The Deep-Dive Series: The Gut Microbiome

You’ve probably already heard of our ‘gut bacteria’ – the good bacteria that live in our gut. However, the gut microbiome also includes viruses and fungi, collectively comprising trillions of microbes, across hundreds of unique species.

The bacteria in a healthy individual share a symbiotic relationship with their host, i.e. they derive food from their host, and in turn provide health benefits. In total, the human body can contain tens of trillions (that’s 10,000,000,000,000) of microbes, outnumbering our own cells 10 to 1!

Although they thrive in areas that are exposed to the environment, like our skin and the reproductive tract in women, a bulk of them are found in the digestive tract, starting with the mouth and primarily in the large intestine. Here, despite being microscopic, they can weigh up to 2 kg through sheer quantity! As they utilise their surroundings to source food and grow, these microorganisms influence our health in a very significant way.[1]


The composition of the gut microbiome
The development of an individual’s gut microbiome begins at birth; the microbial population of the mother’s vagina gets transferred to the child as he/she passes through the birth canal during delivery.[2]

As the child grows, he/she is constantly exposed to new species of microbes, be it through breastfeeding or even playing outdoors. Research shows that our gut microbiome continues to evolve throughout our lives. Our environment, our diets, activity levels and lifestyle habits all influence the gut microbiome, to the extent that up to two thirds of their composition is unique to an individual.

The gut microbiota is mainly composed of strict anaerobes (organisms that thrive in the absence of oxygen). Although hundreds of bacterial species have been detected in the human gut to date, most bacteria in the gut belong to one of four families (phyla):





Of these, Bacteroidetes and Firmicutes generally account for about 80% of the gut microbiome in most individuals. The relative ratio of each family to the other is believed to be associated with health parameters such as our body weight and sensitivity to insulin. It’s also important to look at all these families in context; the members of these families found in our bodies are normally symbiotic, but the same families also contain harmful species that can disrupt our microbiome if present.

In addition to bacteria, other key microorganisms such as archeae, viruses, phages, yeast and fungi are also present in the gut.


How the gut microbiome affects our health
The gut microbiome can have significant effects on various aspects of our health, especially –


1] Our nutrition
The microbes in our gut depend on the food we eat for their own sustenance. Our bodies primarily absorb nutrients in the small intestine. Most of the matter that subsequently moves into our large intestine, like dietary fibre, cannot be digested by us. The bacteria in the large intestine can use this fibre as food and a source of energy.

As they metabolise this fibre, they release a variety of by-products, many of which provide us with health benefits. Vitamin K, vitamin B12, biotin and folic acid are all essential nutrients formed by some of these bacteria.


2] Our immunity
Our immune system is primed by our body’s exposure to the environment. When our body is exposed to certain bacteria, it develops the ability to mount an immune response to it in the future. The largest collection of cells of our immune system are found in our gut.

A healthy gut microbiome contains largely helpful microbes, but they can have almost identical relatives that cause disease. For example, Escherichia coli (E.coli) is a bacterial family commonly associated with severe stomach infections, but it also has subtypes that are not only harmless, but also produce vitamin K in our gut. Exposure to the harmless E.coli could prime and prepare the immune system for exposure to infectious subtypes.

It’s also believed that being exposed to the mother’s bacteria can set the tone of the baby’s immune system. Lab experiments have also demonstrated how instrumental bacteria are to the development of a normal immune system; when germ-free laboratory mice are born without any bacteria, their immune system remains immature and lacks important types of immune cells.[3]

Even certain bacteria such as Bifidobacteria, which are part of the Actinobacteria family, produce short-chain fatty acids, which have been shown to reduce inflammation in the large intestine, thereby reducing the risk of colon cancer.[19]


3] Our mood
Our digestive tract is referred to as our ‘second brain’, as it contains the largest number of neurons (nerve cells) outside our brain.

