The gut ecosystem and microbial diversity

The gut microbiota (also referred to as gut flora) is a vast and diverse reservoir of microorganisms, including bacteria, fungi and viruses, which live in relative balance in healthy individuals.

In this week’s blog, nutrition practitioner Miguel Toribio-Mateas discusses microbial diversity, the huge role it plays in a number of conditions and the effects diet can have on the gut microbiota.

The gut ecosystem and microbial diversity – Miguel Toribio-Mateas

We’ve always known that gut health is important, but over recent years the gut ecosystem known as the “microbiome” has been linked to a number of diseases and conditions, from diabetes and obesity to anxiety and depression.

An internet search for “stool test”, or “microbiome test” may have you confused in no time because there are lots of tests out there. Some are sold directly to consumers, and some are available via practitioners only. A lot of them claim to provide you with answers they can’t give you, like a personalised diet based on your gut bacteria.

Sadly, the science is not quite there yet so at best they can give you guidelines. So today, I am focusing on the areas that I find most clinically relevant in stool tests. And when I say relevant I mean translatable into practical recommendations, because you don’t want to spend hundreds of pounds to go “oh, that was interesting” or “you need more fruit and veg”. You could go shopping instead or treat yourself to a weekend away. Ideally, you want tests that provide information to implement some changes to your diet that have a tangible effect.

Microbial diversity

We know from recent research that microbial diversity plays a huge role in a number of conditions. What does this mean in plain English?

Well, imagine your gut is a city like London. You’d expect to walk around and see people from all different walks of life. That is what makes London such a thriving and fabulous place.  You would soon get bored if everyone looked the same, and the diversity that made London such an amazing place would be lost. Your gut is a bit like that.

What scientists have been realising for some time now, when analysing the bacterial profiles of a variety of conditions, is that people suffering from ill-health tend to have a narrower spectrum of diversity, and that this makes them more susceptible to picking up infections. Why? Because the lack of diversity negatively affects the innate part of their immune system.

Microbial diversity seems to be associated with ageing, alas as we age microbial diversity decreases, however, those who age more healthily tend to have a more diverse microbial community or microbiota living in their guts.

Getting “a Mediterranean gut”?

The “Mediterranean diet” means different things to different people, and it certainly isn’t all the same around the Mediterranean Sea. To most of us it means a diet with plenty of fruit and vegetables that are rich in vitamins, minerals and plant-based nutrients such as polyphenols. Both fibre and plant-based nutrients, or phytonutrients, feed our gut bugs.

In fact, the International Scientific Association for Probiotics and Prebiotics (ISAPP) defines a prebiotic as “a substrate that is selectively utilised by host microorganisms conferring a health benefit”, and updated that definition in 2017 to acknowledge that “established prebiotics are carbohydrate-based, but other substances such as polyphenols and polyunsaturated fatty acids converted to respective conjugated fatty acids might also fit this definition assuming convincing weight of evidence in the target host”.

What does this mean in plain English? Well, it just means that a simpler way to describe prebiotics includes bits of food that aren’t digestible and that nourish and stimulate the growth of specific bacteria. Some examples include culinary spices such as black pepper, cayenne pepper, cinnamon, ginger, oregano, rosemary, and turmeric, to name but a few. All have been shown to have prebiotic effects inducing positive changes in human microbial diversity. Another example is provided by proanthocyanidins (PAs), one of the most abundant types of phytonutrients in the human diet.

These plant-based nutrients (called flavonoids) present in grapes (both in seeds and skins), apples, cocoa, red wine, blueberries, cranberries, bilberries, blackcurrants, hazelnuts, pecans and pistachio nuts are also favourite foods for some of our gut bugs. Brassica (e.g. broccoli, cabbage, cauliflower), and dark and green leafy vegetables (e.g. kale, chard), as well as bulbs (e.g. garlic, onions, spring onions, shallots, leeks) also provide huge amounts of fibre along with phytonutrients that keep gut bacteria happy.

The only downside of fibre is that it can make you windy. You will know if this applies to you in a way that goes beyond the usual inconvenience of the wind. I’m referring to painful bloating or cramping caused by fermentation of the fibre in your gut, which is beyond the scope of this blog.

