Part 10 – Fermented Food Recipes

Today is my last post on the microbiome. Here are three recipes that I regularly make. Go on, give them a try! As your confidence grows, you can expand your repertoire using the many recipes and variations of these, online. A little a day, keeps trouble at bay!

Homemade Sauerkraut

Equipment needed

A large fermentation or mason jar; a large bowl; a rolling pin; a fermentation weight


  • 1 medium head of Cabbage (white or red)
  • 1-3 Tablespoon sea salt or Himalayan rock salt (more for a bigger cabbage)


  1. Finely chop or shred the cabbage. Put it into a large bowl and sprinkle with the salt.
  2. Pound with a rolling pin for about 10 minutes, until the cabbage has leaked enough cabbage juice to cover itself. If it doesn’t, you can add a little filtered water.
  3. Transfer the cabbage into a big sterilised fermentation jar, pressing and coimagesmpacting the cabbage down hard underneath the liquid. If necessary, add a bit of water to completely cover cabbage.
  4. Place a fermentation weight on top of the cabbage to make sure it is all completely submerged (every last little bit!) This ensures proper fermentation and prevents mould growing.
  5. Cover the jar with a tight lid. You will need to lift the lid every couple of days to allow the excess gasses to escape (or you can buy specialised lids online).
  6. Allow to ferment at room temperature (60-70°F is preferred) for at least 2 weeks until desired flavour and texture are achieved.
  7. Once the sauerkraut is ready, pop it in the fridge in smaller jars with an airtight lid and keep the sauerkraut submerged in its own brine. Enjoy a tablespoon with your meals. The sauerkraut’s flavour will continue to develop as it ages.

Homemade Kombucha Tea

Equipment needed

Large glass jar; muslin cloth; elastic band; glass storage bottle(s)


  • Organic Green (or Black) tea bagsdxu76dmas+khhfjgyng%xw
  • Organic cane sugar or just white granulated sugar
  • Kombucha Scooby (Symbiotic Culture of Bacteria and Yeast). Buy online


  1. Boil a full kettle of water.
  2. Put 4 tea bags into your clean glass container, then add 130g sugar.
  3. Pour your boiled water into the glass jar with the tea bags & sugar. Stir and leave to steep for 30 minutes. Then remove the tea bags with a clean spoon.
  4. When the glass jar is cool to touch (feels the same temperature as your hands), gently add the Kombucha Scooby to the sweet tea. (Put all the contents of the packet, liquid included, into your prepared sweet tea). Your Scooby may float or sink, it doesn’t matter. A new, second Scooby will grow on the surface of the liquid in about 2-4 weeks, depending on how warm your room is, or the season you are making it in.

5. Cover your jar with the muslin and secure in place with the elastic band. Place the jar out of direct sunlight at room temperature. Your Kombucha will take about 2 weeks to mature.

6. You will need to periodically taste your Kombucha tea to see when it is ready. The more acidic or sharp it tastes the more fermented it is. If it still tastes sweet, then the bacteria haven’t had long enough to convert those sugars into lactic acid. Note the colour will darken and become cloudier the more mature it is.

7. When you feel it is ready to drink, pour off the Kombucha tea into a clean glass bottle and put it in the fridge. The longer you leave it in the fridge, the fizzier it will get. It won’t “go-off”. Drink a small glass each day, 5-10 mins before main meals. Build up the quantity you drink slowly, to allow yourself to get used to it.


Please remember to leave the Scooby(s) sitting or covered by about an inch of its brewing liquid. Do not let it dry out. It will last like this for up to 4 weeks. Don’t ever put the actual Scooby in the fridge.

You can now make a new batch of pre-made tea (sugar, tea bags and cooled boiled water) to the jar and Scooby. Or, if you don’t want to make any more, just cover the brewing jar, leaving the Scooby in its own juice.

Over time, the Scooby colony will grow upwards, in successive layers. The oldest layer lies at the bottom and is the darkest layer. You can carefully remove the lowest colony layer (clean your hands very, very thoroughly) and give it to a friend or put it in the compost. Eventually, you may want to buy a completely new Scooby.

Homemade Kefir


Equipment needed

Sieve or strainer; glass container or jar; spoon


  • Kefir grains as supplied with some kefir from the bag. I bought mine online.
  • 250ml milk – best is full fat organic from grass-fed cows, or also goat’s, almond or coconut


  1. Put the whole contents of the kefir bag into the clean glass container.
  2. Add your choice of 250ml milk.
  3. Cover the glass container with a muslin cloth and leave it at room temperature for anywhere between 1-3 days (depending on how warm your room is).
  4. It will be ready when it looks thick and clumpy. The longer you leave it out, the more tangy and cultured it will become. If it separates into a clear liquid and clumps, it’s definitely ready.
  5. When it’s ready, pour the liquid kefir through a sieve/strainer set on top of a Pyrex measuring jug or other suitable container. The kefir “grains” should be left behind in the sieve.
  6. Now put your grains back into your next batch of 250ml milk and start all over again
  7. Enjoy your Kefir drink – flavour it, or not, as you wish.