A nerve called the ‘vagus nerve’ forms a direct interface between our digestive tract and central nervous system; it controls the involuntary muscles of our gut, helping food pass food through our digestive tract. Studies have shown that emotional stress can trigger the vagus nerve [4], an example of which is the feeling of ‘butterflies in the stomach’ when we are nervous.

This gut-brain connection works both ways. Certain microbes present in our gut can produce neurotransmitters, including serotonin, which promotes the feeling of ‘happiness’. An imbalance in our gut microbiome can increase the production of these neurotransmitters, which can disrupt our body’s natural balance of this crucial chemical and lead to mood-related disorders.


4] Our skin’s health
Research is exploring the link between our gut microbiome and our skin. It’s believed that dietary changes that affect the gut microbiome can also translate to changes in the skin microbiome, leading to skin issues. While research in this field is still at a nascent stage, breakouts on our skin when we are stressed or have a digestive issue are common, supporting this line of research.


Dysbiosis of the gut microbiome
A disruption in a healthy microbiome is broadly called ‘dysbiosis’. This can refer to a decrease in populations of good bacteria or an increase in microbes that could potentially cause harm.

Dysbiosis could be caused by a number of reasons including, but not limited to, stress, illness, an unhealthy diet or overuse of antibiotics. The effects of dysbiosis are as varied as the causes, and could include:


i] Digestive issues:
The small intestine receives food mixed with the acids from our stomach. Due to the acidic nature of our stomach acid, bacteria cannot thrive here.

Changes to bacterial populations have been linked to an increased risk of several digestive issues. For example, if the stomach’s acidity is compromised due to dietary habits or the indiscriminate use of antacids, bacteria can grow in the small intestine and damage its lining, which can further lead to a host of issues including acidity.

Conditions such as IBS have also been linked to dysbiosis in the gut.  In an Indian study, colon cancer and IBD patients had higher percentages of Bacteroidetes than Firmicutes, compared to healthy individuals.[18]


2] Metabolic issues
Most studies of overweight and obese people show a dysbiosis characterised by a lower dietary diversity.[5]

Studies have shown that individuals with lean and normal-weight individuals tend to have higher numbers of bacteria from the family Firmicutes than Bacteroidetes, compared to overweight and obese individuals. The effect of gut bacteria on weight gain was demonstrated in an interesting experiment, wherein the microbiome from an obese individual and their lean twin were transferred to mice that lacked a microbiome. They found that the mice that received the microbiome from the obese twin gained weight, despite having the same diet as their counterparts who received the lean individual’s microbiome.


3] Increased risk of heart disease
A recent study in 1,500 people found that the gut microbiome played an important role in promoting “good” HDL cholesterol and triglycerides.[8] Certain unhealthy species in the gut microbiome may also contribute to heart disease, by metabolising nutrients found in animal products into trimethylamine N-oxide (TMAO), a molecule that contributes to an increased risk of heart disease.


4] Diabetes
The gut microbiome also may help control blood sugar, which could lower the risk of type 2 diabetes. The ratio of Firmicutes to Bacteroidetes has been shown to affect the way we metabolise glucose. A proposed hypothesis is that certain bacteria can break down nutrients to release sugar, which subsequently enters our blood, which we would normally not be able to do ourselves. Digestive issues caused by dysbiosis can lead to an increased exposure of the immune system to bacterial components, leading to systemic inflammation.


Keeping our gut microbiome healthy
The major determinants of a healthy microbiome, such as our diet, exercise and other lifestyle choices are all elements that are in our control.

A few steps to improve the health of our gut microbiome include:


i) Eating a diverse range of plant-based foods:
Legumes, whole grains, beans, vegetables and fruits contain soluble and insoluble dietary fibre, which are ‘prebiotic’ nutrients that healthy bacteria thrive on. Including a diverse range of these foods in our diet can help good bacteria thrive, keeping our gut microbiome healthy.[11].

