The role of good and bad gut bacteria in the body

The Role of Good and Bad Gut Bacteria to our body

Gut bacteria, we mention it a lot in our Expert Series and there’s a reason for it; good gut bacteria and bad gut bacteria play very different roles in our gut health.

In this week’s Expert Series, we’ve looked at numerous published studies on gut bacteria and deciphered them for you to give you the jargon-free, easy to digest (pun intended) version. Trust us, this was a lot of reading. but we’re here to do the hard work, so you don’t have to.

What is gut bacteria and its role in our gut?

Firstly let’s outline the glossary of terms we’ll be using frequently in this issue (so we’re all on the same page):

Microbiome* – this is the collection of DNA (genes) of microorganisms in a habitat. 

Microbiota* – the collection of microorganisms in a habitat (that is life forms, microbes themselves, as opposed to microbiome which equals its DNA (genes)).

*Both terms are largely interchangeable

Pathogens – bad bacteria displaying harmful unhealthy functions.

Dysbiosis – unhealthy changes in our microbial community. 

Gut bacteria- usually when people refer to gut bacteria, they are referring to the bacteria within the large intestine (colon) where the majority of bacteria within the digestive tract reside.

Imagine, the London underground on a weekday morning with people rushing to get to work, now imagine this at microscopic level and you have a bit of an idea of what our microbiome looks like in our body. It is a diverse, dynamic and colourful community like that population of commuters on the tube.

From the moment we are born, our body and gut are colonised by a collection of bacteria and microbes, and interestingly, the highest numbers are found in our gut. In fact, the first 1,000 days after birth is often coined ‘The Window of Opportunity’, as the gut goes from being (almost) sterile to having a fully established microbiome. This means that particular care needs to be given to our gut health for the first 1,000 days of our life. 

The bacteria, along with the other microorganisms within our gut are responsible for many things including (but not limited to):

  • Metabolism – our gut bacteria regulates gut hormone release which have key roles in insulin sensitivity, glucose tolerance, fat storage and appetite 
  • Immune system regulation
  • Natural defence against infection
  • Strengthen the gut integrity and intestinal lining

What factors influence our gut bacteria?

Birth and early development

There has been a lot of research in the past decade to understand the forces that shape the composition and functionality of the microorganisms that reside in our gut. As mentioned above, research claims that the initial colonisation of the bacteria and the microorganisms in our gut and body start from birth. The method of delivery at birth (whether you were born by vaginal or caesarean section) also plays a role on the initial composition of the microbiota found in our gut and body.

The diversity and stability of our gut bacteria and microbiota continually increases throughout early development and reaches a fully established gut microbiota roughly by the age of three years old, however, this composition fluctuates due to various factors and life events, as explained further below.  


Research has shown that our diet plays a large role in gut bacteria and its structure and function in our gut. Have you heard of the saying “you are what you eat’? Well, to put it in simple terms, this is very appropriate when it comes to our gut bacteria and the food we consume. 

Dietary preferences can have a significant impact on certain strains of gut bacteria and how these strains can dominate other strains too. For example, diets where meat is consumed more have significantly different gut microbiomes to those with plant dominant diets, due to certain bacteria flourishing in the abundance of protein. 

Interestingly, research has also found that our cultural background may also impact the composition of our gut bacteria. For example, in Asian populations where the diet tends to include foods high in starch like rice, these populations are considered to have a notably high abundance of Bifidobacterium, which is bacteria known to produce large quantities of starch-metabolising enzymes.

Certain foods and diets have also been shown to play a large role in the growth of good bacteria in the gut, while others can have the opposite effect and promote unhealthy strains. New guidelines say that we should all be eating 30+ whole food varieties of fruit, vegetables, nuts, seeds and legumes per week. Aftermath: a diverse healthy food plan means diverse healthy microbiota.  

Read more from our previous Expert Series: the worst foods for gut health


Antibiotic treatments dramatically disrupt both short- and long-term balance of our gut bacteria, including the diversity and richness of the bacterial community. The exact effects and time of recovery of our gut bacteria following a course of antibiotics is very much dependent on the individual. ​​The good thing is that microbiome can be restored after antibiotics.

 Top tip: Reducing the use of antibiotics when they are not absolutely essential is key to maintaining this balance.

 There are other factors that impact our gut microbiota including (but not limited to):

  • Frequency of exercise: it is suggested that daily exercise increase gut microbial diversity
  • Lifestyle: Stress, sleep deprivation, smoking and alcohol consumption all have a negative impact on your gut microbiota.
  • Our genetics can predispose us to favour some bacteria compared to others

What is ‘good’ gut bacteria?

You may have heard or read about ‘bad’ gut bacteria and organisms that can cause disease, but our gut also hosts a variety of ‘good’ gut bacteria that can greatly benefit our overall health. 

Note: there are some other parameters to describe microbiota and its health. For instance, the characteristics of a healthy gut microbiota depends on the density (the abundance of bacteria we have in our gut) and diversity (how many species of bacteria we have in our gut). It’s important to note that there isn’t a universal gut microbiota composition as it differs in every individual. It is said that your gut microbiota composition is as unique as your fingerprint!

