Are you struggling to lose weight?

Perhaps you’ve tried restrictive diet after restrictive diet, exercise programs, and more – only to find that your weight doesn’t budge.

What if the answer to achieving and maintaining a healthy weight has been inside of you all along?

The Microbiome

Your digestive system is home to a vast ecosystem of trillions of bacteria that are diverse and complex. (1)

The different bacterial species all work together, much like a community, to ensure your digestive system and body functions appropriately. (2) The correct balance of microbiota can help your metabolism, increase your immunity, and can even enhance your brain functioning. (3)

Gut bacteria is acquired from birth, passed from mother to child (4), and there are many factors that could affect and alter your gut microbiota throughout your life, including:

  • The environment you live in. A large study investigated the differences in gut bacteria in rural and urban dwellers and found that urban people living in America had vastly different bacteria in their stool than those living in rural Malawi and Venezuela. They found that urban American fecal matter was the least diverse out of the groups, although this finding was only observed in adults and not in children. They also observed a difference in the clusters of bacteria found between the regions. (5) Another study showed that at least three species of bacteria differ in composition between people from different countries and continents. (6) These changes in bacteria could also be attributed to the differences in dietary habits between countries.
  • The food you eat. Carbohydrates, fat, and protein all have an effect on your microbiome. Protein-rich diets can encourage Bacteroidetes growth, while the Prevotella species is more dominant in the gut of those eating carbohydrate rich diets. (7). Your diet can have an impact on your gut bacteria in as little as 24 hours. (8)
  • The people you surround yourself with. The old saying that you become who you spend the most time with can also be true for gut microbiota and body weight. In mice studies, researchers found that when they housed obese mice together with lean mice and fed them both low-fat, low-sugar diets, the obese mice that lived together with the lean mice acquired lean bacteria faster than those who lived with other obese mice. (9
  • Your age. Even though a child’s gut bacteria can develop to adult-like maturity by the time they reach 3 years old, your gut bacteria changes as you age. The types of bacteria found in the microbiome are different in children and adults; in babies, more bacteria that make folate are present, whereas in adults the bacteria focuses more on metabolizing the folate from the diet. 

The Role of Gut Bacteria in Obesity

There’s been a lot of research done surrounding the idea that your gut bacteria alters your propensity for obesity and that gut bacteria change as a result of obesity or weight loss diets.

The increased interest in the role of gut bacteria on our metabolic health started when researchers microbiota from obese mice into mice with no gut bacteria and saw that when they did this, the mice with no bacteria gained fat mass, just like their obese counterparts.

Further research showed that when mice are fed a Western diet, they start to develop “obese microbiota.”

Obese microbiota can contribute to weight gain in the following ways: (10)

  • An increase the size of the villi in the small intestine (responsible for the absorption of nutrients) allows them to absorb almost double the energy of normal-sized villi
  • Gut motility slows down, allowing more time to digest food and absorb excess energy
  • Excess energy absorbed leads to increased fat in the liver and an increase in fat tissue throughout the body
  • Suppression of enzymes that break down fats lead to the increased conversion of triglycerides into fat cells

The idea that our microbiome plays a huge role in how we extract nutrients was confirmed in this study where they saw that when they gave germ-free mice a conventional microbiome, they produced 60% more body fat and developed insulin resistance, despite reduced food.

The Firmicutes/Bacteroidetes Debate

For many years, the main bacterial culprits for weight regulation have been thought to be the phyla Firmicutes and Bacteroidetes. If you’ve ever gotten a stool test done, you may have seen your Firmicutes and Bacteroidetes ratio listed. 

Much of the research available points to the fact that too many Firmicutes and too little Bacteroidetes can lead to weight gain. (10)

However, newer research has begun to challenge this mindset.

A study using data from the Human Microbiome Project and MetaHIT to investigate the relationship between gut bacteria and obesity found no difference in the Firmicutes:Bacteroidetes ratio between lean and obese participants. The researchers also found that bacterial diversity was not linked to obesity, which contrasts with the results of other studies. (11)

Another study looked at the gut bacteria in fecal matter from people from four different European countries and found that there was no link between BMI and the Firmicutes:Bacteroidetes ratio. The researchers did find evidence, however, to support the link between gut bacteria and its capacity to harvest energy, which is thought to promote weight gain. (12)

If you’d like to learn more about this topic, I recommend checking out this article.

The reality is that we don’t quite know if the Firmicutes:Bacteroidetes ratio really matters all that much when it comes to weight regulation. But the good news is that many of the interventions that seem to improve your ratio also seem to positively benefit your gut bacterial balance as a whole anyway.

Inflammation: the Underlying Factor Leading to Metabolic Dysfunction

While the research on whether the Firmicutes:Bacteroidetes ratio has much to do with weight regulation remains inconclusive, we do know that dysbiosis, in general, is a big problem when it comes to metabolic health.

