Restoring Your Gut Microbiome to Restore Your Health
“All disease begins in the gut.” It’s a quote attributed to the Ancient Greek physician Hippocrates nearly 2500 years ago. The gut consists of 1000-1500 bacterial species in the microbiome of healthy people. However, modern lifestyles have caused us to lose the diversity in the gut microbiome. Contributors to this problem include things such as antibiotic overuse, pesticides, environmental toxins, and stress. In fact, a single dose of antibiotics can result in an 80-90% drop in numbers of gut bacteria! Antibiotics kill off many lactic acid bacteria which then can cause the pH of the gut to increase, which causes a host of other problems. For example, in an alkaline pH pathogenic bacteria can overgrow. Also, an alkaline pH can also affect proper digestion which can thus lead to nutritional deficiencies. Furthermore, the proportion of the bacteria can shift, which causes us to lose the functionality of the microbiome. This can lead to gut infections which can cause chronic inflammation from the endotoxins from the microbes…and thus downstream effects such as chronic illnesses, autoimmune diseases and even cancer. Dysbiosis is defined as the shifting of proportions of commensal and pathogenic bacteria. This is a big contributor of modern day chronic illnesses. One example is SIBO, small intestinal bacterial overgrowth, which is characterized by the displacement of the large bowel into the small bowel. Researchers are finding that SIBO is really not a bacterial issue, but rather a disruption in motility and terrain that causes bacteria to become displaced and to overgrow where it is not supposed to be. That is, the small intestine. One common cause includes ileocecal valve dysfunction. Other causes can be leaky gut, chronic infections, genetics, environmental burdens and genetic predispositions.
So what is the solution? Many people are blindly taking over the counter probiotics, which can actually cause more harm than good! Take for example most lactobacillus based probiotics such as Culturelle. For someone with SIBO, that can actually make their condition worse and can exacerbate an overgrowth situation. So the goal is not to reseed the gut, but rather recondition the gut, and change the environment to favor regrowth. This is often called gut reconditioning. Below are some general guidelines on ways you can recondition your gut. Keep in mind, it is best to work with a practitioner to ensure you are following the steps correctly.
- Keep your gut acidic but not too acidic. Many people are obsessed with being alkaline! This is a big mistake especially in regards to gastric pH, which must maintain an acidic pH range of 1-2.5 for optimal health (Evans et al., 1988). The alkaline diet and alkaline water are flooding the industry, but your gut needs to be acidic for optimal functioning. According to Beasley et. al, “in light of modern lifestyle changes in diet, hygiene and medical interventions that alter stomach pH, we suggest that stomach acidity in humans is a double-edged sword. On one hand, the high acidity of the human stomach prevents pathogen exposure but it also decreases the likelihood of recolonization by beneficial microbes if and when they go missing.” One role of the stomach acid is it acts as a pathogen barrier. However a potential consequence of high stomach acidity is the difficulty of recolonization by beneficial microbes (Beasley, Koltz, Lambert, Fierer, & Dunn, 2015). A large body of literature now suggests that a variety of human medical problems relate to the loss of commensal gut microbes, whether they failed to colonize during hyper-clean C-section births or were lost through use of antibiotics or other circumstances. In fact, the pH of the human stomach may make humans uniquely prone to such problems, therefore it is important to maintain the proper pH!
2. Take the right Probiotics– did you know that 98% of the traditional probiotics you take do not survive the gastric system? Even those that are enteric coated do not survive! The companies typically test in pH of 2.8 to 3.2 so they aren’t even testing close to the gastric pH! Therefore, 98% of your probiotic are not surviving your GI tract. That does not mean they aren’t benefitting you, but it is not for the reason you think. They aren’t successfully colonizing your gut. However, they may have a temporary favorable metabolic response. This can result in improvements in IBS symptoms, which can be favorable for many people. However, this is really just acting like a bandage, since they are typically NOT successfully restoring your gut microbiome. Did you know that most lactobacillus probiotics are coming from cow intestines? In fact some of the first probiotics were isolated and developed as good fermenting organisms to give us the flavors that we like in products such as cheese and yogurt. They were not chosen based on some profound efficacy they had in the gut! It was merely a matter of convenience. And probiotic manufacturers used this fermenting ideology and developed the wide spectrum of probiotics you see today in the market. This was all done before the Human Microbiome Project. The human microbiome project is really only 4-5 years old, and the lactobacillus probiotic products are truly outdated. With all the wide availability of probiotics, why are we still flooded with an epidemic of leaky gut related health issues? Perhaps they aren’t doing the job they claim to be doing!
Another issue that comes up with the lactobacillus strains is the issue with overgrowth such as SIBO. In fact, if someone has SIBO it is generally recommended they do not take those strains until their SIBO is cleared, if at all. For this population, bifido strains are more suitable. Again you encounter the issue with probiotic survival in the GI tract, but regardless evidence has shown that people with overgrowth such as SIBO should probably avoid most commercial probiotics.