If you want to stop making you kefir for a while you still need to keep it alive by feeding it new milk. You do this by just sieving off the old, unwanted, fermented milk and topping up with lots of new milk (4 cups). Keep it in the fridge to slow growth.

I am here to help, if I can. Please do get in touch. Throughout January 2019 I am offering a free, no-obligations 20 minute chat to discuss any of the issues we have looked at. I have really enjoyed putting this series together for you and I hope you have enjoyed it as much too.

To your very good health, Dawn.

Part 9 – Optimising your microbiome

Caring for our microbiome is like tending to the soil in our vegetable garden. We need to weed it, seed it and feed it.


  1. We can weed-out, kill-off, or out-compete any unbeneficial species
  2. Then we can seed it with fermented foods and probiotics
  3. We need to make sure to feed it with the right diet including prebiotic foods
  4. We need to tend it with a nurturing healthy lifestyle

The dietary changes that you make will have a rapid effect on your microbes. Within days of improving your diet, your microbes will respond. You will need to be consistent to maintain the changes though. Here are some top tips.

Feed your microbiome lots of fibre from vegetables, fruits, nuts, seeds and wholegrains (if you eat grains). Fibre rich vegetables are apples, artichokes, avocados, beans, berries, broccoli, Brussel sprouts, cabbage, celery, greens, figs and kale, to name a few.

Eat a raw green-leaved salad every day – rocket, watercress, herby salad leaves, Pac Choi, chicory, spinach, chard, Chinese cabbage and any type of cabbage. Spice it up with a handful of fresh herbs like coriander, basil, flat leaved parsley or mint. Drizzle with col-pressed extra virgin olive oil and lemon juice, if you like.


Eat 3-4 servings of colourful vegetables at lunch and dinner and a couple at breakfast if you can. Aim for over 10 portions of vegetables per day.

Enjoy a rainbow of colour on your plate. Making a mixture of blended and juiced vegetables is an easy way to pack in the veggies.

If eating such an amount and variety of vegetables is difficult, consider supplementing your diet with additional fibre from psyllium husk, oat bran or inulin. Build up gradually to avoid bloating.

Eat a little fermented food at each meal. Fermented foods have been part of traditional foods in every culture of the world but have sadly been lost in the typical Western diet. First, let’s clarify the difference between picking and fermenting.

Pickling and fermenting are two ways of preserving food. Today, pickled foods are foods that have been preserved by an acid, like vinegar, to achieve a sour flavour. By contrast, fermented foods are preserved using salt, not vinegar. When we ferment vegetables in salty water (with no air in the jar) the normal bacteria found on the food eat the natural sugars from the vegetable and produce lactic acid as a waste product. The lactic acid then preserves the food.

Most people think that the jars of vinegar-pickled vegetables in the supermarket are fermented. They are not. They have been cooked at high temperatures or pressures and therefore don’t contain live probiotic organisms. Fermented foods that have been preserved or “pickled” using only salt and water (no vinegar or high heat) do contain live probiotic microorganisms. This is what you want to eat. You can buy these from health food shops (very expensive) or make them yourself. Here are some to look out for.

  • Naturally fermented sauerkraut
  • Salt pickled vegetables
  • Kimchi (Korean pickled vegetables)
  • Kefir (fermented milk, unsweetened)
  • Live Greek, cow’s, goats or coconut yoghurt
  • Miso – fermented soy (really yummy in soups, bone broth and casseroles – I buy mine from Green Ginger in Corsham)
  • Tamari – gluten-free fermented soy sauce (I use this all the time)
  • Tempeh – fermented tofu cake (might be tricky to find)
  • Tofu – try to find a fermented one
  • Unpasteurised apple cider vinegar (bottle should say “with the Mother” on it)
  • Kombucha tea (you can buy this online or make it)

Stew a batch of cooking apples (leave the skins on). Cooking the apples releases pectin, a naturally-occurring jelly-like starch found in some plants. When eaten, pectin releases a compound that does many helpful things – it neutralises unbeneficial microbes; it stimulates our genes to repair any damage to the intestinal barrier; it stimulates beneficial bacteria to multiply and take up residence in the protective mucus lining of the gut. Enjoy a spoon or two daily, perhaps with live yoghurt, a little raw honey and cinnamon.

Foods high in polyphenols are great to eat because the gut bacteria love them! Polyphenols are just special chemicals found in plants that are really good for our health. Good sources are dark chocolate (yay!), cocoa, red wine, grape skins, green tea, almonds, onions, blueberries, nuts, black tea and broccoli.

