How To Enhance Your Microbiome For Weight Loss + Brain Health

Enhance Your Microbiome For Weight Loss + Brain Health Dr. Will Cole 2

Something alien controls you – it lurks deep inside you, and influences you without you even realizing! But don’t worry, this inner alien community usually works in your best interest. The relationship you have with your microbiome – the trillions of bacteria and yeast that live in your gut and on your skin – is mostly a happy and symbiotic one.

Article continues below

Make Your Life a Cleanse



Get FREE access to these + giveaways, recipes, & discount codes (including 50% off code for video courses) in personal emails from Dr. Will Cole


9 Facts About Your Microbiome

1. Your microbiome is enormously vast

Your microbiome is made up of approximately 100,000,000,000,000 (that’s 100 trillion) living microbes. One trillion dollar bills laid next to each other would extend from the earth to the sun and back with many miles left to spare. Do that 100 times and you start to get at least a rough idea of what’s living inside of you.

2. It’s immensely complex

With hundreds of known diverse bacterial species and many more still unknown, the bacterial diversity of your microbiome is an important part of your health. The more diverse your microbiome, the better (1) your health potential tends to be, and that diversity comes from exposure to the down-and-dirty world, including not just the foods we eat (and how clean they are) but the dirt we work in outside, the animals that we play with, and the very air we breathe. Even how and where you were born! All these things determine the richness and diversity of your gut garden.

3. You are more bacteria than human

Your gut contains 100 trillion bacteria. Compare that to the 10 trillion human cells in your body, you are, in fact, 10 times (2) more bacteria than human, if you are going by cell count! In addition, the genes of your microbiome bacteria outnumber your own by 100 to 1!

4. It’s the foundation of your health

Many seemingly unrelated health problems are now being linked to underlying gut problems such as diabetes and heart disease. Read my previous article here for the full list of health problems associated with microbiome dysfunctions.

5. It holds the majority of your immune system

If you find yourself feeling chronically sick and run down, be sure to check your microbiome health. A staggering 75 to 80 percent (3) of your immune system is produced in your gut! It’s no wonder that many immune issues, including autoimmune diseases, may be linked to hidden gastrointestinal problems.

6. It influences many aspects of your health

You may now be thinking, “I don’t have bloating, diarrhea, constipation, or IBS, so this doesn’t apply to me.” But you don’t have to have gut symptoms to have gut problems. The majority of underlying gut problems don’t have noticeable GI symptoms, but show themselves through systemic effects that manifest in other parts of your body.

7. It affects your weight

I’ve talked to countless patients who have struggled with weight gain since they were little kids. Now, some research suggests that the gut might be the missing link to chronic weight-loss resistance.

One study (4) published in the scientific journal Nature found that weight gain was associated with bacterial imbalances, specifically higher amounts of the bacteria Firmicutes. Another 2015 study (5) found that adults with metabolic syndrome who took a probiotic supplement showed improvements in their triglyceride levels and other risk factors for heart disease.

Also, your sleepy-time hormone (melatonin) is made in the brain – but there’s also a lot of it in your gut! And the health of the bacteria in your gut is essential (6) for healthy melatonin levels. In short, an unhealthy microbiome will mess up your sleep. The problem? Losing out on sleep can make (7) fat cells 30 percent less able to play nicely with your fat-burning hormone, insulin.

Short-chain fatty acids (SCFAs) get made in your gut as a result of bacterial fermentation. In other words, bacteria feed off of the food you eat and they make SCFAs as a by-product. These fatty acids, are important because they prevent gut problems like small intestinal bacterial overgrowth (SIBO). Research is finding (8) that our SCFAs also promote weight loss, and all three types of SCFAs (acetate, propionate, and butyrate) decrease cravings.

8. Your diet can influence your microbiome

A recent study (9) found that polyphenols from foods such as blueberries, coffee, and extra-virgin olive oil play a significant role in the prevention of degenerative diseases by improving your microbiome environment. This is the power you wield with your fork!

9. It's your "second brain"

This gut-brain axis connection is something we look at very closely in functional medicine. For example, anxiety and depression have been linked (10) to lower levels of Lactobacillus helveticus and Bifidobacterium longum bacterial strains in the gut. It always amazes me what bacterial and yeast problems I find in the lab results of patients not coming in for gut problems but for brain problems like depression, anxiety, and brain fog. To have a healthy brain, you need a healthy gut.

