The term ‘good bacteria’ is used a lot, but what does it mean? Who are the good guys in your gut and at what levels do they need to be to constitute ‘good’ and healthy?
Content Outline
- Introduction to the gut microbiome
- What are good gut bacteria?
- Key players: The prominent good bacteria species
- How to support and maintain good gut bacteria
- Summary
Introduction to the gut microbiome
Although it’s easy to think your body is exclusively yours, it’s not. In every nook and cranny, a tenant is renting a bit of space, whether for good, bad, or neutral reasons. Your gut is one of these zones teeming with life, also known as your gut microbiota.
The human gastrointestinal tract is one of the largest structures in the human body, with the average mucosal surface equating to approximately 32m2[i] and up to 400m2 in total surface area. In other words, it’s huge, but it’s also home to trillions of microbes who have co-evolved with humans over thousands of years, forming a mutually beneficial relationship[ii].
This unique ecosystem is comprised of bacteria, archaea, fungi, and viruses that reside in your gut and can have a profound impact on your health.

Figure 1. The positive impact of the human gut microbiota. (Source: Afzaal et al, (2022))
Among these microbes are “good” bacteria, essential allies for supporting digestion, immunity, and mental wellbeing. In this article we’ll introduce you to four key species of good gut bacteria – Bifidobacteria, Lactobacilli, Akkermansia, and Faecalibacterium – and explore their remarkable functions, why they’re termed “good,” and how to support their healthy growth.
What are good gut bacteria?
Good bacteria are the beneficial microbes that support your health in several ways and cause no harm. They are also known as probiotics – live cultures found in foods that when consumed in high enough quantities,, have health benefits – and some of their benefits include:
- fermenting/breaking down dietary fiber and transforming it into useful metabolites (short chain fatty acids (SCFAs, vitamins)
- strengthening the integrity of the gut barrier for better immunity and protection from pathogens
- antimicrobial activity against pathogenic bacteria
- protection against allergens
- protective anti-cancer benefits[iii]
When balanced and enriched with health-promoting microbes, the gut microbiota is an important factor in the prevention of many chronic illnesses and promoting your overall health and wellbeing.
However, when the balance of good and bad bacteria is disturbed, a condition called dysbiosis, it can impact several body systems and organs, causing a variety of symptoms, such as inflammation, digestive complaints, illness, and even lead to chronic disease (Fig. 2).
Figure 2. The negative effect of the human gut microbiota when it is in a state of dysbiosis or imbalance. (Source: Afzaal et al, (2022))[iv]
Therefore, understanding which species and strains are good and how to promote and maintain their presence in your gut is critical.
Key players: The prominent good bacteria species
Your gut is home to countless bacterial species, but some are the real VIPs when it comes to supporting your health. The key species work behind the scenes to keep your digestion smooth, your immune system strong, and your gut barrier intact.
1. Bifidobacteria
Function in the gut: Bifidobacteria are a key component and one of the first colonizers of the human gut microbiome. They have a significant role in digestion, breaking down fiber and transforming it into SCFAs, supporting immune function, and cross-feeding other key species, such as those that produce butyrate, the main energy source for the cells lining the gut[v].
Healthy population range: Bifidobacteria dominates the microbial population in the gut. In infants, Bifidobacteria make up around 60 to 70% of the gut community. In adults, it’s closer to 10 to 15% of the total gut microbiota of healthy individuals[vi].
2. Lactobacilli
Function in the gut: Lactobacilli are bacteria that produce lactic acid which helps to maintain bacterial balance in the gut by preventing the growth of harmful microorganisms. Humans have a mutually beneficial relationship with Lactobacilli because the species aids the digestion of certain dietary components and protects against invaders, in return for a place to stay and nutrients to help them thrive and survive[vii].
There are many different species of Lactobacilli. Some popular examples include:
- Lactobacillus acidophilus is a common gut species that aids digestion and improves symptoms of irritable bowel syndrome (IBS)[viii].
- Lactobacillus rhamnosus reduces inflammation, modulates the gut microbiota, and can protect against pathogenic invasion[ix].
- Lactobacillus reuteri reduces gut inflammation and can improve depression symptoms through its ability to modulate the gut and improve serotonin metabolism[x].