Most people will benefit from increasing the spectrum of plant-based fresh foods they eat daily, alongside other ingredients they may eat as part of their diet, e.g. meat, fish, eggs, dairy, etc. Obviously, this doesn’t apply to vegans, but I was a vegan myself for 6 years during the early 2000s and I had vegan friends with excellent varied diets, whilst others only ate hummus and rice cakes, plus a little soy mince. So regardless of your dietary preferences, counting colours and increasing diversity can be a useful thing to do.

So what happens when you eat a rainbow?

As part of a large-scale open-platform citizen science microbiome research project known as the “American Gut” project, involving over 10,000 participants, researchers found that the wider the diversity in fruits and vegetables consumed by participants, the wider their microbial diversity. This resonates with my own experience, having run and reviewed 100s of stool tests based on the same technique used by the American Gut project. The laboratory technique is called “16S” or “16S rRNA sequencing”, which is like genetic testing of the microbes that live in your gut. 16S tests are the gold standard because they allow researchers to identify which bacteria live in your gut and in what quantities. Based on that, most labs now can compare your diversity score with that of a “healthy person” (normally the average score of a “healthy group”) so that you know how you benchmark against others.

In my experience, food diversity, as in eating lots of different colours every day, tends to translate into an increase in microbial diversity in stool test results. Some labs are going the extra mile to try to benchmark you against people of similar age, sex, food preferences, etc. They’ll need to build up lots of data so that the results are reliable, but it won’t take too long before that happens so you can actually compare your results to others who are more like you than just some random “healthy person” who may be a completely different age to you and live thousands of miles away. We’ll get there eventually! I’d give it another 5 years before we start seeing a lot more fancy stuff like that.

One of my favourite pioneering companies looking at personalisation of diet based on the individual bacterial composition of your gut is MapMyGut. I was involved in the early stages of development of this project along with Professor Tim Spector of King’s College London, and I believe they’re now recruiting participants for a larger scale clinical trial. While that gets going, there are other labs that provide you with detailed diversity and abundance scores, as well as many other interesting aspects that I’ll be covering in part 3 of this blog, coming up very soon.

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

Last updated on 30th January 2020 by cytoffice


16 thoughts on “The gut ecosystem and microbial diversity

  1. Excellent article with important details on herbs and seasonings and why eating food as nature intended is important.

  2. What do you suggest l take for indigestion sometimes l can’t eat because of it and on other times l get it when I’ve eaten l do suffer with anxiety and stress and this doesn’t help matters thanks

    1. Hi Jaci,

      Thank you for your question on our blog. To start with you could try taking a Live Bacteria supplement daily eg Cytobiotic Active. Take at the end of a meal or at bedtime.

      Digestive enzymes can also be useful, however, you mention that sometimes the indigestion is before you eat – it would be useful to understand a little more about your symptoms, when they start etc. You could complete a health questionnaire and we will then send you some written diet and supplement recommendations. This is a free service.

      There is a very simple test you can do at home which gives an indication of stomach acid levels and whether they are high or low (however this test should not be considered diagnostic) – it’s the bicarbonate of soda test and if you email me I can provide you with details.

      In terms of foods – avoid spicy foods and caffeinated drinks which can exacerbate symptoms. If you complete a questionnaire, there may be other foods that we would suggest you remove from your diet for a period of time.

      In terms of anxiety, you could try:
      – L-theanine – one in the morning, ideally on an empty stomach.
      – Pantothenic acid – one, three times per day or acutely can be increased to three
      – Biofood Magnesium – one at breakfast

      Please consider completing a health questionnaire and we can then give you some more personalised advice. I hope this helps.

      Best wishes

      1. Thank you for. Your reply l would like to fill out a question are and any information you can give me

  3. I will fill out a questionnaire I would like any help you can give me on digestion and stress and anxiety I am my husbands full time carer which at times is very stressful l am aged 77 thank you

  4. I have excema and some wart-like lumps on my leg that the hospital says are excema too. Would enzymes do something for me and, if so, which omes?

