Ferment TIM SPECTOR GUT-HEALTH
Includes easy recipes to try at home
The LifeChanging Power of Microbes
Ferment
Also by Tim Spector
Identically Different
The Diet Myth
Spoon-Fed
Food for Life
The Food for Life Cookbook (with ZOE)
Ferment
The Life-Changing Power of Microbes
Tim Spec T or
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Copyright © Tim Spector 2025
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To my long-suffering wife, Veronique –sorry about the state of the fridge!
Introduction
Of all the ways to prepare food, fermenting is surely the most mysterious, miraculous and misunderstood, yet humans have been finding ways to ferment plants, dairy and meat for thousands of years as a means of preservation and enhancing flavour. Fermentation simply means the chemical transformation of any food or drink, with the help of yeast, bacteria or other microbes, often producing bubbles or heat. Whole foods already contain hundreds of compounds; however, once bacteria or fungi have worked their magic, these compounds multiply and foods become vastly more complex. As these fermenting microbes feed on the food or drink, they produce hundreds of new and unique compounds. Wine is infinitely more complex in flavours and chemicals than grape juice, as is cheese compared to milk. We now know that this ancient process of alchemy not only transforms the flavour of the food, making it more complex, varied and delicious, but it also brings a multitude of additional health benefits.
In 2024, one of the largest ever trials of a new supplement was performed, with nearly 10,000 UK volunteers. For three weeks they were asked to take three doses of the supplement daily and monitor changes to their health. The results were amazing. Nearly half of participants (47 per cent) saw improvements in mood, 55 per cent reported more energy, 52 per cent less hunger, and 42 per cent a decrease in bloating. In fact, this trial was organised by my team and ZOE (the science and nutrition company I co-founded), and it wasn’t a new commercial supplement we were testing, but ordinary shopbought fermented foods, such as sauerkraut, kefir, yogurt and kimchi. If these results had been for a new vitamin supplement it would be a blockbuster. That all these benefits could come simply from adding such humble ingredients to your diet is even more astonishing. In
this book, I want to demystify fermented foods and explore why it is that they bring so many benefits. In fact, I hope to convince you to throw away your vitamin supplements and instead try thinking of fermented food as a vastly more nutritious and tasty supplement, with many more proven benefits for your health.
I now get asked about fermented foods more than nearly any other topic. It is these potential health properties and their effect on gut health that has ignited people’s interest. Although I have mentioned fermented foods in previous books, the science is evolving so fast that there is much more to say. For instance, I was recently blown away by research showing that even some dead microbes in our foods can still be beneficial. This means that some beers with dregs of dead yeast in them could have some health benefits, which might partly help to compensate for the negative impacts of alcohol. These kinds of breakthroughs in our understanding of the benefits of fermented foods have not yet been given the prominence and space they deserve. Perhaps one of the reasons that these benefits aren’t better known is that many of us are fearful of fermented foods. We’ve been conditioned to associate them with strange tastes and smells, dangerous bacteria, and slimy, mysterious microscopic creatures. There is much confusion and misunderstanding about how to consume them too. People often ask me if they work at all, given that stomach acid destroys the live microbes. Aren’t probiotic supplements more effective? Isn’t all that saturated dairy fat in kefir and yogurt bad for you? Don’t kombuchas rot your teeth, cause acid reflux or food poisoning? Are they not dangerous if you have cancer or autoimmune disease? Before 2010, when I first started studying gut microbes, I have to confess I was ignorant about fermented foods. Like most people I had seen over-hyped adverts for commercial yogurts that I assumed had no real health benefits. I had no idea that my Stilton contained healthgiving fungi in its blue stripes, or that sauerkraut might contain live microbes. I had not heard of kefir or kombucha, and kimchi was for me just a spicy pickle to be avoided. I enjoyed Japanese food but had no clue that microbial ingenuity was behind the complexity of soy sauce, tofu and miso soup. Being a medical doctor trained in the 1970s I did know quite a lot about alcohol, professionally and personally.
While I knew microbes were involved in the fermentation process to change sugar into alcohol, and could also turn forgotten red wine into vinegar, I didn’t realise that it was fermentation that made my humble cup of coffee so drinkable and yet beneficial for long-term health, and the reason my sourdough bread was both tastier and healthier than supermarket loaves. As I delved deeper, more surprises followed: Marmite and Tabasco sauce, it turned out, were also fermented products.
I started to experiment with fermented foods in my own diet and soon became converted to the cause. I began making my own kombucha with my trusty SCOBY (symbiotic culture of bacteria and yeast), affectionately known in my house as Blob, which I nurtured from a tiny baby blob I had found in the dregs of another bottle. Before long, I found myself adding fermented vegetables to almost every meal and enjoying my sour morning kefir (fermented milk) with nuts and berries more than any other breakfast. I made my own version of kimchi (known in my household as Timchi) from fridge leftovers and found I loved the taste, as well as its benefits for avoiding food waste. I was glad to discover that red wine and maybe even artisanal ciders (in moderation) have a beneficial effect on our heart and our microbes. I now find that I have to be doing some regular fermenting to feel happy as well as healthy.
