Supporting your gut with ‘functional foods’

The gut microbiome refers to the trillions of bacteria, viruses and fungi that live in your gut. The gut microbiota interacts with various organs and systems in the body, including brain, lungs, liver, bone, cardiovascular system and others.

This week’s blog is provided by nutrition practitioner Miguel Toribio-Mateas. In this final blog of a 3 part series, Miguel discusses how the food we eat influences the health of our gut and introduces us to some of the ‘functional foods’ that are considered to support the gut microbiome.

In part 1 of this blog series, Miguel introduced us to the idea of how your gut flora may hold the key to health, and in part 2, he went on to explain how getting to know your gut ecosystem or “microbiome” can give you an edge by providing you with specific details that make your gut unique.

Supporting your gut with ‘functional foods’ – Miguel Toribio-Mateas

Challenging your gut bugs

When your gut misbehaves, it may well be asking for a challenge and in my clinical experience, the use of fibre-rich, brightly-coloured foods (prebiotics) along with live bacteria and other microorganisms (probiotics) is one of the easiest ways to gently “poke” your gut and see what response you get.

Good quality randomised controlled trials are only starting to look at what happens when you eat more or less probiotic foods, or when you add live bacteria / probiotics to your daily dietary regime.

Results from clinical trials can take ages to be translated into guidelines that actually mean something to you, so you’ve got the option to wait for another 10 years until enough clinical evidence has accumulated, or you could start working on your gut today. The worst that can happen is that you’ll get windy, and the potential benefits far outweigh the extra bit of gas.

Your “good” gut bugs thrive when you eat a varied, colourful diet that contains as many colours from fresh foods as possible, on a daily basis. You’ll have heard the saying “eat a rainbow” or “eat the rainbow”, particularly if you’ve been following leading practitioners in functional nutrition and lifestyle medicine.

Any practitioner who uses the type of stool tests I discussed in part 2 will know that increasing the diversity of the foods you eat on a daily basis, i.e. minimising the repetition of foods, not only ensures you get a wider spread of nutrients but it also feeds a wider spread of your gut bugs, cultivating that all-important microbial diversity I’ve referred to in part 1 and part 2 of this blog series.  If you’re unsure of how varied your diet really is, you should take the “50 food challenge”.

This is very simple:

  1. Download my “50 food challenge chart” by clicking on the link below.
  2. Keep track of every different food you eat for a week and aim for at least 50 foods, mostly plant-based and of all colours of the rainbow, the brighter the better.
  3. Do not exclude any groups of foods unless you actually need to for specific reasons that make you feel unwell.
  4. Note down every food only once only within the next 7 days to assess your diet’s diversity. For example, red and white onions count as 2 different foods, bread and pasta count as just one as they’re mostly made from the same ingredient, i.e. wheat. If you start filling out the chart on a Monday and you note down red onions as 1 ingredient, you may add white onions again on a Tuesday, but if you have red onions again anytime in the following 6 days, you can’t note them down again.
  5. Herbs, spices and oils all count as individual ingredients.

Some notes on using the 50 foods challenge chart

Remember that the idea is to increase the amount of foods you include in your diet, not to increase the amount of foods you exclude from your diet. I see more and more people who exclude a number of foods for the most incredible reasons. My approach to exclusion of foods is simple: only do it if they don’t suit your health or if they have a tangible effect you wish to avoid, e.g. weight gain. Working with a practitioner who understands your goals will help you get there more easily.

If you’re just using the chart for yourself, please download in PDF format. If you’re a practitioner, I’ve also included the PowerPoint file I use myself in clinical practice. Feel free to download this version and to customise it with your own logo and credentials. I’m only too happy for you to do so and hope your clients find it as useful and fun as mine do.

Introducing food-based probiotics  

I’ve been working with food-based probiotics such as yoghurt, kefir and kombucha routinely for years. I find that healthy guts get healthier and not-so-healthy guts have a lot to benefit from by getting some of these foods regularly.

Fermented foods can be based on both dairy and non-dairy substrates. For those of you who don’t suffer as a result of having dairy in any tangible way, e.g. gastrointestinal symptoms, skin issues, I would stick with fermented dairy as it has many advantages over fermented non-dairy produce, including better protein content, helpful fats, and contribution to healthy glutathione levels. I’ll give you a couple of examples of how a simple fermented food can help tackle a number of health issues.

Example 1

Nutrition researchers at the University of Tehran conducted a randomised, double-blind, placebo-controlled trial involving seventy-five petrochemical workers who were split in 3 groups. Participants in one of the groups had 100g of probiotic yoghurt daily.

The yoghurt had been fermented to contain two strains of Lactobacillus acidophilus and Bifidobacterium lactis you find in many plain “live” yoghurts you can buy in your local supermarket.

