How the Gut Microbiome Affects Weight Management

June 01, 2022 7 min read

How the Gut Microbiome Affects Weight Management - Layer Origin Nutrition

How the Gut Microbiome Affects Weight Management

If you want to lose weight, you usually need to eat less or exercise more. While this is certainly true, new scientific research is revealing that the gut microbiome may actually determine whether you’ll have the ability to lose any weight at all.

In this article we’ll explore how the microbiota influences weight loss, particularly in the context of diet and exercise. We’ll look at how the microbiota differs between healthy and obese individuals and discuss ways to shape the gut microbiota that can actually help with weight loss.

How is the Composition of Our Microbiome Related to Our Body Composition?

The composition of the human gut microbiota consists of bacteria that are generally regarded as “good” and others we tend to think of as “bad”1.

While this is mostly true, all the bacteria in our guts are thriving off each other, and this relationship keeps us healthy, possibly even lean.

The microbiome isn’t static though – changes in diet, for instance a high fat diet – can dramatically alter its composition. In fact, the microbiome differs substantially between obese and healthy weight individuals; and bacterial diversity is strongly correlated with lower BMI2–45,6.

One species – Bacteroidetes – is often thought to be protective against obesity. This bacteria feed on butyrate which can manipulate metabolic and inflammatory pathways associated with obesity5,6; low abundance of these bacteria may even predict weight gain. Obese individuals tend to have a high abundance of relatively few bacterial species, namely Firmicutes. This bacterium is associated with increased BMI and low resting energy expenditure.

This is just one example of how our health and our gut microbes are intertwined.


Do Bacterial Transplants Actually Cause Weight Loss?

What if you could give an obese person the microbiota of a lean person?

What effect might it have?

Enter fecal transplants. These are exactly what they sound like, although the sample is purified and is presented as a tasteless capsule full of healthy bacteria.

The result is often weight loss and the secret is bacterial diversity.

When you introduce new bacteria, diversity goes up, which contributes to a healthy microbiota, and even weight loss7.

This is a rather unconventional approach and is only truly effective in animal studies and in a few case studies of obese people. You’re probably better off hitting the treadmill, but this definitely highlights how responsive the gut microbiome can be. 

[Read more about Fecal Microbiota Transplants here.]

Does Exercise Alter the Gut Microbiome?

Exercise is probably the best way to lose weight, and it’s also a good way to change the microbiome.

Interestingly, exercise actually causes increases in bacterial diversity, particularly the genus Bacteroidetes. This increases the production of intestinal acetate and butyrate, which further contribute to bacterial diversity.

There is a limit to the beneficial effects of exercise on the microbiota, particularly among long distance runners. It seems that prolonged aerobic endurance exercise, like ultra-running, results in decreases in bacterial diversity8. Runners may also experience decreases in butyrate-producing species, which can lead to decreased immunity after long races.

In any case, exercise can have profound beneficial effects on the gut microbiota that can promote long-term weight loss.

How Does Diet Influence the Microbiota and Weight Loss?

Diet is the most important factor in weight loss9. It is well known that to successfully lose weight, and keep it off, you must expend more calories than you consume.

However, this may not be so cut and dry.

What we eat also influences the composition of our microbiome, and what we feed our microbiota may influence whether we lose weight.

So it may not be as simple as "calories in vs calories out." 

Bacteria such as Prevotella and Bacteroides are generally considered part of a healthy gut microbiome2,3,10. Overweight people tend to have a lower abundance of these bacteria.

But when overweight people go on a reduced calorie, high fiber diet, the numbers of Prevotella and Bacteroides increase.

These individuals also have greater reductions in fat mass than people with a more ‘normal’ gut microbiota10. In other words, low numbers of these bacteria can make you resistant to weight loss.

One common culprit that contributes to obesity is the so-called “Western Diet”, which is really any diet high in fats and refined carbohydrates.

The Western Diet has a microbial ‘signature’, so to speak. This was demonstrated in one of the early breakthrough studies that examined diet-microbe interaction. It showed that mice fed a Western Diet developed a microbiome that had low bacterial diversity, and particularly low numbers of species like Bacteroides4.

This study went one step further and transmitted the ‘Western Microbiome’ to a subsequent generation of mice, which in turn became overweight.

This should highlight how sensitive the microbiome is to dietary alterations, and the degree to which it may influence weight loss or gain.

Can Pre- and Pro-biotics Contribute to Weight Loss?

Pre- and Pro-biotics are dietary factors that influence the structure of our gut microbiota. Probiotics are live cultures, like Lactobacillus or Bifidobacterium and can be found in foods like yogurt, or as dietary supplements.

Prebiotics are foods that contain digestion resistant starches that primarily feed certain bacteria. These are foods like oats or sauerkraut or kimchi.

Probiotics have long been known to help establish a healthy gut, especially among people who consume high fat and high sugar diets12.

Probiotics increase the abundance of good bacteria, and are associated with decreases in BMI and slowed weight gain in general5.

Prebiotics serve as food for our gut bacteria and consist of non-digestible foods like sauerkraut, or human milk oligosaccharides (the sugar in breast milk). Certain bacteria thrive on these, like those that produce butyrate, which helps to increase overall microbial diversity12.

