The zoo in our guts (Your microbiome)

What is the microbiome?

What is this zoo I hear you cry? It’s the 10’s of trillions of extra cells predominantly living in the full length of your intestine. Weighing up to 2kg or nearly 4.5 pounds these cells consist not of human origin but bacteria, viruses, fungi and other critters with even more complex names. Together with their combined extra DNA, it is suggested that we are more ‘other’ than human in this diverse and symbiotic ancient relationship.


The term microbiome is not just for your gut however, it has become a generic term for all microbiota (different critters) that live anywhere on or in our bodies. And there is literally an eco-system of them everywhere, (from your head to your toes) and notably, their disruption or balance can be quite important, being linked to various diseases. Considering how new this research is, it is not surprising that the medical community is taking time to catch up. 

How new is the science?

The first extensive study was spearheaded by US Human Microbiome Project or HMP, starting in 2007, it ended 2016, using brand new gene sequencing technology, they were able to map out many of the main species in rough quantities all over the body. Final results were publicly published in 2019.

The microbiome is now becoming a fast-growing area of research, with $1.7 billion spent over the past 10 years, this is small in comparison to other areas but has contributed to more and more forthcoming research as exciting results appear weekly from so many ongoing studies.

These are often massive studies mainly in the US and UK, that include real humans. The American Gut Project and the British Gut project are 2 examples with now over 11,000 participants.

Twin research

twins sitting at table eating

The British Gut project was set up by the Department of Twin Research at King’s College London in collaboration with the US version, with the TwinsUK project including 15,000 twins and has been running since 1992. The aim was to investigate the genetic and environmental factors in a range of complex diseases and conditions and more interestingly, the data is now being combined with the microbiome research.

dna strand

Combining ‘twin’ and microbiome research together has eluded to many new insights into how the gut can affect our overall health and well being, as twins are 100% DNA identical at birth. Although there are epigenetic changes as the twins grow, literally amending their individual DNA profiles, this is one reason behind the differences seen in twins. The British Gut project was partially introduced to find out what role our microbiome play in these epigenetic changes, but of course they found many other surprises along the way.

red bacteria swimming

Some eye-openers have concluded that our genetics influence the types of bacteria that are favoured in our gut, this has already been tested in other animal studies to find out which strains are specific to which animals. They end up with a kind of blueprint unique to a particular animal. This is now a whole field of study ‘strain specificity’ and a method of understanding how our microbiota might become ‘unbalanced’.

And when I say bacterial ‘strain’, I mean it’s like having a Ford Fiesta car but a different version like an ST compared to a Zetec, to the degree that bacteria can literally signal or influence things that happen in the body. This is leading to a better understanding of nurturing these more ‘favourable’ friends with the food they like and running out of town the ones that are less inviting.

Enter the zoologist

colourful bacteria having a party

As humans, we often prefer to use our imaginations to visualise something that is pretty much impossible to otherwise understand how all this complexity could possibly influence so much of who we are. These little (microscopic) critters are now showing they control our moods, anxieties, cravings and our health to name but a few. 

I like to coin the phrase ‘the Zoo in your stomach‘, I think this came about when realising that eating late at night is not particularly a good idea for a few reasons, I’ll save the specifics, but when you are trying to control your hunger, as you know there are some foods that spike hunger (hormones) more than others.

It became easier to imagine waking up sleeping cages of animals before I put that one piece of chocolate in my mouth, thinking it would be ok. “Just one piece, it will be fine” and then the resulting chaos that resumes, as I devour the rest of the bar and anything else I can find in the cupboards. Most of us have been there, I’m sure I’m not alone on this one.

naughty bacteria awake

I literally picture, waking up one animal with this bit of chocolate and of course, they can’t keep quiet because they want more and proceeds to wake up every other animal and insect of the entire zoo in my stomach. Before long it’s a chaotic party, but without the music or the dancing.

Now, of course, waking up a zoo is far from the truth, we don’t have miniature gorilla’s running around inside us, but there is some truth in how bacteria start to react to the food that you have eaten. Many signals and hormones are triggered when you consume food, insulin and ghrelin are two well-known examples, but bacteria are also in charge of signalling, particularly serotonin (the happy hormone) of which it is estimated that up 90% is produced in the gut, and not in our brains.

colourful bacteria dancing

Those bacteria in your gut produce many of their own chemical compounds and enzymes that signal to other cells to release other hormones, it’s practically a chain reaction, you could even liken it to an explosion! A population explosion? as those chocolate-loving strains dance for joy, reproducing and breakdancing down that sudden sugar intake (unless it’s 70% chocolate, then the dance might be more a tango, I’m literally laughing).

