Your Gut Health May Be Standing In The Way Of Weight Loss: Here’s What To Do

Gut Health And Weight Loss

Something alien controls you. It lurks deep inside you, influencing your weight, immune function, and overall health without you even realizing it! Trillions of microorganisms live in your gut and influence your weight and overall health.

This is the gut microbiome.

There are 3-4 major biomes in your body (including oral, skin, vaginal), but the most important biome is in your gut. Your gut microbiome has more diverse bacteria than any other biome, and it contains most of your immune system.

If I have a patient who wants to lose weight, I first talk to them about the balance of microbes in their gut microbiome.

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I talked about the microbiome on my podcast episode with Kiran Krishnan, a research microbiologist who has conducted dozens of human clinical trials. Here’s what he had to say:

“If [food and consumer products] meet the standards in the 1950s and 60s, then it’s deemed to be safe… Not surprisingly, most of the things we consume, put on us, in us, around us kill our microbes.”

A balanced gut microbiome can help you maintain a healthy weight, but a dysbiotic microbiome can lead to undesired weight changes, metabolic disease, and worse. Keep reading to find out more.

Most of us need a metabolic health reset. Join me on this Metabolic Recharge journey with step-by-step guidance from a functional doctor.

How Your Gut Can Help — Or Hurt — With Weight Management

I’ve talked to countless patients at my clinic who have struggled with weight gain since they were little. Typical dietary and exercise changes weren’t giving them the results they expected. Now, research suggests that gut microbes might be the missing link to chronic weight-loss resistance.

The microbiome is home to around 80% of your immune system and 95% of your “happy” neurotransmitter, called serotonin. (!) This community of microbes controls your mood, weight, hormones, immune responses, blood sugar (glucose), and even your genetic expression. As long as it contains a good mix of beneficial bacteria and yeasts, your body should hum along nicely.

But we’re here to talk about when the gut biome is not well-balanced.

“One of the scariest things to me and what keeps me up at night is this ‘mass extinction’ we’re facing,” says microbiology researcher Karin Krishnan. “What we are is this amazing microbial construct. We’re made up of microbes, we’re run by microbes, we depend on microbes, and we’ve taken this beautiful microbial construct, and we’ve put it in an end-time microbial world.”

Krishnan and I got to talk about what that end-time microbial mass extinction looks like. Between inflammatory Western diets, antibiotic overuse, and the wild chemicals that get into your food and water, no wonder your gut microbiome is in dysbiosis.

You may be thinking, “I don’t have bloating, diarrhea, constipation, or IBS, so this doom and gloom 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 gut symptoms but instead show themselves through systemic effects that manifest in other parts of your body.

What’s The Science Say?

Every year, the gut microbiome’s impact on weight, the brain, the immune system, and the whole body becomes more mainstream. Remember, though, that functional doctors were healing the gut microbiome before it was conventional!

An older study published in Nature found that weight gain was associated with bacterial imbalances before clinical acceptance of the gut microbiota’s existence hit the mainstream. (2) This newer study concludes that regulating intestinal microbes reduces the risk of obesity. (3)

An unhealthy microbiome will mess up your sleep. The health of your gut bacteria is essential for healthy levels of melatonin, your sleepy-time hormone. (4) The problem? Losing out on sleep can make fat cells interact 30% less with the fat-burning hormone insulin. (5)

Short-chain fatty acids (SCFAs) are made in your digestive system as a result of bacterial fermentation. Research is finding that SCFAs promote weight loss, and all 3 types of SCFAs (acetate, propionate, and butyrate) decrease appetite cravings. (6)

Unfortunately, the microbiome-weight relationship is a vicious cycle. Obesity contributes to gut dysbiosis, and dysbiosis contributes to weight gain. Take control of your health and break this vicious cycle.

@drwillcole Can your microbiome tell you to eat more? 💭 Don't miss this week's new episode of The Art Of Being Well with @zbiotics founder, Zack Abbott. 🎧 Listen now and let me know what you think about this one. #taobw #drwillcole #zbitotics #probiotics #microbiome ♬ original sound - Dr. Will Cole

Your Gut Is Your “Second Brain”

This gut-brain axis connection is something we look at very closely in functional medicine. This axis describes the special relationship between your gut health and how your brain functions. Because of how much the gut impacts your brain and mental health, some call the gut the “second brain.”

For example, anxiety and depression have been linked to lower levels of Lactobacillus helveticus and Bifidobacterium longum in the gut. (7) 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.

Guess what — a huge contributor to weight gain is poor mental health. If your gut is unhealthy, your brain will not function well, which can lead to unhealthy weight-changing lifestyle choices, such as: (8)

  • Less physical activity
  • Sleep problems
  • Eating disorders
  • Soda consumption
  • Alcohol consumption
  • Smoking

Check out my Gut Feelings Supplement, designed to support a healthy gut-brain axis and balance your mood.