If you know you have difficulty with your digestion, consider extra digestive support, such as apple cider vinegar or supplemental digestive enzymes.

Stop eating sugar (in all its hidden forms), refined carbohydrates (food made from white flour, white rice, white pasta etc), artificial sugars, refined vegetables oils (sunflower, canola, corn, rapeseed, peanut, soybean oil) and margarines, because they promote the growth of the unbeneficial microbes and yeasts. Avoid food additives like emulsifiers, preservatives and high-intensity sweeteners for the same reason.

Stop eating wheat because the proteins in the wheat damage the intestinal lining cells in susceptible people. (Exploring this is a whole topic in itself).

Eat less commercially-raised red meat (top quality, grass-fed or wild-caught game is ok). Opt more for a Mediterranean diet, high in fruit and vegetables, extra virgin olive oil, oily fish, nuts & seeds.

Evaluate your need for prescription medications. They are usually designed to suppress symptoms, yet symptoms are your body’s way of telling you that there is a problem. Try to search for the cause of your symptoms (you can ask me for help if you like, just message me here) and avoid commonly used stomach acid blockers, anti-inflammatories, osmotic laxatives, steroids, antibiotics and hormones, as these alter our microbiome.

Stress negatively alters gut microbes. Choose a stress management practice that works for you and practice it daily.

Take daily exercise because it increases the butyrate-producing bacteria. Avoid excessive strenuous exercise because it stresses the microbiome.

Studies of sleep deprivation showed an increase in microbes associated with weight gain, altered fat metabolism, obesity and type 2 diabetes. Get 7-8 hours a night.

Eating outside of a normal circadian rhythm (think shift workers) can also be harmful to gut bacteria. Likewise, don’t eat late at night.

On average, though your microbiome will start to change very quickly from better food choices, more sleep, less medications, less sugar and alcohol and regular exercise, in general it will take around 60 days to feel meaningful benefits and reduction of symptoms from consistent changes.

Good luck, be patient and consistent and get in touch if I can be of some assistance to you. Throughout January 2019 I am offering a free, no-obligations 20 minute chat to discuss any of the issues we have looked at.

Coming up tomorrow, in Part 10, the last post in this series, I will give you a selection of recipes you can use at home to add more probiotic foods to your daily diet. I hope you will try and enjoy some of the recipes.

Part 8 – Probiotics and prebiotics



Probiotics are beneficial live microorganisms that we can eat to improve our health. As far as we know, they don’t necessarily take up residence in our gut but can give us benefits as they pass through.

There are two ways to consume probiotics, either from fermented foods or from probiotic supplements. We don’t yet know if probiotics in food (albeit much cheaper) are better than probiotic supplements, or vice versa.

Current objective opinion is that for healthy people, probiotic supplements don’t significantly change the microbiome, but in ill health or disease they can help restore a healthier microbiome.

Summary analyses of hundreds of trials has showed substantial evidence for the benefit of probiotics for treating diarrhoea; constipation; acute upper respiratory tract infections; eczema and dermatitis in children, improving metabolism; lowering cholesterol; reducing infection rates; and lowering markers of inflammation, like C-reactive protein. Promising research is underway regarding benefit for neurological, mood and brain disorders.

The business of probiotic supplements is currently exploding.  Companies are now making targeted probiotics with specific species and strains of bacteria for a specific problem (like a urinary tract infection), or a specific symptom (like diarrhoea) or specific groups of people (women, children, or elderly). We are beginning to understand which combinations of species of microorganisms are most helpful for specific conditions, but much more independent research is still needed (that is, research not funded by the companies selling the supplements).

Here are some of the species you may see and some of the symptoms or conditions they have already been found to be beneficial for. Don’t be put off by the long names, they are quite phonetically pronounced!

  • Lactobacillus Rhamnosus for eczema, diarrhoea and stress
  • Lactobacillus Plantarum for immunity, lowering gut inflammation and IBS
  • Lactobacillus Casei for diarrhoea, constipation, anxiety and depression
  • Lactobacillus acidophilus for reducing gut inflammation
  • Bifidobacteria Lactis – for abdominal symptoms, supporting immunity, weight control and constipation
  • Bifidobacteria Longum – for constipation, lowering stress and improving memory
  • Bifidobacteria Bifidum – is anti-bacterial and helps the symptoms of IBS and ulcerative colitis
  • Bifidobacteria Breve – for constipation in children, improving skin youthfulness
  • Streptococcus Thermophilus – is anti-bacterial and improves skin youthfulness
  • Saccharyomyces boulardii – This is a beneficial yeast. It out-competes unbeneficial yeasts. It can be taken alongside antibiotics to protect against loss of beneficial microbes. It supports good overall immune function

Supplements should list the quantity of colony forming units (CFU’s) on the packet. Start with 5 billion CFU’s (or lower if you need to) and build up to 50 billion or more, monitoring progress as you go. Stop at the level that works for you. If you experience gas, bloating, constipation or loose stool, reduce your intake and then build up more slowly. Generally speaking, the more severe your gut symptoms the higher the dose you will need to take. For example, VSL#3 is the brand containing the most CFU’s with 450 billion in a single dose! It is available online, but you should seek professional opinion if you think you may need this one! Probiotics are safe but seek advice if you are immuno-compromised.

