The Effects of Your Eating Habits on the Microbiome

With the recent studies coming to the fore in the world of science, we have entered an era where we can improve our health with food. Reshaping the host-microbiome interactions through personalized nutrition is considered to be a new method of therapy for both the management and prevention of diseases.

What Affects the Microbiome?

  • Method of birth delivery
  • Use of antibiotics, particularly in the first 2 years of life
  • Factors related to early life experiences such as introduction of supplementary feeding at the right time and with the right food have strong effects on the microbiome.

These factors retain some degree of flexibility and can be modulated by exposure to various environmental factors. Among them, nutrition is a key determinant in the modulation of the microbiome.

Recent studies have demonstrated that the composition of the human fecal microbiome is affected by nutrients. Studies have revealed that the microbiome differed even among healthy individuals and emphasized that nutrition has an important effect on the composition of the gut microbiome.

The microbiome composition is dependent on long-term dietary patterns. Diet alters the composition and function of the microbiome in a way that is unique to each individual. It was found that in the alteration of the composition of the microbiome, 50-60% of the diversity was associated with nutrient content, and 10-20% was associated with genetic differences.

The content of the diet affects the microbiome, and subsequently the products of fermentation. Some fermentation products and metabolites promote intestinal function and health, while others impair digestive and barrier functions. Human studies on this subject have focused on three major macronutrients: carbohydrates, proteins, and fats. These food elements are sources of energy for microorganisms, make up the microbiome profile, and have a profound effect on the microbiome.


Carbohydrates have the ability to alter the microbiome. Dietary fiber is characterized as “microbiota-accessible carbohydrates,” as it can be used by microorganisms to provide energy and a carbon source to the host. The microbiome of agricultural populations around the world showed greater bacterial richness compared to that of modernized populations. This is thought to be caused by dietary fiber.

How does fiber consumption affect the microbiome?

In studies conducted on rats, low intake of fiber caused an increase in Firmicutes and a decrease in Bacteroidetes.
Similarly, in humans, the microbiome from African children consuming high amounts of plant polysaccharides displayed a low proportion of Firmicutes and a high abundance of Bacteroidetes compared to Italian children characterized by the lack of dietary fiber.

The common point of the studies is that indigestible carbohydrates can alter the composition of the microbiome, and that fiber is a key nutrient for a healthy microbiome as well as an important ally of the gut.


The effect of proteins on the microbiome was revealed in 1977. Studies examining the effects of proteins on the microbiome have gained momentum with the development of the 16S rRNA method, which is a new generation sequencing method. In the studies, the participants were given animal proteins such as meat, eggs, and cheese, as well as vegetable proteins such as pea protein. Positive correlations were observed between protein consumption and diversity in most of these studies.

  • An increase in Bifidobacterium and Lactobacillus and a decrease in pathogenic Bacteroides fragilis and Clostridium perfringens was observed with the consumption of whey and pea protein extracts.
  • Pea proteins provided an increase in short-chain fatty acids. Consumption of red meat has been associated with increased trimethylamine-N-oxide (TMAO) levels. Increased TMAO levels have a proatherogenic effect, and increase the risk of cardiovascular disease.
  • The common point of the studies for proteins is the importance of limiting the amount of dietary protein in such a way that it does not exceed the required value in the regulation of the microbiome and adding vegetable protein sources to the nutrition plan.


  • Similar to high-protein diets, high-fat diets cause a decrease in Bacteriotedes and an increase in Firmicutes in the gut, thereby leading to dysbiosis. Dysbiosis developing in the gut increases the risk of obesity and the development of chronic disease as a result of decreased microbiome diversity.
  • It has been suggested that the type of fat is as important in regulating the microbiota as the amount of dietary fat. Dietary fat and carbohydrate are modifiable risk factors that can affect metabolic syndrome by modulating the composition of the human microbiome.

In addition to the composition of the food consumed, its amount also affects the microbiome. Calorie restriction, malnutrition, and low-fat diets triggered changes in microbiome composition in rats. Short-term carbohydrate restriction in humans resulted in a reduction of butyrate-producing bacteria. However, major changes in the microbiome do not occur with short-term dietary interventions. For example, only minor differences were observed in the composition of the gut microbiota in humans after short-term consumption of industrial white bread instead of sourdough bread.

Other areas of concern include the side effects of popular restrictive diets on gut health. These include some strict vegan diets, raw food or “clean eating” diets, gluten-free diets, and low-FODMAP diets that are used to treat irritable bowel syndrome. Most people who do not consume gluten do not have celiac disease or intolerance. A recent large observational study revealed that individuals who restricted gluten had an increased risk of heart disease, potentially due to reduced consumption of whole grains.

Sustainable Weight Loss and the Microbiome

  • The microbiome plays an important role in the development and progression of obesity. Most studies conducted on overweight and obese individuals revealed dysbiosis, which was characterized by lower diversity.
  • Researchers in Imperial College London tried to determine the role of the microbiome in this problem. In their study, rats were fed a high-fat diet to gain weight. When rats switched to another diet to promote weight loss, the researchers discovered an interesting detail and observed that the gut microbiota of the rats maintained the characteristics they gained during the high-fat diet. Even though the diet of the rats was altered, their microorganisms were still optimized for a high-fat diet.
  • With bad eating habits, we create a memory in our microbiome profile that tends to gain weight and obesity. Unfortunately, this memory impairs the sustainability of our weight loss. Although losing weight can be easy for some individuals and weight loss can be achieved in a very short time, the important thing is to ensure healthy and sustainable weight loss at the right time. We often focus on our weight as the sole criterion. However, our weight is a single page in the health history of our body. Learning about the microbiome helps you understand how and to what extent your weight adapts to the complex system functioning in your body.
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