Gut microbiome and weight

What makes losing weight difficult? Genetics, environment . . . and this!

What if weight—already known to be influenced by age, genetics, environment, diet, medications, physical activity, etc.—was now also found to be influenced by the microbes that live in your gut? A recent study published in the journal mSystems confirms just that.

Gut microbes are the reams of friendly resident bacteria, viruses, and fungi that live inside your digestive system. These microbes come in a variety of species and strains and live together as a community called your microbiota. Some microbes help break down food to improve your digestion, while others make health-promoting compounds such as vitamins or anti-inflammatory fatty acids. These microbes are part of the gut-brain connection and they also contribute to your immune responses and mental health.

While everyone’s gut microbiome is unique, some trends have been noted, for example, there is a difference in the gut microbiomes of people with and without excess weight. Now we can add “weight management” to the ever-growing list of physiological functions that are influenced by the communities of these microscopic beings that reside within us.

New research is looking for patterns in gut microbiomes to see which types are associated with certain states of health or disease. One way to do this type of research is using a new technology called metagenomics. This can analyze the genes from an entire community of different microbes, like the kind that lives in your gut.

Everything that’s alive contains genes it inherited from its predecessors. Examples of traits your genes code for include your eye colour, whether you’re left- or right-handed, and if you’re colour blind or not. The same principle applies to gut microbes. By analyzing the genes in the microbes that are in a fecal (poop) sample, scientists can tell which microbes are present in the digestive tract and what their traits are.

So, how do genes in gut bacteria translate to weight management in people?

It’s no surprise that most people who try to lose excess weight have a very difficult time doing it. This particular study looked at the gut microbes of people who were trying to lose weight to see if there were specific types associated with people who had more difficulty versus those who had an easier time losing weight.

The researchers found that bacteria that grow more rapidly are associated with easier weight loss and lower levels of inflammation in their human hosts regardless of their BMI. This means that the people who were able to lose the most weight had more of the faster-growing bacteria in their guts, and they also had less inflammation.

The current hypothesis right now as to why faster-growing gut bacteria would help a person lose weight and have lower inflammation is that these bacteria may consume some of our food. This means that these “hungry” bacteria eat the food we eat, leaving less for us to absorb. It also means that as these faster-growing bacteria digest more food, they’re able to make more of the health-promoting anti-inflammatory compounds for us. So, with less food to absorb and less inflammation, these can result in more weight loss for the person. As research continues, we’ll learn more and confirm if this is the mechanism—or part of the mechanism—as to why faster-growing bacteria tend to be associated with lower levels of inflammation and more weight loss.

Another finding from this study was that bacteria that produce more enzymes to break fibres and starches into sugars (called amylase) were linked to people who had more difficulty losing weight, regardless of their BMI. It’s possible that having more of this enzyme in the gut may contribute to blood sugar dysregulation, and might be why these bacteria are linked with more difficulty losing weight.

“This [study] tells us that the gut microbiome is an important modulator of weight loss, independent of your underlying metabolic health state, baseline diet, or BMI status,” says one of the study authors.

More research is needed before we can make any clinical recommendations to alter the gut microbiome. Right now there isn’t a probiotic supplement or any other product that has been developed and tested to give proven weight loss results. More in-depth, larger clinical studies must be done.

In the meantime, the researchers recommend a few things you can do to nurture a healthy gut microbiome:

  • Prepare your own meals, rather than relying on ultra-processed foods; in other words, move away from a “Westernized” diet
  • Eat more fiber-rich, plant-based, whole foods like fruits, vegetables, whole grains, and legumes


Diener, C., Qin, S., Zhou, Y., Patwardhan, S., Tang, L., Lovejoy, J. C., Magis, A. T., Price, N. D., Hood, L., & Gibbons, S. M. (2021). Baseline Gut Metagenomic Functional Gene Signature Associated with Variable Weight Loss Responses following a Healthy Lifestyle Intervention in Humans. mSystems, 6(5), e0096421.

Backgrounder articles:

About the study:

  • Microbe = one microscopic organism, like a bacterium, or yeast
  • Microbiota = a community of different microbes living together
  • Microbiome = the genes included in a microbiota
  • Conclusion: “Overall, our results suggest that the microbiota may influence host weight loss responses through variable bacterial growth rates, dietary energy harvest efficiency, and immunomodulation.”
  • “These findings…may help optimize the weight-loss protocols in future studies.”
  • The researchers say that it is still too soon to be able to engineer your gut microbiome.
  • There are currently no probiotics or other treatments that we can recommend, but research is progressing and this may become an option one day in the future.
  • Note that all studies have limitations. That’s why it’s important to look at multiple studies, giving more weight to the ones that have a better design to answer the questions being asked. For this one, the researchers enrolled participants into a year-long behavioural coaching program to try to help them lose weight. They took stool samples and other metrics (e.g., blood samples). The final sub-cohort ended up with 15 participants who lost the most weight and 10 who did not lose weight.
  • This means it’s not a randomized control trial as participants were not randomized into an “intervention” or “control/placebo” arm (which would be even better).
  • Study strength is rated a 5.5/7 according to this chart (better than a cohort, but not as good as an RCT):