It’s this diversity that can ‘reset’ the gut, promote metabolic health, and potentially lead to weight loss.


The gut microbiome plays a huge role in body composition and weight loss. What we eat, and how much we exercise, are still the primary factors that determine how much weight we will lose, but the microbiota may have the final say.

Probiotics and prebiotics can help to improve the overall structure of the gut microbiome, leading to improvements in metabolism and even metabolic diseases such as obesity and diabetes, in addition to weight loss.

But there is no magic bullet, and how you look is largely determined by your own genes. That said, research is consistently demonstrating that if we are good to our microbiomes, we just may be able to get into that smaller bathing suit before beach season.


Written By: 

Zach Pierce

Masters in Nutritional Biology (with emphasis in Immunology)

Certified Personal Trainer



(1)        Baquero, F.; Nombela, C. The Microbiome as a Human Organ. Clin. Microbiol. Infect. Off. Publ. Eur. Soc. Clin. Microbiol. Infect. Dis. 2012, 18 Suppl 4, 2–4.

(2)        Kunnackal John, G.; Wang, L.; Nanavati, J.; Twose, C.; Singh, R.; Mullin, G. Dietary Alteration of the Gut Microbiome and Its Impact on Weight and Fat Mass: A Systematic Review and Meta-Analysis. Genes 2018, 9 (3), 167.

(3)        Okeke, F.; Roland, B. C.; Mullin, G. E. The Role of the Gut Microbiome in the Pathogenesis and Treatment of Obesity. Glob. Adv. Health Med. 2014, 3 (3), 44–57.

(4)        Turnbaugh, P. J.; Ridaura, V. K.; Faith, J. J.; Rey, F. E.; Knight, R.; Gordon, J. I. The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice. Sci. Transl. Med. 2009, 1 (6), 6ra14.

(5)        Kong, C.; Gao, R.; Yan, X.; Huang, L.; Qin, H. Probiotics Improve Gut Microbiota Dysbiosis in Obese Mice Fed a High-Fat or High-Sucrose Diet. Nutr. Burbank Los Angel. Cty. Calif 2019, 60, 175–184.

(6)        Turnbaugh, P. J.; Hamady, M.; Yatsunenko, T.; Cantarel, B. L.; Duncan, A.; Ley, R. E.; Sogin, M. L.; Jones, W. J.; Roe, B. A.; Affourtit, J. P.; Egholm, M.; Henrissat, B.; Heath, A. C.; Knight, R.; Gordon, J. I. A Core Gut Microbiome in Obese and Lean Twins. Nature 2009, 457 (7228), 480–484.

(7)        Gomes, A. C.; Hoffmann, C.; Mota, J. F. The Human Gut Microbiota: Metabolism and Perspective in Obesity. Gut Microbes 2018, 9 (4), 308–325.

(8)        Sato, M.; Suzuki, Y. Alterations in Intestinal Microbiota in Ultramarathon Runners. Sci. Rep. 2022, 12 (1), 6984.

(9)        Aragon, A. A.; Schoenfeld, B. J.; Wildman, R.; Kleiner, S.; VanDusseldorp, T.; Taylor, L.; Earnest, C. P.; Arciero, P. J.; Wilborn, C.; Kalman, D. S.; Stout, J. R.; Willoughby, D. S.; Campbell, B.; Arent, S. M.; Bannock, L.; Smith-Ryan, A. E.; Antonio, J. International Society of Sports Nutrition Position Stand: Diets and Body Composition. J. Int. Soc. Sports Nutr. 2017, 14 (1), 16.

(10)      Hjorth, M. F.; Blædel, T.; Bendtsen, L. Q.; Lorenzen, J. K.; Holm, J. B.; Kiilerich, P.; Roager, H. M.; Kristiansen, K.; Larsen, L. H.; Astrup, A. Prevotella-to-Bacteroides Ratio Predicts Body Weight and Fat Loss Success on 24-Week Diets Varying in Macronutrient Composition and Dietary Fiber: Results from a Post-Hoc Analysis. Int. J. Obes. 2019, 43 (1), 149–157.

(11)      Ridaura, V. K.; Faith, J. J.; Rey, F. E.; Cheng, J.; Duncan, A. E.; Kau, A. L.; Griffin, N. W.; Lombard, V.; Henrissat, B.; Bain, J. R.; Muehlbauer, M. J.; Ilkayeva, O.; Semenkovich, C. F.; Funai, K.; Hayashi, D. K.; Lyle, B. J.; Martini, M. C.; Ursell, L. K.; Clemente, J. C.; Van Treuren, W.; Walters, W. A.; Knight, R.; Newgard, C. B.; Heath, A. C.; Gordon, J. I. Cultured Gut Microbiota from Twins Discordant for Obesity Modulate Adiposity and Metabolic Phenotypes in Mice. Science 2013, 341 (6150), 10.1126/science.1241214.

(12)      Aoun, A.; Darwish, F.; Hamod, N. The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss. Prev. Nutr. Food Sci. 2020, 25 (2), 113–123.

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