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, part 2 of a series of 3, 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. In part 1 of this series, Miguel explained how your gut flora may hold the key to health.

Miguel will be speaking about the gut microbiome at our roadshow events throughout 2018, you can find out more about the roadshow, including booking information, by clicking here.


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 in part 2 of this 3-part series 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.


Cytoplan Roadshow 2018 

Cytoplan Roadshow 2018

Following the success of our practitioner education roadshow in 2017, we’re back this year with a different subject. With the amount of science being published on gut health and the gut microbiota, we thought we’d travel the UK and Ireland focusing on how to make sense of the human microbiome.

Nutrition practitioner and doctoral researcher in clinical neuroscience Miguel Toribio-Mateas will be translating complex science into simple but powerful clinical interventions. To find out more about the roadshow, and to book your place, please follow this link.


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 clare@cytoplan.co.uk


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One thought 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.

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