Be prepared to change brands regularly to maximise the number of different species you are taking. Take probiotics with small meals, for better survival rates. You may need them at every meal. Morning is best to improve your digestion for the day, evening would be better for improving relaxation for sleep. Check expiration dates and storage instructions, some need refrigeration, others don’t. Check for other ingredients like lactose, binders and fillers, like corn starch. Check that the product hasn’t been cooked or heated above 40 degrees because this would kill the bacteria.

Not all probiotics bought online, or in supermarkets are rigorously tested to ensure that they survive transit through the gut. Many brands haven’t undergone strict quality control measures. Look carefully at your packaging and any company research available. You get what you pay for, don’t be tempted to buy low cost.

If you are taking antibiotics and want to take probiotics, take the probiotics as far apart in time from the antibiotics as you can, for example take the antibiotics in the morning and the probiotics in the evening. Continue to take the probiotics after you have stopped the antibiotics. Do not take both at the same time, as both will likely negate the benefits of each other! Probiotics are not a magic bullet that simply wipe out the collateral damage caused by antibiotics. Microbiome rebuilding takes time, there is no quick fix. Bringing the right species to the right area of the body is key to improvement.

If you are unsure, seek professional advice when choosing probiotics, as nutritional professionals have a far wider availability of professional brands available to them, than can be bought over the counter. Similarly, as new research becomes available, professionals are able to match probiotic strains more accurately with a person’s problem. Naturally, as a trained and qualified, practising Nutritional Therapist, I can help you with this, so give me a shout if you have any questions or need any advice.



Prebiotics are carbohydrates from plant fibres. We can’t digest these fibre, but our gut microbes can, so in essence prebiotics are “food for the microbes”.

Prebiotic fibre helps the beneficial microbes to grow; provides food for our intestinal cells; helps digestion; reduces inflammation; reduces insulin; reduces cholesterol and reduces the risk of colon cancer.

Foods high in prebiotics are beans, lentils, legumes, dandelion greens, oats, green bananas, Jerusalem artichokes, asparagus, garlic, leeks, onions, nuts, barley, apples, cocoa, flaxseeds, Burdock root (looks like long brown carrots), Yacon root (looks like a long sweet potato), Jicama root (looks like a potato), and seaweeds.

You can also buy prebiotics fibre supplements such as inulin, Fructooligosaccharides (FOS) chicory root, psyllium husk and fructans. Remember to “start low and go slow” – build up gradually.

Have you heard of resistant starch? This is another type of prebiotic food. It is found in potatoes, rice and pasta when you eat it after it has been cooked and then cooled. So enjoy a little of your cold left-over potato, rice or gluten-free pasta.

Coming tomorrow, Part 9 of this series, looking at optimising your own personal microbiome. Keep an eye on your inbox, and see you tomorrow!

Part 7 – New tests & treatments

The microbiome is like a barometer – it reflects if all will be calm or if a storm is brewing. Today’s post looks at some of the tests and treatments currently available.


The most common way to assess your microbiome is via a comprehensive digestive stool test. It can be done privately, and your GP can order one for you (with good clinical justification). This will give you a thorough overview of the health of your gastrointestinal tract. It evaluates how well you digest and absorb your food; it identifies some of the yeasts, bacteria and parasites and what short chain fatty acids they are producing. It also reports on levels of gut inflammation, pH, food fibres and if there is blood in the stool. I use this private test regularly in my Nutritional Therapy work. Clients find it very helpful to see for themselves the microbes they have and how well their gut is functioning. They are also very reassured to see how those markers of gut health improve with nutritional interventions.

The very latest private stool testing identifies microbial RNA (ribonucleic acids) produced from anything and everything living in the gut. It uses new technology called metatranscriptome sequencing. Compared to older technology, this can identify all the bacteria (not just some) plus the yeasts, bacteriophages, parasites, fungi, and viruses, (and names them for you), which older stool testing doesn’t. In addition, the test identifies all the metabolites being produced and the ones missing. The app-based report gives dietary recommendations and foods for improving your unique gut health based on the results. I am about to do this test on myself, so I will keep you posted!