A second group of participants was given a multistrain probiotic capsule containing seven probiotic bacteria including Lactobacillus casei, Lactobacillus acidophilus, Lactobacillus rhamnosus, Lactobacillus bulgaricus, Bifidobacterium breve, Bifidobacterium longum, and Streptococcus thermophilus. Finally, a third group served as control, i.e. they were just given conventional yoghurt containing the starter cultures of Streptococcus thermophilus and Lactobacillus bulgaricus.

Groups 1 and 2 experienced similar improvements in mental health. They felt less depressed and less prone to anxiety and stress as assessed by clinical psychologists. The group who just ate the plain yoghurt with no “special bacteria” didn’t report the same improvements.

Example 2

In another randomised controlled trial, researchers at the University of Connecticut [227] found that pre-menopausal women who ate just 339g (equivalent to two thirds of the large pot of yoghurt you can buy in British supermarkets)  of yoghurt for nine weeks experienced a reduction in inflammation and improved permeability of their gut, i.e. they experienced less “leaky gut” than those women who ate a food that looked and tasted vaguely like a yoghurt but didn’t have any live bacteria in it.

One of the things that this group of scientists measured was “zonulin” a protein that’s produced by gut cells and that increases the “leakiness” of the gut. Measuring levels of zonulin helps us understand how leaky your gut might be. Leaky gut has been associated with a number of health issues, including diabetes, autoimmune disorders and cognitive decline. We’re learning more about it everyday as more human studies document these relationships. The women eating the cultured dairy experienced reductions in zonulin levels, and those who were having the control food didn’t.

One peculiarity of this study is that the yoghurt used in the intervention group happened to be low fat. Personally, I don’t think this had anything to do with the results, based on the fact that yoghurt is naturally low in fat anyway.

Kefir: water or milk?

If you’re a yoghurt eater you may also enjoy kefir, a probiotic drink typically consisting of dairy milk fermented by kefir grains. Kefir is a complex mixture of bacteria and yeasts or SCOBY (which stands for “symbiotic culture of bacteria and yeast”) that live in a complex sugar base. But don’t freak, these complex sugars aren’t like table sugar, so if you live a low sugar lifestyle, don’t let the name “sugar” put you off. The correct term is “polysaccharide”. Albeit more technical, that may put you off less.

People in the Caucasus mountains and in Tibet have been using kefir for centuries, so they may be amused that their traditional drink has now become widely available in many countries around the world as a “functional food”. I am a big lover of kefir because it’s a wonderful multi-strain probiotic in a food matrix. A glass of kefir will provide you with copious amounts of a number of bacterial species, including Lactobacillus paracasei,  Lactobacillus acidophilus, Lactobacillus delbrueckii,  Lactobacillus plantarum and  Lactobacillus kefiranofaciens.

Other more exotic bugs in kefir include Lactobacillus kefiri,  Acetobacter aceti and  Acetobacter rasens. But kefir contains “good yeasts” too. In fact, in excess of 23 different yeast species have been isolated in kefir cultures, the predominant ones being Saccharomyces cerevisiae, Saccharomyces unisporus, Candida kefyr (not to be confused with the potentially problematic Candida albicans which causes thrush!) and Kluyveromyces marxianus. Drinking kefir daily has been shown to improve the function of the gut’s own immune system and to reduce inflammation in the gastrointestinal tract.

This is perhaps why kefir has become favoured by nutrition practitioners as a powerful source of probiotic microbes in a food matrix that’s symbiotic in nature. Other potential health properties that have been reported with regular consumption including antimicrobial activity, i.e. helpful for troubled tums or traveller’s diarrhoea, for example, as well as control of blood glucose and cholesterol, which mean that this would be useful for those whose blood sugar and blood lipids are a little on the high end.

Kefir also helps improve lactose intolerance, but fear not. Non-dairy varieties have become available in both health food shops and supermarkets. I was pleasantly surprised to find water kefir in my local supermarket the other day. Grains are easy to get online. Or you could get them from the UK Fermenting Friends closed group on Facebook, which is a wonderful resource for those with an interest in fermented foods and wanting to make their own kefir at home.

In fact, water kefir grains are naturally dairy-free and are known to ferment a number of non-dairy substrates, including fruit and vegetables juices, and even plain sugared water. These grains contain a variety of microbial species similar to those in milk kefir grains, plus a generous amount of gut-repairing molecules known as exopolysaccharides.

Kombucha and other ferments

Apart from its exquisite taste, I love kombucha for a number of reasons. This fermented tea drink provides a rich source of liver-protecting enzymes along with a myriad of antibacterial and antifungal natural substances that can provide great support for someone suffering from bacterial imbalance or dysbiosis. Plus it’s a natural source glucaric acid, which helps with healthy detoxification.