Types of important gut bacteria:

  • Lactic acidbacteria (LAB): they encompass Lactobacilli, Bifidobacteria plus some others and play a key role in maintaining stability and diversity of the gut microbiome.
  • Bifidobacteria: help modulate the gut microbiota, prevent inflammation and protect from diseases

 There are also strains of good bacteria that can improve the gut’s resistance to pathogenic bacteria (bacteria that can cause disease). Examples include:

  • Commensal bacteria –   (some friendly forms of bacteria like Lactobacilli and Bifidobacteria, found commonly in probiotics)

Not only can good gut bacteria contribute to the gut’s defence system, but they can also:

  • Produce beneficial chemical compounds, for instance Short-Chain Fatty Acids (SCFAs) and vitamins.
  • Help the gut to maintain normal functions such as regulating gut motility (getting our food from A to B).
  • Help to break down some types of food (fibre, polyphenols) our digestive system cannot handle.
  • Help with detoxification (heavy metals and other toxins).

Keep reading on for tips on how to encourage good bacteria to thrive in the gut.

What is ‘bad’ gut bacteria?

As with all things good, unfortunately also comes the bad. Generally speaking, a healthy person has a stable, diverse microbiome (a balance of good and small number of bad bacteria). However, abnormal changes can alter this balance by adding/eliminating the members of microbiota or changing their abundance, a change known as dysbiosis. Dysbiosis is an unhealthy state of microbiome.

Symptoms such as constipation, bloating, diarrhoea, and food intolerances are just a few examples of what can happen when there is an imbalance in our gut microbiota. Did you know that IBS and IBD is also one of the most common diseases in developed countries in Europe, US and Scandinavia?

Other common gut-related diseases marked by dysbiosis include (but are not limited to):

  • Celiac Disease is an autoimmune disease of the small intestine in which the body responds to gluten with an inappropriate immune response causing inflammation and damage
  • Ulcerative Colitis is a chronic inflammatory bowel disease affecting the colon and the rectum 
  • Crohn’s disease is a chronic inflammatory bowel disease associated with an impaired immune response. It is characterised by lesions which can affect the gastrointestinal tract, from the mouth to the anus.
  • Obesity is the excessive or abnormal accumulation of fat in the body and impairs the health Obesity 
  • Diabetes is a metabolic disease, involving elevated blood glucose levels.

How to increase good bacteria in the gut naturally

Now that we’ve uncovered the roles both good and bad gut bacteria can play in our gut health and overall gut health, we can understand the importance of keeping that stable balance to ensure our gut (and us) are happy.

Here are just some tips on keeping a balanced and happy gut:

Improving diet:

  • Increase whole food diversity: as mentioned above
  • Avoid Ultra processed foods: UPFs! This is a biggy. New classification of foods for how processed they are

Here are more tips from Lauren Windas, Registered Nutritionist and Naturopath on how to improve our diet for a happy, healthy gut.

Regular exercise: there are several studies which show that short (acute) and long training sessions have both seen to have a different effect on our gut microbiota and health. Exercise also helps reduce stress hormones, which in turn affect the bacteria in our gut.

Reduce alcohol intake: Alcohol can influence the composition of our gut microbiota leading to dysbiosis. Reducing alcohol intake can help provide relief to an overburdened digestive system.

Read more about alcohol and the effect on our gut health.

Get enough sleep: Sleep deprivation can lead to unhealthy cravings for fatty and sugary foods due to the reduced levels of leptin (inhibits hunger) and increases levels of ghrelin (hunger hormone), and increases cortisol (stress hormone).

Read more about sleep and our gut on our blog – Let’s Talk Sleep

Take our gut supplements:

  • Aguulp for Gut Prebiotic fibres & key vitamins = food for your gut’s good bacteria
  • Gut Probiotic – Probiotic sachet containing 50 billion live bacteria. Packed with 10 probiotic strains, aiming to increase the count of your gut’s good bacteria.
  • Aguulp for Gut & Probiotic Dual Pack Taken together, you will be giving your gut the best chance of an optimum and healthy environment, supporting healthy digestion and general health.

What’s inside your gut?

Get to know your gut - Aguulp Gut Test

Researchers study the gut microbiota through various approaches but the most popular method, which is more readily available and less invasive to us is by stool sampling (yep, poop). At Aguulp, we think that gut testing is very important for anyone who cares about their health, and if you suffer from digestive issues or any of the conditions highlighted on this post, we would recommend trying to understand your body more closely. 

We offer an expert-scientific led Gut Test which measures your key biomarkers known as short-chain fatty acids (SCFA), which are super important for gut health and overall health. The quantity of SCFAs produced by your gut depends on your gut microbiota’s balance of certain bacterial species as well as your diet composition. Analysing your SCFAs gives us an insight into your microbiota state, an understanding of your diet and a snapshot of your current gut health.

Shop our Gut Health Test

More information on our Gut Health Test



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