial toxins. They state, “A significant change occurs in the production of microbial metabolites after enteral feeding in both healthy volunteers and patients with CD [Crohn’s disease]. Many of those detected in CD are toxic and may feasibly lead to the immunological attack on the gut microbiota, which is characteristic of inflammatory bowel disease. The reduction in the production of such metabolites after enteral feeding may be the reason for its effectiveness in CD.”
Proper diet and digestion
A specific carbohydrate diet was developed by Sidney Haas, MD, in the 1940s. It was made popular by Elaine Gottschall in her book, “Ending the Vicious Cycle.”
It presents a reasonable mechanism for at least some cases of Crohn’s disease and ulcerative colitis. Many practitioners have found that this approach helps with other digestive issues like IBS, SIBO, GERD, etc. The diet has been well-studied and found to be effective in many cases of inflammatory bowel disease,70,71,72 as well as cases of IBS and SIBO.
The mechanism that leads to digestive problems that Gottschall suggests is as follows:
Incomplete digestion — Growth of improper GI flora — Irritation of the SI mucosa — Decreased production of enzymes from the SI (disaccharidases) — Incomplete digestion — More improper flora, etc.
Poor digestion can cause inappropriate bowel flora to grow. Complex carbohydrates, in general, seem to have the potential to disrupt the microbiome. This may explain the popularity of ketogenic and Paleo diets.
What disrupts the microbiome?
Drug therapy, especially acid-suppressing medications and antibiotics, can alter the microbiome.26,27,28,29,30 Diet, especially refined foods, and chemical additives can disrupt it as well.
There is some indication that gluten and dairy are often problematic. Eating food that is not well-digested grows inappropriate flora, which is why the specific carbohydrate diet is so effective. Food that is not digested rots and disrupts the ecology of the intestines.
Probiotics — Taking the right kind of bacteria has become a way to improve the intestinal ecology. As more research is being done, we are finding the importance of specific strains. Biffidobacterium, for example, is often beneficial to allergy patients. Increasing floral diversity has been one way to improve the health of IBD patients, and is another example of the use of probiotics for health.
The environment is more important — Many who take probiotic supplements find that they have to keep taking them. The good bacteria do not colonize because of poor living conditions. It is a lot like dropping polar bears off in the jungle or leaving tropical birds in Antarctica. They do not survive. You need to create an environment that is friendly to the new bacteria. Diet, chewing your food thoroughly and addressing the initial phase of digestion need to be addressed if you want the desirable bowel flora to survive.
You want diversity in the microbiome, and the way to get there is with diet. It makes sense. If you eat a lot of grease and fat, you grow bacteria that feed on it. If you eat a lot of sugar and starch, you get bacteria that feed on sugar and starch. Fiber and polyphenols (translation: vegetables) feed healthy flora. Fermented foods also help with diversity.
When addressing the microbiome, it is important to think about the computer term GIGO (garbage in, garbage out). You can take all the probiotics and gut-healing herbs you want, but if you do not address diet, you will not be very successful.
PAUL VARNAS, DC, DACBN, is a graduate of the National College of Chiropractic and has had a functional medicine practice for 34 years. He is the author of several books and has taught nutrition at the National University of Health Sciences. For a free PDF of “Instantly Have a Functional Medicine Practice” or a patient handout on the anti-inflammatory diet, email him at firstname.lastname@example.org.
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