The microbiome is home to around 80% of your immune system and 95% of your “happy” neurotransmitter serotonin. It controls your moodweighthormones, and even your genetic expression, and as long as it contains a good mix of beneficial bacteria and yeasts, your body should hum along nicely.

However, sometimes pathogenic bacteria and yeasts get the upper hand and when that happens, your health can take a wrong turn. This can happen even if you don’t have classic gastrointestinal symptoms. Many people believe that if they don’t have bloating, constipation, diarrhea, or IBS symptoms, they don’t have a gut problem, but that is simply not true. Just like the brain, the mucosal lining of the gut has no pain fibers and you can’t “feel” when pathogenic species start causing health problems for you.

In reality, most people with underlying gut problems do not have obvious GI symptoms but have the downstream effects of a damaged microbiome. Because your gut is foundational to every other system of your body, these effects can crop up anywhere. If you have a chronic autoimmune condition, chances are it has a microbiome component, and it might even be entirely a microbiome problem.

Health Problems That Contribute To Poor Gut Health

Problem #1: Leaky Gut Syndrome

When the gut lining is damaged, undigested food particles and bacterial endotoxins called lipopolysaccharides (LPS) can pass through the leaky spots, causing systemic inflammation and often, autoimmune reactivity throughout your body.

In functional medicine, leaky gut syndrome is seen as an almost precondition for autoimmune diseases and many other health problems. Just because you are eating a Paleo diet does not mean you have completely cured your leaky gut. You may still be eating foods that cause inflammation for you.

Problem #2: Bacterial Dysbiosis

Your inner gut garden must maintain a delicate balance for optimal health, but sometimes, the more pathogenic species overgrow, or bacteria gets into places they aren’t supposed to be. Conditions like small intestinal bacterial overgrowth (SIBO) and other bacterial imbalances are linked to numerous health problems. When someone with dysbiosis or SIBO starts eating a Paleo diet, and they increase their vegetable intake, it can sometimes cause more gut problems like constipation and bloating. It is the underlying microbiome issue, not the vegetables, that is the problem.

Problem #3: Yeast Overgrowth

We all have some yeast in our gut microbiome, but overgrowths of yeast such as candida albicans can cause chronic low-grade inflammation and immune stress. People with an already weakened immune system or autoimmune problem can find a yeast overgrowth to be a trigger for more health problems. While a Paleo diet can help to control yeast, serious cases of overgrowth may need more intervention and some food limitations and additions that go beyond the basic rules of Paleo.

Problem #4: Food Intolerances

Eating a cleaner diet means ditching many of the immunoreactive and inflammatory foods you might have been eating before (such as gluten, sugar, and bad fats), and that’s a great start. However, for some people, especially those who had a very poor diet previous to changing their eating habits, or who have a lot of toxic exposures, intolerances to foods generally accepted as "healthy" may be a factor.

When the gut is chronically damaged and an inflammatory-immune response has been triggered, your immune system can react to even the healthiest of foods. I have seen bone broth, kale, liver, and just about every other nutrient-dense food be a source of inflammation for some well-intentioned people. What works for someone else may not be right for you, and you may need some professional guidance to uncover your exact food intolerances.

Problem #5: Autoimmunity

Autoimmune spectrum conditions are rampant in our modern world. An estimated 50 million Americans have an autoimmune disease, a number which is generally expected to go nowhere but up. Leaky gut syndrome and other microbiome dysfunctions can trigger elevated antibodies and immune inflammation against any organ or tissue, including the gut, brain, and thyroid. Switching to a so-called "clean" diet may not be enough to turn this around.

What To Do Now?

Keeping your microbiome healthy keeps you healthy, and when your microbiome health declines, so does your health. Let’s look at the many things you can do right now to start maximizing the health of your microbiome (and by extension, the health of you).

1. Ask your doctor about functional medicine labs

You may consider yourself a smart health detective, but it’s easy to overdose on Google. Instead of self-diagnosing, ask about labs that can help you quantify what is going on and give you an objective clinical look at why you feel the way you do.

For instance, blood and stool labs can give you a detailed look at your microbiome, the levels of your specific bacteria and yeast, rule out (or in) leaky gut syndrome, give insight into your food intolerances, and measure your autoimmune reactivity.

