A new study published in the BMJ this week has found that if we have out-of-sync bacterial balance in our gut microbiome, known as “dysbiosis”, then we may well be more likely to develop worse Covid symptoms or longer-term coronavirus related health issues. This bacterial imbalance in the gut may also influence the blood concentrations of several inflammatory cytokines and blood markers of tissue damage, both of which can lead to the longer-term or more significant complications associated with the virus.

This was not a huge study, but it paves the way to help prevent the detrimental effects of Covid. The authors particularly note that this information about gut bacteria may help to prevent children developing the Kawasaki type reaction called Paediatric Inflammatory Multisystem Syndrome associated with COVID-19 (PIMS) which can be extremely serious. What is also unknown for sure is whether this imbalance in gut bacteria was present before the person contracted coronavirus, or whether the virus caused a significant disruption to the microbiome. This is what future research may well be able to establish.

Why am I extra excited about this study? Because it found an imbalance of well-known gut bugs that we at NatureDoc can assess in the stool tests that we offer through our clinics. And, we already know how to help rebalance these bacterial strains through diet and food supplements.

Which Bacteria Did They Find?

This study found that people with the worse or longer term Covid-19 health challenges had very low levels of Bifidobacteria, Faecalibacterium prausnitzii and Eubacterium rectale which are three beneficial bacterial strains that are all known to be needed in abundance to regulate the gut response to infections and to keep chronic inflammation at bay.

These researchers also found overgrowth of bacterial strains detrimental to human health in the sickest Covid-19 sufferers and it is assumed that these pesky bacteria are causing much of the systemic havoc that some people with this virus are experiencing. In particular, Ruminococcus gnavus and torques as well as Bacteroides dorei and vulgatus were found in abundance in the guts of those who developed the more marked Covid issues. We rarely see extremely high Ruminococcus in stool tests and even moderate levels may be part of a wider problem.

These four bacterial strains are well known to be troublesome and we really don’t want them lingering in any significant amounts in our intestines anyway, as they are closely linked with inflammatory bowel and irritable bowel syndrome as well as affecting our upper respiratory tract and airways.

The Ruminococcus strains are particularly horrid as they drive up clostridium bacterial strains, which are known to be neurotoxic and can potentially alter mood & mind and the course of child development. Clostridium Difficile is a gut superbug that can cause antibiotic resistant diarrhoea and is usually found alongside its Ruminococcus cousins. When we have plenty of beneficial bifidobacteria living in our gut, this seems to be protective against the unwanted clostridia strains.

Fuelling the healthy bacterial strains generally helps to drive down the numbers of baddies, and if extra help is needed then herbal antimicrobial supplements can be very useful here too – many are probably in your kitchen right now like garlic, oregano, rosemary and thyme. So, this is a good excuse to start adding these to your cooking!

Why Are The Beneficial Bacteria So Important?

Bifidobacteria are super important for human health and are able to produce a number of nutritional compounds including vitamins, short-chain fatty acids (SCFA’s), and organic acids while acting like soldiers to help fight against infection. Also, Bifidobacteria is a building block for making GABA, our brain hormone that keeps up cool, calm and relaxed – without enough GABA we can become anxious and not cope well with stress. Low levels of both Bifidobacteria and F. prausnitzii are also associated with major and moderate depression.

Bifidobacteria helps to make most of our B vitamins which are important for energy production as well as a healthy metabolism. It also helps to make Vitamin K which helps to regulate blood clotting and the health of blood vessels, regulates calcium blood levels and supports bone health.

Bifido strains feed and encourages the proliferation of other bacteria that produce butyrate, the key SCFA that prevents inflammation and nourishes the gut lining.

Those people who were born by caesarean section, who are formula fed as babies or who have regularly taken antibiotics or proton pump inhibitors for reflux are more likely to be lower in bifido strains that those who had a vaginal birth and are breast fed. It is thought that the more bifido strains that a baby has living in their intestines the less likely they will suffer from serious infections.

Faecalibacterium prausnitzii and Eubacterium rectale
F.prausnitzii and E. rectale are also butyrate producers which support the immune system functions of the colon wall and also protects against diseases of the digestive tract.

Butyrate comes from eating plenty of fibre in fruit, vegetables, salads, nuts, seeds and pulses as well as from ghee and butter. It promotes the growth of villi that line the small intestine and help us absorb the nutrients from the food we eat. Consuming enough butyrate producers can enhance sleep patterns too. It also increases the production of mucin, a gel-like substance that coats the inside of the gut and helps us to tolerate a variety of different foods. Butyrate also helps prevents bacteria, toxins and other chemicals from crossing into the bloodstream from the gut.

