Gutbliss - Dr. Robynne Chutkan



Obesity is characterized as excessive amounts of body fat and is diagnosed using anthropometric measurements, including percent body fat, hip-to-waist ratio, waist-to-height ratio, and body mass index. Two-thirds of the US population has obesity or is overweight, more than one third of adults in the U.S. and almost one in five children are obese, and one third of the population worldwide is overweight. In addition to the incredible breadth of symptoms that accompany obesity, the disease makes you twice as likely to die and increases your chances of developing practically every digestive disease. Although obesity is a serious disease no matter where fat is distributed, fat deposition is important in predicting the likelihood of developing certain diseases. Fat deposited around the abdominal region (apple shaped) puts individuals with obesity at a much higher risk for developing metabolic syndrome – a deadly combination of risk factors, including high blood pressure, high fasting blood sugar, increased waist circumference, and elevated triglycerides, that dramatically increases your chances of developing heart disease, stroke, diabetes, and some types of cancer – than those with fat deposited in the hips and legs (pear shaped). Many scientific theories exist as to what causes obesity, and while it is most likely a disease with various contributing factors, studies show a strong association between obesity, lifestyle factors, and gut bacteria. 


Many of the symptoms and complications that accompany obesity are due to visceral fat (butter-colored bundles of fat that wrap around the abdominal organs and is most prevalent in obese individuals with an apple shape) accumulation in the abdomen. Visceral fat is a complex tissue similar in function to other endocrine organs like the thyroid gland. In addition to affecting the function of the liver, pancreas, and other internal organs, visceral fat itself is hormonally active, producing estrogens, proteins, and other substances that can affect insulin levels, blood sugar, cholesterol, and even the reproductive system. Belly fat puts you at higher risk for elevated lipids (fats) in the blood, diabetes, breast cancer, colon cancer, gallbladder problems, high blood pressure, and lots of other health issues, likely related to these hormonally active substances it secretes. The primary symptoms and conditions that are associated with obesity are many and include:

  • Estrogen dominance (a hormone called androstenedione made in the ovaries is converted to estrogen by fat cells)
  • Gallstones
  • Gallbladder dysfunction
  • Cancer (including colon and ovarian cancers)
  • Dysbiosis
  • Infertility
  • Decreased libido
  • Sleep apnea
  • Depression
  • Sexual dysfunction
  • Stroke
  • Heart disease
  • Liver disease
  • Skin conditions
  • Osteoarthritis
  • Type 2 diabetes
  • Metabolic syndrome


The following factors are the most common contributors to obesity:

  • Eating processed foods high in fat, salt, and sugar (including artificial sweeteners)
  • Lack of exercise
  • Genetics & familial lifestyle similarities
  • Sleep deprivation
  • Medications
  • Hormone issues, including hypothyroidism and PCOS

Although these factors contribute to the disease, obesity rates have increased too rapidly to blame genetics as the main cause, and although a diet high in fat and sugar is partly responsible, it doesn’t account for the striking increase in body mass index observed in the world population over the last few decades. Studies now show that maintaining a stable weight is much more complicated than calories in versus calories out; it’s what happens to those calories as they pass through the digestive tract and its gut bacteria that may explain the rapid increase in weight gain.

The following evidence implies that gut bacteria play a major role in obesity:

Diet: The food you eat affects the composition of the bacterial communities in your gut—high-fat, low-fiber diets are associated with a very different microbial profile than low-fat, high-fiber diets—and that microbial composition can in turn influence whether you end up gaining weight. Although diet can contribute to obesity by encouraging an overabundance of calories, certain foods can promote pathogenic bacteria that also contribute to obesity. A sugary, starchy, fat-laden Western diet encourages growth of the wrong type of bacteria in your gut.

Processed grains, refined sugar, & animal fats and proteins: Cutting down on processed grains and refined sugar can affect our microbiome in a positive way but replacing those foods with too much animal protein and fat can be problematic, because they may crowd out the dietary fibers that are an important component of a microbiome associated with leanness. We see a plateau in weight loss in many patients who put themselves on restrictive low-carb diets or Paleo devotees who don’t eat enough vegetables, probably because they’re not cultivating the right microbes.

Microbial Imbalance & Dysbiosis: Some experts who study gut bacteria believe that dysbiosis contributes to many diseases, including obesity. Interestingly, lean people are typically colonized with different bacterial species relative to their obese counterparts. In fact, we can distinguish between leanness and obesity with 90 percent accuracy just from looking at gut bacteria. Several experiments have shown that when we transplant microbes from obese mice into germ-free lean mice, they gain weight and their fat deposition increases, without any change in their diet or exercise regimen. We are now seeing the same thing happen in humans, and although we’re not sure exactly how, “obese” microbes are able to extract more calories than “lean” microbes from the same food, there are a number of ways bacteria can change their energy harvest: by controlling the transit time of food through the digestive tract, which determines how many calories can be extracted and absorbed; by influencing hormones that determine whether calories are deposited as fat versus used as energy; and by themselves consuming extra calories for tissue repair or other tasks.

