The microbial world inside of our body: Gut microbiota and our health

Shambhu Yadav, PhD
Shambhu Yadav, PhD

Postdoctoral Research Fellow at BWH, Cardiovascular Division-Harvard Medical School
Boston, Massachusetts, United States

The advances in science and technology have drastically changed the way humans live. The needs of modern era have given rise to an increasingly sedentary lifestyle. Although, the genetic and environmental factors on health cannot be denied, the sedentary lifestyle have led to a heightened risk of diseases like heart failure, kidney disease, diabetes, cognitive impairment, cancer, and depression. An important cause of these lifestyle diseases is the change in gut microbiota brought upon by changes in lifestyle and diet.

A normal gut microbiome consists of thousands of species of non-pathogenic commensal microorganisms. These organisms play a vital role in the digestion and absorption of what we eat. In addition, they can also influence the efficiency of harvesting energy from our diet. Besides, they also produce bio-active metabolites like amino acids, bile acids, enzymes, peptides, and vitamins in our body. These metabolites contribute substantially to keeping us healthy. Recent research have shown that gut flora also help us to keep our body cells (particularly endothelial cells found in the inner layer of our many vital organs like the heart, kidney, lung, gut, blood vessels) healthy and provide us systemic immunities to fight against harmful bacteria and viruses.   

The population of the gut microbial ecosystem starts assembling during our birth when microorganism colonization increases due to exposure to vaginal, fecal, and skin microbiome. In addition newborn baby’s nutrition from breastfed (found in human breast milk) also affects the microbiota. As we grow, the exposure to the environment while we grow up also leads to an increase in microbial diversity making them an integral part of our body.

Imbalance of Gut Microbiome and Health

The unhealthy lifestyle is negatively affecting the microbiome (leading to loss of beneficial microbes, expansion of pathogenic microorganisms, and loss of microbiome diversity) in our gut leading to complex metabolic disorders and in some cases life-threatening diseases. During the last few decades, the consumption of processed foods has increased drastically. Generally, processed foods contain synthetic additives, like preservatives, sweeteners, and emulsifiers. Although the additives have traditionally been considered safe for human consumption, recent studies have suggested that it is unsuitable for our gut microbiota. Recently, it was discovered that a small molecule called Trimethylamine N- oxide (TMAO) is produced by microorganisms in our gut. Its high levels of TMAO may lead to increased risk of atherosclerosis (formation of plaques in blood vessels). Surprisingly, TMAO is derived from dietary compounds present in our diets, such as Carnitine, betaine, ergothioneine, and Choline (fig.1).

Fig. 1. ZN Wang et al. Nature 472, 57-63 (2011) doi:10.1038/nature09922

How to keep our Gut Healthy?

Since the food we consume can directly interact with microorganisms and increase or decrease their growth in our gut, the best way to improve gut microbiota is by being selective about the food we eat. The main nutrients for healthy microorganisms are indigestible carbohydrates (e.g. plant derivative glycans) that our digestive system cannot metabolize. So, increasing dietary fibers and consuming short-chain fatty acids (SCFA) in a diet and reducing saturated and trans fats intake can help maintain microbiota. A reduction in the consumption of processed foods in our diet may help to keep the microbiota healthy.

Several studies suggest that the diet having rich micronutrients and high fiber like fruits and vegetables are crucial for a healthy microorganism’s ecosystem in the gut. In addition, having prebiotics(non-digestible food ingredients) in our diet can prevent many diseases.

Another way is the consumption of prebiotics derived from plant sources which are predominantly catabolized and fermented by gut bacteria. This results in reducing the pH in our intestine limiting the growth of pathogenic microbes. There are few examples, Clostridium difficile (causes diarrhea ) and Staphylococcus aureus. However, care has to be taken while taking prebiotics since it may be counter productive in some cases. For example, a gut sensitive person might experience bloating on increasing prebiotics in their diet. Therefore the affects of prebiotics may be subjective depending on the gut microbiota ecosystem. In general, the administration of a balanced and high fiber rich diet can maintain the homeostasis of our gut flora and save us from many of these diseases.

Another approach that is being touted as beneficial for gut-microbiota is, probiotic rise in biotics, but it is still unclear whether commercial probiotics are beneficial.  So, our balanced diet should be according to the health condition, location, metabolic condition, age, gut-microbiota, and food preferences. 

Future of Gut Microbiome

The recent advances in the field of nutrition have given rise to a new concept of “personalized diet’.  Humans have diverse habitats, genetic makeup and dietary habits leading to diverse gut flora composition.  It would be interesting to see if individual gut microbiome can be targeted by altering the lifestyle and diet habits based on ones genetic makeup and environmental niche. A personalized diet can modulate our gut microbiome homeostasis and protect us from various life-threatening diseases like heart failure and diabetes.

Most of the information discussed in this article is from the following studies:

  1. Wang, Z., Klipfell, E., Bennett, B. et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472, 57–63 (2011).
  2. Zmora, N., Suez, J. & Elinav, E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol 16, 35–56 (2019).
  3. Wetzel D, McBride SM. The Impact of pH on Clostridioides difficile Sporulation and Physiology. Appl Environ Microbiol. 2020;86(4):e02706-19.
  4. Piewngam, P., Zheng, Y., Nguyen, T.H. et al. Pathogen elimination by probiotic Bacillus via signalling interference. Nature 562, 532–537 (2018)


Disclaimer: This article is for knowledge and educational purpose and not proposed to any kind of personal medical advice. 


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