Omega-3, allies of the gut microbiota: discover their prebiotic properties!

A growing body of research confirms how important gut wellbeing is for health. And gut wellbeing depends on the balance of the microbes that live inside it: the gut microbiota. Through your diet you can take in substances – prebiotics – that help you maintain this delicate balance. And what about Omega 3? What is their role?

They are fats, but they are “good” ones. They have marked anti-inflammatory properties. They are good for the heart, the brain and vision. They are allies in sport. How many times have you heard these things said about Omega 3?

About some of the benefits of taking them there is no longer any doubt. About others there is consistent evidence, confirmed day after day by the results of new research. And scientific studies suggest there are still others you may never have heard of, such as the ability to promote the wellbeing of the population of microbes that lives in our gut: the gut microbiota.

This is the property referred to when we say that Omega 3 are also prebiotics. But what exactly do they do to support the health of the gut microbiota? And why does this action interest us so much?

The point is simple: the microbes that live in our gut – and what they do inside it – profoundly influence our state of health.

What the gut microbiota is and what it does

Let’s start with the definitions: as mentioned, the gut microbiota is the set of all the microorganisms (bacteria, fungi, viruses, …) that populate our gut. All these microorganisms have a genetic heritage that adds to our own genetic heritage; the set of all these microorganisms and their genetic heritage is called the “microbiome”.

The microbes that live in the gut – and their genetic heritage – are particularly abundant compared with those living in other body districts (such as the vagina or the oral cavity). And they do not sit in the gut doing nothing: for example, they produce molecules we are unable to produce and digest substances we are unable to digest.

Consider that they even regulate the way the body processes and uses Omega 3. In particular:

• some influence their absorption;
• others transform them into molecules endowed with other properties.

Everything they do contributes enormously to our health because it interacts continuously with our body, and this interaction influences our health in a great many respects – not only, as one would intuitively think, at the gut level, but, for example, also at the level of the immune system, cardiometabolic health and mental health.

What comes into play are the substances produced by the microbiota, which influence – directly and indirectly – various functions of our body.

Gut dysbiosis: definition, causes and consequences

When the gut microbiota moves away from its state of balance (eubiosis) we speak of “dysbiosis”. This term denotes all the circumstances in which some microbe takes over the others, moving the microbiota away from eubiosis.

Unfortunately these are very common conditions. Among the most frequent causes are:

• dietary habits (for example, a diet low in fibre, or an excess of protein or fat);
• taking medication (such as antibiotics);
• infections.

For example, an infection that triggers episodes of diarrhoea inevitably alters the balance of the gut microbiota.

Every time the balance of the microbiota is altered, its functions are altered too. Two crucial points are the reduction of substances that protect the gut environment and the alteration of the gut’s permeability barrier – with possibly significant consequences not only at the gut level, but also on all the other functions of the body influenced by the microbes that live in this organ.

Omega 3 for the balance of the gut microbiota

Fortunately it is possible to act on the gut microbiota to promote its balance and counter dysbiosis and the associated problems. One of the main modulators of the gut microbiota is diet, a source of substances with a prebiotic effect.

Prebiotics are substances that selectively nourish gut microbes, producing beneficial effects on the host’s health. The best known are plant fibres, but today research attributes prebiotic effects to other molecules of dietary origin as well, such as polyphenols and Omega 3.

In particular, Omega 3 have been associated with:

• greater diversification of the microbiota (that is, of the variety of the microbes that make it up), considered an indicator of eubiosis;
• the proliferation of bacteria with anti-inflammatory properties (such as bifidobacteria, lactobacilli and Akkermansia muciniphila) and of producers of beneficial substances, the short-chain fatty acids (Short-Chain Fatty Acid, SCFA);
• the reduction of pathogens linked to inflammation and metabolic diseases (such as Desulfovibrio, Escherichia coli and Helicobacter);
• an increase in microbes that are allies of the gut barrier (A. muciniphila) and a reduction in bacteria that damage it (such as Ruminococcus and Oscillibacter);
• a better ratio between Firmicutes and Bacteroidetes, which is altered, for example, in obesity and fatty liver.

The prebiotic effect of Omega 3 might also mediate their very well-known benefits, in particular those for the cardiovascular system and those for the brain. Moreover, the scientific literature suggests that Omega 3 may also be useful in other specific conditions associated with changes in the microbiota, such as obesity, type 2 diabetes, polycystic ovary syndrome and chronic inflammatory bowel diseases.

In this last case they would help the microbiota recover a composition typical of more desirable states of health, with improvement of the altered gut barrier and an increase in SCFA producers. And, again thanks to the increase in SCFA producers, they would appear to help lower the inflammation associated with acne.

In addition, the effects of Omega 3 on the gut microbiota enhance their anti-inflammatory properties, which are due to the fact that in themselves they already:

• are the precursors of less inflammatory molecules than those produced from other fats, as well as of mediators specialised in switching off inflammation;
• inhibit pro-inflammatory factors, such as NF-kB, and activate anti-inflammatory pathways, such as those mediated by the PPAR-γ receptor.

This means that by taking Omega 3 you can exploit, directly, their anti-inflammatory properties and, indirectly, those of the microbes nourished by the Omega 3 you have taken. So how can you ensure a good dose of these fats?

The best dietary sources of Omega 3

The best-known source of Omega 3 is oily fish. It is better to favour small-sized fish, such as anchovies and sardines, and even better if wild-caught. This second characteristic ensures both a good presence of Omega 3 and a good ratio between Omega 3 and Omega 6.

The latter, in fact, are polyunsaturated fats that are just as important for health, but with effects that tend to be opposite to those of Omega 3, with a greater inflammatory potential and very abundant in the modern Western diet.

The effects of Omega 6 on the microbiota would also be opposite to those of Omega 3, and a ratio between Omega 6 and Omega 3 that is excessively unbalanced in favour of the former could attenuate the benefits of taking the latter, at the gut microbiota level too.

Nuts (in particular walnuts), oilseeds (flax, chia, …) and the oils derived from them are also all sources of Omega 3 that we can include daily in our diet, but compared with fish they do not provide the biologically active Omega 3 (EPA and DHA) ready for use, but rather their precursor (ALA), which unfortunately is used by our body very inefficiently.

Another interesting source is microalgae, rich above all in DHA, from which an oil can be obtained that, just like fish oil and krill oil, contains Omega 3 in their biologically active form, and which can be used to produce food supplements suitable also for those who are allergic to fish or shellfish or who do not eat fish out of personal choice.

Discover in the Omegor Shop all the products with which you can add an extra dose of high-quality Omega 3 to your diet!

And listen to episode 13 of the podcast Perle di Benessere: you will discover all the potential of Omega 3 as prebiotics!

References

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• Cao B et al. Diabetes Obes Metab. 2025.
• Huang Y et al. J Dermatolog Treat. 2024.
• Kerman BE et al. Curr Opin Clin Nutr Metab Care. 2024.
• Kumar M et al. Nutrients. 2022.
• Rousseau G. Mar Drugs. 2021.
• Vijay A et al. Gut Microbes. 2021.
• Xia J et al. Nutrients. 2024.
• Zhang H et al. J Ovarian Res. 2023.
• Zou B et al. Front Nutr. 2025.