Hormones: Polycystic ovary syndrome (PCOS) is associated with high levels of androgens and affects between 5 to 10% of women of reproductive age. Classic symptoms include excessive facial hair, male pattern baldness, acne, obesity, irregular menses, decreased fertility, and insulin resistance. Most, but not all women with PCOS will have multiple ovarian cysts demonstrated on ultrasound. Some studies have raised the possibility that obesity causes PCOS, rather than the other way around. What we do know is that addressing insulin resistance and obesity through a diet that restricts gluten and refined sugar improves a lot of the symptoms of PCOS, including bloating. High androgen (male hormone) levels, infertility, and irregular menstrual patterns in PCOS can usually be resolved with dietary modification and weight loss.

Genetics: What you’re eating has an impact on whether you gain weight, and genes have some influence, too, especially over where you gain it—they help dictate whether you end up a belly-prominent apple or a thigh-heavy pear. The Genetic Investigation of Anthropometric Traits consortium (GIANT) identified 13 new areas with variations in the DNA, that correlated with whether people were apple or pear shaped. Not surprisingly, the correlations were stronger in women. Although the identified genes only explained variations in fat distribution in about 1% of the population, the research suggests that for some of us, specific biological mechanisms may play a role in determining where fat is stored in our body. Other research shows that genetics are not the only cause of obesity. Researchers at Washington University in St. Louis took gut bacteria from identical twins (who have the same genes), where one was lean and one was obese, and transplanted them into germ-free mice. Within weeks, the mice that received microbes from the obese twin became obese, and the ones who received microbes from the lean twin stayed lean— validating the concept that our microbes, not our genes, may be primarily responsible for changes in our weight.

Super-Sanitized Lifestyle: In the developing world, we’re seeing lower rates of bacterial colonization in the gut as modern practices like chlorinated water, hand sanitizers, and the widespread use of antibiotics, whittle down our microbiome. The fallout has been increasing rates of modern plagues like autoimmune diseases, asthma, and allergies, but obesity is also one of the consequences of our super sanitized lifestyle.

H. pylori: Less than 10 percent of school age children now harbor H. pylori, a number that’s decreased dramatically from decades ago because of widespread use of antibiotics. In later life, H. pylori may be associated with stomach ulcers and other problems, but in childhood it seems to have a more protective effect, including keeping ghrelin—the “hunger hormone” produced in the GI tract that makes us want to eat —in check. Without H. pylori’s influence on ghrelin, children may be missing the cues that tell them when to stop eating.

Antibiotics: Studies show that children prescribed large amounts of antibiotics are at higher risk for obesity later in life. Antibiotic exposure before birth can be a major hazard, too: antibiotic use in pregnant women in the 2nd and 3rd trimester is associated with an increased risk for obesity in their babies. In animal studies, combining antibiotics with a high-fat diet seems to be a synergistic factor that’s associated with even more rapid weight gain, and the same is true in humans. Babies exposed to antibiotics as newborns have an 84 percent increase in risk for obesity because of the effect on their developing microbiome, and like C-section babies, much higher rates of asthma, allergies, and autoimmune diseases later in life.

Chemicals: Triclosan is an antimicrobial agent found in consumer products like soaps, detergents, and some brands of toothpaste. Despite being marketed as antibacterial, household soaps and sanitizers containing triclosan don’t offer any real benefit over conventional soap and water, but they may confer additional risk, including higher rates of food allergies and a higher body mass index in people with detectable levels of triclosan in their urine, which in some studies was as high as 75 percent of U.S. households. Widespread use of chemicals like triclosan, coupled with the prevalence of pesticides and preservatives in our food, may be altering our microbiome in ways that contribute to the rising trend in obesity.

Exercise: We know that exercise is good for us, but it turns out it’s also good for our microbes. A 2014 British study compared stool samples from 40 professional rugby players during their training season to healthy men of the same age who weren’t avid exercisers. The athletes had more bacteria, greater species diversity, and significantly higher levels of the species that are associated with low rates of obesity and obesity-related diseases. The rugby players also ate a lot more fruit and vegetables. The study authors concluded that, “exercise seems to be another important factor in the relationship between the microbiota, host immunity and host metabolism, with diet playing an important role.”


