What is a biome?
A biome is a biological community that has evolved in response to its environment. A rainforest is one example of a biome, supporting lots of different ecosystems or communities of living organisms, like animals, plants and microbes, which interact with one another.
What is a microbiome?
A microbiome is a community of microscopic organisms, such as bacteria, fungi and viruses, which inhabit a specific environment.
‘If I told you about a fellow creature that shares our food and habits, travels with us, has evolved with us to know what we like and dislike, and that we provide protection for, you might assume I was talking about your beloved dog or cat. In fact I’m talking about something a million times smaller and invisible to the naked eye.’
This is Professor Tim Spector talking about microbes1.
Tim Spector goes on to say ‘…our bodies contain 100 trillion of them, as many as all the cells in our body, and weighing over four pounds in our guts alone – where most of them live.’ This is the Gut Microbiome.
de Vos et al2 consider the human microbiome to consist of microbes, along with their genes and by-products, that have colonised our body since birth. Whilst all sites on our body are colonised, the largest numbers are found in the gut.
What does the gut microbiome do?
Evidence is mounting around the gut microbiome’s significance to health, along with a growth in public interest as to how the gut microbiome can be adapted by dietary choices.
Prior to the 1980s, gastric ulcers were thought to be caused by excess acid in the stomach. Treatment ranged from diet modifications, drugs and even radical surgery where ulcers refused to heal. However, in the 1980s two Australian researchers discovered that a bacterium known as Helicobacter pylori was causing the ulcers to form. Now, most gastric ulcers are treated with antibiotics and antacids. James Kinross states that since this discovery, a new era of microbiome research has begun. Scientists worldwide are questioning if the microbiome might indeed be responsible for other chronic diseases like cancer and dementia3.
There are reportedly 500-1,000 species of bacteria living within the human gut and improvements in DNA sequencing have allowed researchers to identify many of these species4
European Society of Neurogastroenterology & Motility (ESNM)5 list the functions of the gut microbiome as follows:
- Defence – against harmful microorganisms and toxins as well as modulating the immune response.
- Nutrition – digesting foods which human enzymes are unable to break down, e.g. fibre. This digestion produces beneficial molecules, for example short chain fatty acids such as acetate, butyrate and propionate. As well as facilitating the absorption of minerals from the diet, such as magnesium, calcium and iron, the microbiome also produces vitamins, for example vitamin K and B vitamins (though not in amounts sufficient to achieve the Recommended Dietary Allowance).
- Behaviour – affecting mental wellbeing.
What makes a healthy gut microbiome?
Van Hul et al6 state that although there is an undoubted link between a healthy gut microbiome and gut health, it Is difficult to align a definition of gut health and functionality alongside microbiome composition. They go on to say that scientific and medical viewpoints of a healthy gut range from simply the absence of detectable disease to a more comprehensive perspective, which emphasises the points listed by ESNM above as well as microbial diversity.
This is supported by Einstein4, who says part of the problem in distinguishing a healthy gut microbiome from an unhealthy one is because evidence is seeming to show there is no one version of a healthy gut microbiome.
It pays therefore to be mindful when buying food products claiming to support gut health, given the lack of consensus around what constitutes a healthy gut.
In 2023, ZOE, ‘a nutrition science programme leading the gut health revolution’, were identifying 30 of the hundreds of species of bacteria living in our gut4, as either ‘good bugs’ or ‘bad bugs’. These are listed below.
| 'Good bugs' | 'Bad bugs' |
|---|---|
| Veillonella atypica | Escherichia coli |
| Romboutsia ilealis | Flavonifractor plautii |
| Bifidobacterium animalis | Clostridium sp. CAG:58 |
| Bifidobacterium animalis | Ruthenibacterium lactatiformans |
| Veillonella dispar | Clostridium spiroforme |
| Prevotella copri | Clostridium leptum |
| Oscillibacter sp. PC13 | Blautia hydrogenotrophica |
| Clostridium sp. CAG:167 | Ruminococcus gnavus |
| Roseburia sp. CAG:182 | Clostridium bolteae |
| Firmicutes bacterium CAG:170 | Clostridium symbiosum |
| Haemophilus parainfluenzae | Collinsella intestinalis |
| Firmicutes bacterium CAG:95 | Eggerthella lenta |
| Eubacterium eligens | Clostridium bolteae CAG:59 |
| Oscillibacter sp. 57_20 | Clostridium innocuum |
| Faecalibacterium prausnitzii | Anaerotruncus colihominis |
Source: Author’s personal microbiome report (2023)
James Kinross, however, claims it is nonsense to say there are good and bad bacteria8.
In December 2025, ZOE scientists identified ‘100 specific gut bacteria species that serve as reliable markers for heart and metabolic health’ known as the ‘ZOE Microbiome Health Ranking 2025’. Using machine learning techniques, of the 50 species favourably associated with health, 22 were unknown, i.e. without taxonomic names. Of the 50 species unfavourably associated with health, 44 were known species, several of which are already attributed to detrimental health effects. Although the team concede ‘it is currently not possible to disentangle the effects diet plays to improve cardiometabolic health via the microbiome’7. It is also worth noting that a significant majority of the participants in the ZOE PREDICT studies, from which this data is gleaned, were female.
The composition of your gut microbiome is under the influence of factors personal to you, such as your age, sex, ethnicity, genetic make-up, and how your immune system functions. It is also impacted by external factors, such as where you live, who you live with and interact with socially, your exposure to pollutants, how physically active you are, stress, pharmaceuticals and of course your dietary habits6 9 10.
