How the human gut microbiota is shaped by diet

The human gut microbiota yields about 100 trillion microorganisms, involving bacteria, viruses, yeasts, and parasites. At birth, the human gut is mostly sterile and gets colonized by its mother's microbiome. The type of delivery, cesarean or vaginal, plays an essential role in determining the newborn's microbiome. The healthy gut microbiota comprises mainly the phyla Firmicutes and Bacteroidetes, while the Bifidobacterium genus is the most abundant Actinobacteria. Microbes also colonize other regions of the gastrointestinal system whose composition differs from the gut microbiome.

Gut microbiota is one of the key components of the intestinal ecosystem that helps protect the gut barrier, nutrients, and drug absorption, the regulation of human metabolism, and shaping and maturation of the immune system. Alpha diversity of the gut microbiota has been indicated to be a reliable marker of microbiome health. An increase in diversity and stability is observed during the first years of life, indicative of the microbiota's maturation.

Several factors, such as genetics, age, environment, diet, and lifestyle, can influence gut microbiota. Since dietary habits differ as per geographical factors, the variations can also be seen in the microbiota of different populations. Diet-based changes have been observed irrespective of the age of the population. While different diet compositions can impact the microbiota profiles, consuming an unbalanced diet over some time, along with an unhealthy lifestyle, can also impact the microbiota. People with obesity and overweight have been reported to show a lower gut microbiome diversity.

Individuals with different body mass indexes (BMI) are observed to have different gut microbiomes with metabolic imbalances associated with a less healthy microbiome. Children with overweight or normal BMI have been observed to show a higher diversity than those underweight. Akkermansia muciniphila, which has been found in the mucus layer of the intestine, has been reported to be a beneficial organism for the modulation of basal metabolism in rodents and humans. The decrease in Akkermansia due to obesity can lead to gut barrier failure and an increase in the gut inflammatory response. A healthy diet leading to improvements in gut microbiota can be helpful not only in case of metabolic disorders but also in inflammatory diseases. Therefore, each nutrient and dietary approach has a specific impact on the gut microbiota.

A new study in the journal Best Practice & Research Clinical Gastroenterology aimed to summarize the impact of specific nutrients as well as diets on the gut microbiota as well as the future perspectives of using diet as a therapeutic microbiome modulator.

Study: The role of diet in shaping human gut microbiota. Image Credit: CI Photos / Shutterstock

Effect of nutrients on gut microbiota


Dietary carbohydrates are of two types, dietary fibers (resistant carbohydrates) and digestible carbohydrates. Digestible carbohydrates include polysaccharides, monosaccharides, and disaccharides which are rapidly degraded in the small intestine and released as glucose in the bloodstream. Their increasing use in the modern Western diet (WD) has increased concerns about their associations with the onset of non-communicable diseases (NCDs). In addition, short-term exposure to a high-sugar diet in mice has been reported to increase susceptibility to colitis by reducing short-chain fatty acids (SCFAs) production and increasing gut permeability. 

However, dietary fibers are essential for a healthy gut. Fibers are made of non-starch polysaccharides, non-digestible oligosaccharides, resistant starches, and lignin. They yield monosaccharides and SCFAs through saccharolytic fermentation by colonic gut bacteria. The type and amount of SCFAs depend on the number of dietary fibers consumed and gut microbiota composition. Non-digestible complex carbohydrates and allied microbiota-accessible carbohydrates (MACs) have been reported to lead to the proliferation of a broader spectrum of microbial species with specific properties and release specific metabolites. They are being made available as prebiotics for the gut microbiota to metabolize into SCFAs and promote the growth of Lactobacillus and F. prausnitzii. Such effects can, in turn, lead to increased insulin sensitivity, improved gut barrier function, and ameliorated lipid profile. Several studies have reported that consumption of MACs such as inulin can result in softer stools, cognitive improvement, and reduce the growth of opportunistic diarrhoeal pathogen Clostridium difficile.


Proteins comprise amino acid chains linked by peptide bonds and digestible by the main phyla in the distal colon. Proteolytic fermentation results in the formation of SCFAs in lower amounts than saccharolytic fermentation, branched-chain fatty acids (BCFAs), and potentially toxic substrates. The production of such metabolites and the balance of gut microbiota populations is based on the quantity and quality of dietary proteins digested by gut microbiota. Diets rich in animal proteins can increase bile-tolerant anaerobic bacteria which further increases TMAO, a compound associated with cardiovascular diseases (CVD). Additionally, the consumption of high amounts of animal-based proteins, as in a traditional Western diet, can increase the growth of sulfate-reducing bacteria (SRB) that increases gut inflammation through the production of hydrogen sulfide (H2S).

On the contrary, consumption of plant-based proteins can increase the abundance of beneficial bacteria such as Lactobacillus and Bifidobacterium and decrease those of Clostridium perfringens and Bacteroides fragilis. Furthermore, consumption of pulses has been reported to result in positive gut microbial changes in rodents and humans. Therefore, a diet rich in plant-based proteins can be an excellent alternative to a diet rich in plant-based proteins to reduce gut inflammation. Additionally, they comprise several bioactive compounds and resistant starches, which might benefit gut microbial homeostasis.


Dietary fat quantity and saturation can impact the gut microbiota and metabolic health. A high-fat diet (HFD) can result in dysbiosis, which can further lead to gut permeability, increased insulin resistance, and adipose tissue inflammation. Such dysbiosis can be reversed by following a standard diet. Additionally, high-fat diets containing milk fat with a high sulfide concentration can increase gut inflammation and cause a defective mucus layer.