Battle of Waterloo

different colourful bacteria

You could even go as far as likening those micro battle troops, in full combat as they fight for dominance over the other. Strains of bacteria have been identified as preferring different food types, nutrient types and chemical compounds. As humans, we only possess a limited amount of enzymes, these are chemicals that breakdown other compounds to put it simply. A bit like when a fly spits on your food to liquefy it. Loverly!

Instead, bacteria break down the nutrients that humans eat and use them to create their own food. Only the difference is, between them, they have multiple times more enzyme producing ability than we do.

strawberry dropping in milk

Some of us might not be able to genetically breakdown that milk in your coffee because of the lactose, but there are bacteria that can. March in those troops! or lactase producing bacteria to be precise. This is where the story starts to get exciting, all those different types of insoluble fibres we were always told that were simply not ingested or broken down, well now we know there is an enzyme for that! And guess who produces it. They produce thousands more enzymes that we, as mammalians can, and the rich diverse chemicals they produce are beneficial to both themselves and to us.

Not to make things sound any more complicated but they have some unusual habits, not only can they influence our own cells, turning our genes on and off (gene expression) but they can also swap genes with one another, called gene transfer, this often allows for even more exotic enzyme production to breakdown and make use of the foods and fibre that we eat. The interactions that happen in the gut are so mind-boggling complex that scientists are only just starting to get to grips with the sheer scale.

Drug dealers

colourful pills

Although to picture this huge battle of ‘Napoleonic’ species would be nice to picture for us with OCD, it’s been more likened by some as badly organised safari park, with individuals mingling and hanging out closely with each other, like a communal busy market offering favourable resources to one another, but without the bartering or exchanges of cash, just dodgy chemicals. Gangster!

Some of these chemical compounds are even Vitamins, yes they also deal in supplements. Its has long been known that vitamins can be produced in the gut but now they know which are the ring leaders of the operations and what are they supplying. Mainly B vitamins are on the wanted list. B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenic), B6 (pyridoxine), B7 (biotin), B9 (folate), B12 (cobalamin) and even Vitamin K. There is now a comprehensive hit list of those involved in producing vitamins some even deal in more than one vitamin. The boss!

I’ve mentioned in a previous article about ‘The benefits of raw ginger‘, that bacteria also produce Short Chain Fatty Acids or SCFA’s, these consist of a collection of acids, acetate, propionate and butyrate and are of the biggest interest at the moment, recognising their importance in lowering inflammation.

Knowing that there are strains of bacteria that produce the right chemical compounds that lower inflammation and those that do not, this is where nurturing those ‘good guys’ becomes a focus for improving your health.

Enter prebiotics and fibre

To encourage specific strains to grow (strain specificity) requires the right types of food that they prefer. As we have mentioned, they can be fussy eaters, although some are like me and not very fussy at all (former self, are you listening?).

Prebiotics are really any food in the form of a carbohydrate (the majority are of plant origin) that contain some form of dietary fibre. Often grains, fruits, vegetables, nuts, and legumes, but others arguably are not plants, say seaweed (Algae) often used in Japanese cuisine and mushrooms which are fungi.

psyllium husk

We can categorise these dietary fibres (see below) into soluble and insoluble, divided into characteristics of fermentability, solubility, and viscosity. Tough fibres like cellulose are classed as insoluble and poorly fermented, they are partially broken down but very slowly and will predominantly pass through the gut. Psyllium husk on the other hand, although again poorly fermented is extremely soluble in water, becoming gel-like. This can increase the water in the intestine to reduce constipation and interestingly increasing diversity (different types and strains) of SCFA producing bacteria.

This last comment is where the surprises are showing in the science community. What was once thought of as just a ‘bulking’ agent “to make you regular”, is now known to add diversity to the gut microbiome! Each form of fibre has different benefits, and the constant reminder that building a diverse and healthy zoo can be achieved by mixing and rotating these different forms of fibre in our daily diet.


