An Introduction to the Microbiome

What is the Gut Microbiome?

Hippocrates said: “All disease begins in the gut”.

Modern-day research appears to be showing just how right he was. However, it is not the health of the gut itself that has such an impact – but rather the 100 trillion bacteria that make their home there, forming what is often referred to as ‘the microbiome.’

Bacteria get a lot of bad press. We’re encouraged to use anti-bacterial solutions and to regard all bacteria as ‘germs’, and therefore the enemy. But whilst there are bad bacteria, we now know beyond any doubt that there are also many different good bacteria. And we need them if we want to be healthy.

The Importance of the Gut Microbiome:

There are over 1000 distinct bacteria species living with the microbiome, and each can have an impact on our health. Many people don’t realise how vital the good bacteria in our gut microbiome are. Here are just some examples:

  • Helping with weight regulation: Research has shown that naturally slim people have a different biome to those who struggle to lose weight. (1) It would also appear that some bacteria can actually make us crave sugary foods, making it harder to stick to a healthy eating plan. (1)
  • Supporting healthy digestion and elimination: Good bacteria play a vital role in the health of the digestive system, helping to reduce wind and bloating as well as supporting healthy bowel function. (2,3)
  • A healthy microbiome could prevent food intolerances: Good bacteria help to keep the gut wall healthy, preventing allergens from leaving the intestines. If the gut flora is not balanced correctly, the wall can start to break down, allowing allergens to leave the gut and leading to the development of food intolerances. (4)
  • Supporting the immune system: Up to 80% of our immune function is influenced by the gut. Studies have indicated that a reduction in the level of good bacteria can increase the number, and severity, of infections. (4)
  • Fighting holiday tummy: The major fear of every holidaymaker is that they could be struck down with ‘holiday tummy’. It has been shown that taking a good bacteria supplement can prevent traveller’s diarrhoea. (5)

An imbalance of bacteria within our gut microbiome can have an impact on our digestion, our immunity to infections, our brain function and our skin health.

Let’s look at these in more detail:

Gut Bacteria and the Immune System

Did you know: The gut contains cells that form 70% of our immune system, so the health of your gut has a huge impact on the health of the rest of your body. And what keeps the gut healthy? Your good bacteria!

No matter how hard we try, nothing in our environment is truly sterile – from the bathroom to the kitchen to our food. Our intestinal immune system – supported by the microbiome – encounters more bad bacteria and protects us from more illnesses than any other part of the body.  

This link between gut bacteria and the immune system is therefore extremely important for our immune health. Every day that we do not get ill after eating food or putting our hand to our mouth, we have the good bacteria in our gut to thank for it. 

Types Of Good Bacteria For The Immune System

The three specific bacteria which have been shown to be specifically helpful in supporting our immune health are:

  • L. plantarum – Bacteria like L. plantarum help to keep the cells lining the gut wall healthy. Without the right type of good bacteria, this wall can start to break down – a problem known as ‘leaky gut’.  Leaky gut is linked to recurrent illness, allergies and food intolerances.
  • Lactobacillus acidophilusBacteria like L. acidophilus produce lactic acid, which keeps all the other good bacteria healthy and happy and creates a hostile environment for the unfriendly bacteria.
  • Bifidobacteria bifidum – As well as keeping the gut healthy, certain types of good bacteria like B. bifidum help the immune system directly. The immune system response to bacteria includes reducing inflammation and encouraging the growth of infection-fighting cells.

These types of good bacteria have a number of different roles in supporting our immune health and have been shown to work well as a team. Therefore, when looking for a good bacteria supplement to support immune health, these would be the three bacteria to look out for.

The Role Of Bacteria In Digestion

As well as keeping our immune system healthy, the bacteria in our gut also help to keep nasty, pathogenic bacteria under control and can stop them from causing havoc with our innards. 

For this reason, it has long been thought that taking a daily supplement of good bacteria may help to prevent and treat holiday tummy. Science has now backed this hypothesis up concluding that the use of certain probiotics can help to prevent traveller’s diarrhoea.

