Decoding the Diversity of Gut Microbiome

Reviewed by

Shifa Fathima

Decoding the Diversity of Gut Microbiome

The human body harbours a plethora of microorganisms. Trillions of microbes in your body constitute the human microbiome. The microbiome is a collection of bacteria, fungi, viruses, protozoa and their genes, which are naturally present in every organ such as the skin, liver, gut and many more where it silently functions for the well-being and good health of humans.

Microbiome Diversity

Your gut is home to several microbial communities including bacteria, fungi, viruses and archaea. They make up thousands of genera of these microbes. The different genera and species belonging to different types of microbes constitute the microbiome diversity. It is similar to having a hall full of different people having different heights and weights, wearing different coloured clothes. Some may have the same surname, but they may belong to different families. Similarly, the microbiome constitutes a variety of shapes, sizes and functions; hence, it is called microbiome diversity.

Any imbalance in this diversity results in a reduction of a particular type of microorganisms while elevating another species. In the gut, several factors such as your diet, age, stress, or some kind of disease may result in the increase or decrease in the microbiome diversity that indirectly affects your metabolic health. Persistent imbalance in the microbial community gives rise to conditions such as diabetes, irritable bowel, obesity and even cancer. (1,2)

There also exists a connection between the skin microbiome and the gut microbiome of an individual which is called the gut-skin axis. Therefore, any disturbance in the gut microflora will not only affect your gut health but will also be responsible for your skin diseases.

Uniqueness of Microbiome

The most important characteristic of the microbiome is that it is unique to every person. Your diet age and environment decide which microbes you will have and in what density. (3) A study that did genome sequencing for infants showed that there was a very less common microbiome among the infants thus proving its uniqueness. (4) Disturbances of the gut microbiota were also responsible for the deaths of infants that were born preterm. The microbiome of male and female infants was also found to be different. Female infants gut microflora had more population of Clostridiates and a comparatively lesser fraction of Enterobacteriales than males during the early stages of life. Additionally, babies that were fed their mother’s breast milk had a more diverse profile of gut microflora and also a higher population of Clostridiales and Lactobacillales species than the babies who were not fed with their mother’s milk. All these findings indicate the uniqueness of the microbiome right from birth.

Measuring Microbiome Diversity

A microbial census counts the type of microbes existing in your gut microbiome. The best way of doing this is by gene sequencing procedures. The concept is known as metagenome sequencing. Using some already existing data and marker genes, the microbiome that exists in a particular sample can be identified. If nothing matches the previous data or the markers, your computer program will generate new data. Up to 95% of matching seen in the sequences are considered to belong to the same species. This is important as bacteria tend to throw bits of DNA and evolve into a different species very often. Bacteroides and Firmicutes are common in the gut. Thousands of species fall into these larger communities. (3,5)

Decoding Microbiome Diversity

Using marker genes, the scientists will run the samples that they collect from different subjects and amplify the sequencing. A computer will try to match these DNA and genome sequences and come up with data that suggests how many organisms belong to a particular type of microbe family. One such study performed by Cong et al. on 29 preterm infants, used their stool samples to find the gut microbiome of these 30-days-old infants. The study yielded interesting results that showed that the gut microbiome of these infants was completely diverse. (3)

Counting Microbiome Diversity

Measuring the microbiome diversity provides information on the richness and evenness of a particular species belonging to a microbial community. A community that has only a few species is less rich than a community that has several species. A study showed that diversity was different in males and females and also changed according to dietary habits. As one counts the microbiome diversity, it becomes easy to understand the reasons for a particular digestive disorder or poor metabolic health that a person may have. Every individual needs a proper balance in the diversity and type of microbes within his/her microbiome community. Any imbalance in this affects the metabolic health of the individual.


We can now conclusively infer that the gut microbiome is diverse and this diversity is unique to every individual. Your gut microbiome will develop based on what you eat depending on your habits and lifestyle. Metagenomics helps quantitatively evaluate the degree of difference in gene content between strains of the same species of gut bacteria from different people. While we are moving towards personalised and tailored treatments for individuals, your diverse genome of the gut microbiome will help in finding which treatment exactly suits you. With the help of newer techniques to measure the microbiome diversity, it will be easier to detect susceptibility to different diseases and interventions required depending on your unique microbiome.

Back to Top