Gut Microbiome 101

Understanding the human gut microbiome

The gut microbiome is a complex and dynamic ecosystem with trillions of microbes coexisting in a symbiotic relationship with the host. In this mutually beneficial relationship, microbes interact with each other and the host to influence a wide range of physiological processes, including digestion, nutrient absorption, immune function, and metabolism.

Recent advances in sequencing technology have allowed researchers to begin to unravel the complexities of the gut microbiome and its interaction with the human body. For example, studies have shown that the gut microbiome can influence the severity of inflammatory diseases such as Crohn’s disease and ulcerative colitis.

While the exact mechanisms by which the gut microbiome influences human health are still being studied, it is clear that this complex ecosystem plays a critical role in overall well-being.

So, here’s your guide to understanding the basics of the human gut microbiome.

 What is the human gut microbiome?

The gut microbiome is the existence of trillions of tiny microorganisms living in the human gastrointestinal tract – the mouth, oesophagus, stomach, small intestine, large intestine, rectum, and anus. Humans also have a microbiome in the nose, the mouth (oral microbiota), and any other location in which the body interfaces with the outside world. There is even a microbiome on the skin.

The gut microbial community is incredibly dense, with thousands of species inhabiting it. The vast majority of species that exist in the gut microbiome are gut bacteria, however archaea, eukaryotes, fungi, protozoa, and viruses also exist.

It may seem unusual to have all these microorganisms living in and on the human body, however, they can be immensely beneficial to human health (gut health, hormone health, brain health and immune health).

What does the gut microbiota do?

The well-balanced gut microbiome offers a range of benefits to the host in the form of physiological functions that help:

  • Strengthen the integrity of the intestinal mucosal barrier
  • Protect from disease-causing pathogens
  • Support functional immune responses

Additionally, the gut microbiota ferments non-digestible dietary fibres and resistant starch to produce a variety of short-chain fatty acids (SCFA). As the main microbial metabolites, SCFAs play several key roles that support intestinal health. There are three major SCFAs: acetate, propionate, and butyrate.


Butyrate is the main energy source for human colonocytes (epithelial cells of the colon), it helps to keep the lining (mucosal layer) of the intestines healthy so it can absorb vitamins, water and electrolytes. It has also been linked to regulatory effects on blood sugar (glucose) control, body weight, inflammatory markers and cholesterol ratios.


Propionate is primarily produced from Beta-glucan fibres, which are found in whole grains like oats, barley and rye. When fermented in the large intestine, propionate acts as a mechanism linked with controlling blood glucose levels and appetite regulation.


Acetate is indicated to be a crucial source for butyrate’s functionality. This cross-fermentation process may explain acetate’s role in immune regulation. Plus, as the most abundant short-chain fatty acid, acetate reaches the peripheral tissues via the intestinal lumen where studies have shown its use in the metabolism of cholesterol and lipogenesis.

Randomised controlled trials (RCT) have shown that higher production of short-chain fatty acids is associated with a lower rate of diet-induced higher body weights.


Gut dysbiosis explained

Turns out, what a healthy gut looks like is different for each person based on a countless number of factors, including where you live, what you eat, whether you had a pet as a child, and even the method of how you were born, and if you were breastfed.

Because of this, there’s a near-infinite number of possible combinations of bacterial species that exist on and inside the body, symbiotically (in a mutually beneficial relationship). This makes it impossible to say there is a single type of “healthy” gut microbiome. This also makes it difficult to provide a hard definition of exactly what dysbiosis is across the board.

Generally speaking, gut dysbiosis is a disruption of the complex gut microbial community.

While the exact cause of gut dysbiosis is not yet known, it is believed to involve a combination of lifestyle factors, such as diet and antibiotic use.

The development of the human gut microbiota

Research shows that the development of the microbiota begins from birth. By the age of 3, the composition, diversity, and functional capabilities of a microbiota resemble those of adult microbiota. This adult state is considered a microbiome “set point” that shapes the gut flora for life.

What microbes a person has early in life can impact their human biology and health potential throughout their entire life.

Factors that influence the gut microbiome at birth

Mode of delivery

For humans, the first major exposure to microbes occurs during birth and differs depending on whether delivery occurred vaginally or by C-section.

With newborns delivered through the vaginal canal, the microbiota contains a high abundance of lactobacilli as a reflection of the maternal vaginal microbiota.

In contrast, newborns delivered by C-section don’t experience inoculum exposure to the vaginal canal. Their microbiota is depleted and instead colonised by facultative anaerobes such as Clostridium species.

Infant feeding patterns

During the first few months of life, whether a baby is fed breast milk or formula can impact the composition of their microbiome. Breast milk is associated with several benefits for a baby, including increased resistance to infections, lower risk of high body weight, and decreased risk of allergies.

Factors that impact the gut microbiome after birth

Diversity is the hallmark of a healthy microbiome, with the composition of the gut microbiome being subject to several factors, including diet, age, antibiotic usage, and environment.


Current research suggests that diet is one of the most important factors that shape the gut microbiome. Studies suggest that different diets can lead to dramatic shifts in gut microbial composition. For example, a high-fat, high-sugar diet has been linked to an increase in Firmicutes bacteria, whereas a diet rich in fibre and plant-based foods has been associated with an increase in Bacteroidetes bacteria.

Firmicutes are a family of bacteria that inhabits the gut. Many members of the Firmicutes family produce butyrate that helps to keep the colon healthy. Bacteroidetes are one of the most abundant bacteria in the gut. They act as a probiotic to help reduce inflammation, regulate and inform the immune system, and produce butyrate.

