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Gut Microbiome and Metabolism

Consider this one body system when you want to influence your metabolism


Where is your mind going to when you read that word?

To your body shape? To the amount of energy you expend each day? Or are you instead thinking about the way your body uses the food you eat at each meal?

And while each one of these relates to one another and is a function of your body’s metabolism, today we’re going to explore this intricate body process a little further. By the end of this post, you’re going to fully comprehend the role your metabolism plays, and the factors that influence it in the greater environment of health and disease.

What is the metabolism, anyway?

Metabolism, as a verb, is any process that involves changing one compound to another, which then performs a specific function. When we relate it to the energy processes of the body, which is what we refer to as metabolism in our day-to-day lives, we’re talking about the conversion of the food we eat into nutrients that can then be used for the body to function.

There are many factors that influence our metabolism, which include both the efficiency of the conversion of food and the rate at which these nutrients can be used. Hormones, the types of food you eat, your body composition of muscle to fat mass, your age, genetics, gender, and levels of physical activity1.

What about your balance of gut bacteria? Do you think that they play a role in energy metabolism?

Of course, they do; and unfortunately, they’re often forgotten about when it comes to this essential process.

The gut microbiome is ever-changing

Current research into the gut microbiota, which refers to the trillions of bacteria, fungi, viruses and collective microorganism that live within your digestive tract, has allowed us to gather significant amounts of information about the role they play in health and disease2. We already know that too many of one species, and not enough of another, can predispose an individual to obesity3, but this imbalance, called dysbiosis, can also influence our metabolic health4.

While these little critters are tough, they do change markedly across the lifespan of an individual. As you change your habits, you have more stress, you take antibiotics when you’re sick, or you start eating different foods, your gut microbiome shifts and changes accordingly5. Sometimes for the better, and sometimes for the worse.

One of the most significant influencing factors on these changes in gut microbiota is your diet. Research has shown that it can happen within 4 days of a dietary change!6 You can imagine why when you think about your eating habits. Apart from sleep, it’s something every living creature must do to survive… And some of us do it far more than others, which is one crucial factor that changes the composition of the gut bacteria that then goes on to influence metabolism.

Let’s take the standard westernized diet, for example. It’s packaged, processed, refined, based on convenience, sugary, low in fibre and high in saturated fat. That about sums it up! And when we look at the gut microbiome of people who eat this way every day? It’s little wonder there’s an imbalance, where metabolically-rich species are in lower supply we’ll refer to as B for Bacteroidetes, than those that negatively impact metabolic health we’ll call F Firmicutes7.

Interestingly, in experiments done on mice, when their diet is shifted from one that resembles a more westernized diet to one that is more plant-based and fibre rich, not only do their gut bacteria change for the better, they also lose weight.

It’s all because of the way the gut microbiota acquire and harvest energy, and how they influence the metabolic pathways8. More F-type species harvest more calories from food than B-types, which means you could be ‘eating’ more calories than you think, and so put on weight due to the increased storage of these additional calories as fat9. Because these gut bacteria also influence nutrient absorption and utilization, they can further impact the risk of metabolic disorders and diseases like heart disease, obesity and diabetes10. Then there’s inflammation…

When one type of bacteria outnumbers another, it can lead to heightened inflammatory responses. When there’s more inflammation in the gut, as is the case in obesity and other metabolic disorders, the situation only gets worse. The consequences include leaky gut syndrome (where inflammation increases, nutrient absorption and utilization is hampered even further, food sensitivities can arise and overall health and wellbeing is compromised), and more changes in the balance between more helpful and less helpful types of bacteria.

So, how do you put a stop to this vicious cycle of poor metabolism, struggling with weight issues, and generally poorer health?

Strategies to optimize your gut microbiome for metabolic health

As mentioned, it’s possible to modulate these effects with diet. Strategies to increase the helpful B-type bacteria and reduce the F-types include11:

  1. Including more fibre into the diet.
  2. Eating a variety of whole foods at each meal.
  3. Managing your calorie intake by not eating too much or too little.
  4. Staying away from processed and refined foods.
  5. Eating whole grains.
  6. Taking probiotics (where it is deemed necessary), or eating probiotic-rich foods like yogurt, sauerkraut, kimchi, tempeh, and drinking kombucha.
  7. Eating prebiotic foods like bananas, inulin, chicory root.
  8. Managing blood sugar levels by eating smaller, more frequent meals.
  9. Balancing carbs, fats and proteins at every meal.

Weight management and metabolic health goes far deeper than the calories in versus calories out theory. When we begin to consider what our gut microbiome is doing, and whether it is working for or against us, we can begin to figure out the interventions we need to make to improve its function, and thus have better control of our metabolism and overall metabolic health.


  1. Sergi G., Trevisan C., Zanforlini B.M., Veronese N., Manzato E. (2018) Age-Related Changes in Body Composition and Energy Metabolism. In: Masiero S., Carraro U. (eds) Rehabilitation Medicine for Elderly Patients. Practical Issues in Geriatrics. Springer, Cham.
  2. Matheus, A., et al. (2013) Impact of diabetes on cardiovascular disease: an update. Int. J. Hypertens. 2013, 653789.
  3. Ng, M., et al. (2014) Global, regional, and national prevalence of overweight and obesity in children and adults during 1980-2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet 384, 766–781.
  4. Janssen, A., & Kersten, S. (2015) The role of the gut microbiota in metabolic health. FASEB Journal.
  5. Sommer, F., Bäckhed, F. (2013) The gut microbiota: masters of host development and physiology. Nat. Rev. Microbiol. 11, 227–238.
  6. Sonnenburg E., et al. Specificity of polysaccharide use in intestinal bacteroides species determines diet-induced microbiota alterations. Cell. 2010 Jun 25; 141(7):1241-52.
  7. Turnbaugh, P.J., Ridaura, V.K., Faith, J.J., Rey, F.E., Knight, R., Gordon, J.I. (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci. Translat. Med. 1, 6ra14.
  8. Nicholson J., et al. Host-gut microbiota metabolic interactions. Science. 2012 Jun 8; 336(6086):1262-7.
  9. Jumpertz R., et al. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am J Clin Nutr. 2011 Jul; 94(1):58-65.
  10. Kallus S., & Brandt L. The intestinal microbiota and obesity. J Clin Gastroenterol. 2012 Jan; 46(1):16-24.
    Rios-Covian, D., et al. Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health. Front Microbiol. 2017; 8: 376.
  11. Rios-Covian, D., et al. Shaping the Metabolism of Intestinal Bacteroides Population through Diet to Improve Human Health. Front Microbiol. 2017; 8: 376.

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