Healthy population range: There are more than 200 known species of Lactobacilli and yet only a few are consistently linked to the gut with the most abundant being:
- L. casei
- L. delbruckeii
- L. murinus
- L. plantarum
- L. rhamnosus
- L. ruminus
Despite their presence being crucial for human health, Lactobacilli account for less than 1% of the total microbial population (around 0.3%)[xi].
3. Akkermansia
Function in the gut: Akkermansia, specifically A. muciniphila, has been identified as a next-generation probiotic because it has some unique properties. Unlike other probiotics that ferment specific dietary components, A. muciniphila is a mucin degrader which means it uses the mucins that make up the mucosal layer in the gut as an energy source. So it can thrive without being reliant on you, by degrading mucins, it encourages more mucin to be produced, strengthening the gut lining[xii].
The presence of A. muciniphila is associated with a lower incidence of metabolic diseases such as obesity and type 2 diabetes[xiii]. It’s associated with the guts of lean people and improved weight management and lower inflammation.
Healthy population range: Having only been discovered in 2004, A. muciniphila has since been identified as one of the most prominent bacterial species in the human gut, accounting for 0.5 to 5% of the total bacterial population[xiv].
Can you have too much A muciniphila?
Possibly. Some mice studies are showing that too much A.muciniphila in your gut can cause some side effects including minor inflammation. For example, Qu et al., (2023) found that overcolonization of A. muciniphila in mice with colorectal cancer or colitis resulted in mucin being degraded in the gut lining without increasing mucin production.
This disruption coupled with altered tight junctions resulted in an unhealthy gut mucosal environment, increased inflammation, and allowed the microbiota to cross into the circulation in the cancer model. Therefore, there is a possibility that overcolonization could contribute to the progression of some intestinal diseases via the degradation of mucins in the gut lining[xv].
That’s why it is important to focus on keeping the gut microbiome balanced and not favouring one species over another. Keep reading for our top tips for supporting and maintaining balance in the gut.
4. Faecalibacterium prausnitzii
Function in the gut: Faecalibacterium prausnitzii is one of the major butyrate producers in the gut. Butyrate is a crucial SCFA that provides energy for the cells lining the gut and has many other important roles including anti-inflammatory and antioxidant effects. Research has shown that F. prausnitzii is present in nearly everyone’s gut[xvi].
Healthy population range: F. prausnitzii is one of the most abundant bacterial species in the gut[xvii], representing more than 5% of the total gut microbiota[xviii].
How to support and maintain good gut bacteria
Here are some of the practical ways you can help nurture beneficial gut bacteria:
- Focus on a fiber-rich diet: Wholegrains, fruit, vegetables, beans, and legumes are all excellent sources of prebiotic fibre, which will help to keep your beneficial bacteria nourished.
- Incorporate fermented foods: Fermented foods, naturally contain probiotics and are a great source of health-promoting bacteria. Some tasty examples include live yogurt, kombucha, kimchi, kefir, and miso.
- Stay active: Regular physical exercise is important for promoting a diverse and healthy microbiome.
- Avoid antibiotic overuse: Antibiotics, although a medical breakthrough, can kill both good and bad bacteria in your gut, so it’s best to only use them when necessary and you’re sure they are going to do some good.
- Get a microbiome test: If you want to understand what your gut microbiome looks like, get a microbiome test. You’ll need to supply a small fecal sample and send it away for analysis. You can use your results to help you target the areas of your gut that need attention and improve your overall health and wellbeing.
- Choose good quality prebiotics: Human milk oligosaccharides (HMOs) are (in our opinion) the best example of prebiotics because they are so integral to a healthy microbiota in both adults and infants. You can maximise the benefits of HMOs when you combine them with probiotics, such as our SuperHMO Prebiotic Mix. HMOs can support the growth of all the good bacteria species listed in this article. We also offer our popular Akkermansia muciniphila probiotic.
Summary
The key to a healthy gut microbiome is having your good and bad bacteria in balance, or a state of eubiosis. Species like Bifidobacteria, Lactobacillus, Akkermansia muciniphila, and Faecalibacterium prausnitzii are just some of the examples that are critical for your health. By supporting their growth with a balanced diet and healthy lifestyle, you can support your digestion, immunity, and mental wellbeing.
Taking care of your gut microbiome is an investment in your long-term health, one you can proactively promote with our PureHMO products.
Written by: Leanne Edermaniger, M.Sc. Leanne is a professional science writer who specializes in human health and enjoys writing about all things related to the gut microbiome.