Balancing Gut Bacteria For Better Health


The gut microbiota describes the population of bacteria, fungi, viruses and protozoa that have taken up residency in your gastrointestinal tract. Despite there being 100 trillion organisms in there, overcrowding isn’t a problem since they have the equivalent of 2 tennis courts space and bacteria are 10 to 50 times smaller than a human cells.

Around 90% of your gut microbiome is made up of bacteria most of these organisms can be categorised into 5 phyla or communities – mostly Bacterioidetes and Firmucutes with smaller amounts of Verrucomicrobia, Actinobacteria and Proteobacteria.

These bacteria are tiny chemical factories producing thousands of metabolites that affect the cells throughout the body. The exact makeup of the microbiome is unique to every individual. Studies on twins have shown that although we inherit some of our bacteria our lived experience – the foods we eat, drugs we use, environment we’re exposed to – are all much bigger determinants of microbiota consumption.

There is evidence that certain bacteria are found in people with specific health conditions but we can’t yet say that these bacteria cause the condition. But we can use poo and blood samples to look at particular metabolites produced by our microbiome.

The good guys in the gut produce substances called short-chain fatty acids (SCFAs) the most predominant SCFAs are acetate, propionate and butyrate. Butyrate is the main energy source for the cells in our large intestines and is involved in how we regulate our blood sugar. Propionate is involved in the feelings of fullness and in generating blood sugar. And acetate, the most abundant SCFA plays a role in appetite regulation, and regulating cholesterol levels.

More SCFAs is associated with lower diet induced obesity, reduce chronic inflammation and reduced insulin resistance. Some of the other products include certain B vitamins and other chemicals that seem to reduce the risk of developing type 2 diabetes.

Each bacterial community produces different chemical products so it’s important to have a varied population of bacteria. People with inflammatory bowel disease, psoriatic arthritis, type 1 diabetes, atopic eczema, coeliac disease, obesity, type 2 diabetes, and arterial stiffness have less diverse bacterial populations than healthy people.

So what causes the microbiome to get out of balance? The good bacteria in your body can be influenced by stress, surgery, illness, trauma, antibiotics or unhealthy dietary patterns.

Sugar alternatives like sucralose, aspartame and saccharin have been shown to upset the balance and diversity of the gut microbiota in animal studies. Food additives commonly found in processed foods has also been show to affect the gut microbiota of animals with two commonly used emulsifiers reducing the Bacteroidates and Verrucomicrobia phyla and increasing inflammation promoting Proteobacteria.

Making positive changes to the gut microbiota are possible and can happen within relatively short periods of time. A 2.5 times increase in butyrate production among African Americans was observed after researchers asked African American and rural African participants to take part in a two week diet swap.

To help the good guys flourish you’ll want to:

  • Stay hydrated with water and non-caffeinated drinks
  • Avoid foods that your sensitive, intolerant or allergic to
  • Probiotics in the form of supplements or food are often needed to reestablish a balanced gut flora. Eat probiotic foods or take supplements that contain the good gut bacteria such as bifidobacteria and lactobacillus species . Fermented foods, such as yogurt, miso and tempeh are good sources of probiotics. Prebiotics work to selectively stimulate the growth of beneficial microorganisms already in the colon.
  • Prebiotics are available in many foods that contain a fiber called inulin, including garlic, leeks, tofu and by consuming the high soluble fiber foods that good bacteria like to eat call prebiotics.
  • Eat plenty of high fibre foods – low fibre intake reduces the production of the short chain fatty acids and detrimentally shifts microbiota metabolism  to produce potentially harmful metabolites. There is reliable evidence that shows that the Western diet degrades the barrier in the large intestines, provoking an immune response and leads to inflammation.

The individuality of the gut microbiota suggests a need personalisation in our diet and lifestyle functional medicine practitioners like myself understand the importance of re-establishing a healthy microbiome and functional testing can help to shed light on the makeup of your gut bacteria and the metabolites they produce to understand how this is affecting your health.


Rothschild D, Weissbrod O, Barkan E, et al. Environment dominates over host genetics in shaping human gut microbiota. Nature 2018;555:210-5

Hakim H, Dallas R, Wolf J, et al. Gut microbiome composition predicts infection risk during chemotherapy in children with acute lymphoblastic leukemia. Clin Infect Dis 2018doi:10.1093/cid/ciy153

DeVadder F, Kovatcheva-Datachary P, Goncalves D, et al. Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits. Cell 2014;156:84-96

Frost G, Sleeth ML, Sahuri-Arisoylu M et al. The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism. Nat Commun 2014;5:3611

Nettleton JE, eimer RA, Shearer J. Reshaping the gut microbiota: Impact of low calorie sweeteners and the link to insulin resistance? Physiol Behav 2016;164(PtB):488-93

Chassaing B, Koren O, Goodrich JK, et al. Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature 2015;519:92-6

O’Keefe SJ, Li JV and Lahti L. Fat, fibre and cancer risk in African Americans and rural Africans. Nat Commun 2015;6:6342


Hello, I’m Leah! Functional health consultant and founder of The Thrive Practice. Driven by data and supported by science, I’m unerringly obsessed with exploring your unique biochemistry to methodically get to the root of your health issues. So, you can achieve real and lasting relief.


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