The Importance of Gut Bacteria

Bacteria and the microbiota explained

Each of us has our own unique make up of microorganisms living on or inside us. Most of these microorganisms are bacteria but also include archaea, viruses and eukaryotic microorganisms. These microorganisms are also called microbiota and live on the skin and in the gut, mouth and vagina. Some are essential for human health and survival. We provide the microorganisms with the right environment and nutrients to allow them to survive. In exchange they help us by producing vitamins, assisting energy metabolism, immune support and digestive function.

What is the role of gut bacteria?

We have an estimated 100 trillion bacteria living in our gut that can weigh up to an astounding 2kg! These essential microorganisms play an important role in maintaining our health, weight and wellbeing. Some of their functions include:

  • Helping to digest foods and medications
  • Supporting the production of vitamin B and vitamin K
  • Increasing the energy taken from foods and altering appetite
  • Supporting the immune system and protecting us from foreign pathogens by providing a physical barrier and maintaining a healthy intestinal mucosa
  • Enabling healthy digestive function

What are the different types of gut bacteria?

There are more than 1000 types of bacteria that have been found living in the human gut and each of us has approximately 150 to 170 species that are dominant. Most of us share the same one third of these bacteria, although the remaining two thirds of bacteria are unique to each of us.

Our gut bacteria are mostly from the Firmicutes and Bacteroidetes phyla, with fewer being Proteobacteria and Actinobacteria phyla.3 Phyla is just a term used to classify the bacteria just like we use the name ‘dog’ to describe the canine species. Then each phylum we have a number of bacterial genera. Genera is a sub-classification to further describe the bacteria in a phylum, just like we use specific breeds of dogs to classify types of canine species such as ‘dalmations’ or ‘poodles’. Some of the most common bacterial genera include Clostridium, Ruminococcus, Enterococcus, Lactobacillus, Bifidobacterium and Akkermansia that belong to the Firmicutes phyla and Bacteroides and Prevotella that belong to the Bacteroidetes phyla.

The diagram below further details some of the most abundant bacteria that we see in a healthy gut and where these bacteria are located:

Our gut is also home to a variety of pathogens such as Campylobacter jejuni, Salmonella enterica, Vibrio cholera, Escherichia coli (E. coli) and Bacteroides fragilis although these make up less than 0.1% of our microbiota.

What influences gut bacteria?

Our gut bacteria are constantly changing in response to our diet, lifestyle and environment. The gut bacteria we have as an infant is vastly different to what we have as an adult. Some of the major factors that influence our gut bacteria include our age, geographical location, diet and birth method, as well as our lifestyle behaviours such as antibiotic usage, our participation in exercise, ability to manage stress and avoidance of smoking.


Lactobacillus and Bifidobacterium are the predominate genera of gut bacteria for infants. Once infants stop receiving breast milk and start eating a varied diet the Lactobacillus and Bifidobacterium bacteria decrease and account for only a small percentage of bacteria in the large intestine. Their bacterial composition changes and begins to reflect what is seen in an adult’s microbiome.

The bacteria most abundant in adults are Firmicutes and Bacteroidetes. These two phyla then remain dominant into mature age, although mature adults have less Bacteroidetes and more Firmicutes compared to younger adults. 5 6 Learn more about how age impacts your microbiome. (add in internal link to “Gut Bacteria Over the Lifespan”)


Gut bacteria can vary based on ethnic background and geographical location. There have been differences in gut bacteria seen between individuals living in the Unites States and individuals living in rural communities in Venezuala and Malawi.

Mature adults living in long-term care have less diversity in their bacteria compared to mature adults living in the community. This suggests that not only the country, but also the location of where we live can impact our gut bacteria.


A Western diet high in sugar, fat and refined carbohydrates and low in fibre has been shown to reduce gut bacteria diversity. Reduced diversity is associated with the development of a number of digestive, mental health and immune conditions whereas more traditional diets high in fibre and complex carbohydrates that are followed in rural African and South American countries lead to greater bacterial diversity.

Diet is also an influential factor in an infant’s gut bacterial development. Breastfed babies have been shown to have higher numbers of Bifidobacteria compared to formula fed babies. Bifidobacteria has been associated with healthy immune development and is why breast feeding is encouraged for healthy gut bacteria development. 


