The Microbiome: Bacteria in the Gut

Author profile picture
Samuel Anthony
Sep 11, 2022
Green bacteria in the gut microbiome

Defining the Microbiome and Gut Bacteria

The microbiome describes the collection of trillions of bacteria, fungi, viruses and other single-celled organisms residing in our body.

Most commonly, discussion surrounds the microbiome of the gut - but your skin, lungs and the majority of your body are home to their own biome of life.

Some estimates find the human body to be 10% human and 90% microbial. Others claim a balance of 1:1.

All we can safely say is they drastically outnumber us with around 30-50 trillion organisms inside all of us.

The gut microbiome, which is becoming recognised as quite the powerhouse for human survival, sits predominantly in the large bowel/intestine (known as the colon).

Fun fact: the microbiome can explain the function of a once-thought-to-be-redundant organ: the appendix.

It is now thought that the microbiome stores a copy of itself, via a sample collection of microbes, in the appendix in case of emergency.

This way, should something sweep through our system and harm microbial life (e.g. antibiotics), we may have a backup!

The Relationship between Western Diets and Disease

Before we get into the impact a healthy gut microbiome can have on the immune system, we should cover the relationship diet has with our health.

Western diseases include heart disease, colon cancer, Crohn's disease, diabetes, asthma, and many other diseases which are most often associated with elevated inflammation.

It is also important that we drop any idea we may have of diseases as transferrable physical substances and understand their reality as a state of the body not at ease (think: dis-ease).

The China Study is said to be one of the most comprehensive nutritional studies to have been carried out and has evidenced the strong relationship between food and disease.

The study attributed western diets high in processed foods, meat and dairy with a vast array of diseases.

We have great power over our health with nutrition. As Hippocrates is often famously quoted, "all disease begins in the gut".

In understanding western diets as largely responsible for associated ailments, we also understand natural, higher fibre diets as capable of healing the body.

Plant based whole food selection of whole grains, vegetables including avocado and fruits including tomatoes and banana.

Bacteria, the Microbiome and Disease

So back to the microbiome and the relationship between bacteria and disease.

In the mid-1800s the belief was that disease was caused by something known as "miasma".

Miasma, known as 'bad air' or 'night air', was the believed cause of diseases at the time.

Miasma was quite literally the belief that the air went 'bad' and caused illness.

Since Louis Pasteur's Germ Theory was published in the late 1800s, the belief has shifted greatly to a view that microbes - more specifically bacteria - cause disease.

This was again simplistic as the accepted view very quickly became 'all bacteria = bad'.

Pasteur even provided a means to destroy bacteria with heat via a process he coined: Pasteurisation.

The relationship between microbes and disease is truthfully much more complex.

Since then several scientists have found not only that many bacterial species do not cause disease at all, but in fact, many can actually be beneficial to our bodies in fighting diseases off.

The change in the believed cause of disease:

Miasma > Bacteria > Microbial Imbalance (dysbiosis)

Dysbiosis - a condition of the microbiome in which the organisms are out of balance - is now what is associated with causing disease.

Either too much of a particularly harmful species or too little of species vital for our immune system are primary causes of dysbiosis.

In fact, with over 70% of the immune system said to reside in the gut, the role of bacteria in keeping us healthy has been ignored for far too many years.

Insoluble Fibre and Short-Chain Fatty Acids (SCFAs)

So just how can the microbiome improve our chances against disease?

A key explanation is the help they provide us with digesting food.

They can consume our food alongside us, breaking it down into compounds that we can use for various bodily tasks - even sleeping (see next chapter).

On top of this, they can also break down (ferment) foods that we otherwise could not digest.

Insoluble fibre is a type of carbohydrate (glucose chain) that our digestive system cannot digest - be it the acidic stomach, small intestine or large bowel alone.

Bacteria can break down (metabolise) these previously indigestible foods and turn them into compounds known as metabolites that are small enough to pass through into our body and be utilised by our systems.

Short-chain fatty acids (SCFAs) are just one of these metabolites and bring a multitude of benefits for gut health and systemic immunity.

When bacteria break down insoluble fibre into short-chain fatty acids - e.g. butyrate and acetate - they can strengthen the gut wall and prevent inflammatory compounds from entering the blood and regulate the immune system and significantly reduce the risks of developing those western diseases mentioned earlier.

Whole food plant-based diets are high in insoluble fibre - fruits, vegetables, whole grains and pulses all contain this resistant carbohydrate.

From treating loose bowels to inflammatory diseases, keeping our diets rich in whole food sources of fibre, encouraging good bacteria to flourish and ferment those fibres is essential.

A bedside alarm clock

The Role of Gut Bacteria for Sleep and Immunity

Without a harmonious microbiome, diverse with beneficial bacteria, the chances of good sleep ever occurring are low.

The immune system gently raises your inflammation when you first fall asleep to encourage healing.

The cycle of gradual increases in inflammation leading up to sleep and the decreasing before morning would not be possible if it were not for our microbes.

