Gut Microbiome In Human Health And Disease: How Food Shapes Microbiota?

 Author: Paulami Dam, Junior Research Fellow

Do you know? The human body is the home of several to numerous bacteria, viruses and fungi - both good and bad.  They are collectively called the microbiome. Do you know? Nearly 100 trillion bacteria reside in your gut [1]. Yes! Inside your gut. Your gut microbiome is as wide and fascinating as the universe. Now scientists are amazed to explore this unique universe inside us. They are showing keen interest in two subfields of gut microbiome research. 

  • From cardiovascular diseases to cancer progression, from autoimmune disorders to drug metabolism, scientists began precisely investigating how gut microbiota impacts and improves health conditions. 

  • In turn, science is also looking for how gut microbiota is being influenced. Herein, a lot of attention is being paid to individual diet preferences. How does food affect the gut microbiome?

Let’s discuss the role of the gut microbiome in health promotion and disease prevention.

Gut microbiome in human health and disease


Every individual possesses a unique microbiome which is specified by their DNA. An infant is primarily encountered by microorganisms during the parturition and lactation period via the mother's body. Hence, the first set of microbes in one's body is solely dependent on the network found in the mother's system. Afterwards, exposures to environmental factors and food can alter the gut microbiome - either positively influencing the health or impacting negatively. Negative impact induces the access of external pathogens and increases the risk of diseases. Several sources discussed how the gut microbiome is linked with human health and diseases [2,3,4].

  • The gut microbial community surprisingly synthesizes essential amino acids and vitamins including vitamin B and vitamin K. Point to be noted, only bacteria have the enzymes required to produce vitamin B12; plants and animals lack these enzymes.

  • Complex carbohydrates (for example, starch or dietary fibre) are not easily digested in the human body. Bacteria present in distal gut secret microbial enzymes and help in their digestion.

  • Bacteria work on the undigested toxic dietary residues and form significant metabolic by-products like small chain fatty acids. 

  • Some metabolic by-products act as the source of nutrition and provide energy to gut tissues. Nevertheless, they perform in the muscle function and prevent chronic disorders as well. By-products like small chain fatty acids have direct anti-inflammatory properties. Anti-inflammatory effect protects from several chronic diseases. 

  • The gut microbiome within a healthy individual protects from external pathogenic organisms. They compete with the invading microorganisms and exclude them from the gut environment. Moreover, natural gut bacteria play a significant role in enhancing local immunity via acting on the pathways associated with the immune system and producing antimicrobial proteins against the invaders. 


In your gut there are two types of bacterial community: one, which is beneficial for your gut health, is good bacteria and another, which is pathological and causes several diseases, are bad bacteria. Two communities interact with each other. A balance between them keeps your gut healthy. When the balance is interrupted, diseases can emerge viz. irritable bowel syndrome, type-II diabetes, obesity, heart disease, cancer, autoimmune disorders, metabolic diseases, and neurological disorders. Journal of translational medicine reported the role of the microbiome in human diseases [2].

  • In type-II diabetes patients were reported with a less productive gut microbiome. Production of metabolic byproducts was decreased. Vitamin metabolism was reduced. Bacteria showed less movement in the gut environment.

  • Obesity and irritable bowel disease exhibit a disrupted gut microbial community with an altered ratio of specific bacterial populations.

  • Research confirms that the gut microbiome can produce some compounds which have the ability to induce the pathogenesis of neurological disorders such as Alzheimer’s disease.


All of the following elements, together, form a microbiome that is unique to each individual.

  • Genetic makeup
  • Immune and metabolic setup
  • Environmental exposure and lifestyle
  • Drugs and medications
  • Food habit and diet preferences

How diet affects the gut microbiome?


Proteins, fats, and carbs are by far the most commonly mentioned and essential nutrients in food sources. The kind of food and amount of nutrients can significantly alter the gut microbial communities. This impact is linked to the metabolites found in the food. 

  • Studies have shown that dietary changes can cause immense and transient changes in microbial community structure within 24 hours, indicating that nutrition performs a major role in the formation and maintenance of the gut microbiome [2]. 
  • Foods influence the pH of the gut which in turn determines the type of bacteria specific to the environment. Bacterial digestion of dietary fibres lowers the pH of the gut through fermentation.  Low pH often promotes the growth of good bacteria along with restricting the growth of bad bacteria inside the gut [4]. 
  • Prebiotics boosts up a person's good health by modulating gut bacterial composition [5].
  • As compared to rural populations, consuming western diets with low fibres and vegetables results in the disappearance of several key microbes in the gut microbiome of individuals belonging to western metropolitan societies [5].
  • For instance, studies confirmed that a completely plant-based diet or entire animal-based diet alters the microbiome structure in individuals. Vegetarians have a more beneficial bacterial community in their gut. A vegetarian diet promotes an anti-inflammatory effect in the intestine and levels up more than carb-rich urban food choices. The alteration was also observed between groups fed with whole-grain diet and refined grain diet. A gluten-free diet was reported to induce the rise of harmful bacterial communities. Low fibre and high-fat diets exhibit a larger number of pathogenic bacteria whereas a high fibre and low-fat diet show the opposite. [5, 6].
  • Additionally, a high-fat diet or high sugar diet subjects the gut microbiota to disruption of the body's biological clock and affects the metabolism [6].


We're approaching a time in which we can progressively manipulate our health through diet and analyze this nutritional effect via observing gut microbial structures. The Mediterranean diet, which includes a variety of fruits and vegetables, grain products and unsaturated fats, is often regarded as the gold standard for a better living. In the near future, dietary changes to alter microbial diversity might have considerable therapeutic benefits. However, there seems to be a significant gap in the current knowledge of how dietary choices affect the microbiome and how the microbiome affects the host's immune response and acts in the progression or restriction of diseases. New tools, new methodologies and new approaches are required for the translation of clinical research into clinical practices. 


  1. Can gut bacteria improve your health? Harvard health publishing. Harvard Medical School.
  2. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., Bhutani, T., & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of translational medicine, 15(1), 73.
  3. Gut feelings: How food affects your mood. Harvard health publishing. Harvard Medical School. 
  4. The microbiome. Harvard T.H. Chan. School of public health. 
  5. Rajoka, M. S. R., Shi, J., Mehwish, H. M., Zhu, J., Li, Q., Shao, D., ... & Yang, H. (2017). Interaction between diet composition and gut microbiota and its impact on gastrointestinal tract health. Food Science and Human Wellness, 6(3), 121-130. 
  6. Leeming, E. R., Johnson, A. J., Spector, T. D., & Le Roy, C. I. (2019). Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration. Nutrients, 11(12), 2862.

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