As you now know, the vast majority of microbes should be in your large intestine, or colon. However, in some people with upper abdominal bloating, feelings of fullness, pain and fluctuating stool (all very common symptoms) there is a test to see if large amounts of colonic microbes have moved upwards into the small intestine. The test is called a Small Intestinal Bacterial Overgrowth (SIBO) test and you can do it yourself at home. It’s a breath test to capture the gases (hydrogen and methane) given off by the bacteria after a test drink. This is not a test commonly done on the NHS.

Have you heard of faecal transplants?  Hospitals are now transplanting filtered faecal microbes from healthy individuals into those with diabetes, obesity, Crohns and ulcerative colitis (UC) to rapidly improve their microbiomes. The results to date are very promising and this is likely to be a fast-expanding field of gastroenterology. I know, you think it sounds rather yukky, but anyone with debilitating Crohns or UC will tell you, if it offers relief from a lifetime of pain, steroids and drug side effects, it’s more than worth it.

I appreciate the sometimes awkward, personal side of bowel and digestive issues, and I know it can be difficult to talk to people about such problems. If you have any concerns, you can talk to me, I am a trained and qualified Nutritional Therapist, as well as being a practising osteopath for 24 years.  We can talk in total confidence, and trust me, I have heard it all before and I just might be able to offer an understanding ear and some helpful advice. If you are at all interested and want testing, please contact me and I’ll arrange to have tests sent out to you at home, and I’ll explain to you how testing is quick and easy.

Look out for Part 8 tomorrow, when I’ll explain the difference between probiotics and prebiotics, and how and why you need both in your diet. See you then.

Part 6 – Microbiome and disease

The differences between peoples’ microbiomes is one reason why we each have different susceptibility to different diseases.

Microbial imbalances are thought to contribute to disease through the cross-talk between the microbes, the chemical waste products they produce and our immune cells. When toxic, this drives an inflammatory response.










Dysbiosis is the name given to an imbalance between beneficial and unbeneficial microbes; typically too many “bad” ones and too few “good” ones. Research is currently unravelling which microbes are beneficial, which ones are neutral and which ones are harmful.

Dysbiosis causes bloating, cramps and abdominal pain as the microbes produce gas and other chemicals, which can distend and irritate the gut. Mild, sub-clinical gut disorders are increasingly common these days. Many people are living with tolerable, but uncomfortable, levels of bloating, gas, digestive disorders and irregular bowel movements. They are called functional disorders, like IBS, because the functionis affected but there is no pathology. While not life threatening, such disorders can be frustrating to live with and may be a sign that your microbiome needs some attention. It’s best not to ignore these symptoms for the long term; dealing with them sooner, rather than later, may help prevent more serious conditions developing years down the line.

There is considerable mounting evidence that dysbiosis in the gut is also associated diseases, both inside or outside the gut. Gut conditions like inflammatory bowel disease, ulcerative colitis, coeliac disease, colorectal cancer and non-gut conditions like allergy, asthma, diabetes, cardiovascular disease, obesity, autoimmune conditions and some neurological diseases. As yet, it is currently debated as to whether or not dysbiosis is a cause, or consequence, of a given disease.

Let’s look at some of these.

Weight gain and obesity

Refined carbohydrates and sugar are foods which feed the unfavourable microbes and yeasts, which then grow and multiply in our gut. A fungal overgrowth, like candida, can trigger more sugary food cravings and weight gain.

The unfavourable microbes make toxic compounds, some are called lipopolysaccharides (LPS). The LPS cause irritation and inflammation when they escape the gut and get into the bloodstream. The inflammation leads to insulin resistance, weight gain and type 2 diabetes.

Diabetics commonly lack the beneficial butyrate-producing bacteria. Among other things, these bacteria help to control blood sugar and insulin levels after a meal. Foods that help the butyrate-producing bacteria to multiply are typically high in resistant starch. Resistant starch is high in cooked and cooled rice, potato and pasta, also fibre from vegetables, oats and legumes. So enjoy your cooled “left-overs” straight from the fridge! Supplements high in resistant starch are inulin (please note spelling, that is inulin, not insulin!) and potato starch.

Obese people have been typically found to have a high number of Firmicutes species compared to low numbers of Bacteroidetes species. It is thought that the Firmicutes could be extracting more calories from the food and promoting more fat storage.


Researchers are finding more and more specific species of bacteria associated with certain cancers, for example helicobacter pylori with stomach cancer; Fusobacterium nucleatum and Escherichia coli with colon cancer; Chlamydia with cervical cancer; Clostridium with liver cancer, and other mouth bacteria associated with pancreatic cancer.This doesn’t mean to say that those bacteria are causing the cancer, they may just be taking advantage of the compromised cells. Research is ongoing.

This may mean that we might be able to detect a pro-cancerous environment years before cancer is detectable, by understanding what bacteria belong where and monitoring how they change over time.