Exercise can also impact our gut bacteria. Participating in 30-60 minutes of exercise three times a week can increase bacteria that produce short chain fatty acids. We need short chain fatty acid producing bacteria to provide us with energy and support metabolism and healthy weight management.


Stress can impact gut bacteria by impairing colon function and altering the bacterial ratios in the gut. Stress can lower the number of Lactobacillus bacteria in the gut, which may be of concern as Lactobacillus are important for healthy gut function.


Smoking impacts the composition of gut bacteria, as it increases the bacterial ratio of Bacteroides to Prevotella.

Antibiotic use

Antibiotic use has been shown to disrupt gut bacteria and may contribute to an imbalance of gut bacteria, also known as gut dysbiosis. Antibiotics are often taken to destroy harmful bacteria, although they can also destroy our beneficial bacteria and lead to bacterial imbalance. Imbalances of gut bacteria can interfere with the normal function of bacteria and these imbalances have been associated with a number of health conditions and increased risk of infection. While antibiotics have a role in fighting bacterial infections it is important not to overuse them to maintain healthy gut bacteria.

Birth method

How we are born can impact the development of our gut bacteria. Infants born by caesarean have been shown to have less gut bacteria at one month of age compared to infants born naturally.

While our gut bacteria have complex names that may be hard to recall, the important thing to remember is that maintaining a healthy balance of these bacteria is necessary for healthy gut function. Eating a healthy diet, avoiding overuse of antibiotics, exercising regularly and managing stress can all support the development of beneficial bacteria and bacterial diversity necessary for gut health.

How gut bacteria change over the lifespan

The bacteria living in our gut, known as microbiota, change as we age with infants, adolescents, adults and mature adults having different microbiota communities. By one year of age we have developed a unique microbiota profile and this continues to change over the course of our life based on our diet, environment and overall health.

There are gut bacteria developments and differences across each of the life stages from infancy through to mature adulthood.

Infancy and early childhood

The gut microbiota of a newborn is understood to have less bacterial diversity. An infant’s microbiota has a predominant proportion of the phylum Firmicutes (of which Lactobacillus and Bifidobacterium are the bacterial genera), and includes a reasonable proportion of the phyla Proteobacteria and Actinobacteria Between two and five years of age the microbiota develops in composition and diversity to what is seen in adults with Firmicutes and Bacteroidetes becoming the dominant bacterial phyla present.

It is believed that our microbiome develops toward an adult-like microbiota in the first three years of life. The microbiome is our gut environment where bacteria live. The mother’s health during pregnancy, the time, place and method of birth, antibiotic usage, breastfeeding, diet, geographical location, family environment and hygiene are all factors that can impact the development of an infant’s gut bacteria. As infancy and childhood are important life stages in developing a healthy gut, care should be taken to support microbiota development through a healthy pregnancy, natural birth when possible, breastfeeding when possible and refraining from the overuse of antibiotics.

Infants born by caesarean have been shown to have a fewer number of Bacteroidetes and Bifidobacteria compared to those infants vaginally delivered. While infants who are formula fed have been shown to have fewer Bifidobacteria compared to breastfed infants. Bifidobacteria is a gut microorganism of interest as high levels of Bifidobacteria have been associated with healthy immune development and maturation.


Adolecents share a similar number and type of gut bacteria to that of adults with Bacteroidetes and Firmicutes the dominant bacterial phyla. Variations exist in bacteria at the genus level, which are subspecies of bacteria. Adolescents have been shown to have a higher number of Bifidobacterium and Clostridium, belonging to the Firmicutes phyla.

Bifidobacterium is recognised as being a predominate bacteria in children and for being the first species to take residency in a newborn’s gut, potentially explaining why adolescents have an elevated number of these bacteria.


The adult microbiota is more complex and stable with greater diversity compared to that of infants, children and adolescents. Microbiota diversity is considered to be beneficial for maintaining health. Bacteroidetes and Firmicutes are the two bacteria types that make up a healthy gut microbiota throughout adulthood, provided there are no challenges to the gut environment. Frequent antibiotic usage, poor diet and recurrent infection can impact the abundance of these bacteria and alter the microbiota.

Mature adulthood

Mature adults have been shown to have less diversity in their gut bacteria compared to younger adults. They have a reduced number of Lactobacilli, Bacteroides, Prevotella and Faecalibacterium prausnitzii bacteria that have been associated with greater frailty.