The bacteria which have been shown to be particularly helpful include:

  • Lactobacillus acidophilus – This bacteria has been shown to improve the production of lactic acid – creating an environment which encourages the growth of other, friendly bacteria. L. acidophilus also creates an undesirable environment for the harmful bacteria, keeping them under control.
  • Lactobacillus casei – This bacteria has also been found to be helpful in changing the gut environment for the better. Therefore, the combination of L. casei & L. acidophilus would be helpful in encouraging the growth of the good bugs whilst helping to eliminate the bad ones.
  • Lactobacillus plantarum – This bacteria continuously fights disease and prevents entry of pathogenic microorganisms that might otherwise cause disease, as well as prevent them from growing.
  • Streptococcus thermophilus – This bacteria can withstand very high heat as the name suggests. It has several benefits for digestion & health, including the prevention and relief of diarrhoea.

If you do want to take a good bacteria supplement to help prevent holiday tummy upsetting your break, look for a product that contains at least these four strains. You should also choose a product with at least 10 – 30 billion good bacteria per capsule. The bacteria should also be heat stable – after all, you don’t want them to die off in the heat of your holiday!

Good bacteria supplements have also been shown to be beneficial for those suffering from bowel complaints, such as IBS.

The Microbiome and Mental Wellbeing

How does the gut affect the brain? Over the past few decades, there has been a lot of research into answering this question and bettering our understanding of gut-brain communication – also known as the gut-brain axis. 

Scientists have discovered that human beings have a ‘second brain’ in the gut – a number of endocrine cells stretched out along the digestive tract. This ‘second brain’ in the gut contains the same amount of cells as found in a dog’s brain! 

These cells are in direct communication with the brain, via the vagus nerve. Communication is not one way either; the gut influences the brain, and the brain responds. 

Researchers have been delving into whether, as adults, the health of our gut microbiome and the bacteria which live there has an impact on our mood and stress levels. 

They’ve discovered that certain bacteria residing within the microbiome produce a large number of neurotransmitters, which help and support the brain and mood. We now know that:

  • 95% of Serotonin (our happy brain chemical) is actually produced in the gut and then sent to the brain.
  • Dopamine production is also largely reliant on our gut flora – dopamine is important for motivation.
  • GABA (an anti-anxiety neurotransmitter) is also synthesised by good bacteria.

It is therefore clear that there’s a strong link between gut bacteria and mood, motivation and behaviour. 

If the bacteria involved in the production of these neurotransmitters were depleted, this could lead to increased levels of stress, anxiety and low mood. This also appears to be something of a cycle, as stress and poor sleep are known to reduce the levels of good bacteria living in the gut. 

Types of Good Bacteria For The Brain & Mood

So, how can we keep the gut-brain axis healthy? There are certain types of good bacteria that are shown to help support the microbiome and mental health:

  • In trials, it has been shown that supplementing the diet with a combination of L. acidophilus, L. casei and Bifidobacteria bifidus significantly improved mood and motivation. (6)
  • L. rhamnosus has also been shown to have beneficial effects in the treatment of low mood and anxiety. (7)
  • Combining these bacteria with a B Vitamin complex – which can be used to support a healthy mood and mental performance – could provide the missing piece of the puzzle for many people looking for some extra support for stress or low mood. It could also be a key combination for stressed, busy people who are feeling fuzzy-headed or forgetful. 

Thanks to this research, we understand more about the vital role good bacteria play in the management of stress, anxiety and low mood, and that the connection between gut bacteria and mood shouldn’t be overlooked.

Gut Health and Skin Problems

While the relationship between the gut and the brain is often described as the gut-brain axis,  this idea is taken a step further with the concept of the gut-brain-skin axis, which identifies how gut health and skin problems are interlinked. 

This theory is quite simple and makes a lot of sense. Simply put, our emotional health impacts our gut flora, which impacts our skin health, which in turn impacts our emotional health, and so on, in a constant cycle.

Did you know that 40% of those people who suffer from inflammatory bowel diseases also struggle with some form of skin disorder? Or that unbalanced gut flora is ten times more common in people who are suffering from acne rosacea?

This link between gut health and skin problems is not new.

Researchers as far back as 1930 suspected a link between gut health and skin health and modern research has confirmed the importance of this relationship.

Many studies have shown that stress and gut inflammation can result in a reduction in the antimicrobial peptides produced by the skin, causing an increase in infection and inflammation. In fact, many skin conditions including acne, rosacea, psoriasis and dermatitis have now been shown to be linked to increased levels of unfriendly bacteria in the gut.