As cancer rates are rising, microbial diversity is decreasing. Is there a connection to explore? Researchers have discovered that both people and mice with cancer who had been given antibiotics, tended to have poorer cancer outcomes to immunotherapy.

Autoimmune disorders

Diseases such as multiple sclerosis, lupus, Hashimoto’s (low thyroid), coeliac disease and rheumatoid arthritis develop because the immune system is overactive and making autoantibodies against particular groups of body cells.

The reason why the body makes autoantibodies is through the mechanism of mistaken identity. This means that the immune cells attack and kill our own cells that have certain markers on them (a bit like a birthmark or tattoo) that may look like a pathogen.

For example, Hashimoto’s is an autoimmune disorder whereby the body makes autoantibodies against the thyroid gland in the neck. This progressively damages the gland and its ability to function to regulate our energy. Symptoms of low thyroid are chronic tiredness, hair loss, IBS, panic attacks, weight gain and constipation. It’s now easy to get a full set of thyroid tests with an at-home finger-prick blood test that you submit through the post. If you would like a test, it’s quick, cheap and easy, just ask me and I’ll have a test sent out to you,

Neurological disorders

People with psychological disorders (anxiety, depression, autism, bi-polar, schizophrenia, Parkinson’s and Alzheimer’s) have been shown to host specific species of gut bacteria, which are different to the microbial species of people with no neurological condition.

Researchers have proposed that the “bad” microbes indirectly alter brain function via inflammatory signalling molecules through the nerves that link the gut and the brain (gut-brain axis) and by directly crossing the blood brain barrier.

Specific probiotic strains have produced mixed, but promising results for improving symptoms of conditions such as anxiety, depression and memory. They have been called psychobiotics.

Heart disease

 There is a strong connection between gum disease and heart disease. Bacteria in the mouth enter the blood stream via the inflamed gums. Immune cells in the blood then mount an inflammatory response in the arteries. If this goes on for decades, it is believed this inflammation contributes to atherosclerosis and cardiovascular disease.

Trimethylamine N-oxidase (TMAO) is a compound made by the gut bacteria when we specifically eat animal foods – fish, red meat, eggs & dairy. TMAO seems to make our platelets stickier, which increases our risk of clots, leading to heart attacks and strokes.

Lactobacillus may help to reduce cholesterol when taken as a probiotic.

I hope you are enjoying this short series, learning about your microbiome and gut health. If you have any questions, or if you would like to have a private chat about your own health, head over to this page and send me a message and we’ll arrange a time to talk.

Coming up tomorrow, Part 7, all about the latest tests and treatments available. Keep an eye on your inbox!

Part 5 – Gut-brain communications

Imagine a web of communication (some of it wireless) between all our cells. Microbes are the key link in this communication.

vortex-blue-2A significant proportion of the calories we eat don’t get absorbed into the bloodstream for use by our bodies. Instead, the food is eaten by the microbes further down in our colon. As the microbes eat the food they produce waste products. The waste products are important communication molecules.

Initially, the waste products give signals to our gut lining cells and gut immune cells, starting the conversation, if you like. Thereafter, some of them may get absorbed into our bloodstream and continue the ‘conversation’ anywhere in our body. This can be good or bad, depending on the microbes and what messages they are sending.

The beneficial microbes make helpful communication molecules like short chain fatty acids and vitamins which keep us healthy. Unhelpful and pathogenic microbes produce toxins called Lipopolysaccharides (LPS) and others, and inflammatory signalling molecules that can contribute to disease processes like high blood pressure, diabetes and other inflammatory conditions.

Butyrate is another communication molecule made by our beneficial gut bacteria. It is essential for gut health, immune health and brain health. Butyrate helps to prevent cancer, speed our metabolism and reduce inflammation – which is key to good health. We can measure our levels of butyrate in a stool sample. Please contact me if you would like me to arrange a stool test for you – it’s easier than you think and can be done alone at home and sent in the post. If low, you will know to focus on feeding the butyrate-producing bacteria to reduce inflammation and improve health.

There are other messenger molecules too. The gut microbes, together with our gut cells, make neurotransmitters. Neurotransmitters are chemical molecules which allow nerves to pass their messages from one nerve to another throughout the body.

Serotonin is a neurotransmitter made in large quantities in the gut. Serotonin helps to make us happy and helps us to sleep well. We need to keep our gut healthy so that we can make enough of this happy hormone.

