Fish Oils: a powerful fuel for microbiome diversity and gastrointestinal health

By Karen Jones Nutritional Therapist

The gut microbiome refers to the collection of trillions of microbes that live within the gastrointestinal tract.  Research shows these organisms play a crucial role in digestive, immune and mental health. Any imbalance can lead to a wide range of issues, from digestive distress like wind and bloating, to broader systemic challenges such as obesity, diabetes, Alzheimer’s, cardiovascular disease, inflammation, and cancer.

Positively influencing the microbiome is a major health goal for many.  “Seeding” the microbiome using probiotics and feacal transplants has often been the approach, but this has limited long term benefits as it fails to focus on influencing the intestinal terrain and the growth factors that nourish the microbiome towards health.

One way to do this is to encourage microbial diversity.  While there are several key bacteria associated with a healthy microbiome, greater overall diversity leads to a more resilient and functional microbiome.  A little-known fact is that some of the greatest influencers of microbial diversity are the long-chain omega-3 fatty acids; docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA). 

It appears that the ideal DHA:EPA:DPA ratio for influencing the microbiome is similar to that found in wild salmon.  Docosapentaenoic acid (DPA) is the third ‘forgotten’ omega-3 fatty acid, also found in oily fish but only recently effectively extracted.  DPA has many health benefits, including acting as a reservoir of omega-3 fatty acids in the body.

Higher DHA levels exert more profound effects on the microbiome

While the many health benefits of omega-3 fatty acids are well known, their effects on the microbiome are not, even though many of their health benefits are actually mediated through it.  Here’s what is currently known: DHA appears to be the key omega-3 for influencing the microbiome and has greater anti-inflammatory effects in the gut.  It does this through circulating in the blood, by incorporating into the cells that line the GI tract and by acting as an intermediate to anti-inflammatory compounds known as D-series resolvins and protectins. 

Resolvins resolve inflammation, while protectins protect against inflammation starting.  By lowering gut inflammation, these compounds help to promote microbial diversity.  Their discovery has helped to explain why DHA supplementation produces better results than EPA in reducing gastrointestinal inflammation and in improving microbial imbalances or “dysbiosis”.  

Higher levels of circulating DHA are associated with increased levels of bacteria in the Lachnospiraceae family.  These are the main group of bacteria that transform dietary fibre into short-chain fatty acids (SCFAs).  SCFAs, especially butyrate, have been shown to exert multiple beneficial effects and protect against any overgrowths of unwanted bacteria, such as Clostridium difficile.

Higher levels of Lactobacillus and Bifidobacteria species, known for their beneficial probiotic effects, are also associated with higher DHA levels.   Multiple studies show their roles in improving metabolic diseases (obesity and diabetes), cardiovascular diseases, neurological diseases (Parkinson’s, Alzheimer’s and multiple sclerosis) and musculoskeletal conditions (including osteoporosis and gout).

Higher DHA levels are also linked to higher feacal concentrations of N-carbamylglutamate (NCG), an extremely beneficial substance produced by a healthy microbiome. NCG preserves the integrity of the intestinal lining by reducing oxidative stress in the gut, helping to reduce intestinal permeability and inflammation.

Another superstar microbe, Akkermansia muciniphila, is boosted by both DHA and EPA.  Akkermansia plays a critical role in the health of the mucin layer that protects the intestinal lining and helps maintain its proper structure.  Higher levels are associated with improved barrier function, reduced intestinal permeability (leaky gut), and improved insulin sensitivity.  

DHA produces favourable effects on butyrate production

As mentioned earlier, DHA helps to increase the levels of butyrate-producing bacteria. Butyrate is the primary energy source for the cells that line the GI tract and controls their proper growth and replication.  This means that higher levels help to maintain the functional integrity of the intestinal lining and reduce abnormal intestinal permeability or ‘leaky gut’.

Not surprisingly, colon cancer risk is linked to lower numbers of butyrate-producing bacteria.  Butyrate protects against colon cancer through its effect on cellular energy but also on immunity, through positively influencing the function of regulatory T-cells.  These cells help the immune system recognise the difference between an infectious organism and self, so play a key role in preventing autoimmunity as well.

Higher butyrate production is also linked to weight loss. In fact, the changes in microbiome composition produced by DHA support weight loss, improved metabolism, and better blood sugar control.  Interestingly, some of the key benefits of a ketogenic diet, such as appetite control and better metabolism, are because it increases the body’s own production of butyrate. 

Higher butyrate levels also improve conditions affecting the brain and have clear anti-inflammatory effects, especially in inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis.  Fish oils have also been shown to be beneficial for patients with IBD, perhaps through this mechanism.

The ratio of EPA and DHA in systemic inflammation

As well as having a profound effect on microbiome composition, a higher ratio of DHA to EPA also appears to have greater anti-inflammatory effects. 

One study, ComparED, compared the two.  Healthy men (n=48) and women (n-106) with abdominal obesity and low-grade systemic inflammation consumed 2.7g of either DHA, EPA or corn oil for 10 weeks.  DHA supplementation resulted in the greatest reduction in inflammatory markers such as C-reactive protein, interleukin-18 and tumour necrosis factor. “DHA is more effective than EPA in modulating specific markers of inflammation as well as blood lipids”, the authors concluded.

In another study, subjects were given 4g of either DHA or EPA as part of a test meal to evaluate the effects of each on vascular function after the meal.  DHA significantly reduced overall cardiovascular risk, producing a 13% decline, while EPA had no effect.  These beneficial effects were the result of DHA being metabolised into protective compounds known as oxylipins.  EPA can also be converted into its own versions of these, but those derived from DHA are much more effective at reducing the risk factors for heart disease. 

Final comments

While the science of how to influence the microbiome is in its infancy, there is an emerging pattern that focuses not on probiotics, but rather on how to influence the terrain of the gastrointestinal tract.  The growth of microorganisms in our intestinal tracts is a lot like the planting of grass.  If the lawn is overrun with weeds and competing grass types, or the soil is poor or arid, all the grass seeding in the world is not going to produce a lush green lawn. The focus must be on improving the terrain first to enable the desired change.  It appears that omega-3 fatty acids are able to promote the proper intestinal terrain, in particular, DHA.


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