2. Evaluate your stress

Eating clean but still being chronically stressed sabotages your good attempts to help your body heal. Chronic stress has been shown (11) to suppress the immune system, decreased blood and oxygen flow to the intestines, and increase gut lining permeability. It’s hard to get better with all that going on. That’s why I suggest finding ways to regularly de-stress. Learn mindfulness meditation, tai chi, yoga, or just spending more time in nature. That is an important piece to your healing puzzle.

3. Cut out the junk

This one should be a no-brainer, but just in case you need a little more motivation to avoid the drive-through, know that one of the most important things you can do for a healthy microbiome is to avoid processed foods, which can cause inflammation in your protective gut lining and damage a healthy balance of gut flora, giving pathogenic bacteria the upper hand and crowding out the beneficial bacteria that do so many good things for you.

4. Take antibiotics and NSAIDs only when essential

Many of us spent our younger years on antibiotics for every sniffle or ear ache, then later learned to pop over-the-counter pain pills like ibuprofen with every ache and pain. Both these medications can tip the microbiome balance in a bad direction, so limiting antibiotics and NSAIDs is essential to provide a good environment for your microbiome. (See also these other culprits and how to minimize them to maximize your microbiome’s health).

5. Eat living food

With every meal, you either increase your microbiome’s health, or decrease it. “You are what you eat” might be better stated as “You are what your microbiota eat.” In other words, eat living plant food, the more variety, the better, as these are the foods that best feed the beneficial bacteria in your gut garden. However, remember that what works for one person doesn’t necessarily work for everyone, and you may need to experiment to find the living plant foods that work best for you. For example, people with SIBO (small intestinal bacterial overgrowth) or IBS tend to do better avoiding foods high in FODMAPS (Fermentable Oligo-, Di-, Monosaccharides And Polyols), which include many plant foods such as onions and garlic, at least until the condition is resolved. Fortunately, plant food choices are vast and diverse, and anyone should be able to find vegetables and fruits that help their microbiomes and bodies thrive.

6. Eat fermented food

If it’s fermented, pickled, or cultured, it has good bacteria in it, so fermented foods like sauerkraut, kimchee, and kefir can help to recolonize your gut with beneficial bacteria. Although some people with dysbiosis don’t do well with these foods or have to lay off them temporarily while healing, for many others, they can be great microbiome supporters.

7. Try natural medicine

Some of the gut-boosting natural compounds I’ve found useful include L-glutamine, slippery elm, marshmallow root, and deglycyrrhizinated (DGL) licorice. These are great natural substances that can aid in repairing the protective lining of your gut.

8. Advanced strategies

There are some other next-level protocols that can improve gut health, depending on your situation, although they should all be done under the guidance of an experienced health practitioner. Personally, I’ve found many cases of microbiome dysbiosis or gut dysfunction respond well to condition-specific intermittent fasting regimens, involving food restriction for set amounts of time to allow for better gut healing and a microbiome reset.

Fecal bacteriotherapy is another experimental treatment in which a patient receives a fecal transplant from a healthy donor. This has in some cases successfully reset the microbiome in people who were very sick or weight-loss-resistant. This might sound too gross for some, but I’ve seen therapies like this do wonders for people’s health when they haven’t been able to find relief elsewhere. Again, however, this is not a DIY project and must be managed by a professional.

9. Increase your bacterial diversity

Probiotics are a great tool to balance your microbiome, and a combination of bifidobacteria, enterococcus, and lactobacillus has been shown (12) to have a positive effect on small intestinal bacterial overgrowth. They encourage healthy bacterial populations. I am also a fan of soil-based probiotics to further broaden the varieties of microbes in your gut. Eating a variety of fermented foods like sauerkraut, kimchi, kombucha, and coconut kefir is another great way to introduce different bacterial strains, to promote healthy bacterial diversity.

10. Optimize conditions for short-chain fatty acid levels

SCFAs are made when you eat healthy prebiotic and high-fiber foods. Load up on nutrient-dense leafy greens like spinach, kale, Swiss chard, and watercress, as well as other super plant foods. To increase the fat-burning butyrate, I also suggest bringing Hi-Maize Resistant Starch into your diet to boost butyrate in your large intestine. Hydroxymethyl butyrate can also be supplemented.