Gamma-Aminobutyric Acid(GABA) is another neurotransmitter produced by our gut microbes. GABA helps to keep us calm. It balances stress neurotransmitters like cortisol. Acetylcholine, histamine, melatonin are other important chemicals produced in the gut to enable the body’s cells to communicate with each other.

imagesIn addition to these chemical messenger molecules, we also have physical lines of communication. We have millions of nerves that connect our gut and brain, and its been called the “gut-brain axis”. The vagus nerve is one of the biggest nerves that connects our gut to our brain. It sends signals both ways. For example, if you are stressed, not only does the brain send distress signals to the gut reducing the digestive process, but the gut bacteria then communicate back to the brain, via the vagus nerve, telling it what’s happening down in the gut and what to do about it.

And finally, a very important gut-brain connection is through our immune system. This is a huge and complex system of communication. One important thing to know is that together our gut immune cells and our microbes control the levels of inflammation in our body and this is believed to be key in helping to prevent degenerative diseases like cardiovascular disease, metabolic syndrome, diabetes and dementia.

We’re half way, that was Part 5, and we have another 5 still to come.

I hope you are enjoying this series and learning something useful from all of this. Look out for Part 6 tomorrow when we will take a look at your microbiome and links to different diseases – important stuff!

See you tomorrow.

Part 4 – Microbiome and antibiotics


Antibiotics originated as one life form producing something against another life form. For example, penicillin is a substance produced by fungi which stops the growth of bacteria. Modern antibiotics are synthetically made and have been in widespread use to fight bacterial infections. They have saved many lives and speeded the recovery from infection for most of us, but remember, they cause collateral damage to the beneficial microbes and diversity of your microbiome.

When we take antibiotics, our resident beneficial microbes are also killed. The more we take, the more are killed. In time and given opportunity, our microbes do repopulate our gut, but they don’t necessarily grow back the same, or as plentifully, as they were before.

Taking too many antibiotics can leave us more susceptible to antibiotic resistant bacterial strains, like clostridium difficile, gonorrhoea and MRSA. Resistant bacteria can cleverly pass on their antibiotic resistance, thus out-competing other species.

Prescription antibiotics aside, massive quantities of antibiotics are fed to animals each year to combat infections and speed up growth. Overusing antibiotics in animals can also lead to antibiotic resistant bacterial strains becoming a problem. These resistant bacteria can then pass into our food chain if we don’t handle and cook meat properly.

Another route of contamination is from eating food crops that have been sprayed with animal manure fertilizer, which is infected with antibiotic resistant bacteria. Resistant bacteria in supermarket foods can be surprisingly common. You’ve probably heard of food recalls due to infection with Salmonella, Campylobacterand E.coli.

The message is simple. Avoid antibiotics as much as you safely and responsibly can. Only take them if your doctor insists they are essential.

If you do have to take a course of antibiotics it is advisable to try to restore your beneficial microbes as best you can, with probiotic foods and probiotic supplements. The probiotics will try to out-compete the harmful species by colonising the layer of protective mucus covering the gut lining.

Generally speaking, you want to take your probiotics away from taking the antibiotics and keep taking them after you finish taking the antibiotics. For example, if you take the antibiotics morning and evening, then take the probiotics at midday. We will look at probiotic options in Part 8; where to source them, which brands to choose, how many to take and for how long.

I hope you are enjoying this blog series so far. If you are interested in having a chat about your microbiome, your diet and lifestyle, and your gut health, head on over to my site and make an appointment with me for a free, no-obligation, 20-minute chat. No hard sell, just a chance for you to ask any questions.

Look out for Part 5 tomorrow, all about the fascinating connections between gut health and brain health. The complex and intricate connections between our gut and our brain were largely unknown until recent times, but new research is emerging all the time now, and our knowledge is increasing every year. Find out more tomorrow! See you then.

Part 3 – Microbiome and your immune system

About 70% of our immune cells are housed in the lining of our gastrointestinal system, or gut. Our gut is the biggest immune organ of the body. Likewise, it’s also where the majority of our microorganisms reside. This is not a coincidence. It makes complete sense. The food we eat is the largest exposure of foreign material that we bring into our body, so it makes sense for our immune system to reside in our gut. The outside world is literally experienced through the filter of the gut microbiome (and of course through our lungs), defending us against unwanted microbes and toxins.


It’s like an internal ecosystem – a biological community of interacting organisms in their physical environment (our gut). The more diverse the number of beneficial microbial species our gut hosts, the better our immune system will work and the healthier we will be.

A delicate interaction occurs between us and our microbes. The gut immune system is constantly working hard to distinguish between beneficial bacteria and potential pathogens (unwanted invaders). When we lose our microbial diversity (all those different species of microbes) we lose “tolerance”. When our immune system goes wrong, it’s basically losing tolerance. It fails to adequately deal with all that is presented to it, and often reacts to things that it shouldn’t react to. Thus, digestive inadequacies, allergies, food intolerances and autoimmune conditions are mostly the result of an immune system losing tolerance.