Types of Good Bacteria For The Skin

The bacteria shown in research to be supportive of skin health include L. Plantarum, L. Rhamnosus & L. Reuteri.

These bacteria have been studied in skin health, and it appears that they may help to reduce the numbers of the following ‘unfriendly’ bacteria:

• Staphylococcus aureus – a bacteria linked to skin infections, pimples, boils & cellulitis

• Pseudomonas aeruginosa – thought to be responsible for skin inflammation, infection and dermatitis.

• Propionibacterium acnes – the bacteria linked to the development of acne and oily skin.

• Staphylococcus epidermidis – an opportunistic bacterium which has been linked to the worsening of all skin conditions.

How To Restore Healthy Gut Flora

Many things in life can influence the gut microbiome, and our beneficial bacteria can be killed off by:

  • A high sugar diet 
  • Stress 
  • Artificial sweeteners 
  • Processed foods 
  • The Pill or HRT 
  • Antibiotics 

When possible, reducing these factors are all ways in which you can help improve gut bacteria. 

Alongside this, many nutritionists advocate regular intake of good bacteria supplements – often referred to as probiotics. Scientists have discovered that using specific good bacteria could help to support us after illness, and act as a helpful preventative measure.

Replacing Gut Bacteria After Antibiotics

Antibiotics are helpful when we are ill; however, in addition to killing off the bad bacteria that are making us poorly, they also kill off the vital good bacteria.

Research has indicated that taking antibiotics can cause such damage to our gut microbiome that, even one year after finishing a course of antibiotics, the gut flora will not fully recover. (8)

It becomes easy to see how people can sometimes get stuck in a nasty cycle of almost constant infections. 

For this reason, replacing gut bacteria after antibiotics is important. Many nutritionists will suggest that: 

  • Anyone who has used antibiotics in the previous 12 months should use a good, broad-spectrum, probiotic supplement. This should provide at least 30 billion good bacteria per capsule.
  • Anyone currently taking antibiotics should use a high-strength good bacteria supplement alongside them and for at least a month afterwards.

Choosing A Good Bacteria Supplement

When choosing a probiotic supplement, there are certain considerations to keep in mind:

1. Strength – There is thought to be around 100 trillion bacteria in the gut, so a supplement of 1-2 billion is really a drop in the ocean. Look for at least 10 billion as a daily top up, or 30 billion to rebuild after antibiotics, or upset.

2. Strains – Check labels; a good broad-spectrum supplement should contain at least five or more. You may also want to ensure that certain strains are present in a formulation, as they all have a specific job to do.

Types Of Good Bacteria To Look Out For

These are some of the best probiotic supplements to support the body, and the combinations to look out for:

  • L. acidophilus and L. casei are a great combination, as they help to create an environment which encourages the growth of other good bacteria.
  • L. plantarum is also important, as it is said to help prevent leaky gut issues.
  • B. bifidus and L. reuteri have been linked with supporting a healthy immune response.
  • B. lactis and S. thermophilus have been found to help improve digestive comfort.

Written by Jenny Logan DNMed. (Jenny is a Nutritional Therapist who has worked with clients in health foods stores and private clinics for over 20 years, and is Product Development & Training Manager at Natures Aid)


  1. C Menni et al; Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain; International Journal of Obesity (2017) 41, 1099
  2. Sridevi Devaraj; The Human Gut Microbiome and Body Metabolism: Implications for Obesity and Diabetes; Clin Chem. 2013 Apr; 59(4): 617–628.
  3. Sridevi Devaraj, Gut microbiota role in irritable bowel syndrome: New therapeutic strategies; World J Gastroenterol. 2016 Feb
  4. G Vighi, et al; Allergy and the gastrointestinal system; Clin Exp Immunol. 2008
  5. Meta-Analysis of probiotics for the prevention of travellers’ diarrhoea McFarlan LV Travel Med Infect Dis 2007
  6. The effects of probiotics on depressive symptoms in humans: a systematic review; Caroline J Wallace; Ann Gen Psychiatry 2017
  7. Ingestion of Lactobacillus strain regulates emotional behaviour and central GABA receptor expression in a mouse via the vagus nerve; Javier A Brails et al; Proc Natl Acad Sci USA; 2011
  8. A. E. Perez-Cobas et al; Gut microbiota disturbance during antibiotic therapy: a multi-omic approach. Gut, 2012

Comments are closed here.