Gut microbiome: An organ you didn’t know about!

Our body is home to millions of microorganisms, some good and others bad for our health. We live in homeostasis with these organisms. The largest population of these microorganisms resides in our intestines which has earned these gut dwellers the name “Gut microbiome”.

Nobel Laureate and American microbiologist Joshua Lederberg defines the term Gut microbiome as the totality of microorganisms - bacteria, viruses, protozoa, and fungi - and their collective genetic material present in the gastrointestinal tract. Microbiomes are responsible for encoding over 3 million genes that are vital for metabolite production in our body. Comparatively, the human genome only consists of 23,000 genes. So basically, 99% of the genetic material in our body is microbial and the vast majority of those are located in our gut.

Although we all house the same bacterial groups in our bodies, the microbiome composition in each of us is as unique as our fingerprints. However, this doesn’t mean gut microbiota is a genetic trait, rather it responds to various social, physical, mental, and environmental triggers. The most common of which include: birthing, infant feeding methods, stress, environment, diet, medication, lifecycle stages like ageing and adolescence as well as comorbid diseases.

Since the dawn of mankind, we have lived in symbiosis with these microorganisms but only in recent years, we began the exploration of its relationships with our physiological system. Many recent evidences suggest a link between human health and metabolism through gut microbiome. It has been linked with the pathophysiology of nutrition-related chronic diseases such as obesity and diabetes. Linkages have also been found on its influence on systemic functions such as immunity and brain functionality. As nutritional biologist and microbiome specialist Riley L. Hughes stated: No doubt! That it (microbiome) is now considered an “ORGAN.”

The benefits of gut microbes can be understood through its major metabolic products that include short-chain fatty acids and its byproducts; acetate, propionate, and butyrate, which are vital for gut health. It provides energy for epithelial cells, enhances epithelial barrier integrity, and also provides immunomodulation and protection against pathogens.

The hallmark for good gut health is its richness or diversity in microbiome species and their plethora of genes. Another key indicator for a healthy gut is the resilience and restorative power of the microbiota during any stressful triggers such as antibiotic treatment or irregular diets. No wonder nutrition-related diseases such as obesity, diabetes, as well as neurodegenerative disorder have been linked to an imbalance in gut microbiota composition; a term called - dysbiosis.

Dysbiosis and Nutrition-related diseases

Dysbiosis refers to the alteration in microbial community that results in decreased diversity and quantity of commensal bacteria. These bacteria supply the host with nutrients and defend the host against opportunistic pathogens. Many researchers in this field have suggested the linkage between gut dysbiosis and chronic health conditions such as inflammatory bowel disease, Type-2 diabetes cardiovascular disease, obesity, and cancer


The gut microbiome has a significant impact on nutrient metabolism as well as energy expenditure. Microbial diversity has been proven to prevent weight gain. A comparative study on the diversity of the microbes between normal and obese individuals revealed that obese individuals have less diverse microbes than normal individuals. This breakthrough research has drawn a clear connection between obesity and gut health. Similarly, the majority of studies done in humans demonstrate that the ratio of Firmicutes to Bacteroidetes is also significantly higher in obese subjects. Firmicutes have been negatively linked with resting energy expenditure which means a high firmicutes population leads to lower resting energy expenditure which can contribute to obesity in the longer run. (Aoun et al., 2020) Furthermore, a recent study conducted also noted that overweight and obese individuals with high Firmicutes/Bacteroides ratios have better health outcomes when following a high fiber and whole-grain diet than those with low Firmicutes/Bacteroides ratio which further establishes the link of microbial diversity in the gut and its relationship with obesity. (Hjorth et al., 2018)

Type- 2 diabetes

Type – 2 diabetes is often associated with inflammation. Many gut microbes stimulate anti-inflammatory cytokines and chemokines thereby reducing inflammation. For example induction of IL-10 by species of Roseburia intestinalis, Bacteroides fragilis, Akkermansia muciniphila, Lactobacillus plantarum, L. casei may contribute to improvement of glucose metabolism since overexpression of this cytokine in the muscle protects from ageing-related insulin resistance.

Likewise, gut permeability is typical in diabetic individuals. Gut microbes up-regulate the expression of tight junction genes thereby reducing gut permeability. Gut microbiota also influences glucose homeostasis and insulin resistance in major metabolic organs such as the liver, muscles, and fat, as well as affects the digestion of sugars and the production of gut hormones that control this process.

Finally, gut microbes have also been shown to work together with anti-diabetic drugs to maintain diabetes although limited research is there in this area. (Gurung et al., 2020)

Cardiovascular disease

Hypertension is the major risk factor for cardiovascular diseases. Recent studies have shown the linkage between short-chain fatty acids and the modulation of blood pressure. SCFAs can function to stimulate host receptor pathways that impact renin secretion and therefore blood pressure regulation. Likewise, dyslipidemia, an abnormal amount of lipid in the body, is another risk factor for cardiovascular diseases. Secondary bile acids produced by gut microbiota are shown to regulate lipid metabolism positively in humans regardless of body mass index. Similarly, the metabolic product of gut microbes TMAO also has been linked as a potential promoter for the process of atherosclerosis.