3. Think about Spore Based– Many people are starting to move to soil based organisms (SBO’s). The idea comes from our ancestors were so close to nature that they were in contact with bacteria that resided in dirt, which may be indicated in human health. Although this move is closer to what was found in nature, the issue again is the inability to colonize the gut. Only a few strains are able to survive the harsh pH of the gut to properly colonize, and most over the counter SBO’s are a blend of some ineffective strains. For therapeutic purposes, you need to select strains that are able to colonize the gut. Again, the exposure can be beneficial to up regulate the immune system, but they more than likely are not colonizing and living there (Kirshnan, 2017). There are a few organisms within the soil that do function as true probiotics and have the natural ability to survive the gut, and are able to colonize in everyone, and hence are considered “universal colonizers”. Not all soil based organisms are able to form spores, and not all spore based probiotics are derived from soil either. You need a probiotic that consists of all these characteristics: can get into gut and colonize and perform significant functions inside the gut (Kirshnan, 2017).
If you have SIBO, Crohn’s or IBD-Be careful with traditional probiotics! As mentioned earlier, people with SIBO are advised to stay away from conventional probiotics. Introducing more lacto or even bifidobacterium strains can exacerbate the situation. In addition, people with Crohn’s also have an overabundance of lactobacillus acidophilus. So you could be increasing your risk of Crohn’s and IBD if you take too many conventional probiotics. It is amazing how so many people are taking such strong probiotics such as VSL#3 and could actually be doing more harm than good! VSL#3 can be useful in many people, but it needs to be used with caution on a case by case basis. Spore based probiotics can actually kill off the overgrowth that is characteristic of SIBO, so they can act as the police. It is not the only treatment, but can be a critical part of the treatment protocols. So again, if you have an overgrowth related condition, consider spore based and drop your lactobacillus based probiotics. One way to avoid complications is to work with a practitioner who can run a number of tests to see what your microbiome status is. Two key tests are an organic acids test and a GI stool analysis. “Test, don’t guess!”
If you are using natural antibiotics like berberine, oregano oil, and other herbs-they can also kill some beneficial bacteria. They can be used for certain conditions in the short term (2-6 weeks), but long term can have really deleterious effects on the body. Do not use any natural anti-microbials long term to save your gut integrity.
Spore based are the best option for children-particularly for children with overgrowth disorders like PANDAS (strep overgrowth), spectrum disorders, ASD, mood disorders that can be implicated in overgrowth of certain bacteria. There have been studies done on infant mice that early exposure to bacillus subtilis is helpful for stimulating the immune system and also can work with bacteria associated with GALT (gut associated lymphoid tissue) which is your immune tissue in your gut.
4. Your diet is your biggest driver of the structure of your microbiome-the more diverse your diet, the more diverse your microbiome. Increase the diversity of your foods, try new foods, and focus on roots, tubers, cruciferous vegetables and leafy greens. The prebiotics feed your good bacteria in your gut, which you want to encourage the growth. Visit a different ethnic grocery store and try some new foods your body has not been exposed to!
5. Consider intermittent fasting-Really high calorie diets can disrupt diversity! One of my favorite tools to enhance health is to restrict your calories and food intake. It is a very effective method to increase the diversity of your gut microbiome. There are certain microbes within that grow very well in a fasted state, such as akkermansia muciniphila, which is a healthy gut microbe for inflammatory bowel metabolism and leaky gut. In a paper dated in May 13, 2013, researchers at the University of Louvain, Belgium concluded that this strain of gut bacteria has the amazing ability to promote weight loss in humans (Silvers, 2017). Signals of this rapid change in the gut are sent to the brain via the vagus “This triggers a remarkable chain reaction in your body resulting in an increased metabolism—your body gradually rids itself of excess weight, lowers inflammation and strengthens the immune system” (Silvers, 2017). This bacteria makes up 3-5% among hundreds of other gut bacteria, but levels drop sharply in obese individuals (Silvers, 2017). It does very well in fasted state because it feeds off the mucous layer and helps regenerate the mucosal layer. In fact the study in 2013 states that “this human mucous colonizer can be used for the prevention or treatment of obesity and its associated metabolic disorders” (Silvers, 2017). This bacteria can talk to other bacteria in your body to help establish mutually beneficial relationship with you to stimulate and promote a number of beneficial physiological processes. “If you feed and nourish your Akkermansia muciniphila colony, then they will in exchange promote your body’s metabolism, lower inflammation, deal with harmful microorganisms and help control weight” (Silvers, 2017). Right now there aren’t any probiotics with this strain, so intermittent fasting seems to work best. An 8 hour feeding period is the most effective strategy; try to have 14-16 hours a day where you are fasting. “This is one of the most important things you can do for you microbiome” (Krishnan, 2017)
6. Consider strain specific prebiotics-Prebiotics are fermentable and digestible carbohydrates bacteria can use. However, if you have overgrowth, they can also feed off of them and can make people feel worse. So you do need to be careful. If you have SIBO, you may want to considering cycling on and off prebiotics with intermittent fasting to get the benefits of both worlds. XoS is a good prebiotic that tends to be specific for bifidobacterium and selectively grow bifido strains which can be helpful for those with lactobacillus overgrowth. Another one is a kiwi fiber. Beneficial microflora strains like Lactobacilli and Bifidobacteria greatly benefit from regular kiwi consumption, one human trial found, acting to balance out these “good” bacteria while promoting healthy bowel movements and aiding the body in better assimilating nutrients from food (The Science of Eating, 2017). This bacteria is associated with a reduced risk for diabetes, metabolic syndrome, IBD and cancer. “This study concluded that consuming kiwis acts quickly to exert these effects, “fertilizing” Bifidobacterium and Lactobacillus so that they grow stronger and more populous. These prebiotics found in kiwifruit help improve the overall functionality of the digestive system, while at the same time bolstering the immune system, a bulk of which resides in the gastrointestinal tract”(The Science of Eating, 2017). The kiwi fiber (New Zealand) specifically targets this microbe. FOS can also be beneficial if it is tolerated, but many people do not tolerate it. Akkermansia (mentioned above) also responds well to prebiotics. Psyllium husks are bacteria’s favorite food, and a simple and effective way to promote the growth of akkermansia and other probiotic bacteria residing in your gut. Other prebiotics include plant tannins such as pine bark. Polyphenols (clover, ginger, star anise, spearmint, moringa, curcumin, schizandra, bilberry, blueberry, mexican oregano, thyme, rosemary. Also flax seed meal, psyllium, vegetation, and hard fruit skins. If no SIBO, then inulin and onion, cabbage, cruciferous vegetables. Try to consume at least 32 grams of fiber per day.
