gut microbiome


Meet your Gut Microbiome!

It is very hard to imagine that more than half of the cells in our body belong to other species: the microbes that live in our nooks and crannies.  We have evolved to live in harmony with them over millions of years yet we haven’t given them much thought up until now.  Thanks to recent advances in testing we have been able to study this minuscule world in more detail and understand its contribution to our health.  There are 20,000 human genes but millions of microbial genes.  As the Zoe Project puts it “the most important thing for human health isn’t even human”.

Most of the bacteria live in your gut and are known as the gut microbiome. 

The bacteria can be divided into potentially harmful or beneficial ie health-promoting.  A lack of diversity or too many harmful bacteria can contribute to many common gastrointestinal (GI) symptoms such as gas, bloating, indigestion, abdominal pain, diarrhoea and constipation.  The health of the microbiome is a major player in irritable bowel syndrome and inflammatory bowel disease.  Research has also linked an imbalance in bacteria to a growing list of non-GI conditions such as Alzheimer’s, anxiety, asthma, autism, chronic fatigue syndrome, depression, diabetes (Type I and Type II), eczema, kidney stones, metabolic syndrome, MS, obesity, Parkinson’s and rheumatoid arthritis. 

The message is very clear: a healthy microbiome is essential for our long term well-being

In return for board and lodgings let’s have a brief look at what the microbes do for us and how this has such an impact on our health.

Nutritional Status

The bacteria in the colon produce many times more carbohydrate digesting enzymes than we do in the small intestines to digest all the fibres that we can’t.  In ancestral times, the short-chain fatty acids (SCFAs) produced from the fermentation of these fibres provided extra fuel in times of food shortage and prevented starvation.  SCFAs are a vital energy source for the intestinal cells which are replaced every 5-7 days.

The bacteria also produce B vitamins and vitamin K.  B vitamins are water-soluble so we can’t store them, we need a constant supply from our diet.  We can also take up the vitamins produced by the bacteria – it’s like having a backup internal supply.  Folate in particular can be made in the gut in larger amounts than we get in the diet, so low levels on a blood test may be due to low dietary intake and low levels of beneficial bacteria, particularly bifidobacteria which is known to produce all the B vitamins.  The exception is B12: it can only be absorbed in the lower part of the small intestine along with a substance called intrinsic factor so we can’t make use of any produced by bacteria in the colon.

A vital way bacteria increase our nutritional status is through their action on polyphenols.  Polyphenols are micronutrients found in colourful plants associated with an array of health benefits.  Polyphenol rich diets, like the Mediterranean diet, provide significant protection against many conditions and diseases due to their potent antioxidant and anti-inflammatory effects.  Polyphenols travel through the small intestine largely undigested.  Bacteria convert them into more biologically available metabolites.  An example is phytoestrogens.  These are lignans and isoflavones found in plants like soy and flax which can have a weak oestrogenic effect.  The metabolites produced by the bacteria have a stronger oestrogenic effect.

The action of bacteria on the foods we eat gives us far wider health benefits.

Brain Health

For centuries Eastern medicine has called the gut the second brain and this connection to the nervous system is engrained in our language with descriptions like “gut feeling” and “butterflies in the tummy”.  Did you know that the GI tract is lined with more than 100 million nerve cells and the gut can “talk” to the brain within seconds using electrical signals in the way that neurons do, through the vagus nerve which travels from the gut to the brain stem?  It is a two-way interaction called the gut-brain-axis.

Some members of the microbiome can make neurotransmitters, including GABA, noradrenaline, serotonin and dopamine.  Dopamine is a mood-boosting neurotransmitter, involved in reward, which may explain why eating makes us feel good.  Up to 90% of serotonin (the happy feel-good neurotransmitter) is made in the gut where it helps to regulate bowel movements.

The relationship between the gut and the brain is very complex and IBS is an example of one of the consequences of disruption.

Immune Health

As well as digesting the foods we eat, the GI tract forms a barrier between its contents and the rest of the body and the intestinal wall contains around 70% of the cells that make up your immune system. The intestinal immune system balances active and suppressive immune responses as it is continuously exposed to beneficial compounds (products of digestion, helpful bacteria) and toxic compounds (pathogenic microorganisms like viruses, harmful bacteria and yeasts). A healthy gut drives a healthy immune system so you get sick less often. An unhealthy immune response may send your body into attack mode. This over-reaction forms the basis of auto-immune disorders.

Inflammation is the common thread between many health conditions. The balance of microbes in the gut can either decrease or increase inflammation.

You can meet your microbiome through testing. At The Verve Clinic we offer the ultimate gut health and microbiome test which has biomarkers for inflammation, immune function, digestion, beneficial and pathogenic bacteria (including helicobacter pylori), yeast and parasites. There’s nothing like getting to know your body better!

Let’s look at some of the things that influence gut health.