Fibres that are highly fermentable while also possessing high solubility and viscosity include β-glucan (beta-glucan and not to be confused with gluten) and pectins. Naturally found in whole grains such as oats and barley (β-glucan) and fruits such as apples (Pectin). Gel-like fibre usually has the benefit of slowing glucose absorption and of course that dreaded insulin spike.

Cellulose InsolubleNone/Slow fermenterCell walls of all forms  of plant
Lignin InsolubleSlow fermenter Sesame and flax seeds
Chitin InsolubleSlow fermenter Mushrooms, fish scales, crustaceans
Hemicellulose Insoluble/SolubleSlow fermenter Cell walls of all forms  of plant
Resistant starch
Insoluble/SolubleViscous/Slow FermenterOats, cooked & cooled rice, green bananas
PsylliumSolubleViscous/Slow FermenterPsyllium husk
GumsSolubleViscous/Slow FermenterGuar, acacia
Beta glucanSolubleViscous/Slow FermenterBarley, oats
PectinsSolubleViscous/Slow FermenterApples, strawberries
Polyols  (FODMAP)SolubleFast fermenter Erythritol,  xylitol
Saccharides (FODMAP)SolubleFast fermenter Root vegetables, onions, chicory

What is a FODMAP?

fruit & vegetables

Non-gel highly fermentable types are where we enter the now-infamous FODMAP’s which stands for 
Fermentable Oligo-, Di-, Mono-saccharides And Polyols:

  • Oligosaccharides: Wheat, rye, legumes and various fruits and vegetables, such as garlic and onions.
  • Disaccharides: Milk, yoghurt and soft cheese. Lactose.
  • Monosaccharides: Various fruit including figs and mangoes, and sweeteners such as honey. Fructose.
  • Polyols: Certain fruits and vegetables including blackberries and lychee, as well as some low-calorie sweeteners including erythritol and xylitol.

The term FODMAP has become synonymous with a low-FODMAP diet. Originally just a theory in a 2005 published paper. It was proposed that “a collective reduction in the dietary intake of all indigestible or slowly absorbed, short-chain carbohydrates would minimise stretching of the intestinal wall. This was proposed to reduce stimulation of the gut’s nervous system and provide the best chance of reducing symptom generation in people with IBS”. Reproduced from its Wiki page (Low FODMAP Diet). IBS is an acronym for Irritable Bowel Syndrome.

onions & garlic

The low FODMAP diet was originally developed by a research team at Monash University in Melbourne, Australia and went on to do further studies and papers to understand how the diet actually worked with patients suffering from IBS type symptoms. They have since published a lot of data, categorising food into the various groups to guide people through the maze of what is classed as high and low FODMAP.

Proof in your pudding!

The premise is that you start by eating a relatively low list of FODMAP foods and when your symptoms improve you would then start to introduce these foods back into your daily diet. It clearly works for the majority (up to 75%) although a bit complex, they do encourage you to use an expert to help you through the maze, making it a challenge to do without some form of significant planning and research. But then again, Weight Watchers or Slimming World with their array of ‘syns’ can be equally hard without guidance from various online resources and offline clubs.


One piece of advice seems to point to remembering that the various foods can be almost dose-dependent. If a particular food gives an upset stomach, then likely there may be a threshold before it becomes a fermentable problem. You just need to find out what that threshold is! An example might be, eating a handle of peanuts, no harm done, finish the packet and 2-3 days later your microbiota is in a bit of state (I speak from experience).

Some foods in guidance tables have been as listed high AND low in FODMAPS, this really highlights a few things. In my table above, as simple as it is, many foods contain many different and important types of fibre, if you search for more comprehensive lists, it becomes very clear how complex plants are, leaving aside other forms of nutrient density.

The SCFA smoking gun

Knowing that real food is digested and fermented the full length of your intestine and not just the beginning or end seems to be one of the most important findings, and knowing how important the short-chain fatty acids produced by our internal zoo are to the health of our overall biology including a strong healthy immune system. A diet containing as many different types of real food is not just a slogan, it’s a necessity.

sushi roll

Is there a particular food that produces more SCFA? In one particular study, and nearly all studies I’ve looked at, all forms of fibre produce SCFA’s, it doesn’t matter if its white rice, baked beans, seaweed, oats or flax seeds, if your critters can break it down, then there is a benefit.