For some cardiovascular diseases such as myocardial infarction, the severity of the disease is altered by gut microbiomes. Hence, following a diet that modulates gut health positively can reduce the severity of myocardial infarction. Last but not the least, there is growing literature that supports the relationship between gut microbiome and heart failure also referring to it as the “gut hypothesis of heart failure.” This hypothesis says that the reduced output from the heart, as well as congestion in the system, leads to increased bacterial translocation as well as increased endotoxins released from the bacteria that contribute to the underlying inflammation seen in patients with heart failure. (Tang et al., 2017)

Nutrition and gut health

The relationship between nutrients and gut health is two-way. The presence of healthy microbes means proper digestion and absorption of the nutrients while the type of food you eat also alters the microbes in the gut. Out of many nutrients, many studies have evidently shown the relationship between macronutrients such as protein, carbohydrate, fats, polyphenols, and gut microbes.

Protein: A majority of the studies have shown protein consumption positively correlates with overall microbial diversity. For example, consumption of whey and pea protein extract has been reported to increase gut commensal bacteria while whey additionally decreases the pathogenic bacteria.

Carbohydrate: Both digestible, as well as non- digestible carbohydrates, have shown to impact the gut microbiota. Digestible carbohydrates from foods reduce the pathogenic bacteria while non-digestible carbohydrates increase the commensal bacteria. While both these classes increase the bifidobacteria, a genus of bacteria that is known to play a key role in the gut barrier, as well as plays a defensive role against pathogens.

Fats: Generally fats that come from a vegetarian diet or plant have shown a significant role in increasing commensal bacteria in the gut. However, saturated fat from animal sources decreases these commensal bacteria which can lead to inflammation and can further lead to metabolic disorder.

Polyphenols: Foods such as colorful fruits, seeds, vegetables as well as tea are rich in polyphenols. It increases those genus of bacteria that poses cardioprotective and anti-inflammatory benefits. (Tomova et al., 2019)

Foods for gut health

Following are the foods that can help you maintain a healthier gut.

- Fermented Foods

  • These foods are a natural source of probiotics. Probiotics are defined as live microorganisms which have beneficial effects on the body.

  • Sources: Fermented dairy products such as yogurt, curd, kefir, fermented vegetables (eg: pickled cucumber or radish), kimchi, kombucha, miso, gundruk, tama, etc.

- Prebiotic Fiber

  • Probiotic feed on non-digestible carbohydrates called prebiotic.

  • Sources: Onions, garlic, flaxseeds, yacon roots, whole grains such as barley and oats, apples, bananas, asparagus, etc.

- Plant-derived Protein

  • Plant-based protein sources have greater benefits to the gut.

  • Sources: Peas, chickpeas, lentils, mung beans, nuts and seeds, etc.

- Polyunsaturated Fatty acids

  • Sources: Walnuts, sunflower seeds, flaxseeds, fatty fishes such as trout, etc.

- Plant-based diet

Lifestyle tips that can help to maintain a healthy gut

  • Exercise regularly

  • Get enough sleep

  • Reduce your stress

  • Hydrate

No wonder, the gut microbiome is now proposed as an organ considering its impact on mental as well as physiological well-being. So the next time you go on your healthier diet spree; be sure to add few fermented food products because a happy gut will lead to a happy you.


· Aoun, A., Darwish, F., & Hamod, N. (2020). The Influence of the Gut Microbiome on Obesity in Adults and the Role of Probiotics, Prebiotics, and Synbiotics for Weight Loss. Preventive Nutrition and Food Science, 25(2), 113–123.

· Gurung, M., Li, Z., You, H., Rodrigues, R., Jump, D. B., Morgun, A., & Shulzhenko, N. (2020). Role of gut microbiota in type 2 diabetes pathophysiology. EBioMedicine, 51.

· Hjorth, M. F., Roager, H. M., Larsen, T. M., Poulsen, S. K., Licht, T. R., Bahl, M. I., Zohar, Y., & Astrup, A. (2018). Pre-treatment microbial Prevotella-to-Bacteroides ratio, determines body fat loss success during a 6-month randomized controlled diet intervention. International Journal of Obesity (2005), 42(3), 580–583.

· Hughes, R. L. (2020). A Review of the Role of the Gut Microbiome in Personalized Sports Nutrition. Frontiers in Nutrition, 6.

· Tang, W. H. W., Kitai, T., & Hazen, S. L. (2017). Gut Microbiota in Cardiovascular Health and Disease. Circulation Research, 120(7), 1183–1196.

· Tomova, A., Bukovsky, I., Rembert, E., Yonas, W., Alwarith, J., Barnard, N. D., & Kahleova, H. (2019). The Effects of Vegetarian and Vegan Diets on Gut Microbiota. Frontiers in Nutrition, 6.