The role of diet on the gut microbiome

Dylan Bowe | Last Updated – 30/12/2023 | 4 Minute Read

The gut microbiome is composed of roughly 100 trillion microorganisms – such as bacteria, fungi and viruses, and is located within the human gastrointestinal tract. Research has shown that the gastrointestinal microbiome can play an important role in modifying the risk of several diseases such as obesity, type 2 diabetes, cardiovascular disease and cancer. Along with this, the quality of a person’s diet can affect their gut and cause alterations potentially both short and long term. Therefore it is vital to understand this role of diet including the effect of different macro and micronutrients as this may have implications on disease risk. The research in gut health can be daunting to individuals without a science background, as there is a lot of discussion of different bacterial groups or different cell types with lots different names. However, I believe it is vital to make this information as digestible as possible (pardon the pun!) in order to educate and empower as many people as possible. After reading this short article, hopefully you will have a better grasp of the human gut microbiome, and how diet can effect it and in turn, our overall health. 

The gut microbiome can be seen as similar to rush hour traffic in a city, with thousands of people hustling and bustling around, busy roads and footpaths, each individual having a different role or job to do. Within the 100 trillion microorganisms in our gut, there are 1000s of species of bacteria, all with various roles to help the body run smoothly. DNA determines a person’s gut microbiome and it is unique to each individual. Exposure to microorganisms happens quite fast – during delivery at birth and through consumption of breast milk as an infant. Within the gut microbiome most microbes/bacteria are beneficial, but some can be pathogenic (cause or promote disease). This is usually fine as there can be a balance between the good and bad microbes, but when there is a illness, overuse of antibiotics or a poor diet present, the balance can become skewed and the body may have a higher risk of disease.

The consumption of protein including both animal and plant based, has been investigated in relation to the gut. Protein consumption is positively correlated with microbial diversity, for example, consuming whey and pea protein extract can increase gut protective species Bifidobacterium and Lactobacillus, while whey can also decrease pathogenic Bacteroides fragilis. However, other research indicates that red meat intake can increase trimethylamine-N-oxide (TMAO) levels in the blood, which is a compound that can possibly increase risk of cardiovascular disease. Along with this, studies in mice have shown a correlation of IGF-1 levels with a high protein intake which can increase risk of cancer and diabetes. It is important to follow guidelines provided by a registered dietitian or nutritionist, as consuming too much of anything can be a bad thing, and animal protein including eggs and red meat can be included in a healthy diet once combined with positive dietetic changes such as a high fruit and veg intake or regular exercise. 

The consumption of high saturated and trans-fat diets has been thought to increase risk of CVD through upregulation of LDL cholesterol and total cholesterol. However some fats can be ‘health promoting’ such as mono and polyunsaturated fats, which may reduce disease risk. These healthy fats can be found in avocados, fish nuts and olive oil. A diet high in fat can reduce Lactobacillus and also A. muciniphila, both of which are associated with healthy metabolic states. Carbohydrates are probably the most researched nutrient for altering the gut microbiome, and for this research, exist in two varieties: digestible (such as glucose fructose etc) and non-digestible (fibre and resistant starch). When subjects are fed high levels of glucose fructose or sucrose in the form of dates, there is an increase in healthy Bifidobacteria with reduced pathogenic Bacteroides. Fibre does not break down in the small intestine, instead it goes through fermentation in the large intestine, where microbes can utilize the carbohydrates to provide the host with energy. This dietary fibre is classified as prebiotics, sources of prebiotics include raw oats, soybeans and unrefined wheat or barley. Diets low in prebiotics have been shown to reduce total bacterial abundance, while diets high in them increases healthy species of bacteria in the gut. There is some dietary controversy with artificial sweeteners such as aspartame and sucralose and health. These compounds are often used in food or drinks in order to reduce sugar content while still maintaining sweetness. This can be beneficial if an individual is adhering to a caloric deficit and trying to lose weight, however large consumption of these sweeteners can directly oppose the microbial shifts caused by carbohydrates therefore artificial sweeteners may be unhealthier to consume for gut health than naturally occurring sugars. 

Another important aspect of the diet to improve the gut microbiome is probiotics. Fermented foods containing lactic acid bacteria such as cultured milk and yogurt, represent a source of ingestible microorganisms that may beneficially regulate intestinal health and possibly treat inflammatory bowel disease. These foods enriched in beneficial microorganisms are classified as probiotics. There are also other health benefits from consuming these fermented foods such as alleviation of GI intolerance symptoms and accelerated intestinal transit time (time from consumption to excretion of food). It is extremely important to have a varied diet that does not exclude any food group in order to have a diverse, healthy gut microbiome. The close relationship between diet, the gut microbiome and health suggests we can improve our health by modulating our diet. One way in which microbiota can influence host health is by modulating the host’s immunity. A variety of different species of microorganisms can cause different effects such as Bifidobacteria dampening inflammation and upregulating anti-inflammatory T regulatory cell expression. The mechanism of how this gut flora modulate immune responses is not yet clear and research is constantly looking into this. Along with immunity, the gut can affect metabolic health. Individuals with obesity have a higher Firmicutes to Bacteroidetes ratio, and a calorie deficit was shown to lower this ratio. The gut microbiome is an emerging topic in the nutrition research sphere and there is constantly new research being published on its effect on disease and health. From what we know now, it is important to have a varied diet, high in fibre, fruit, vegetables and including animal and plant protein, along with mono and polyunsaturated fats. People tend to look for a magic pill or an easy fix when trying to improve their health, but more often than not, the best advice may be the most underwhelming. Eat your vegetables, fibre, protein, fats and some fermented foods (in conjunction with a healthy lifestyle)  and your gut microbiome should be extremely diverse and healthy.

Further reading:

The gut microbiota at the intersection of diet and human health, DOI:

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