Microbiome health – Herbal Allies for the Gut, Digestion, Emotions and the Mind

Microbiome health – Herbal Allies for the Gut, Digestion, Emotions and the Mind

First of all what is the Microbiome?

Imagine, for a moment, the rainforest, teaming with life – from the ants scuttling on the forest bed, jaguars prowling through the bushes, howler monkeys swinging overhead and birds of every shape and colour flitting through the trees. On a microscopic level, this is what our microbiome is like. Being labelled as a ‘supportive organ’ because of the impact it plays in ensuring all the key roles of daily health take place, it consists of trillions of thousands of different kinds of microorganisms called microbes or microbiota – so many in fact that there are 100,000 times more microbes in your gut than there are people on Mother Earth. 

These different species include bacteria, fungi, viruses and parasites – I know it sounds pretty strange, but in the average healthy human body these little friends co-exist in symbiosis throughout the body, with the largest concentration of them being found within the small and large intestines – living in the mucus layer which lines the intestinal walls and therefore allowing them to have direct communication with immune cells.

This home also allows for the microbes to have a relation with the brain – becoming aware of stress signals and even of contentment and joy through the vagus nerve.

Around 90% of the neurons in this fascinating nerve are actually transporting information from the gut to the brain – with recent studies showing that the brain isn’t only aware of gut microbial health but that they actually have an influence over our moods, behaviour and even how we process perceptual information.

Every individual has a plethora of unique microbes which is determined by DNA as well as infant exposure during birth and through breast milk. The microorganisms exposed to the baby are directly passed down from their mothers and what is existing within her microbiome – later on in life diet and environment have an influence on exposure to microbes which can either be beneficial of detrimental to health. The extensive communications which signal throughout the body with these wonderful microbes allows for higher textured and varietal biological potential – meaning that their ability to aid our bodies in day to day life wellness can exponentially grow with their growth.

Within all systems there are both helpful and harmful microbes, however they are usually coexisting in a state of symbiosis, without any danger of disease manifesting. That being said, if there is a disturbance to the balance of the microbiome from illness, diet, antibiotics and any other bacteria killing medications dysbiosis occurs, where these usual interactions which play such a key part of our daily lives, struggle and can cause one to become more susceptible to disease and illness.

How Microbiota benefit the body:

Basically put, microbes aid in stimulating the immune system, synthesise vitamins and amino acids (Vitamins B & K), aid in digestion and detoxify the body from potentially harmful chemicals and foods. Complex carbohydrates such as starches and fibers are broken down by the microbes with digestive enzymes – the fermented indigestible fibers produce short chain fatty acids which the body uses as a nutrient source, as well as being vital for muscle function, prevention of chronic diseases related to the gut and even aid in treating Crohn’s disease, ulcerative colitis and diarrhoea. Due to their immune stimulating action they are protective from pathogens which can enter the body through contaminated foods and water.  

Starchy herbs, including yams, have been found on eating vessels (30,000 years ago) and known to be consumed seasonally for eons. The Tanzanian Hadza hunter-gatherer populations digested rich carbohydrates as well as starches – these starches allowed for a great source of nutrition for the microbes and their ecology within the body. This would have allowed for the hunters to have prolonged energy for their long journeys to find food.


Having a disrupted microbiome not only disrupts the neural functioning of the gut and therefore the success of digestion, processing of nutrients and detoxification but research shows that it can also have an influence on levels of anxiety, inflammation, trigger depression, cause an overactive immune response, be potentially stimulating of autoimmune disorders and more.

With over 70% of immune cells targeting the digestive tract, our gut-immune response can cause immune dysregulation which can therefore lead to autoimmune disease, Alzheimers disease and chronic ailment. The microbes also have an influence on the guts production and secretion of neurotransmitters of which there are 30 – one being Serotonin the “happy chemical” of which 95% of it is made in the gut.

The Enteric Nervous System:

The Enteric Nervous System (ENS) is what scientists have come to call “the little brain”, and referred to as the digestive nervous system which consists of hundreds of millions of neurons which connects the brain and the ENS. It is a quasi-autonomous part of the nervous system (which is so extensive that it can operate independent of the Central Nervous System (CNS), although they are in communication) and includes neural activity which controls mucosal transport and secretions, modulates immune and endocrine system, motor functions and local blood flow. Consisting of two thin layers of more than 100 million nerve cells which line the entire gastrointestinal tract, from the oesophagus to the rectum, it controls all digestive processes, absorption, secretion, GI blood flow and more.  