How much fibre is too much fibre?

hadza member peeling a tuber
A member of the Hadza peeling a tuber.

Can you get too much fibre? Well, it doesn’t seem so so far if your Microbiota is well trained and fighting fit and of course if you don’t have IBS. The Hadza tribe, a modern hunter-gatherer people of Tanzania, Africa, is now in the spotlight for their love of roots and tubers. It’s not the only thing they eat as they are seasonal eaters, but at times, they consume 100 – 150g of fibre per day. Compare that with our western diets we are talking 5 to 10x more than many of our western diets and still 3 times more than the governments 30g per day recommendation. Specific types of fibre are not on the radar yet.

It is actually quite difficult to obtain excessive amounts of fibre if only eating real unprocessed food. With the exception of bowel sensitivity or constipation, you need to be absorbing the right types of food and in the right quantities before moving on up the ladder.

Mass extinction!

mass extinction

The Hadza diet and their microbiome were studied for over a year and compared with other hunter-gatherer cultures around the world, including Peru, Venezuela and Papua New Guinea, with a mixture of both industrialised and more traditional cultures.

They found that the more traditional cultures shared their high diversity and range of bacteria populations, even though they were countries apart. The more western-style diets, often devoid of fibre had lost the many species to almost extinction.

baobab fruit
Baobab fruit.

But what was the cause of this critter massacre? with the Hadza, they followed a very cyclical diet, switching from a range of very high fibre, tubers, berries, Baobab fruit and honey if they could find it. There are awesome pictures online of one fellow, face deep in a huge honeycomb, bees a buzzing as they look on in dismay at their hard work disappearing before their numerous eyes. To a diet high in meat, protein and fat. In the 6 months of the dry season, the animals are easier to catch as they become more predictable. From zebra, giraffes, monkeys and birds, you name it they catch and sometimes, even steal from lions.

two lions resting

Now at this point, I can hear a few people shouting see?? they eat meat and they have diversity. But unfortunately, after extensive research across so many separate studies, concluded that during this time of eating meat, the Hadza microbiome diversity diminished to somewhat near western or more industrialised cultures. Considering their starting point, it was quite a surprise.

The Diet Myth

Tim Spector, the author of literally my favourite book ‘The Diet Myth (The real science behind what we eat)‘, spent 3 days with the Hadza (and the BBC to document) to test a few theories. After baseline stool samples and three days of eating their highly fibrous diet, Tim’s microbiota increased diversity by 20%. This also diminished within days after, but the conclusion was clear, that changing your diet has very profound and fast-acting impacts.

Tim Spector is Professor of Genetic Epidemiology at Kings College London and in charge of the UK’s main microbiome project mentioned earlier. He has many stories of how fast our microbiome can be impacted by either very poor but more importantly by very good plant biased diets. The evidence is becoming overwhelming.

But seriously what makes plants so special?

rows of herbs & spices

We have established that bacteria are the victims of the fibrous underworld, consuming large quantities and in their secret chemical labs, creating even more weird and wonderful compounds to supply to their neighbours and in fact, anyone else nearby that might benefit, including our own human cells, including the cells of our immune system.

Dodgy dealings indeed. These innocent transactions are certainly to our benefit, improving our immunity and helping to lower inflammation.

green tea

But fibre is not the only kid on the block, plants contain other important, biological compounds that are even less well known in their interactions with our crowded zoo of critters and microbiota. Polyphenols are on the tip of everyone’s smoothie. There are now literally thousands of studies on the how red grapes or green tea positively affects our health, but not so many studies on how these amazing phytochemicals actually do their stuff whilst on their safari trip travels of the gut.

It has been eluded that up to 95% of the polyphenols you eat, bypass the small intestine and travel all the way to the large intestine where they are broken down into smaller metabolites. There is where it seems much of the magic happens, as the 5% of smaller molecules get absorbed into the gut higher up, lower down they rely on our friendly bacteria break them down into nutrients our bodies can utilise

All plants are not equal when it comes to these magical polyphenol potions, I’ve talked about Ginger in ‘The benefits of raw ginger‘ and compounds like gingerol, shogaol and zingerone, exploring how powerful these are in lowering inflammation etc. And some explanation of how this might be achieved.