Monounsaturated fatty acids (MUFAs) have been reported to increase gut microbiota diversity and show positive health effects. Medium-chain fatty acids (MCFAs) have also been indicated to improve cognitive and metabolic functions. Medium-chain triglycerides (MCTs) have been observed to improve gut microbial equilibrium and gut barrier integrity. Polyunsaturated fatty acids (PUFAs) are also termed "essential fatty acids" since they must be obtained from the diet and cannot be synthesized by the body. High intake of omega-6 PUFA, and saturated fats, as well as reduced intake of omega-3 PUFA, have been indicated to result in gut barrier alterations and metabolic disorders.

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Food additives

Food additives such as emulsifiers and non-nutritive artificial sweeteners (NAS) are available in many (ultra-) processed foods. They are used to improve texture, prolong shelf life, and give stability. However, consumption of NAS can lead to glucose intolerance and impairment of insulin sensitivity. The consumption of the natural sweetener steviol glycoside has not been observed to be associated with significant gut microbial variations, however, few studies have reported harmful effects.

Certain dietary emulsifiers such as polysorbate 80 and carboxymethylcellulose have been indicated to alter the composition and localization of the gut microbiota, promote gut and systemic inflammation, and increase bacterial translocation. Consumption of emulsifiers has been observed to reduce gut microbial diversity and impact the composition of the gut microbiota. However, further research is required on the nature, frequency, amount, dietary components, as well as synergy between food additives concerning the onset of NCDs.

Impact of different dietary approaches on gut microbiota

Western diet

The Western diet (WD) involves high regular consumption of refined sugars, animal proteins, saturated fats, and processed foods. Long-term consumption of WD can result in obesity and metabolic disorders. Various studies have reported a decrease in gut microbiota diversity and compositional changes on prolonged consumption of WD. WD has been observed to decrease levels of beneficial bacteria and increase the abundance of bacteria relevant to dysbiosis and diseases. Such compositional shifts could increase lipopolysaccharides (LPS), impairment of gut barrier integrity, TMAO, and other inflammatory molecules that could lead to severe cardiovascular and metabolic outcomes.

Mediterranean diet (MD)

MD is based on regular fiber intake, nuts, and olive oil. Adherence to MD can increase beneficial bacteria and improve the diversity and richness of gut microbiota. MD has been observed to induce a microbial profile that produces more SCFAs and can help to prevent the development of disease and promote the metabolic health of the host. Moreover, MD could also restore some microbiota species and microbial dysbiosis in older individuals and those with metabolic syndrome.

Vegan/Vegetarian diet

A vegetarian diet comprises avoiding all types of seafood and meat. A vegan diet is a subgroup of vegetarian dietary patterns that excludes all animal products. The  replacement of animal-based foods with plant-based foods can increase the intake of insoluble fiber and resistant starch. Vegan and vegetarian diets have been observed to increase the abundance of Faecalibacterium prausnitziiKlebsiella pneumoniaeClostridium clostridioforme, and Bacteroides thetaiotaomicron. However, few studies have reported these diets to reduce potentially harmful metabolites. No significant gut microbial changes have been observed at a family level due to short-term consumption of a vegetarian diet. The vegetarian diet has also been observed to decrease propionic acid production. Further research is required to understand the benefits and risks of vegan and vegetarian diets on gut health.

Gluten-Free diet (GFD)

GFD helps restore normal intestinal mucosa in coeliac patients and those with non-celiac gluten sensitivity. GFD, along with pre-and probiotics, can help in the recovery of gluten tolerance. Consumption of GFD in healthy people for a prolonged time can result in dysbiosis. Compared to a high-gluten diet, a low-gluten diet has been observed to reduce the inflammatory response, improve bloating, as well as reduce fasting and postprandial hydrogen exhalation.

Low-FODMAP diet

A diet without foods comprising all fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) has recently gained popularity for treating patients with irritable bowel syndrome (IBS) and inflammatory bowel disease. Intestinal bacteria cause fermentation of FODMAPs resulting in gas production and increased fluid secretions in the intestinal lumen. A low FODMAP diet has been indicated to reduce many gastrointestinal symptoms such as bloating, cramping, abdominal pain, constipation, gas production, or diarrhea. However, these diets can also adversely impact the gut microbiota in the long term. Several studies suggest that a low-FODMAP diet can alter gut microbiota composition. Nonetheless, further research is needed to determine whether such alterations are harmful and persist for a long period of time.

Ketogenic diet (KD)

KD is a high-protein, high-fat, and low-carbohydrate dietary pattern. KD is clinically advised for patients with GLUT1 Deficiency Syndrome and drug-resistant epilepsy. KD can also be used for rapid weight loss in obese patients. Studies have indicated that KD can lead to gut inflammation and decrease the abundance of beneficial bacteria. Further studies are required to assess the role of gut microbiota variations during KD in healthy individuals.


Diet is one of the most important factors impacting gut microbiota and human health. Recent research focuses on the need for the development of personalized nutritional interventions as a predictor of weight loss success in patients following a caloric restriction diet. Many such diets can have a beneficial impact on the gut microbiota and can lead to improvement of the overall health of the individuals. Newer studies must analyze the potential role of microbiota-accessible carbohydrates (MACs) as modulators of gut microbiota. A combination of specific diets with other gut microbiota approaches, such as FMT, can also be a promising field of research.

Journal reference:
  • Rinninella, E. et al. (2023). The role of diet in shaping human gut microbiota. Best Practice & Research Clinical Gastroenterology. doi:

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Written by

Suchandrima Bhowmik

Suchandrima has a Bachelor of Science (B.Sc.) degree in Microbiology and a Master of Science (M.Sc.) degree in Microbiology from the University of Calcutta, India. The study of health and diseases was always very important to her. In addition to Microbiology, she also gained extensive knowledge in Biochemistry, Immunology, Medical Microbiology, Metabolism, and Biotechnology as part of her master's degree.

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