Did you know that there are trillions of microbes living in and on our bodies? Did you know that these tiny little organisms, that can only be seen under a microscope, affect us in many different ways? These microbes include bacteria, fungi, viruses, and all of their genetic material, and are collectively known as the microbiome.

Even though we cannot see its composite members, the microbiome helps keep us healthy by influencing our immune and digestive systems and protecting us against pathogens. However, if the microbiome becomes unbalanced, it can also cause disease. Our microbiome has a crucial role in our health, which is why it’s so important to understand what it is and how it affects us.

What is the microbiome?

The microbiome is a collection of trillions of microorganisms - including different species of bacteria, fungi, parasites, and viruses - found in and on our bodies. In fact, it is estimated that the number of bacterial cells in our body matches that of our own cells.¹

The majority of these microorganisms are found in your small and large intestines, and together form the gut microbiome. However, they can also be found all over your body, including your mouth, your skin, your nose, your respiratory system and other body parts.

Your microbiome first develops when you are born and depends on how you were delivered. Within twenty minutes of being born, if you were delivered vaginally, your microbiome would resemble that of your mother’s vagina.

However, if you were delivered via Caesarean section, your microbiome would resemble that of your mother’s skin.² The composition of your microbiome continuously changes throughout the first three years of your life, after which it becomes more stable. However, small changes still happen throughout your childhood, teenage years and adult life.³

The microbiome interacts with your body in a symbiotic way, meaning that both the microbiome and you benefit. These interactions include:³

• Commensalistic interactions: when one organism benefits, while the other is neither harmed nor helped
• Mutualistic: when both organisms benefit from the interaction between them
• Pathogenic (parasitic): when one organism (pathogen or parasite) benefits, while the host (you) is harmed
• Neutral: when neither of the organisms is harmed or helped by the interaction between them

How does the microbiome benefit your health?

Your microbiome has many roles in your body and can benefit your health in a number of ways, which include:

Improves digestion and nutrient absorption

Some of the microbes in your microbiome can help you digest food more efficiently. For instance, some complex carbohydrates cannot be easily broken down by your own digestive enzymes, but they can be broken down into smaller, easily digestible parts by some microbes.⁴ The microbiome also helps with the absorption of macro- and micronutrients, such as magnesium, iron and calcium.³

Produces vitamins 

Some bacteria in the intestines, like Bifidobacterium spp., Bacteroides spp., and enterobacteria, are responsible for producing essential vitamins, such as:^3,4

• Vitamin K: needed for normal blood clotting and bone formation
• Folic acid (Vitamin B9): needed for DNA and RNA formation as well as normal protein metabolism. It also helps with making healthy red blood cells
• Vitamin B12: needed for red blood cell and DNA formation. It is also essential for the normal function and development of the brain and nerve cells

Immune system regulation and protection against pathogens

The microbiome has an important role in maintaining normal immune system activities, including regulating the development of immune cells and the inflammation triggered by infections.³ 

Some helpful microbes in the microorganism actually create an unfavourable environment for pathogenic microbes. They stop pathogens from accessing useful nutrients and produce and release an antimicrobial substance called bacteriocin, which prevents pathogenic microbes from growing - preventing them from infecting you.³

Central nervous system development

The microbiome is also known to play an important role in the normal development of your central nervous system.⁵

What can affect your microbiome?

Several things can affect your microbiome, such as:

Diet and nutrition

When you are a baby, the development and composition of your microbiome is affected by the composition of breast or formula milk you are fed.⁶ As you grow up, your microbiome will in turn be affected by your dietary choices. Your diet can affect your microbiome in either a positive or a negative way.

For instance, sweeteners such as sucralose, aspartame, and saccharin (which are found in diet sodas, dairy desserts, and sweets, for example) have been shown to negatively affect the diversity and balance of the gut microbiome.⁷ Food additives, such as emulsifiers, which are found in many processed foods, have also been shown to negatively affect your microbiome.⁷ 

In contrast, high-fibre diet and vegetarian diets have been shown to have a positive effect on the gut microbiome compared to non-vegetarian diets.⁶

Antibiotics and other medications

It was shown by a large Dutch-Belgian population study that medications such as laxatives, inflammatory bowel disease medication, female hormones, antidepressants, antihistamines can significantly affect your microbiome.⁸ 

Antibiotics are another class of medication that can affect your microbiome. While antibiotics kill disease-causing bacteria, they can also destroy beneficial species, disrupting the balance of your microbiome. This can lead to the unwanted growth of pathogenic microbes.⁶

Genetics

Genetics can also affect the composition of your microbiome. It has been noticed that related individuals have more similar microbiomes than unrelated individuals, and that identical twins have more similar microbiomes than non-identical twins.⁹

Use of probiotics 

Probiotics are live microbes that can have a positive effect on your health and microbiome. The most commonly used probiotic species are Lactobacillus, Bifidobacteria and yeasts, such as Saccharomyces boulardii. These help promote a healthy and balanced microbiome, and can even help your body fight off harmful microbes.⁶

The role of microbiome in disease

The microbiome plays an important role in keeping us healthy - and if it becomes unbalanced (in a process called dysbiosis), your risk of developing several different diseases may increase. Some examples include:

Cancer 

Your microbiome can affect your risk of developing cancer, as well as how quickly any cancer grows and how you respond to anti-cancer treatments. For instance, infection with H. pylori, Fusobacterium or Clostridium bacteria can increase your risk of developing gastric cancer. Similarly, patients with breast cancer are more likely to have Bacillus, Staphylococcus, or enterobacter species in their breast tissue than healthy people.⁴

Inflammatory bowel disease (IBD) 

The gut microbiome is known to differ between healthy individuals and individuals with inflammatory bowel disease. People with IBD have been shown to have decreased diversity in bacterial species, reduced numbers of Firmicutes and Bacteroidetes bacteria, and increased numbers of Proteobacteria strains compared to healthy people.¹⁰

Atopic diseases

Atopic diseases include conditions like asthma, eczema and food allergies. It is believed that the lack of exposure to microbes in countries with high levels of hygiene can affect the microbiome of young children, disrupting the development of their immune system and triggering the development of allergies.¹⁰ Importantly, epidemiological studies report more cases of atopic diseases in children who were delivered by caesarean sections, formula fed, or were given antibiotics soon after birth.

Type 1 diabetes 

Bifidobacteria are thought to have a protective role against type 1 diabetes, while Proteobacteria are believed to be a risk factor.¹⁰ Additionally, it has been shown that delivery by caesarean section increases a child’s risk of type 1 diabetes by 20%.¹¹

Cardiovascular diseases

An unbalanced microbiome has been associated with an increased risk of cardiovascular disease.⁴

Summary

• The microbiome consists of trillions of tiny microorganisms, such as bacteria, fungi, and viruses, that you cannot see but you are affected by in many important ways
• When the microbiome is balanced, it can help keep your immune system working correctly and protect you against pathogens, help with your digestion, aid vitamin production, and help you in other ways too
• However, when the microbiome becomes unbalanced, it can promote the development of several conditions including cancer, IBD, allergies, metabolic diseases, and even cardiovascular disease
• The content of your microbiome can be affected by several things, such as diet and medications. However, you can promote a healthier microbiome by using probiotics and eating a healthier diet