Three factors determine if we will lose tolerance:

  1. Our genetic predisposition
  2. Our exposure to a bad environmental event or trigger, like an infection
  3. How permeable our intestinal lining cells are

For most people, improving the integrity of the intestinal barrier is the most practical way to improve immune tolerance.

Increased intestinal permeability, commonly referred to as “leaky gut”, can be thought of as micro-tear’s in the gut lining cells. This is the start of the trouble. Many things in our modern lifestyles can damage this delicate lining. Stress, toxins, undigested food particles, gluten, antibiotics, acid-blockers, processed foods, low fibre diets, pathogens, drugs, alcohol and infections are the main ones. These can lead to unwanted substances (microbes, particles of food, pathogens) getting directly into our blood stream and triggering long-term inflammation.

leaky gut


Be on the lookout for Part 4 tomorrow, we’ll take a look at your microbiome and antibiotics, and what happens to your microbiome when you are prescribed a course of antibiotics, and what you can do afterwards to help yourself restore good order.

Part 2- Functions of the gut microbiome

microbiome700Our microbes:

Help us digest our food.

Protect our gut lining cells from pathogens and toxins.

Help teach and mature our immune system to function properly.

Make B vitamins, Vitamin K and amino acids (proteins).

Break down, by fermentation, non-digestible dietary fibre that we eat.

Regulate our metabolism (how much energy we get from food) and help to regulate our weight and how much body fat we store.

Make waste products called short chain fatty acids (SCFA’s) that provide food for our gut lining cells. These are important communication molecules.

Influence sleep, mood and brain function.

Regulate the repair and growth of our body’s cells.

Are key to our health and disease.

Coming up tomorrow in Part 3, we’ll take a look at your microbiome and how it forms a crucial, and major, part of your immune system. Few people realise how important our gut is when it comes to immune system, tomorrow I will explain more.

See you then!

The Human Microbiome


For many months now, I’ve been researching and listening to lectures about the human microbiome. My short, easy to digest (ha, ha, pun intended!) blog series is about how our gut microorganisms significantly influence all aspects of our health (and disease) and how to turn this knowledge into healthy new habits. I hope you find it helpful and I welcome any comments or questions.


This post is Part 1 of a 10-part series. Here is the outline of the series:

Part 1 – In the beginning

Part 2 – Functions of the microbiome

Part 3 – Microbiome and your immune system

Part 4 – Microbiome and antibiotics

Part 5 – Gut-brain communications

Part 6 – Microbiome and disease

Part 7 – New Tests and treatments

Part 8 – Probiotics and Prebiotics

Part 9 – Optimising your microbiome

Part 10 – Fermented food recipes

Part 1 – In the beginning

The microbiome is a community of microbes living in, and on, your body. Microbes are bacteria, fungi, yeasts and parasites. They are found in every part of your body, particularly your gut, but also your eyes, skin, sinuses, mucus membranes such as your mouth, lungs and vagina and in your blood. In the gut the microbes live in a healthy, thick, protective layer of mucus lining the gut walls.

A baby’s first exposure to microbes is through the vaginal canal. As the baby moves down through the birth canal, it gets covered in its mother’s microbial secretions and also swallows some of the microbe-rich vaginal mucus. Also, breast milk is full of healthy bacteria, prebiotics (food for the microorganisms) and of course colostrum, a nutrient dense, antibody-rich, immune-supportive first milk.

Our mother’s genetics, the food she ate, her lifestyle (e.g. smoking or alcohol consumption), her medication use, antibiotic use and any infections she had, all contribute to the microorganisms passed onto her baby.

Our microbiome is established within the first 6 months of life. After the second year of life, the resident microbial species becomes relatively stable.

Early exposure to bacteria in our environment helps our immune systems to develop. The microbiome literally shows and teaches the developing immune system what it has to face and deal with. A healthy, microbiome is crucial for the maturation of a baby’s developing immune system.

Less exposure through sterile wipes, hand sanitizers and harsh cleaning chemicals reduces our exposure to germs. Long term, this can leave us more exposed to infection or allergies because we lose that early exposure which we need while our immune systems are developing.

As adults, we host 100 trillion microbes in our gut, between 3-6lbs in weight! We have ten times the number of bacterial cells compared to our own cells and 100 times the number of microbial genes than our own genes.

The microbiome houses 40,000 different species of bacteria; 5 million species of fungi and 30,000 species of parasites – some of them are beneficial, some are not. Generally speaking, the greater the number of different species we host (called microbial diversity) the healthier we are.

Most microbes in the gut belong to one of four groups or species: FirmicutesBacteroidetesActinobacteria or Proteobacteria.

As we age, our immunity gets progressively less effective (for several reasons) – so it’s important to focus on helping it work as efficiently as we can. When we nurture and look after our microbiome, it will in return, look after us.