Fruits and vegetables also contain polyphenols, which in addition to being powerful antioxidants, also promote the growth of certain beneficial bacteria. [10]


ii) Eat probiotic foods or supplements
Fermented foods such as yogurt, sauerkraut, kefir, pickles and idli all contain healthy bacteria, mainly Lactobacilli (part of the Firmicutes family), and can help maintain a healthy microbiome.[12] .

We can even introduce healthy bacteria to our gut through a probiotic supplement, especially to address the dysbiosis caused by antibiotics. However, this is best done under the guidance of a healthcare practitioner. [17]


iii) Limit your intake of artificial sweeteners
Artificial sweeteners have been shown to be detrimental to the gut microbiome.

Aspartame, for example, has been shown to increase the growth of a family of bacteria, Enterobacteriaceae, by serving as a preferred food source, which can promote dysbiosis. In fact, even stevia, which is often used as a sugar substitute/non-caloric sweetener, also interferes with the growth of Lactobacillus in the gut.[21]

Animal studies have shown mice fed with artificial sweeteners have an increased risk of obesity and insulin resistance, believed to be, at least in part, because of changes to the gut microbiome.


iv) Don’t self-medicate with antibiotics
Antibiotics are important medicines used to treat infections and diseases caused by bacteria, such as urinary tract infections and strep throat.

However, one of their drawbacks is that they affect both good and bad bacteria, even in cases of short-term use. Antibiotics usually cause a short-term decline in beneficial bacteria, such as Bifidobacteria and Lactobacilli, and can temporarily increase harmful bacteria like Clostridium.[22] Therefore, antibiotics must be used only when necessary and prescribed by a doctor.

As we delve deeper into the nuances of how our habits affect our health, we continue to find fascinating ways in which our gut microbiome comes into play. While the research continues, we can do our best to maintain their numbers and help them keep us healthy.



Sender R, et al. PLoS Biol. 2016 Aug; 14(8): e1002533.
Bull M.J, et al. Integr Med (Encinitas). 2014 Dec; 13(6): 17–22.
Shreiner  A.B, et al. Curr Opin Gastroenterol. 2015 Jan; 31(1): 69–75.
Carpenter S, American Psychological Association, That Gut Feeling: September 2012, Vol 43, No. 8. Available from
Peter J, et al, Nature volume457, pages480–484 (22 January 2009).
Ridaura V.K, et al. Science. 2013 Sep 6; 341(6150): 10.1126/science.1241214.
Pozuelo M, et al. Sci Rep. 2015; 5: 12693.
Fu J, et al. Circ Res. 2015 Oct 9;117(9):817-24.
Kostic A.D, et al. Cell Host Microbe. 2015 Feb 11;17(2):260-73.
Hindustan Times, Here’s how a super combo of gut bacteria and broccoli may keep bowel cancer away: Jan 13, 2018. Available from
Heiman M.L, et al. Mol Metab. 2016 Mar 5;5(5):317-320.
Hindustan Times, Curd for good gut bacteria, here’s how it helps improve your immune system: Jul 04, 2018.  Available from
Palmnas M.S, et al. PLoS One. 2014 Oct 14;9(10):e109841.
Dewulf E.M, et al. Gut. 2013 Aug;62(8):1112-21.
Madan J.C, et al. JAMA Pediatr. 2016 Mar;170(3):212-9.
Cardona F, et al. J Nutr Biochem. 2013 Aug;24(8):1415-22.
Hajela N, et al. Indian J Med Res. 2014 Jan; 139(1): 19–26.
Bamola V.D, et al. Microb Ecol Health Dis. 2017; 28(1): 1322447.
Wu H.J, et al. Gut Microbes. 2012 Jan 1; 3(1): 4–14.
Segain J.P, et al. BMJ Journal. Butyrate inhibits inflammatory responses through NFκB inhibition: implications for Crohn’s disease. Available from:
Denaina I, et al. Lett Appl Microbiol. 2014 Mar;58(3):278-84.
Phillips M.L. Environ Health Perspect. 2009 May; 117(5): A198–A205.

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