According to Van Hul et al6 some of the markers that could be considered to constitute a healthy gut microbiome are outlined below…
Diversity
A large number of different species is generally regarded as beneficial.
Composition
One possible health marker is the Bacillota/Bacteriodata ratio; a higher proportion of Bacillota may have an association with obesity, whereas increased Bacteriodata may be linked to leanness. As previously seen in the literature, the same caveats to these associations apply, i.e. the complex nature of the microbiome and conflicting evidence from study data.
Functional diversity
Studies have found that whilst two individuals may only share around 45% of bacterial species in their guts, their gut microbiomes have 82% of metabolic pathways in common, meaning different species can perform the same functions so potentially offering some resilience for the host.
Metabolites
Short chain fatty acids (SCFAs) such as acetate, butyrate and propionate are by-products of the bacterial fermentation of dietary fibre. A source of energy for the cells of the colon, these metabolites have a role in maintaining the integrity of the gut barrier as well as the modulation of the immune response. However, the accurate measurement of SCFAs is complex, requiring specialised spectrometry techniques and their levels can change due to the complex interplay between the composition of the gut microbiome and differing dietary patterns.
Variants
Severe disease can be caused by some strains of Escherichia coli, enterohaemorrhagic E. coli as one example, whilst other strains are benign.
Lastly, a look at diet and specifically probiotics, prebiotics and fermented foods. Unsurprisingly, food and beverage companies are capitalising on the growing focus on gut health.
Probiotics
A probiotic is defined as ‘live microorganisms that, when administered in adequate amounts, confer a health benefit on the host’11. By association the probiotic should contain sufficient microorganisms that are alive by the time they reach the site of proposed action in the gut. Found in dairy foods such as yoghurts and aged cheeses, alternative sources such as kefir, which is a fermented milk, are now becoming more mainstream. Other non-dairy probotics are covered in the section on fermented foods below. Probiotic supplements are also available.
Prebiotics
A prebiotic is defined as a substrate, usually dietary fibre, that serves as a nutrient for microorganisms living in the gut and ultimately confers a health benefit to the host. Prebiotics can also be taken as a supplement in the form of powders, gummies and capsules.
For more detail on prebiotics see the post Dietary Fibre.
Fermented foods
First used as an ancient practice for food preservation, the current reported gut health benefits of fermented foods have caused a resurgence in their popularity. Live, harmless bacteria (two main groups include Lactobacillus and Bifidobacterium) or yeast consume the natural sugars in a food source. In an anaerobic environment (absence of oxygen), these microorganisms grow and multiply, producing organic acids, such as lactic acid and carbon dioxide. This is fermentation. Examples of fermented foods include, kefir (milk), kombucha (sweetened tea) and kimchi (spiced vegetables). Food fermentation can be carried out at home, using a salt brine or rubbing salt into the vegetables to create the anaerobic conditions. It may take 1 – 2 weeks for the desired result to be achieved.
A few tips on fermented foods…
- Some, but not all fermented foods can be probiotics
- Vegetables pickled with vinegar are not generally probiotic
- If a fermented food has been pasteurised, it may still contain the healthy by-products of fermentation but it is likely the microbes will have been de-activated due to the heat treatment
- Foods that do contain live cultures generally need to be stored in a refrigerator
- Cask-conditioned beer (real ale) is a probiotic beverage which can offer limited probiotic benefits. As with all alcoholic beverages it should be consumed in moderation
- Check food labels to be sure what you are buying
The gut microbiome is a vast subject, touching many other areas not mentioned in this post, for example the effect of ultra-processed foods on the gut microbiome, food as medicine, personalised nutrition, farming, antibiotic use in farming, pharmaceuticals, the immune system, the gut-brain axis. Continuing research is much needed to overcome the challenges to distinguish causations rather than correlations between our health and our gut microbiome.
References
- SPECTOR, Tim. 2020. The Diet Myth The Real Science Behind What We Eat. London: Weidenfeld & Nicolson, pp 14
- de Vos W M, Tilg H, Van Hul M, et al. Gut microbiome and health: mechanistic insights Gut 2022; 71:1020-1032
- Kinross, James. 2024. Dark Matter The New Science of the Microbiome. UK:Penguin Life, pp 48
- Eisenstein, Michael. The hunt for a healthy microbiome. Nature 577, S6-S8, 2020 doi: https://doi.org/10.1038/d41586-020-00193-3
- About gut microbiota (2022). Gut Microbiota for Health. Available at: https://www.gutmicrobiotaforhealth.com/about-gut-microbiota-info/ (Accessed: 14 March 2026)
- Van Hul M, Cani PD, Petitfils C, et al. What defines a healthy gut microbiome? Gut 2024;73:1893–1908. doi: https://doi.org/10.1136/gutjnl-2024-333378
- Asnicar, F., Manghi, P., Fackelmann, G.et al. Gut micro-organisms associated with health, nutrition and dietary interventions. Nature 650, 450–458 (2026). doi: https://doi.org/10.1038/s41586-025-09854-7
- Kinross, James. 2024. Dark Matter The New Science of the Microbiome. UK:Penguin Life, pp 330
- Cresci GA, Bawden E. Gut Microbiome: What We Do and Don’t Know. Nutr Clin Pract. 2015;30(6):734-46. doi: https://doi.org/10.1177/0884533615609899
- Kinross, James. 2024. Dark Matter The New Science of the Microbiome. UK:Penguin Life, pp 149-155
- Hill C, Guarner F, Reid G, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014; 11(8): 506-514