Mature adults over the age of 65 living in long-stay care have also been shown to have less microbiota diversity compared to mature adults living in the community. Maintaining diversity of microbiota species is important for health and well-being.

While age can impact our gut bacteria, it is not the only factor that influences the health and diversity of our bacteria. Environmental factors such as diet, antibiotic usage, stress, infection and birth method all play an important role in determining bacterial diversity and overall gut health.

To help maintain the health of your gut bacteria it is recommended to restrict overuse of antibiotics, manage your stress, participate in regular exercise and consume a healthy diet rich in dietary fibre, prebiotics and probiotics.

Good vs bad bacteria

While bacteria are essential for our survival, not all bacteria are beneficial. There are a number of beneficial and potentially harmful bacteria that have been associated with human health and disease.

Many of the ‘good’ bacteria, recognised through research, for supporting human health belong to the Lactobacillus and Bifidobacteria genus. Some of the most well researched bacteria species are included in the table below, along with some of their documented uses. Each of these studies used specific bacterial strains at particular dosages to achieve clinically significant outcomes that may be relevant only in the population group studied.

However if the gut environment is in poor health there are a number of ‘bad’ bacteria that can cause harm. These include Clostridium difficile, Klebsiella pneumoniae and some types of Escherichia coli. These bacteria, and the symptoms and conditions that they have been associated with, are outlined in the table below.

Escherichia coli, Clostridium difficile, Enteroccus faecalis and Enterococcis faecium also have a role in causing gut inflammation and have been associated with a number of inflammatory bowel conditions. Other potentially harmful bacteria that have a role in bloating are Anaerotruncus colihominis, Ruminococcus callidus and Lachnospira pectinoschiza.

The presence of ‘bad’ bacteria in the gut is not always detrimental to health, as it isn’t just about the type of bacteria you have in your digestive tract. The ratio of your ‘good’ to ‘bad’ gut bacteria also matters. Imbalances in the ratio of ‘good’ to ‘bad’ bacteria is known as dysbiosis and can be caused by poor diet, antibiotic and toxin exposure, stress, hygiene and bacterial infections. Dysbiosis may be associated with the development of number of health conditions.

Supporting the maintenance of beneficial gut bacteria through your diet, lifestyle and environment is an effective approach to reduce the risk of dysbiosis and minimise the potential health complications that may follow.

How our diet affects gut bacteria

When you decide what to eat for your next meal will you be considering the trillions of bacteria living in your gut? It could be a wise idea, as our gut bacteria are strongly influenced by our dietary choices.

Our gut bacteria have a number of important roles in helping to keep us healthy. They help us with digestion, vitamin B and vitamin K production and support our immune system. For our gut bacteria to perform these roles they feed on indigestible fibre in the large intestine. These indigestible fibres are often called prebiotics and come from what we choose to eat.

Emerging research is showing that a 'traditional' diet can impact our gut bacteria and some interesting findings have been observed.

One study swapped the diets of rural Africans and African Americans for two weeks and found a number of differences in their gut bacteria. The rural Africans traditionally eat a high-fibre and low-fat style diet and this was swapped with the high-fat and low-fibre diet of African Americans. At the end of the two weeks the rural Africans eating the high-fat and low-fibre diet had impaired production of the short-chain fatty acid butyrate. Butyrate is what bacteria produce by feeding on undigested fibres, or prebiotics, in the large intestine. Butyrate is needed as an energy source for our intestine cells, for reducing inflammation and supporting gut healing. Interestingly the African Americans who were eating the high-fibre and low-fat diet had increased production of butyrate and improved gut health.

Another study compared the traditional diets of two groups of children from Europe and rural Africa. The European children were consuming a Western diet and were compared to African children living in rural Burkina Faso eating a traditional high fibre diet. The African children had a higher ratio of Bacteroidetes to Firmicutes which has been linked with the maintenance of a lean body mass. The African children showed greater microbiota diversity, including many anti-inflammatory bacteria that are able to reduce inflammation associated with the increased risk of illness and disease. The African children also had more short-chain fatty acids that are necessary for providing cells with an energy source.