America: It’s Worse Here Than Anywhere Else

American diets are filled with highly processed foods, mysterious additives, lots of sodium, and unnatural sugars and carbohydrates. This inflammatory combo means that the microbes in American guts are very out of balance and more prone to unhealthy weight gain.

Just about anywhere else in the world, even the “unhealthy” foods people eat are better for us than some of the “health” foods in the United States. American diets are shortening American lives.

Krishnan adds:

“Most of the food we eat is covered with herbicides and pesticides, which are strongly antimicrobial. Everything around us works against us. The water we drink, with the chlorine and fluoride in there that acts as an antimicrobial… You go outside, and your neighbor is using Roundup around his or her garden, right? All of that is running off into your own drinking water.”

8 Strategies To Improve Gut Health And Start Losing Weight

Keeping your microbiome healthy keeps you and your body weight healthy. When your microbiome health decreases, your weight is bound to increase. Let’s look at the strategies you can implement right now to start maximizing your microbiome health, your weight management, and, by extension, your overall well-being.

1. Get Tested

Ask a functional doctor about comprehensive lab tests. Diagnostics can help you understand the root cause of your weight gain and gut issues.

You may consider yourself a health detective, but it’s easy to overdose on Google. Instead of self-diagnosing, ask about labs that help you quantify what is going on in your gut. You want an objective clinical look at why you feel the way you do. Then you can objectively treat that underlying problem.

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 confirm leaky gut syndrome, give insight into your food intolerances, and measure your autoimmune reactivity.

LISTEN: The Metabolic Recharge Protocol — Sustainable Weight Loss Without Big Pharma Side Effects

2. Cut Out The Junk

This one should be a no-brainer, but in case you need a little more motivation to avoid the drive-thru, know that one of the most important things you can do for a healthy microbiome is to avoid processed foods that cause gut inflammation and unhealthy weight gain.

Want to learn more about inflammation? Read The Inflammation Spectrum, my handy book about learning to love your body enough to nourish it with delicious, healing foods.

To avoid processed food, you must know what it looks like. Processed food includes:

  • Fast food
  • Frozen meals
  • Processed meats
  • Fried foods
  • Cereals
  • Chips
  • Cookies
  • Sweetened beverages or foods
  • Most packaged items
  • Almost anything a grocery store outside meat and produce sections

3. Consume Probiotics

Probiotics (AKA beneficial bacteria) have many health benefits, including balancing your microbiome and losing weight. Probiotic supplements restore and improve gut microbiota, and the “use of probiotics has been shown to reduce BMI (body mass index) and total body fat,” according to this recent study. (9, 10)

I am a particular fan of soil-based probiotics to broaden the variety of microbes in your gut.

“Increase the diversity of your diet in baby steps,” microbiologist Krishan suggests, “use some intermittent fasting, start going outside more, take your soil-based probiotic — just these 4 things alone will be a huge impact on your microbiome and your overall health.”

Can probiotics help with weight loss? Yes, some probiotic strains support healthy management, especially weight loss from visceral fat burning.

Supplements are great, but adding probiotics to your diet is great, too. If it’s fermented, pickled, or cultured, it has good bacteria in it. Eat fermented foods, including:

  • Sauerkraut
  • Kimchi
  • Kombucha
  • Kefir

Although some people with dysbiosis don’t do well with these foods or have to lay off them temporarily while healing, many others find them to be great microbiome supporters.

4. Consume Prebiotics

Prebiotics essentially promote the growth of healthy probiotics, which play an important role in healthy weight management, by offering yummy “food” for probiotics to feast on in the form of fiber. Beneficial short-chain fatty acids (SCFAs) are made when you eat healthy prebiotics and dietary fiber.

Load up on nutrient-dense prebiotic leafy greens, such as:

  • Spinach
  • Kale
  • Leeks
  • Swiss chard
  • Watercress
  • Artichokes

Other high-fiber prebiotic foods include whole grains, legumes, garlic, and onions.

5. Intermittent Fasting

Personally, I’ve found that intermittent fasting (IF) regimens have a positive effect on gut microbiome dysbiosis and stubborn weight gain. This involves food restriction for set amounts of time to allow for better gut healing and a microbiome reset. (11, 12)

Talk to a dietitian or your doctor before trying a new diet.

I’m a huge fan of IF. For more guidance, check out my book, Intuitive Fasting.

6. Sparingly Use Antibiotics And NSAIDs

Many of us spent our younger years on antibiotics for every sniffle or on over-the-counter pain pills like ibuprofen for every ache and pain. Both antibiotics and NSAIDs (non-steroidal anti-inflammatory drugs, like ibuprofen) may impact your microbiome balance and lead to weight gain.

Limit antibiotic and NSAID use. This limitation is essential in providing a good environment for your microbiome. In special cases, you may need them to survive, but doctors have historically over-prescribed antibiotics and over-recommended NSAIDs.

Krishnan explains:

“We, of course, completely overuse antibiotics. In prescriptions, in food processing, in cattle farming — in all of these areas we’re exposing ourselves towards awful antibiotics.”

See also these other anti-gut culprits and how to minimize them to optimize your microbiome’s health.

