The gut microbiome helps to keep us in tip-top shape

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  • Symbiotic bacteria, particularly those in the gut, play an important role in the development and maintenance of the human body.
  • Most researchers agree that we acquire our first microbiota, i.e. micro-organisms in or on the human body, at birth.
  • Supplementation of the diet with prebiotics can lessen changes in the gut microbiome associated with diseases.


World Microbiome Day was celebrated on 27 June in recognition of the often-overlooked contributions that our resident microbes make to our health as well as the role that microorganisms play in maintaining healthy global ecosystems. It is, therefore, fitting that the theme for 2022 was “Celebration of The Microbial World”.

Microscopic organisms, such as bacteria, fungi, viruses, and archaea, amongst others, are everywhere. They live in and on water, soil, food, plants, animals, and humans. In fact, for every human cell, there are approximately 1.3 bacterial cells. These microorganisms cover our entire body, including our skin, eyes, genitalia, mouth and gut.

Within each of these habitats, communities of microbes called “microbiomes” are formed. Some bacteria are simply along for the ride, while others – the symbiotic bacteria – offer a mutually beneficial relationship. These symbiotic bacteria, particularly those present in the gut, play an important role in the development and maintenance of the human body.

First microbiota acquired at birth

The human gut microbiome – the microorganisms that live in our intestines – is one of the interesting features of our bodies. The gut microbiome plays a crucial role in early childhood-to-adult development and has a direct influence on the immune system, hence its importance in health and disease. It has a high metabolic capacity that exceeds that of the liver, and its genetic information outnumbers that of all the other cells of the human body combined.

Although frequently debated, most researchers accept that we acquire our first microbiota (micro-organisms in or on the human body) at birth. Delivery mode (vaginal or C-section delivery) greatly influences the gut microbiome of newborns. Babies born vaginally have a gut microbiome that closely resembles their mother’s vaginal microbiome, while the gut microbiome of infants delivered by C-section is more their mother’s skin microbiome.

After birth, the choice of diet (breast milk or formula) influences the bacterial colonisation of the newborn’s gut. The gut microbiome of exclusively breastfed babies is dominated by specialised bacteria which break down the healthy sugars in breastmilk. Following the introduction to solid food, the infant gut microbiome gradually becomes more complex – a transition that can take up to three years.

In adults, the complexity of the gut microbiome peaks with the formation of a robust core microbiome. The microbiome helps protect us from infection, helps us digest food and medicine, and produces vitamins and hormones that are essential for our health. While the gut microbiome can buffer some changes, changes in diet, bacterial infection, antibiotic use, and stress can greatly affect it.

Reduced microbial diversity

In recent years, changes in the gut microbiome have been increasingly recognised for their contribution to disease susceptibility. The different bacteria that make up the gut microbiome work closely together to maintain the health and function of the human body and prevent disease. Disturbance of the composition of the gut microbiome (termed "dysbiosis") promotes inflammation and disease.

Dysbiosis occurs because of an unhealthy diet and excessive use of leads to reduced microbial diversity. In fact, decreased microbial diversity during adulthood has been associated with more than 100 diseases including obesity, type 1 and 2 diabetes, allergic conditions such as asthma, a variety of cancers as well as neuropsychiatric conditions such as depression, anxiety, and schizophrenia.

The gut microbiome plays a key role in preventing intestinal diseases such as colon cancer and inflammatory bowel disease. The human body cannot digest dietary fibre which is found in whole-grain products, fruit, vegetables, beans, peas and other legumes as well as nuts and seeds. Thankfully the gut microbiome has the capacity to ferment fibre into readily usable short-chain fatty acids including butyrate.

Butyrate alters the immune system and protects against the development of colon cancer. A diet low in fibre contributes to dysbiosis and inflammation which, in turn, contributes to the development of certain diseases. When we eat food rich in fats, the liver digests the fat into primary bile acids which are further digested by the gut microbiome into secondary bile acids. One of these secondary bile acids – deoxycholate – promotes colon cancer.

Building microbiome literacy

Recently, the gut and the brain have been found to interact with each other indirectly through what is termed the “microbiota-gut-brain axis”. The gut microbiome plays an essential role in brain development. During critical neurodevelopmental periods such as early life, dysbiosis negatively impacts neurodevelopment and can lead to neurological and neuropsychiatric disorders later in life.

Unlike our DNA, the microbiome is dynamic and can therefore be altered for improved health and well-being. Supplementation of the diet with prebiotics (non-digestible foods that bacteria digest), probiotics (living beneficial bacteria) or synbiotics (a combination of probiotics and prebiotics) can lessen changes in the gut microbiome associated with disease by increasing the abundance of beneficial microbes within the gut, and consequently, good health outcomes.

Even in the absence of diagnosed disease, incorporating prebiotics and probiotics into your daily life, through a healthy diet and supplementation, can help feed the beneficial bacteria in your gut and can aid in boosting your immunity. 

As highlighted by American board-certified gastroenterologist and member of ZOE's Scientific Advisory Board Dr Will Bulsiewicz “... what appears to be the most important thing for human health, isn't even human”. No doubt, the gut microbiome is crucial for our physical well-being. We should therefore continue to build microbiome literacy and create more public awareness about the importance of microorganisms in our lives.

*Lauren Martin and Natasha Kitchin are students in the Neuropsychiatric Genetics Research Group in the Faculty of Medicine and Health Sciences (FMHS) at Stellenbosch University. Dr Matsepo Ramaboli is a post-doctoral research fellow at the African Microbiome Institute in the FMHS.

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