Microbiome - antibiotics

The decrease in the diversity of bacteria in our microbiome compared to traditional tribes is probably due to a few generations of antibiotic use as well as a decline in the amount of fibre we are consuming since food processing arrived. Other factors include an increase in caesarean births, hygiene methods, other medications and the effects of chemotherapy and radiotherapy. The core bacteria that we now see may not have been so dominant in our grandparents’ time.

Each course of antibiotics changes the composition of the microbiome so they act on a new ecology. Recovery to a stable state takes time, influencing the function of the immune system, our ability to resist infection and our capacity for processing food, especially the benefits derived from phytonutrients. Alterations can last up to 16 months.

Routinely taking antibiotics just once a year could mean the gut may never function properly

It is very important to take antibiotics as guided by your doctor but you can limit the damage and take steps to restore the microbiome. Take a clinically proven probiotic strain at the same time as taking antibiotics and then continue with the probiotics for a few weeks afterwards. Nourish the good bacteria by eating a diet diverse in plant fibres and polyphenols. After the course of antibiotics has finished you can add in a prebiotic supplement. They come in powder form and are easy to take as they mix with food or drink which is especially useful for the elderly and children who may have a more limited diet.


Microbiome - probiotics

Probiotics are live strains of beneficial bacteria in supplement form.  They are particularly beneficial taken at the same time as antibiotics to help to reduce side effects like diarrhoea and prevent overgrowth of the more antibiotic-resistant bacteria.  Probiotics have been well-researched for many conditions such as IBS, inflammatory bowel disease and anxiety.

Characteristics of bacteria and their efficacy are strain-specific.  To take advantage of the research, match the probiotic to the condition.  Consult with a professional, do your own research on PubMed or use a brand that carries a range of probiotics.

The only way to increase the number of all the beneficial bacteria is to feed them the right food.  If your beneficial bacteria levels are very low or it is difficult to have enough plant fibres eg because of IBS or illness take a prebiotic supplement.

Fermented Foods

Microbiome - fermented foods

Microbial cultures have been used for making beer, wine, yoghurt, cheese, tempeh, sauerkraut, kimchi, green olives and sourdough bread for thousands of years. It has long been a component of our diet as a method of preserving and storing food.

Many fermented foods are made by airborne bacteria which grow and produce lactic acid, a natural preservative which neutralises invading microorganisms. The flavour, texture and nutritional profile of the food is often improved. It’s fascinating that every culture has a “culture”, like sauerkraut from Eastern Europe, and kimchi from Korea.

Like probiotics, fermented foods will only temporarily improve diversity as the bacterial count (millions) is a drop in the ocean to the bacterial count in the colon (trillions). They can help to crowd out harmful bacteria and the compounds produced during fermentation may be more biologically active due to the “outsourcing” of the fermentation process. The nutrition of the food is enhanced whilst also making it easier to digest.

Probiotics and fermented specific foods will not repopulate the colonic bacteria but are important tools in a multi-layered approach to restoring a damaged microbiome


Microbiome - prebiotics

Prebiotics are fibres that escape digestion and selectively feed the beneficial bacteria.

The two main families of prebiotic fibres: fructo-oligosaccharides (FOS) and galacto-oligosaccharides (GOS).  These are available as supplements and found in certain foods, generally the ones known to cause wind!

As an extract, they have a sweet flavour which makes them very easy to take and they do not impact blood sugar levels.  Inulin is a FOS fibre readily available in health shops.  GOS is less likely to cause GI side effects so is a better choice if you suffer from IBS, gas or bloating.  As a bonus, it also helps to maintain hydration of the skin improving skin health.

Good food sources: 

  • FOS: artichokes, garlic, onions, leeks, asparagus
  • GOS: beans, lentils, cruciferous vegetables, beetroot, rye sourdough, sunflower seeds, pumpkin seeds

Resistant Starch

Microbiome - resistant starch

Resistant starch resists digestion in the small intestine so it reaches the colon and feeds the beneficial bacteria.

The cooking and cooling of some root vegetables and grains like potatoes, pasta and rice turn some of the digestible starches into resistant starches.  The same thing happens when oats are soaked overnight rather than cooked as porridge.

It is also found in black beans, adzuki beans, red lentils, chickpeas and kidney beans.


Microbiome - polyphenols

Foods rich in polyphenols are like sweets for your bacteria who reward us with active anti-inflammatory and antioxidant constituents and plenty of SCFAs.

The great news is that they are found in foods that look and taste delicious like berries and dark green leafy vegetables.

Colour counts.

Not only do we need the greens, but purple, red, black, brown, orange and yellow. Eat a rainbow is a cliché but it is crucial to your gut health.

Plant polyphenols and dietary fibre are the main sources of food for your beneficial bacteria. Aim to have 30-40 different vegetables, fruits, grains, nuts and seeds every week.

Variety is key and – aim to have a little of a lot.