This is because when we have unhealthy, unbalanced bacteria (dysbiosis), it leads to intestinal permeability and chronic, low-grade inflammation. This inflammation is highly associated with obesity and metabolic conditions like insulin resistance and diabetes.

If you have imbalanced gut bacteria, you develop localized inflammation within the gut, which contributes to intestinal permeability or “leaky gut”.

Leaky gut means that the cells that make up the gut barrier open up and allow larger particles into the bloodstream, like lipopolysaccharides (LPS). Once in the bloodstream, LPS causes chronic low-grade inflammation throughout the body.

This low-grade inflammation is associated with many diseases, but especially with metabolic disorders like obesity and diabetes.

Here is a list of the many different conditions LPS has been associated with:

Rodriguez-Castaño GP, Caro-Quintero A, Reyes A, Lizcano F. Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle. Frontiers in Genetics. 2016;7:224. doi:10.3389/fgene.2016.00224.

What Diet and Lifestyle Factors Increase LPS Concentrations?

Diet is probably the most studied contributor to LPS concentrations. When researchers do these diet studies, they’re typically comparing a high-fat, low-carb diet with low-fat, high-carb diet.

Pretty much across the board, it’s the high-fat diets that lead to a negative change in gut bacteria and higher LPS levels. (You can see one example here.)

Four weeks on a high-fat diet increased counts of LPS-containing bacteria and caused what researchers have deemed “metabolic endotoxemia” (essentially, high LPS concentrations causing chronic low-grade inflammation) in mice. This high-fat diet contained 72% fat (corn oil and lard), 28% protein, and <1% carbohydrate. When researchers used a 40% fat diet, they saw increases in LPS concentrations, but not as high as on a 72% fat diet. Metabolic endotoxemia caused increased fasting glucose levels, insulin levels, and levels of whole-body, liver, and adipose weight gain. (13)

Interestingly (though perhaps not so surprising to those who have been in the Paleo/Real Food world for a while), it is diets high in omega-6 fats that cause this reaction. Alternativately, diets high in fats like coconut oil or fish oil seem to be protective against high LPS levels. (14, 15)

How much you exercise also plays a role in your circulating LPS concentrations. High intensity exercise is associated with lower levels of LPS compared to being sedentary. (16)

If you’ve got a lot of stress in your life, you’re unfortunately promoting the growth of LPS-containing bacteria, which can lead to increased concentrations of LPS in your whole body. (17) (Want to learn more about how devastating stress can be for you digestive system? Read my article on the topic here.)

Though I hope most of you aren’t exposed to cigarette smoke on a regular basis, it also causes LPS-derived inflammation. (18)

A Healthy Gut Means A Normal Weight

OK, so you probably understand by now that high concentrations of LPS in the body seem to be responsible for many of the modern metabolic disorders we see today like obesity, insulin resistance, and diabetes. So how can you prevent getting high concentrations of LPS in your system and help yourself lose weight or prevent metabolic disease?

Here are my top tips:

  • Eat a varied diet with plenty of plant matter to get fiber, prebiotics, and polyphenols
    • Fiber and prebiotic intake have been shown to improve the cluster of symptoms seen in metabolic disorders and improve gut health. (19) Prebiotics also seem to ameliorate LPS-induced inflammation. (20)
    • Polyphenols reduce counts of LPS-containing bacteria and increase counts of beneficial bacteria as well as prevent metabolic endotoxemia and improve intestinal permeability. (21, 22) I’ve written an entire article about the benefits of polyphenols for gut health here.
  • Consume a moderate fat diet and reduce exposure to omega-6 fatty acids
    • I think a higher-fat diet is likely ok provided you have sufficient fiber and prebiotic intake, but to err on the side of caution, I’d recommend that most people consume a moderately-high fat diet (30-60% of calories). Within this amount, your fats should come from healthy options like omega-3s, coconut oil, olive oil, avocado oil, and pastured animal fats.
  • Consume probiotics regularly
    • Several studies have shown improvements in LPS concentrations, body weight, glucose metabolism, insulin and leptin sensitivity, among other benefits with probiotic treatment. (23, 24) Please note that probiotics’ effects are strain-specific, so we don’t know if all strains are equally as effective in this regard.
  • Exercise appropriately
    • As mentioned above, high intensity exercise seems to have a beneficial effect on LPS concentrations. In addition to this, exercise modulates the microbiome and gut health in a very beneficial way. (25)
  • Manage your stress levels
    • As I discussed previously, stress hormones seem to promote the growth of LPS-containing bacteria. Stress also causes intestinal permeability, meaning that LPS can then more easily get out of the gut and into other tissues, causing system-wide inflammation.


Join my newsletter to download my 5S Protocol to Optimize Digestion at Mealtime. In it, I’ll teach you how to stimulate the production of digestive enzymes and stomach acid, calm your system so it’s in “rest and digest” mode, and slow down to allow the proper breakdown and absorption of your nutrients.

Making sure you are optimizing your digestion is a great first step in improving your gut health!

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