Whilst these types of bacteria are helpful in maintaining gut health, when there are too many of one type and not enough of another, this can reduce the overall health-promoting activities of all of the bacteria present. This imbalance results in gut dysbiosis which can be a risk for certain diseases.


Age is another factor that can influence the gut microbiome. The composition of the gut microbiome generally changes as humans age, with a decrease in diversity and an increase in Firmicutes bacteria. These changes have been linked with a variety of age-related diseases, such as Type 2 Diabetes, and inflammatory conditions.

Antibiotic use

The use of antibiotics is another significant factor that can impact the gut microbiome. Antibiotics can kill both good and bad bacteria, leading to an overgrowth of bad bacteria and a decrease in good bacteria. This disruption to the delicate balance of the gut ecosystem enables a period of vulnerability for pathogens to potentially take over and increase the risk for disease.

Environmental factors

As a complex and dynamic ecosystem, the human gut microbiome is constantly changing in response to its environment. The environment of a newborn is a natural source of microbes that can inhabit different microbiomes on the body to strengthen a healthy gut.

Later in life, environmental factors of geographical location, surgery, smoking, depression, and living arrangements can also impact the diversity of microbes in an individual gut microbiome.

The gut-brain axis

The gut-brain axis is the connection between your digestive tract and the brain. It’s an important system because it allows the gut to communicate with the brain, which can affect mood, health, and more.

The gut-brain axis is made up of two parts: the enteric nervous system (ENS) and the central nervous system (CNS).

The ENS is a network of nerve cells that controls digestion and other processes in the intestines. It has its own set of neurotransmitters – chemicals that carry signals between neurons.

The CNS contains all of the body’s nerves that connect to each other throughout the body. This includes both spinal cord nerves (the part of your nervous system just above where they connect to the spinal column) and brainstem nerves (the part of your nervous system that connects directly with the skull).

The gut-brain axis works by using these two parts to communicate back and forth: when something happens in one place, it causes an automatic response somewhere else. For example, if you eat something spicy or drink alcohol with no food in your stomach, you might feel nauseous or get a headache because these things activate certain receptors in your GI tract; those signals are then sent back through to the brain.

Eat a variety of plant-based foods

Consuming a variety of plant-based foods, such as whole grains, nuts, seeds, fruits and vegetables (and the diverse fibre they contain) is a great way to foster diversity in the microbiota and provide gut bacteria with the fibre required to thrive.

Fibre is essential to the health of the gut microbiome. It helps prevent constipation, which can lead to gut dysbiosis. Fibre also helps to regulate inflammatory responses which support an anti-inflammatory action in many chronic conditions such as irritable bowel disease (IBD), Type 2 Diabetes, some cancers, and heart disease.

Plant-based foods also contain prebiotics, which are non-digestible carbohydrates that serve as food for probiotic bacteria. The probiotic bacteria can feed on prebiotics and grow in number and diversity – this can help maintain a healthy balance between good and bad bacteria in the gut.

Avoid sweeteners and processed foods

Sweeteners that are used to replace sugar as a “healthier” alternative are generally recognised as safe by regulatory agencies, however, some animal studies suggest some sugar alternatives may disrupt the balance and diversity of the gut microbiota.

Emulsifiers – a type of food additive commonly used in processed foods – have also been shown to negatively impact the gut microbiota by disrupting the mucus layer, leading in the direction of inflammation and metabolic syndrome.


Probiotics are live microorganisms that can offer health benefits to the host in support of a healthy gut microbiome. The most common types of probiotics include lactobacillus and bifidobacterium species. Certain probiotic strains are also used to make fermented foods like yoghurt, kefir and sauerkraut.

Probiotics can be sourced from a variety of products, including food and dietary supplements.


Prebiotics are indigestible fibres that confer health benefits to the host. Although they aren’t digestible by the human body, prebiotics can selectively nourish the beneficial bacteria in the gut.

Prebiotics can be found in foods like whole grains, fruits, and vegetables, and in prebiotic supplement form.


The Human Microbiome Project

Established by the National Institutes of Health (NIH), The Human Microbiome Project (HMP) was a research initiative that facilitated the characterisation of microbial communities in the human body of almost 300 young, healthy people with the aim to understand how the microbiome impacts human health and disease.

During the period of 2007 and 2012, next-generation sequencing was used to analyse samples from human anatomical sites, including the nasal passage, oral cavity, skin, gastrointestinal tract, and urogenital tract. This enabled scientists to catalogue the different types of microorganisms that inhabit the human body and explore whether a core healthy microbiome exists, and how a person’s microbiome may affect their susceptibility to disease.

Turns out, that no two gut microbiomes are the same. The human gut microbiome is malleable, in that it’s constantly changing in response to lifestyle, environmental, and dietary factors. The microbial diversity present in the gut one day, may not be the same on another day. The only way to learn precisely what’s going on in the gut is through human genome testing methods, sometimes involving a stool sample.


How to test your gut microbiome

Lower bacterial diversity has been reproducibly observed in people with inflammatory bowel disease, psoriatic arthritis, atopic eczema, coeliac disease, obesity, Type 2 Diabetes, and arterial stiffness, than in healthy controls. So, if you’re someone who cares about the state of your health, it makes sense to uncover what’s going on inside your gut.

Using advanced metagenomic sequencing, testing your gut microbiome is possible.

Metagenomic sequencing is a highly advanced method of sequencing human DNA from an entire community of microorganisms in a sample. Most commonly used to analyse the diversity of bacteria living in a unique microbiome, metagenomic sequencing can identify what species of bacteria are present in a sample, what they’re capable of, how they interact with each other, and how they compare to the average balanced microbiome of a healthy population.

Interested in finding out what’s going on in your gut? Take Vidality at-home gut microbiome test and address your insights with personalised prebiotics blends.



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