Modern day research has built on the decade old finding that mood can be affected by digestive issues, finding that the ENS may in fact trigger big emotional shifts for people who have IBS or bowl issues. This illustrates that irritation or imbalances in the gastrointestinal tract communicates with the CNS and causes a mood altering response.


Lifestyle Tips:


Just as in the forest I mentioned at the beginning of this study, one of the best ways to maintain a healthy microbiome is through diversity and abundance. A high diversity means resilience, whereas a low one means vulnerability and a diminished ability to fight infections which can be caused by medication, pathogens, poor diet, viruses or pathobionts. The easiest way to achieve a happy microbiome through diversity is eating a broad range of foods – especially looking hat fibre rich sources and fermented foods.

Physical movement

Exercise has shown to modify the microbiome of the gut due to the overall health benefits – this can include short walks after a meal or a yoga practice in the morning. This aids in stimulating digestion and avoiding constipation and bloating

Good old H20

Drinking water throughout the day has shown to aid the mucosal lining of the intestines as well as aid the good bacterial in the gut to maintain balance and health. Water also aids in the processing of food through the intestines, and therefore encouraging healthy bowel movements.

Herbal allies:

First and foremost we need to focus on the prebiotics – these are compounds which aid the growth and activity of beneficial microorganisms - like the bacteria and fungi living in your gut. The following herbs are great in their prebiotic action but also in their immune supporting and overall gut nourishing activity.

 DANDELION (Taraxacum Officinale)

  • Eaten wild, dandelion greens aid in increasing the good bacteria in your gut, reducing constipation and boosting immune function. They are high in fibre, including inulin fibre
  • A highly nutritious weed which contains amazing amounts of antioxidants and vitamins
  • Best known to fight inflammation, aid blood sugar level control, reduce cholesterol, lower blood sugar levels, is a diuretic which detoxifies the body and gets rid of excess fluid, is a liver tonic and supports general GI health.

SLIPPERY ELM (Ulmus Rubra)

  • This mucilage rich medicine is soothing and loaded with prebiotic starches – supporting a healthy mucous layer within the GI tract and therefore serving as a phenomenal source of nutrients for beneficial microbes. .
  • In Native American medicine it was taken orally to treat coughs, diarrhoea, sore throats, and stomach discomfort such as bloating and indigestion.

 REISHI (Ganoderma lucidum & G.spp.)

  • We all know that Reishi is a well LOVED medicine for the Aether family, but did you know that along with it’s many other benefits it has shown to aid in modulating the microbiota in the gut – having a prebiotic effect 
  • It has a plethora of healing abilities, being a three treasure tonic as well as being an amazing adaptogen, anti-inflammatory, nervine tonic, protective against side effects of stress, being immune modulating and protective, is an antioxidant, heart, brain, liver and kidney protective, reduces cholesterol and even aids in increasing the process of apoptosis in the body (the scheduled destruction of cancerous cells)

 BURDOCK (Arctium lappa)

  • An incredible blood tonic – as a food and medicine Burdock is rich in inulin making it a phenomenal prebiotic.
  • Traditionally used as a bitter tonic to aid in detoxification, support skin health
  • It has also proven to be a great anti-inflammatory

 CODONOPSIS (Codonopsis pilosula)

  • A well-loved “spleen qi tonic in Traditional Chinese medicine, Codonopsis is able to support healthy digestion and the assimilation of nutrients - containing inuline-like fructans which had in feeding and supporting the microbiome
  • Rich in prebiotic fiber and starches

CACAO (Theobroma cacao)

  • I know, is there anything is medicine can’t do? Cacao is in fact a prebiotic medicine!
  • When Cacao beans are consumed they begin to break down in the colon, producing nitric oxide which has a benefit to the cardiovascular system – hence why it can sometimes physically be felt that blood flow in the chest and heart is increased.
  • Containing Flavanols – this is where it has a powerful prebiotic benefit which can aid with the growth of healthy gut bacteria and thus a healthy microbiome.
  • As a medicine it is rich in vitamins, minerals (iron, calcium, beta-carotene, magnesium and zinc), Omega 6 fatty acids and contains tryptophan which is a building block for serotonin, lowers blood pressure, is cardioprotective, aids in brain health and finally contains phenylethylamine which is related to amphetamine – this is the chemical released in the brain when falling in love.

Honourable mentions:

Sea moss, Triphala, Moringa, Lions mane, garlic, onion, alums, miso paste as well as White Button mushrooms (Agaricus blazei, bisporus, similar spp.) which have shown to increase the activity and presence of Prevotella (the good bacteria) in the gut therefore acting as a prebiotic.