11. Check out personalized functional medicine care

There is no “one size fits all” approach to regaining your health. We are all different. Customized and advanced natural solutions are at the heart of functional medicine, which can help you tweak and augment your diet to get you to where you want to be.

As one of the first functional medicine telehealth clinics in the world, we provide webcam health consultations for people around the globe. 

Photo: Stocksy

Start Your Health Journey Today



  1. Le Chatelier, E., Nielsen, T., Qin, J. et al. Richness of human gut microbiome correlates with metabolic markers. Nature 500, 541–546 (2013).
  2. American Society for Microbiology. (2008, June 5). Humans Have Ten Times More Bacteria Than Human Cells: How Do Microbial Communities Affect Human Health?. ScienceDaily. Retrieved May 28, 2020 from
  3. Furness JB, Kunze WA, Clerc N. Nutrient tasting and signaling mechanisms in the gut. II. The intestine as a sensory organ: neural, endocrine, and immune responses. Am J Physiol. 1999;277(5):G922‐G928. doi:10.1152/ajpgi.1999.277.5.G922
  4. Turnbaugh, P., Ley, R., Mahowald, M. et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444, 1027–1031 (2006).
  5. Ahn HY, Kim M, Chae JS, et al. Supplementation with two probiotic strains, Lactobacillus curvatus HY7601 and Lactobacillus plantarum KY1032, reduces fasting triglycerides and enhances apolipoprotein A-V levels in non-diabetic subjects with hypertriglyceridemia. Atherosclerosis. 2015;241(2):649‐656. doi:10.1016/j.atherosclerosis.2015.06.030
  6. Galland L. The gut microbiome and the brain. J Med Food. 2014;17(12):1261‐1272. doi:10.1089/jmf.2014.7000
  7. Impaired Insulin Signaling in Human Adipocytes After Experimental Sleep Restriction Josiane L. Broussard, David A. Ehrmann, Eve Van Cauter, Esra Tasali, and Matthew J. Brady Annals of Internal Medicine 2012 157:8, 549-557
  8. Kallus SJ, Brandt LJ. The intestinal microbiota and obesity. J Clin Gastroenterol. 2012;46(1):16‐24. doi:10.1097/MCG.0b013e31823711fd
  9. Taira T, Yamaguchi S, Takahashi A, et al. Dietary polyphenols increase fecal mucin and immunoglobulin A and ameliorate the disturbance in gut microbiota caused by a high fat diet. J Clin Biochem Nutr. 2015;57(3):212‐216. doi:10.3164/jcbn.15-15
  10. Messaoudi M, Lalonde R, Violle N, et al. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br J Nutr. 2011;105(5):755‐764. doi:10.1017/S0007114510004319
  11. Gareau MG, Silva MA, Perdue MH. Pathophysiological mechanisms of stress-induced intestinal damage. Curr Mol Med. 2008;8(4):274‐281. doi:10.2174/156652408784533760
  12. Fan YJ, Chen SJ, Yu YC, Si JM, Liu B. A probiotic treatment containing Lactobacillus, Bifidobacterium and Enterococcus improves IBS symptoms in an open label trial. J Zhejiang Univ Sci B. 2006;7(12):987‐991. doi:10.1631/jzus.2006.B0987

Shop This Article

Purchase personally curated supplements
and Dr. Will Cole’s books!

Shop Dr. Will Cole

The information on this website has not been evaluated by the Food & Drug Administration or any other medical body. We do not aim to diagnose, treat, cure or prevent any illness or disease. Information is shared for educational purposes only. You must consult your doctor before acting on any content on this website, especially if you are pregnant, nursing, taking medication, or have a medical condition.

Our articles may include products that have been independently chosen and recommended by Dr. Will Cole and our editors. If you purchase something mentioned in this article, we may earn a small commission.



Evidence-based reviewed article

Dr. Will Cole, DNM, IFMCP, DC is a leading functional medicine expert who consults people around the globe, starting one of the first functional medicine telehealth centers in the world. Named one of the top 50 functional and integrative doctors in the nation, Dr. Will Cole provides a functional medicine approach for thyroid issues, autoimmune conditions, hormonal imbalances, digestive disorders, and brain problems. He is the host of the popular The Art Of Being Well podcast and the New York Times bestselling author of Intuitive Fasting, Ketotarian, The Inflammation Spectrum and the brand new book Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.