Your Microbiome – Get Trillions To Help Your Wellbeing!


Dr. Katy Willis
GP in West London


They’re not enemies, they are our friends and positively benefit our health. They help our digestive system, our mood, our immune system and can even help us lose weight. They are little tiny gut bugs, bacteria, that live in your gut. They are also called the microbiome if you want a collective name for them.

There are up to 4000 different varieties of gut bugs, and the more variety we have the better, for our health and wellbeing.

The microbiome – a collection population of commensal microbe living symbiotically with a multicellular organism. (Turnbaugh et al, 2007) 

At any one time, your gut contains about 1.5kg of gut bugs.


Yuck, or good? 100 years ago, the major cause of human death was an infection, so, of course, there was a drive for hygiene and cleanliness. Together with the discovery of antibiotics, this worked, and today infection only causes a minority of deaths. But I think we’ve taken it too far. We have been trained to hate bacteria, to use anti-bacterial soap and wipes all the time, cleanliness is next to godliness and other such sayings.

However, our gut bugs are very important, and have beneficial functions, and losing them, and losing their diversity can be harmful to our health.

We all have gut feelings, gut-wrenching sadness, we spill our guts, we have our bowels in an uproar, stomach in knots…

– let’s look at the positive importance of our guts to our health, weight loss, and wellbeing.

What we eat affects our gut bugs, and helping our gut bugs is one of the easiest ways to improve our health and wellbeing.1

If you like visuals, here are a couple of excellent short videos that explain:

This is a 2.5-minute introduction to gut bugs and tips on getting a great gut full of happy gut bugs by Dr Rangan Chatterjee, a GP in Manchester. Short and sweet.

This is a 5 minute cartoon that explains how the food we eat affects our guts and our gut bugs by Shilpa Ravella, highly recommended.

So, what do our gut bugs do?

  1. Our gut bugs regulate our digestion
  2. Our gut bugs regulate our body weight
  3. Our gut bugs regulate our immune system
  4. Our gut bugs regulate our mood


1. Our gut bugs regulate our digestion

Our gut bugs break down food the body can’t digest, and they produce important nutrients for us. They love to eat fibre and vegetables.

2. Our gut bugs regulate our body weight2

People who are overweight may have variety in their gut bugs3. Changing the makeup of your gut bugs can help you lose weight. Our gut bugs decide how much energy we extract from the type of foods we eat and control our hunger signals, cravings, sugar spiking.

Having an unhealthy gut can mean chemicals leak through into our bloodstream and interfere with our hormone (leptin) that tells our brain we don’t need to eat any more, so we end up feeling hungry all the time.

Getting healthy gut bugs through a well-balanced diet,  the Mediterranean diet, reducing carbohydrates, and/or intermittent fasting will help you lose weight.

Which diet is right for you?

A good gut bug to have is akkermansia muciniphila. Studies show this bug is associated with better weight control, better insulin sensitivity. Obese people have less akkermansia, and so do people eating an industrialised diet (processed foods/diets). Akkermansia feeds and grows on onions, garlic, leeks, artichoke, yams, agave, bananas, Brussel sprouts, okra, cauliflower, broccoli, chicory root. You can boost your levels of akkermansia by eating polyphenol-rich foods, and by fasting (as they feed off your mucus, not your food!).

Another good gut bug to have is bacteroides, which is associated with a lean body type and less gut inflammation.

3. Gut bugs regulate our immune system

Gut bugs regulate our immune systems and protect against harmful germs. (Gut bugs are the good guys in the germ war!).

For example, our friends bacteroides, as well as helping weight regulation, help break down fibre from vegetables, producing a chemical called butyrate, which is great to protect us from bowel cancer and is very anti-inflammatory. Butyrate also keeps your gut lining strong, stopping toxins getting into your body. Foods producing butyrate include oily fish, grass-fed beef (NOT standard beef), walnuts, flaxseeds.

Another example is lactobacillus, which is good at protecting your guts from bad bugs such as candida, and boosting mood by producing serotonin, the feel-good hormone. It is present in many yoghurts.

Yet another example is Bifidobacterium, again present in yoghurt, and cheese. Bifidobacterium breaks down otherwise indigestible fibre and protects the gut from pathogens.

The term ‘leaky gut’ is when the gut wall becomes leaky, allowing toxins through from the gut to the bloodstream causing inflammation and affecting tummy health and mood, e.g. bloating, heartburn, pain, gas, cramps, tiredness, general aches and pains, even some autoimmune conditions, obesity, dementia and depression.

Inflammation is supposed to be a short (acute) process to protect us, e.g. if you sprain your ankle it gets hot, swollen and red – the acute inflammation helps the area heal, and settles down quickly. However, if inflammation is longstanding and goes on and on (chronic), our bodies believe they are under attack and the immune system goes into stress mode. This chronic inflammation is behind many modern diseases.

70% of our immune system activity is in the gut. Therefore, our diet relates directly to our immune system, because everything we eat goes into the gut as a foreign body. Our immune cells in the gut decide whether to react to the food or whether to welcome it – if it does react, we have inflammation. Our gut bugs are the first line of defence against ingested pathogens, making it hard for pathogens to colonise.

There is a life-threatening gut infection called Clostridium Difficile – if you take poo from a healthy person and put it in an infected person poo from a well person (sterilize it somehow and stick it in somehow, technically known as Faecal Transplantation) the infected person gets better – this has been so successful it is now the standard treatment for this infection.

Getting the good gut bugs in improves our immune system. Improving your gut bugs can help allergies and asthma and eczema as well as colon and digestive health. And this can start happening within 48hours (see below).

