How Gut Health Affects Your Weight

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I think we can all agree that the type of foods we eat directly impacts our weight. If we choose to eat a high-calorie diet full of processed sugary foods and drinks with lots of carbohydrates, weight generally goes up assuming exercise stays the same.  On the contrary, if we choose to eat a calorie- and carbohydrate-restricted diet higher in good fat and protein, weight generally goes down.

What about the old saying “calories in, calories out” in regard to weight loss: does eating less and exercising more always lead to weight loss? Not really, because:

  • Metabolism is VERY complex and unique to each and every person
  • The type of calories you consume matters
  • The health of your GI tract matters

For example, those following the ketogenic diet (high fat, low protein, low carbohydrate) tend to lose weight rather quickly as the body is in a state of ketosis, which is its fat-burning mode. The ketogenic diet, which is typically higher in calories, may be helpful for weight loss, but it may not be beneficial long-term for supporting the gut microbiome as a high fat diet may negatively affect diversity of microorganisms in the gut.   

Research shows that the gut-brain axis can influence metabolism via many different mechanisms, and microbes are partly responsible for this. We know that microbes directly influence the following, mainly through communication with the vagus nerve:

  • Immune system function via cytokine production
  • Short chain fatty acid production (e.g., butyrate)
  • Neurotransmitter production (e.g., serotonin)

We Have Mice Studies, But Limited Human Studies

Researchers have revealed some pretty interesting connections between gut microbes and weight, but we don’t have many human studies to back up their findings. For instance, if bacteria from obese mice are transplanted into the intestines of germ-free mice (mice bred with a sterile gut, i.e., no gut microbiome), the germ-free mice tend to gain weight. Think about that for a moment. 

What we do know from human trials is lean twins tend to have greater diversity of gut microbes compared to obese twins. What this means is that certain bacteria, like Bacteriodetes, may play a role in the breakdown of dietary fibers and utilization and production of energy by the body.

Findings like these do not necessarily suggest that human fecal microbial transplants from lean people into overweight people will lead to weight loss. These types of studies are being conducted right now, though, so this scenario might be a possibility in the future. 

What About Chronic Exposure to Antibiotics?

One of my favorite books on gut health is called Missing Microbes, written by Martin Blaser, MD, from New York University. In this book he discusses the evolutionary development of our microbiome, the importance of certain “missing microbes” like H. pylori, and the impact the environment has had on gut microbiome diversity.  

For example, Blaser found that when mice are administered low levels of antibiotics similar to what livestock receive, they can put on 15% more body fat than mice not given low dose antibiotics. Blaser goes on to explain that in certain areas of the USA, particularly the South where antibiotics are heavily used, the obesity rates are higher. This makes a stronger case for buying organic and pastured-raised animal products to minimize exposure to antibiotic residues. 

Inflammation in the Gut

If you have ever known anyone that’s suffered with an irritable bowel disease (IBD) like Crohn’s disease or ulcerative colitis, you know keeping weight on can be a problem for them. There are many reasons why IBD can lead to weight loss or the inability to gain weight, but chronic inflammation in the gut is likely the major cause. 

When the gut is inflamed, the cells lining the intestine are more likely to be damaged and absorption of nutrients is affected. As the body does not receive an adequate supply of nutrients from food, basic metabolic functions are disrupted, and muscle growth and fat storage are less likely to occur. When IBD sufferers are given steroids and/or supported through personalized medicine treatments, weight usually stabilizes and tends to return over time. 

Dysbiosis and Sugar Cravings

Dysbiosis is a term used to describe an imbalance of gut flora. It usually indicates an overgrowth of an organism, like yeast or bacteria or even a parasite. Dysbiosis can develop for many reasons such as frequent antibiotic use or chronic stress or poor diet, and I find that many people with chronic gut issues have dysbiosis. 

What I’ve seen clinically, and experienced personally myself, is that overgrowth of yeast can cause sugar cravings. Yeast throw a party when sugar and simple carbohydrates are present; eating these foods keeps the party going. 

When patients come in and complain of the following constellation of symptoms, I like to rule out yeast or candida overgrowth in the intestines:

  • Sugar and carbohydrate cravings
  • Skin rashes, or pruritus (itching of the skin)
  • Fatigue
  • Brain fog
  • Joint pain
  • Itchy anus
  • Yeast infections

Of course, this presentation of symptoms can be due to many factors, but if I hear all or some of the above symptoms, I’ll investigate further and try to build a stronger case by running a stool test and candida antibodies on blood work. Once I’ve backed up my findings and I’m certain that yeast overgrowth is present, I’ll treat the dysbiosis with antifungal herbs and major dietary changes to kill and starve off the yeast, respectively. Usually within 8 weeks, sugar cravings are down and weight tends to plateau or even decrease as dietary habits improve.   

On a personal note, it took me decades to realize the harm sugar and refined carbohydrates were doing to my microbiome. As a young child I craved and ate a LOT of sugar. My belly frequently had access to sugary cereals, ice cream, sodas, chips, candies, and desserts. Even until age 35, I wanted to eat something sweet after dinner every single night! It wasn’t until I had been practicing medicine for almost a decade that I realized that I had dysbiosis, so I took antifungal herbs, and drastically reduced my sugar and carb content.

I cannot tell you how freeing it is to be in control of the sugar cravings, rather than the sugar cravings controlling me! It took a lot of experimentation to find out which sugars were more problematic, but over time my relationship to sugar and carbs (think tortilla chips!) has changed for the better. On the occasion that I crave something sweet after dinner, I’ll have some fruit or stevia-sweetened chocolate, which are much healthier options for supporting a healthy yeast population.

Heal Your Gut to Promote Healthy Weight

Research into the microbiome is exploding right now, and I predict that in the next 5–10 years, we’ll have a much stronger understanding of how the health of the gut impacts weight, and ways to manipulate the gut to reduce weight gain. At this time, it’s difficult for me to recommend specific treatments to reduce weight as metabolism is very complex and many factors, including genetics, are involved with weight gain. 

What I can suggest are the following as ways to strengthen and promote a healthy terrain in your gut, which may indirectly impact weight over the long term. 

  • Eat more fiber-rich foods, and minimize processed sugary foods.
  • Identify and treat underlying inflammation and/or dysbiosis in the gut.
  • Reduce excessive exposure to antibiotics and/or foods that may contain antibiotic residues.
  • Eat a vast assortment of fruits, vegetables, and grains (if you tolerate grains) to promote greater diversity of microbes.
  • Consume more fermented foods, which are rich in probiotics, fiber, and often prebiotics.
  • Exercise and/or move your body every day.
  • Reduce chronic stress in your life by incorporating more stress-reducing practices like meditation, yoga, mindful breathing, prayer, or positive intention/thoughts.
  • Take probiotics like Lactobacillus as certain strains have shown to improve insulin sensitivity.



Blaser, Martin. Missing Microbes. Oneworld Publications. England. 2014. 

Dr. Drew Sinatra

Meet Dr. Drew Sinatra

Dr. Drew Sinatra is a board-certified naturopathic doctor and self-described “health detective” with a passion for promoting natural healing, wellness, and improving quality of life by addressing the root cause of illness in patients of all ages. His vibrant practice focuses on treating the whole person (mind, body, and spirit) and finding missed connections between symptoms and health issues that are often overlooked by conventional medicine.

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