While we still do not understand what exact diet is best for our gut bacteria, we do know that adding fibre and prebiotics is an effective way to improve gut bacteria diversity and encourage the maintenance of healthy gut bacteria. Look after your gut bacteria by including plenty of fibre and prebiotic rich foods into your diet. Some good sources of fibre include fresh vegetables, wholegrain bread and pasta, brown rice, kidney beans and rolled oats. Whereas some prebiotic rich foods your gut bacteria will appreciate could include a prebiotic honey, asparagus, onion, garlic, Jerusalem artichoke and chicory.

How to improve your gut health

We have over 100 trillion bacteria living in our gut and looking after these bacteria and their environment, called the microbiome, is essential for healthy gut function as well as our overall health.

Diet and lifestyle habits such as medication use, alcohol, stress, poor sleep and a poor diet can impact our microbiome by causing an imbalance of the beneficial and harmful bacteria in our gut. This imbalance is known as dysbiosis and may contribute to a number of health conditions affecting not only the gut itself, but also aspects that are immune mediated.

If you are concerned about your gut health or are looking to optimise your digestive function here are some scientifically researched ways you can improve your gut health.

1. Eat a fibre rich diet

Choosing to eat a high fibre diet rich in fresh vegetables, fruit, beans and legumes supports digestive health and allows regular bowel movements. Fibre is a component of food that is not digested in the small intestine and ferments in the large intestine or colon.

Fibre also promotes the growth of beneficial gut bacteria such as Bifidobacteria that reduces gut inflammation and promotes gut healing. Consumption of a high fibre diet has also been shown to reduce the risk of a number of digestive conditions such as constipation.

It is recommended that Australian women consume 25g of fibre daily for healthy gut functioning and Australian men consume 30g of fibre daily. 

2. Include prebiotics in your diet

Eating prebiotic rich foods can help raise the number of good bacteria in your gut to support digestive health. A prebiotic is an indigestible fibre that promotes the growth of beneficial bacteria in the gut to benefit health and wellbeing.

Prebiotics may improve bowel regularity and digestive function. They have also been associated with supporting calcium absorption, modifying blood glucose responses, acting as a fuel for colonic bacterial fermentation and assisting gut transit time.

Some good food sources of prebiotics include Jerusalem artichokes, chicory, garlic, onion, leek and pre-ripe banana. You may need to eat large quantities of these foods to consume a beneficial amount of prebiotcs. To get a high dose of prebiotics to support a healthy gut you could also use a prebiotic supplement, such as a prebiotic honey supplement.

3. Add probiotics to your diet

Including probiotics in your diet through supplementation or food sources, such as yoghurt and kefir, can help support a healthy gut. Probiotics are beneficial live microorganisms that can provide us with health benefits when consumed in adequate amounts.

Probiotics support gut health by breaking down indigestible food particles, producing vitamins, supporting nutrient absorption and competing with harmful microorganisms in the gut to maintain a healthy balance of bacteria. They can be particularly beneficial when you have taken a course of antibiotics and your gut bacteria have been challenged.

4. Eat fermented foods

Fermented foods and beverages have been associated with increasing the microorganism diversity in the digestive system to support gut health. Some of the best fermented food sources include yoghurt, sauerkraut, kimchi, kefir, kombucha, tempeh and miso.

Fermented foods or beverages have been exposed to a yeast or bacteria and had their carbohydrates and sugars converted to alcohol or organic acids. This fermentation can alter the flavour of the food or beverage, extend its shelf life, increase its nutritional value and also increase the number of good bacteria present in the food.

5. Manage your stress

Learning to reduce or manage your stress can help support healthy gut function. Stress can impact gut functioning by altering gut motility and secretions and impairing gut healing.

Exposure to chronic stress has been linked with a number of gastrointestinal disorders.

If you are frequently feeling stressed, some effective ways to manage your stress could include mindfulness meditation, breathing exercises, cognitive behavioural techniques, yoga and Tai Chi.

6. Get regular exercise

Exercise has been positively associated with gut health. Exercise may be able to boost microflora diversity and increase the number of beneficial bacteria that live in our digestive tract to improve our health and wellbeing.

Exercise has been shown to improve the balance of bacteria in our gut that may help to manage gastrointestinal, metabolic and weight issues.

For those keen to improve your gut health quickly, it is reassuring to know that gut bacteria respond to dietary changes in as little as three days. A study has shown that gut bacteria can be improved after three days of following a predominately plant based diet high in fibre.

So, now is the perfect time to implement some of these recommendations to help promote digestive health and your general wellbeing!


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