Without enough butyrate to fuel our gut, we can become more sensitive to anything that we ingest as well as chemicals and toxins that we are exposed to in our environment. This can manifest in the development of new allergy-type reactions, constipation or diarrhoea, fatigue or a foggy brain. When we have low levels of butyrate in our gut, we can also start to show signs of nutrient deficiencies, even if we are eating a nutritious balanced diet, and this can in-turn get the ball rolling for more symptoms to develop.

Many people who have had Covid-19 or suffer from Long Covid report “brain fog” where they are unable to concentrate for long periods of time, their short-term memory has become worse, they have become forgetful or developed poor word retrieval. Some with Long Covid have also developed anxiety or depression and a few people have developed psychosis. Interestingly butyrate also upregulates the level of brain-derived neurotrophic factor (BDNF) in a damaged brain, which can help to restore short-term memory and word retrieval.

Also, many people who have had complications from contracting the virus have had damage to their blood vessels or have been found to have heart muscle scarring and/or a build-up of fluid in the heart muscle or the pericardium surrounding the heart. Again, all three of these friendly gut bacteria have been found in much lower quantities in people with many cardiovascular health challenges and it is thought that building up the population of these butyrate producing bacteria may be a step towards mending the damage.

How To Boost Up A Depleted Microbiome

So, here are some pointers that we have learned over the years to help you make some better-informed dietary and lifestyle choices for your family, that might give your gut the makeover it needs:


  • Cut back on highly processed convenience foods especially those containing white flour, white sugar, artificial sugars, hydrogenated fats, emulsifiers and preservatives.
  • Adopt a Mediterranean diet rich in fresh fruits, vegetables, salads, meats, fish, wholegrains, nuts and seeds as well as olive oil and herbs and spices.
  • Eat plenty of fermented foods: Live yoghurt, kefir, sauerkraut, kimchi, miso, apple cider vinegar, sourdough bread.
  • Consume dietary polyphenols which are the coloured pigments in fresh fruits, vegetables, cocoa, green tea and foods high in antioxidants. Therefore, aim to “Eat The Rainbow” of fruit and veg every day.
  • Aim to eat at least 30 different plant-based foods every week to include vegetables, fruits salads, nuts, seeds, pulses, wholegrains, quinoa, buckwheat. The veggies could include three different coloured peppers or different coloured carrot varieties or a mix of salad leaves. Try yellow and green kiwi fruits and a mix of berries.
  • Meat: Eat good quality locally sourced, free range or organic. Not too much.
  • Fructo-oligosaccharides (FOS)/inulin: chicory, endive, dandelion root, Jerusalem artichoke, garlic, onions, leeks, asparagus, bananas, burdock, oats, seaweed, apples & flax seeds.
  • Arabinoxylans: found in all major cereal grains, including rye, wheat, barley, oats, sorghum, maize, millet, psyllium, flaxseed, bamboo shoot and rye grass. The highest content of arabinoxylan is found in rye, followed by wheat, barley, oats, brown rice and sorghum.
  • Resistant starches: Plantains and green bananas (as a banana ripens the starch changes), beans, peas, and lentils, whole grains including oats, teff and barley. Cooked and cooled rice, pasta, toast or potatoes.
  • Galacto-oligosaccharides (GOS): Cow’s milk, legumes (e.g. red kidney beans, chickpeas, baked beans, split peas, lentils), cashews and pistachios, soybeans, and oats.
  • Fucoidan: Brown algae and brown seaweed. Try Seagreens Culinary and Mineral Salt.
  • Omega-3 rich diet: Oily fish including salmon, sardines & mackerel. Flax, chia, hemp, walnuts, omega 3 rich whole organic milk, omega 3 enhanced eggs or take an omega 3 supplement.


  • Open your windows to let a mix of bacteria come into your home
  • Spend time in nature – sit in your garden or go for a walk, a run or a bike ride
  • Let kids get muddy
  • Own a pet
  • Wash rather than peel your veggies


These are prebiotics and probiotics that have specifically been found to increase the levels of Bifidobacteria, Faecalibacterium prausnitzii and Eubacterium rectale:

If you wish to investigate this further, you can discuss your gut health in depth with one of our NatureDoc clinical team. During your consultation your practitioner can arrange stool testing, and then provide full interpretation of the results. This includes a personalised gut health plan to help restore a better balance of gut flora, which in turn should help to improve your overall health.

Lucinda Recommends

Bionutri – Ecodophilus
Fushi – Organic Grass-Fed Ghee
Metabolics Inulin Fibre Prebiotic Powder


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