But they are only a few of more than 4000 identified, spices, dried herbs, beverages, berries, seed, nuts, vegetables and even oils.

Some examples of the highest quantities:

  • Spices: Cloves, star anise, ginger, cumin, cinnamon.
  • Dried herbs: Peppermint, oregano, sage, rosemary, thyme, basil
  • Beverages: Cacao, green tea, black tea, red wine.
  • Dark berries: Black chokeberry, strawberry, raspberry, black grapes.
  • Seeds: Flaxseed, celery seeds.
  • Nuts: Hazelnuts, pecans, almonds, walnuts.
  • Vegetables: Artichokes, onions, spinach, broccoli.
  • Fruits: Apples, pomegranate, peach, lemons.
  • Oils: Extra-virgin olive oil, rapeseed oil.


bowl of pottage misu

Eat as many different types of real food as possible as often as possible. I have identified some pretty simple methods of preparing very dense and rich combinations of healthy fibrous foods that are incredibly tasty and deeply filling.

Anything from super salads (that don’t contain rocket, replace with spinach leaves), crazy fibre muesli yoghurts to the rediscovered idea of a medieval-style pottage, consisting of thick soup or stew made by boiling vegetables and grains.

I love the fact that this was the original ‘fast’ food (it was always available). To quote Wikipedia “It could be kept over the fire for a period of days, during which time some of it could be eaten, and more ingredients added. The result was a dish that was constantly changing.” I can confirm I have tried this (not over a continuous fire) but I have experimented with many more Asian style ingredients, lemongrass, lime juice, miso paste, crushed wakame seaweed, it’s worth trying I can tell you. 

bowl of pottage

The advantage of pottage is the sheer amount of herbs and spices that you can experiment with all at once, remember the diversity? Maybe not recommended for FODMAP’ers initially, but something to aim for if you can.

Pottage consistently remained a staple of the poor’s diet throughout most of 9th to 17th-century Europe. We seem to keep coming back to the old ways somehow.

Fibre + Polyphenols = Happy harmonious zoo

what are FODMAP's

I used to look at fruit smoothies as a crazy idea, all that sugar? This is about quantities again, would you eat a huge bowl of raspberries, blackberries and watermelon. In one go. Likely not, when you blend it up, it’s easier to consume, it’s not something we were likely designed as humans to do.

Taking into account we are not removing the fibre and many fruits are high in many types of fibre, especially gel-forming sticky types, the combination of high polyphenols, fresh antioxidants and incredibly rich fibre is a clue to why a regular size glass size with a meal, will not produce those serious sugar spikes that you might think.

melon smoothie


colourful bacteria having a party

Our microbiome is more like a final frontier, forget space, there is more going on inside you than you can imagine, the complexity is overwhelming, but its importance is equally profound. The science is relatively new but the speed of discovery is astounding and exciting.

What is clear is that simple changes in diet, including more plants in our diet, have very dramatic changes within hours not even days. Both ways, good or bad, so put down doughnut and pick up some 70% chocolate!

Other types of microbiome are being explored all over the body and new science being unravelled every day. With new products focused on say, a healthy mouth! With new natural toothpastes, that claim to remineralize your enamel, natural ingredients that don’t contain fluoride but potentially to be a better job

The microbiome of the skin, and those dry and itchy skin problems that plague most of us, problems often caused by bacteria overgrowth or an unbalance caused by the use of so many chemicals that kill the good bacteria as well as the ones causing the inflammation, corrected by simply using the right topical but natural ingredient.

These things, I’ve personally found only after reading the science, then digging around in Amazon to look for proof. The components of MCT oil is not something Streptococcus Aureus enjoys the studies say, again their balance is the cause of excessively itchy skin. Manufacturers will move more and more towards trying to balance the underlying problem involved instead of just sticking a plaster on it and hope it goes away. Amazon reviews at least give you a choice to do your own research.

We are moving fast towards a better understanding of how we can live healthier lives, cutting through so much of the conflicting noise and nonsense.

And remember your gut bacteria don’t like junk food, even if you do! No, wait! that’s wrong, the good bacteria don’t like it.

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Useful links:

Priorities for the next 10 years of human microbiome research

British Gut project

American Gut project

Study points to how gut bacteria evolved host specificity

Can changing the microbiome reverse lactose intolerance?

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