7. Avoid foods laden with pesticides and choose organic when possible-Glyphosate and weed killers found on non-organic foods has a huge impact on the microbiome.
Fermented foods are not a good source of probiotics! They die during the process of entering the gut, but they do help create a healthier terrain for your gut and can be a good effective fertilizer and act as a good substrate for growing the good bacteria. For those with Mast cell issues or are histamine intolerant, they can be problematic. However, spore based probiotics are tolerated well with people with histamine intolerant. An option for these populations is to ferment your own foods with the spore based strains. They like warmer temperatures, and when they ferment they can produce interesting isoflavones, K2 at high levels, methylated B vitamins, coq10, 13 MTD (potent anti-cancer compounds). Be aware that they will not colonize the gut once they are fermented, but they will have the secondary health benefits mentioned.
So why the focus on the gut microbiome? Studies show the gut microbiome can influence the microbiome of other parts of the body. It can control what grows in other areas such as the vaginal or skin microbiome. These are parts of the body you do not want a lot of diversity. The dysfunctions in these areas of the body originate in the gut. So think of the gut as the control center of the body’s microbiome. The theory is that the spore based probiotics can lower systemic inflammation, since leaky gut is the major driver of systemic regulation due to an up-regulation of pro-inflammatory cytokines. Interestingly, the Spore based probiotics have been shown to lower the systemic inflammation in studies using conventional blood draws, as seen in circulatory cytokine and inflammatory markers. The spores can actually shut down the leakiness in the gut which will facilitate lowering the systemic inflammation. This is really exciting news for those with chronic inflammatory conditions!
There was also a significant drop of triglycerides by 50 points in 30 days. They are a great marker on stress on liver and inflammation inn body. They are produced by the liver in response to stress, constant detoxifying and large amounts of inflammation in the body. By lowering this marker it is demonstrating it can lower both systemic and local inflammation in the body. Inflammation is the number one cloaking mechanism by bacteria and fungus. You do not want inflammation in your body. When your body is constantly inflamed, it creates an increase in your innate immune system, which can lead to destruction of your cells and can allow pathogenic cells like cancer cells and infections flourish.
If you want more information on Megaspore, which is only available from practitioners, you can use the contact form below or email me at email@example.com. It is often used to complement any other protocols you are doing and should not be used as a stand-alone therapy.
Fill out the contact form below if you want to try this product, they are currently retailing at $55 per bottle.
Beasley, D. E., Koltz, A. M., Lambert, J. E., Fierer, N., & Dunn, R. R. (2015). The Evolution of Stomach Acidity and Its Relevance to the Human Microbiome. PLoS ONE, 10(7), e0134116. doi:10.1371/journal.pone.0134116
Evans, D. F., Pye, G., Bramley, R., Clark, A. G., Dyson, T. J., & Hardcastle, J. D. (1988). Measurement of gastrointestinal pH profiles in normal ambulant human subjects. Gut, 29(8), 1035-1041.
Flesh, Fiber, Skin & Seeds: The incredible Health Benefits of Kiwi Fruit (n.d.) Retrieved from http://thescienceofeating.com/2016/12/27/flesh-fiber-skin-seeds-the-incredible-health-benefits-of-kiwi-fruit-2/
Microbiome Medicine with Kiran Krishnan. (2017, April 21). Retrieved from https://www.youtube.com/watch?v=IolxUHdiX3Y&feature=youtu.be
Silvers, Ken. (2017, October 1). Akkermansia Muciniphila: Weight Loss Bacteria at Your Service. Retrieved from https://www.probioticscenter.org/akkermansia-weight-loss/