7. Evaluate Stress

Eating clean can’t completely heal your gut if you’re still chronically stressed. Constant stress has been shown to suppress the immune system, weaken gut lining permeability, and increase weight. (13, 14, 15)

I suggest finding ways to regularly de-stress, including these fantastic stress relievers:

  • Mindfulness meditation
  • Tai chi
  • Yoga
  • Spending time outside
  • Reducing screen time, especially before bed

“Going out for a walk or a hike, going outdoors in a natural environment,” Krishnan recommends, “that interaction with nature is so powerful for your microbiome.”

8. Try Natural Medicine

Natural medicine is often superior to pharmaceuticals that lead to adverse effects and addiction. Using herbs may promote gut health and healthy weight management without those nasty side effects.

Some of my favorite gut-boosting natural compounds include:

  • L-glutamine
  • Slippery elm
  • Marshmallow root
  • Deglycyrrhizinated (DGL) licorice
  • Green tea (chock-full of anti-inflammatory polyphenols)

These are great natural substances that can help repair the protective lining of your gut and lead to a healthier body weight.

Kick The Stubborn Weight For Good

There is no one-size-fits-all approach to losing weight and regaining your holistic wellness. We are all different. Customized natural solutions are at the heart of functional medicine, which can help you tweak and augment your diet and lifestyle to get your gut and weight where you want.

Ready to try something that works for sustainable weight loss? Join my Metabolic Recharge, a 90-day program designed to help you kick the stubborn weight for good by developing a healthy gut and better habits.

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  1. Furness, J. B., Kunze, W. A., & Clerc, N. (1999). Nutrient tasting and signaling mechanisms in the gut. II. The intestine as a sensory organ: neural, endocrine, and immune responses. American Journal of Physiology-Gastrointestinal and Liver Physiology, 277(5), G922-G928.
  2. Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027-1031.
  3. Noor, J., Chaudhry, A., Batool, S., Noor, R., & Fatima, G. (2023). Exploring the impact of the gut microbiome on obesity and weight loss: a review article. Cureus, 15(6).
  4. Galland, L. (2014). The gut microbiome and the brain. Journal of medicinal food, 17(12), 1261-1272.
  5. Broussard, J. L., Ehrmann, D. A., Van Cauter, E., Tasali, E., & Brady, M. J. (2012). Impaired insulin signaling in human adipocytes after experimental sleep restriction: a randomized, crossover study. Annals of internal medicine, 157(8), 549-557.
  6. Kallus, S. J., & Brandt, L. J. (2012). The intestinal microbiota and obesity. Journal of clinical gastroenterology, 46(1), 16-24.
  7. Messaoudi, M., Lalonde, R., Violle, N., Javelot, H., Desor, D., Nejdi, A., ... & Cazaubiel, J. M. (2011). Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. British Journal of Nutrition, 105(5), 755-764.
  8. Michels, N. (2021). Poor mental health is related to excess weight via lifestyle: A cross-sectional gender-and age-dependent mediation analysis. Nutrients, 13(2), 406.
  9. Dahiya, D., & Nigam, P. S. (2022). The gut microbiota influenced by the intake of probiotics and functional foods with prebiotics can sustain wellness and alleviate certain ailments like gut-inflammation and colon-cancer. Microorganisms, 10(3), 665.
  10. Aoun, A., Darwish, F., & Hamod, N. (2020). The influence of the gut microbiome on obesity in adults and the role of probiotics, prebiotics, and synbiotics for weight loss. Preventive nutrition and food science, 25(2), 113.
  11. Paukkonen, I., Törrönen, E. N., Lok, J., Schwab, U., & El-Nezami, H. (2024). The impact of intermittent fasting on gut microbiota: a systematic review of human studies. Frontiers in Nutrition, 11, 1342787.
  12. Shalabi, H., Hassan IV, A. S., Al-Zahrani, F. A., Alarbeidi, A. H., Mesawa, M., Rizk, H., ... & Aljubayri IV, A. A. (2023). Intermittent Fasting: Benefits, Side Effects, Quality of Life, and Knowledge of the Saudi Population. Cureus, 15(2).
  13. Bae, Y. S., Shin, E. C., Bae, Y. S., & Van Eden, W. (2019). Stress and immunity. Frontiers in immunology, 10, 420512.
  14. Madison, A., & Kiecolt-Glaser, J. K. (2019). Stress, depression, diet, and the gut microbiota: human–bacteria interactions at the core of psychoneuroimmunology and nutrition. Current opinion in behavioral sciences, 28, 105-110.
  15. Kumar, R., Rizvi, M. R., & Saraswat, S. (2022). Obesity and stress: a contingent paralysis. International Journal of Preventive Medicine, 13(1), 95.

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.

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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 Gut Feelings: Healing the Shame-Fueled Relationship Between What You Eat and How You Feel.

Gut Feelings Dr. Will Cole 6

Gut Feelings

Healing The Shame-Fueled Relationship
Between What You Eat And How You Feel