Other fermented foods that have become popular of late are sauerkraut and kimchi. Not only are they rich in probiotic bacteria, they’re also rich in fibre. So if you’re a novice start with small amounts to avoid getting windy. I find them both incredibly useful clinically, plus I love their taste. I could eat them all day long!

Final words

Apart from being touted for a range of health benefits, probiotic or “functional foods” (as some have started to call them) such as kefir, kombucha, sauerkraut and kimchi  provide some people with an appealing way to supplement their live / probiotic microbes. Selected probiotic supplementation can be helpful too.

However, we all need to be mindful of the complexity of the gut ecosystem and the fact that the relationships between our gut tissue, the bugs that live there and rest of our body is equally complex, so I’d stay away from “protocols” that promise health based on the same “one size fits all” principles for everyone. Given that the science is evolving rapidly in this area, a little trial and error is required, with the reassurance that you’re working with food and that tends to be an extremely safe thing to do. In any event, I hope that the tools I’ve discussed over this 3-part blog have provided useful answers to some of your questions.


The “50 food challenge” chart was published recently in Miguel Toribio-Mateas’ review article entitled “Harnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions”, available to read / download as open access (free of charge) from the peer-reviewed journal Microorganisms. It’s a great educational read that has received good reviews by clinicians around the world. We encourage you to click here to access the paper’s full text and hope you find it as useful as we have.

Miguel is a doctoral researcher in cognitive ageing who’s experienced the research process from the laboratory bench – having completed a lab-based Masters in Clinical Neuroscience focusing on brain ageing – to the delivery of science findings in the consultation room, delivering quality individualised nutrition care to his clients from 2009. Miguel’s background includes 15+ years in senior training roles in life sciences and medical publishing, and he has trained scientists and researchers around the world.

With many thanks to Miguel for this blog; if you have any questions regarding the health topics that have been raised, please don’t hesitate to get in touch with Clare via phone; 01684 310099 or e-mail

Related Cytoplan Products

Acidophilus Plus – Containing Lactobacillus acidophilus and a further 8 live native bacterial strains, plus a small amount of fructo-oligosaccharides (FOS).

Cyto-biotic Active Powder – A live native bacteria powder comprising 9 strains plus a small amount of the prebiotic inulin which stimulate the growth of bifidobacteria and other healthy native bacteria in the gut. With antibiotic resistant strains and stable at room temperature – so no need to refrigerate.

Fos-A-Dophilus – Contains 6 strains of live native bacteria, plus a small amount of prebiotic. It is designed to have activity throughout the whole GI tract.

Saccharomyces Boulardii – A unique, natural and safe microorganism, with a wealth of research data, which has been used worldwide as a food supplement for more than half a century.

Last updated on 25th February 2020 by cytoffice


15 thoughts on “Supporting your gut with ‘functional foods’

  1. This is a fantastic article by a well respected practitioner. One I will be directing my patients too. Very informative and practical. Thank you.

    1. Wonderful to hear that Dr Quinton.
      I hope the GP’s at my local surgery will become just as enlightened

    1. Hi Helen, thank you for your question. You can get a list of functional doctors here and functional nutritionists here – if you need anything else, please let me know. Thanks, Miguel.

  2. I am a big fan of fermented food. Thank you for giving me so much scientific information about their benefits to share with my family and friends..

  3. Thank you for this excellent series Miguel and your very generous PDF access. I have learnt a lot about fermented food from you.

  4. I have found that a kefir drink before breakfast every day has helped to restore my energy levels, even though I’m in my 60s

  5. “Download my “50 food challenge chart” by clicking on the link below.”

    I did not see the link…

    1. Hello, thank you for your message. They are under ‘Some notes on using the 50 food chart’ in the second paragraph. Miguel has provided a PDF format and a PowerPoint. Thanks, Abbey.

  6. Hi, this is so helpful. When using the chart, do dairy products count as one? For example, milk, cheese, yogurt, kefir? Or can they be included as separate entries?

    1. Hi Caroline, thank you for your comment. Miguel recommends that every type of milk counts as one ingredient, e.g. sheep’s milk yoghurt would count as one and goat’s milk yoghurt would count as another one. If your cheese was cow’s milk that would be a third, and if you kefir was made with coconut milk, that’d be four ingredients. Hope this helps. Thanks, Abbey.

    1. If you are healthy, with good digestive function and including fermented foods in your diet, then it may not be necessary for you to take a daily probiotic supplement. A multi-strain probiotic will provide you with different strains than kefir, so might help to support microbial diversity – but perhaps if you don’t have any digestive symptoms, you could take a month’s course of probiotic supplement every 6 months or so, rather than every day. However, if you do have gut complaints, you may benefit from the additional supportive strains as found in one of our probiotic supplements.

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