Obesity is a diagnosis based on anthropometric measurements, including percent body fat, body mass index (BMI), or waist circumference (WC). A body fat percentage of 24 in men and 37 in women, a BMI of 30 and above, and a WC of 40 inches in men and 35 inches in women, are considered obese. As percent body fat, BMI, and WC increase, so does disease risk. While BMI can be a good predictor of obesity and disease risk, it does not consider percent body fat and therefore is not an accurate measurement in those with a very low percent body fat. While body fat percentage does take body fat into consideration, research associating body fat percentage ranges to disease risk is lacking. Waist circumference is both a valid predictor of obesity and disease risk, as it measures the adiposity around the mid-section, which is the best predictor in risk of metabolic syndrome. 

Another useful number in diagnosing body fat and disease risk is waist-to-height ratio (WtHR or index of central obesity). WtHR is used to measure the amount of fat that accumulates around the abdomen, in relation to height. If your waist circumference is more than half your height, even if you’re not overweight, you may have more belly fat than you thought, which puts you at a higher risk of developing metabolic syndrome, a condition that dramatically increases your chances of developing heart disease, stroke, diabetes, and some types of cancer. Measure your waist circumference by placing your tape measure midway between the top of your hipbones and the bottom of your ribs. Release your breath normally and wrap the tape around your waist. If your WC is approaching 31 inches for women and 37 inches for men, your health is at risk. If your WC is approaching 35 for women and 40 for men, you are considered obese and are at risk for serious health problems. Now, compare your weight circumference to half your height. If your WC is more than half your height, you are at a higher risk for developing metabolic syndrome.


Recommended integrative treatments for obesity include the following:


The calories in what we eat may not directly affect our weight as much as we thought, but our diet has a profound effect on our gut bacteria, which in turn affects how we harvest energy and nutrients from our food. Even if we swap out our microbes for ones associated with leanness, if we’re not eating the right mix of foods to nourish and sustain those microbes, they’re not going to survive or reproduce for very long. The best way to treat obesity is through diet, by increasing the amount of high fiber plants you’re consuming and cutting back on animal protein and refined sugar. 


Exercise is one of the best things you can do to treat obesity. Not only because it burns calories (obesity is not as simple as burning more calories than you consume), but also because it promotes stress reduction and encourages a social, active, and healthy lifestyle. Not to mention, studies show that beneficial microbes thrive on exercise!

Stress Reduction

Although initial stressors send signals to the body to suppress hunger to address a stressful situation, persistent stress (which is the type of stress most Americans experience daily with busy schedules and hectic lifestyles) has the opposite effect. In a state of constant stress, the body releases a hormone called cortisol, which increases hunger and the physical drive to eat. Reducing stress, along with diet and exercise, is a first line therapy for obesity, and even if all other lifestyle factors are in place, without stress reduction, losing weight and overcoming obesity is a challenge.


Our lifestyle choices – as individuals and as a society – affect our microbiome and thus our weight. Modern practices like C-sections, antibiotic use, fattening of livestock with antibiotics, and the widespread use of chemicals in personal care products – are killing off our beneficial bacteria and allowing “bad” bacteria to take over. Like almost every aspect of our health, our microbes are intimately involved with whether we end up obese or not. Figuring out how to cherish and protect them is key to achieving and maintaining a natural, healthy weight. 

Fecal Microbiota Transplant

While it may seem that a simple solution to the obesity epidemic is to simply replace our not-so-great microbes with better ones, it turns out that’s not so easily done. Gut bacteria have a very short lifespan—just minutes, in many cases. Even though we can temporarily change our microbial composition by inoculating ourselves with different bugs, we tend to revert to our “old” microbiome pretty quickly, so, creating lasting change can be a challenging process.

Obesity, diabetes, and metabolic syndrome are associated with a disordered microbiome and are natural candidates for FMT therapy, but we still need large-scale clinical trials that can tell us how effective FMT really is for these conditions. Pilot studies investigating the effects of transferring stool from lean donors to obese recipients showed improved insulin sensitivity and increased production of beneficial short chain fatty acids, although most studies were too short to assess meaningful changes in weight. FMT by itself is probably not helpful for obesity, diabetes, or metabolic syndrome without a significant dietary change – which for some people may be all they need to effect meaningful changes in their microbiome without FMT. While there is anecdotal evidence to support the use of FMT in the management of obesity, we’re still waiting on more extensive clinical trials to document a clear benefit. Obesity (along with metabolic syndrome and diabetes) is therefore categorized as a potential indication for FMT.

Many scientific theories exist as to what causes obesity, and while it is most likely a disease with various contributing factors, studies show a strong association between obesity, lifestyle factors, and gut bacteria.


Dr Robynne Chutkan
Dr. Chutkan's Newsletter
Read the latest news and research from Dr. Chutkan’s blog. From the most up to date science on the microbiome, to the best in gut-derived wellness – we are your complete guide to gut health! Sign-up now and receive free access to our 7-Day Microbiome Reboot Course.