    Thank you

    1. Dear Diana,
      Proteolytic enzymes, such as Bromelain, taken away from food have been shown to have anti-inflammatory properties. As inflammation is a major driver of eczema they could be useful to you. I would also look at digestive heath as leaky gut (this is where the gut lining is damaged and inflamed and therefore allows larger molecules to pass across and into the blood stream trigger inflammation) is strongly associated with eczema. Live bacteria supplements, as well as nutrients such as vitamin A and D, are important for maintaining the integrity of the digestive system. Also other anti-inflammatories such as omega-3 fatty acids and curcumin can be useful. Other nutrients which are important for skin health are vitamin A, vitamin E, zinc and selenium.
      Hope this helps.

    2. Just getting over terrible Diverticulitis, lost 34 lbs, gained back 10 lbs.
      Eating fruits, fibrous veggies, chicken and fish.

      What next, for leaky gut and fungus?


      1. Hi Shirley,

        Thank you for your message. In order to fully answer your query, I really need a little more information. We do have a free health questionnaire service – if you complete and return a health questionnaire we will send you some written diet and supplement recommendations. In the meantime in terms of diet – you do not mention healthy fats, it would be important to include foods such as olive oil, avocado, ground nuts and seeds – start with very small quantities – and of course oily fish.

        In terms of supplements to get started with I would suggest:
        – An all round multivitamin and mineral (e.g. CoQ10 Multi, start with 1 per day for 7 days then increase to 2 per day). This multi is low in iron so suitable for post menopausal women and for men. Plus
        CytoProtect GI tract – 3 per day for 2-4 weeks then reduce to 2 per day for a further 4 weeks, then review
        Psyllium – 2 capsules per day with a large glass of water.

        Other supplements to consider in addition would be Sacharomyces Boulardii, essential fats and possibly at a later date some anti-microbials.

        It is important that you are getting sufficient fibre to avoid constipation – Psyllium that I have suggested can be useful (we have a product in capsules which can be taken at up to 3 x 2 capsules per day, start with 1 dose of 2 capsules). It is really important to ensure you drink a large glass of water with each 2 capsules of psyllium.

        I hope this helps.

        Best wishes,

  5. I have a question about microbes, if you think you can comment, I’d appreciate it. All these fruits and vegetables we’re supposed to be eating are coming from all around the world, as well as cheeses, meats and jarred goods. Do you think the microbes we get from these foods are in the air? Do they land on the foods before we ingest them? Like sourdough stuff? Or are they literally made inside the foods we eat? Thanks!

    1. Dear Alice,
      Thank you for your comment.
      Microbes in food come from many sources – certainly via the air would be one source. Microbes will also be present from soil where the food has grown, water, animal (including human) contact. One hundred years ago, before refrigeration, it has been estimated that every mouthful of food we ate had 1000 times more microbes in it than it does today. They are not made inside the foods we eat, but will replicate and grow inside the foods we eat. Fermenting food makes good use of this to create foods such as yoghurt, certain cheeses, sauerkraut etc. On the other hand, as you know, some microbes will spoil food and may cause food poisoning if ingested.
      Best wishes, Clare

  6. This relates to health after 50
    Hi my name is Beverley and I’m 58. I’ve had Type 1 diabetes for 20 years, also I’ve had gastric issues due to a sliding hernia and very long term fatigue issues. I have been diagnosed with sleep apnoea but only just in the moderately SA band. I’ve used cpap for a year and I’m no less tired. In the last 10 years my health as deteriorated. I did take 40mg a day of Omeprazole with gavisgon when I coughed at night. I have reduced that medication to 20mg a day as my oesophagus seems to manage on that level. When I get symptoms it’s like a tight band around my rib cage with a lot of trapped wind in my chest. I take 40mg of statins and in the last year I have felt muscle weakness in my legs. I’m seeing my endocrinologist this week and I’m going to ask him if I can manage with a half dose and see how that effects my cholesterol levels. I also take the anti-depressant Paroxetein because I’ve had many emotional stresses in my life. In February this year I had a mastectomy because the breast clinic found a large amount of DCIS in my right breast. As a result of this I stopped taking hrt, Kiloferm 2mg/1mg. Lastly I constantly get loose stools From reading the article about health after 50 and with the conditions I have and the drugs I take it’s no wonder that I’m so extremely exhausted. So much so that I can’t work because I fall asleep so very easily.
    Thank you for reading my email, any suggestions please?

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