This particular cycle helps shape our circadian rhythm alongside chemicals/hormonal signals produced by our body and ensures sufficient consistent sleep.

Melatonin (the darkness hormone) signals the body to fall asleep.

Melatonin is made from serotonin (the happy molecule).

90% of the serotonin in our body is produced in the gut by our microbiome.

Someone with gut dysbiosis may not be able to sleep sufficiently.

Regularity and quality of sleep are associated with various aspects of our health and energy levels and without a high fibre diet, we can expect issues with our sleep.

Consistent, quality sleep can help regulate systemic inflammation and improve your immune health.

To summarise: sleep helps microbes; microbes help sleep; sleep and microbes benefit immune health.

Probiotic food kombucha in glass jars good for microbiome and bacteria

Prebiotics and Probiotics: what's the difference and are they worth it?

What are Prebiotics?

Prebiotics describe ideal food sources for microbes.

Complex carbohydrates, e.g. indigestible fibre, are an example of a prebiotic food.

When preparing the gut for better microbial balance, we choose prebiotic foods - or plant-based whole foods.

What are Probiotics?

Probiotics are fermented foods or foods that contain living microbes.

There is plenty of controversy surrounding probiotics, with many arguing that they simply cannot work.

The difficulty with probiotics - i.e. adding bacteria to your microbiome by consuming them - is incredibly complex.

Firstly, probiotic yoghurts cannot guarantee the organisms are still active and alive at the time of consumption, nor the time they make it to the large bowel.

Secondly, the microbiome population within our body is in the trillions.

Probiotic health drinks with hundreds, maybe thousands, of organisms would be a drop in the ocean, making very little difference.

This is an area that studies are yet to catch up with and it is advisable to take any health claims from companies promoting probiotics with a pinch of salt.

A man running outdoors to improve microbiome health with exercise

Improve your Microbiome

Exercise and the Microbiome

Regular exercise has been shown to increase microbial diversity in the gut.

Greater diversity can also improve energy levels in the body, so consider this an adaptation to exercise.

Guidelines recommend 30 minutes of cardiovascular activity five times a week.

A daily walk, jog or cycle can make a positive difference to your microbiome.

High Fibre Whole Food Diets and the Microbiome

Their high fibre content and the ingredients your gut needs for serotonin - whole food plant based diets are a great way to increase diversity in the microbiome.

With the primary food source being fibrous plant foods, calories are typically much lower than with meat-based diets - meaning you tend to eat a little more.

This brings the body a little closer to our natural diet: that of roaming foragers like our ancestors.

Consistent, high-fibre, high-polyphenol foods make whole food plant-based a strong diet choice for gut health.

This said, increase your fibre slowly! Too much too fast can cause discomfort.

Remember, insoluble fibre is indigestible - so no bacteria to help you then it will pass the whole way through.

If you have an active disease, causing strictures in your bowel, instantly opting for high fibre can increase your risk of blockages.

Regardless of your condition, it is advisable to increase fibre intake very gradually - aim for months!

A final note on fibre: aim for 30g at the very least, push for 60-70g. Take your time!

Close up of a boxer dog outdoor

Pets and the Microbiome

Pets! A great source of bacteria in our lives.

Unlike a lot of humans, pets are not afraid to get muddy and most, if not all, love the outdoors.

They are home to many millions of their own microbes.

Spending time around pets can increase your exposure to a diverse range of bacteria, fungi and viruses.

Conclusion: an active, whole food plant-based lifestyle for microbiome health

Stay active, eat well, spend time outdoors, work on improving sleep and utilise this organ unto itself: The Microbiome.


Be the first to leave a comment below.

Leave a comment

Please note, by submitting this form your name and comment will be stored and displayed on this website publicly for other users to see. We respect your privacy.

Thank you! Your submission has been received! We will review your comment before publishing.
Oops! Something went wrong while submitting the form.

Sources & References

Plant-Based Nutritionist & Fitness Coach
View website
Facebook logo
Instagram logo
Pinterest logo
Twitter logo
YoutTube logo
TikTok logo
View profile
Green arrow pointing forward
Gordon Ramsay sharpening his knives

Is Gordon Ramsay Vegan?

Gordon Ramsay has been a dominant figure in the world of gastronomy for decades. As the world witnesses a remarkable surge in the popularity of veganism, a pivotal question arises: Is Gordon Ramsay vegan?

Read More
Soy in the form of silken tofu in a blue bowl

Is Soy Bad for You?

In plant-based diets, few ingredients have garnered as much attention and controversy as soy. Let's explore how brands like Tofoo champion organic sourcing to address these concerns.

Read More
High-protein tempeh on barbeque skewers with a vibrant orange plant-based dipping sauce.

Which Vegan Foods are High in Protein

Explore the world of plant-based protein with our comprehensive guide. Discover high-protein vegan foods, learn about amino acids, and unlock delicious recipes. Embrace a nourishing, sustainable, and vibrant plant-powered lifestyle today.

Read More