4. Gut bugs regulate our mood

There is also a role for the gut, and therefore diet, with mood4.  Research shows that if you take poo from a well person5 (sterilize it somehow and stick it in somehow, technically known as Faecal Transplantation) and give it to a depressed person, they perk up, and vice versa. Wow.


How? Well, thinking is:

  • Depression increases inflammation in the gut and around the body. The gut microbiome improves the immune system and decreases inflammation. The microbiome also alters neuroinflammation in the brain.
  • Depression is often linked with high levels of the stress hormone cortisol. The gut microbiome alters adrenal output (where this hormone is made).
  • Depression is linked to a leaky gut, increasing inflammation, the microbiome alters this.

Gut bugs secrete most of our body’s serotonin, the ‘feel-good’ hormone. Having a healthy balance of gut bugs means we then have more serotonin, which means a better mood, less anxiety and depression6.

Gut bugs also speak to the brain about how we interpret pain signals. Healthier gut bugs can improve our chronic pain.7

This is all great, but how do I get happy gut bugs, and a healthy gut, and therefore lose weight, get a better immune system and feel better?8

The bottom line is to eat lots of different sorts of veg11. If you eat lots of different coloured veg each day, your gut will start to change within 48 hours for the better. Read on!

Diversity is key. Of the 250,000 edible plant species on planet Earth, we use less than 200. 75% of the world’s food comes from 12 plants and 5 animals. Branch out. We think that diversity is best for health as each bug is there for a different purpose, e.g. one for mood, one for vitamins, one for absorbing nutrients, one for the immune system etc.

The industrialised diet has hugely reduced bug gut diversity (by about a third). This reduction relates to the increased chronic disease we have in the West. From hay fever increase to cancer increase, from obesity to autoimmune disease, even diabetes.

Antibiotics kill off gut bugs. People often feel ‘wiped out’ after antibiotics – well, their guts are.

It’s possible to increase our gut bug diversity.

The more different types of plants you eat the more diverse your microbiome.

5+ veg of different colours a day

A change in what you eat will start changing your microbiome within 2 days. Getting 5 (or more!) different veg into your diet every day increases your gut bug diversity. The more different colours we eat the better (as different colours have different phytonutrients that help the heart, reduce cancer, inflammation and reverse brain aging).

Chemicals in veg that help us:

  • Polyphenols are one sort of phytonutrient that are antioxidant and lower inflammation (lower CRP levels), slow ageing, reduce BP, improve brain health and blood sugar control, help the heart, gut bugs. Polyphenols are in spinach, broccoli, red onions, asparagus, red lettuce, shallots, carrots, artichoke and green and black olives, and berries, dark chocolate, coffee, nuts, black and green tea, rosemary, thyme and peppermint.
  • Flavonoids – are powerful antioxidants to fight allergies, inflammation and infection, and encourage your body to burn fat. Found in berries, plums, grapes, tomatoes, green tea, parsley. Of interest, green veg have chlorophyll in, which increases satiety and controls hunger
  • Prebiotics – Prebiotics are nutrients that can be metabolized by gut bugs, things that human enzymes can’t metabolise. They reduce depression and anxiety, help constipation, gut bug diversity, bone health and heart disease. Found in onions, leeks, garlic, chicory, Jerusalem artichoke, asparagus, bananas
  • Probiotics – fertilisers for the microbiome, connected to improved gut health, decreased inflammation, improvements in cognitive abilities. They are the live bacteria and yeasts e.g. yoghurt, cheese, fermented foods.
  • Fibre – meals rich in fibre increase the diversity of our microbiome, therefore help our mood, immune system and weight, and also, studies show,  improve our amount of deep sleep and help us get to sleep faster. We eat 10 times less fibre than our ancestors. Gut bugs love plant-based fibre e.g. broccoli. They eat it and produce anti-inflammatory chemicals that reduce heart disease, stroke and dementia.
  • Exercisenot a food! But exercise helps the microbiome diversity
  • Sleep not a food! But sleep helps the microbiome diversity
  • Fasting – definitely not a food! But fasting also helps the microbiome diversity (see Akkermansia)

So, eat your rainbow veg! Eat them raw, lightly cooked, curried, stir-fried or casseroled. Buy them fresh, frozen or tinned, doesn’t matter which. This free chart from a GP in Manchester, Dr Rangan Chatterjee, may help you get them in:

Reduce sweeteners, sugar, processed foods (as these all reduce gut bug happiness and diversity) for gut health.

Your gut will thank you for eating well, your brain will work better, your mood will lift, your immune system will work better, your appetite will be more regulated.

Start eating healthier now


1 Influence of Diet on the Gut Microbiome and Implications for Human Health

2 A fun blog

3DiSalvo, David. Gut Feeling: How Intestinal Bacteria Could Manipulate Your Brain. Forbes 2014.

4Mayer et al. Gut Microbes and the Brain: Paradigm Shift in Neuroscience. The Journal of Neuroscience 2014. 34:15490-15496.

5 Evrensel A et al:

6 Jacka FN et al: SMILES trial: Change to a Mediterranean may be effective in treating depression.

6 Perry, Douglass. Depression, anxiety come from the gut: Surprising new research suggests ‘prebiotics’ can help. The Oregonian 2015.

6 Pennisi E, Evidence Mounts that gut bacteria can influence mood

6 Stewart, L:

7 Manning D:

8 Edermaniger L:


Dr. Katy Willis

GP in West London

Katy has been a GP in West London for over 25 years.

She is a qualified coach with the Association for Coaching and has an interest in well-being and mental health.