Doctors like me used to be taught that all microbes were dangerous and our job was to wipe them out, whether inside or outside the body, with antibiotics and antifungals, and that our food should effectively be sterile in order to be safe. I know from emails I receive that many doctors are still worried about some patients eating even yogurt. We have forgotten that for millennia, before the widespread use of fridges, our ancestors purposefully added natural live microbes to make their food safe to eat. They understood what we have since forgotten: that microbes are generally our friends. If we help them along by manipulating the environmental conditions, they will rapidly colonise a cup of milk or some vegetables in salty water and produce chemicals that change the acidity or, when put into sugar, produce acetic acid or alcohol, which allows only friendly microbes to grow. This stops the food going rotten, keeps more harmful
species away and adds greater complexity of flavour. It also – we now know – brings extraordinary benefits for our health, benefits that we scientists are only just beginning to understand fully.
For many of us, at least in the UK , fermenting has become a bit of a niche pursuit. My first encounter with fermentation was aged about sixteen when my parents bought me a home brewing kit, probably thinking it was safer for me to get slightly tipsy with friends at home than going to the sort of pubs where they didn’t ask your age. It turned out that I might have been safer there, as what my brews lacked in taste and clarity, they made up for in power, leading to a very special type of hangover. My father (a medical scientist) brought home an old 40-litre storage vessel from his lab and, after some disastrous efforts and odd microbial overgrowths, I had a brew that was drinkable, albeit for an undiscriminating teenager and his friends. I still remember the distinctive tastes of the malt in a tin and the yeasty ferments at the bottom of the container, which accompanied me to my first year of medical school, before it was discarded for other social pursuits and better ale. I would never have guessed that decades later I would be writing a book on the subject of fermenting, and that I would be evangelical about its benefits for our health.
Now, in the 2020s, there is growing curiosity about ferments, but the world of fermentation can seem bewildering too. Some of this is down to the brilliant but deceptive marketing of products such as ultra-processed yogurts with a dozen added chemicals and fake fruits, which claim to be healthy because of a few strains of microbes added at the last minute before packing. Many food companies try to entice us by using words like microbes and fermentation. We often do not know if by the time we buy a ‘fermented’ food the microbes are dead or alive, as there are pitifully few food labelling rules to help ensure the consumer is informed.
When it comes to experimenting with fermenting ourselves, many of us don’t know where to start. Perhaps you’d like to try fermenting yourself but are afraid of kitchen explosions. Perhaps you tried making sauerkraut once, but didn’t like the taste or were worried it would make you ill. My hope with this book is to persuade you to try fermenting at least one food or drink yourself, even if it’s just
sticking some garlic cloves in a pot of honey. I will show you how ferments work in your own body and can improve your health, and why we should all aim to consume at least one fermented food every day. And even if you never plan to experiment yourself, I will help you spot the best (and worst) products in shops, and at the very least increase your admiration for the humble microbes – inside our bodies and in our food – that do all the work.
I often talk about the importance of the four Ks: Kefir, Kimchi, Kombucha and Kraut, but in researching this book I have come across hundreds of ferments that were new to me and discovered many new tips and recipes. At the end of the book I’ve shared the best and simplest recipes that you can try at home, with minimal equipment and simple ingredients, ranging from making your own style of kimchi to honey-fermented garlic. I want you to learn from my trials and errors, to encourage you to roll up your sleeves and try fermenting to improve your own health too.
My main focus is on foods that contain live microbes when they are served, rather than those that get killed by baking or roasting, boiling or in alcohol. But, as the new science now shows us that certain microbes can still have health benefits beyond their grave, I will also tell you more about these ‘dead’ or ‘not-so-live’ microbe products that could still provide life after death. The chances are that these are foods that you already enjoy, whether it’s coffee, tea, sourdough bread, wine or beer.
This book is intended to titillate your imagination, taste buds and gut microbes and expand your understanding of what our ancestors called cold cooking. By understanding more about this cooking that occurs outside your body in jars you will learn much more about the cold cooking that occurs every day inside your body and how important it is for your life and soul.
But first, to better understand what makes a fermented food, let’s begin with something that is very much alive, teeming with different life forms . . .
p A r T o N e
What is Fermentation?
Voyage of the
microbes – from field to fermenting jar
Picture a field in the countryside at sunset. The late summer sun is hazy and paints orange hues on the outermost leaves of the humble purple cabbage. It sits proudly above the soil that has been its home for the last six months. The soil and its microbes, with the infinite web of mycelium, have supported its growth from tiny seed into a complex, multi-leaf, colourful structure. Its intricate food matrix holds everything together in a neatly packed pattern. The deeply coloured purple leaves hold hundreds of polyphenols (defence chemicals), which have protected the cabbage from any damage resulting from changes in temperature and availability of water, and which will go on to provide additional fuel for the microbes living in the gut of anyone lucky enough to eat it.
This red cabbage is ready to be harvested. Whether it was grown with organic or small-scale farming methods with minimal use of pesticides and fertilisers, or sprayed with both to encourage a quick harvest, tens of millions of microbes will have colonised the folds of the leaves and its crevices. The cabbage is picked, washed and packed up to be transported to supermarkets or farmers’ markets, in plastic or wooden crates, almost always refrigerated for freshness.
By the time the red cabbage meets its final owner – you or I – the outer leaves will have come into contact with washing agents, hands, plastic, transport, more hands and maybe some supermarket shelves. All these processes are likely to affect the microbial diversity of the outer sections, but plenty of microbes remain. Now it is on your chopping board and you’re about to transform this wonderful piece of natural architecture into something even more extraordinary. First, you remove the outer leaves of the cabbage (keep them for
later) and give everything a good rinse under a running tap. Next, you chop the cabbage into thin slices, admiring the beautiful patterns that lie inside and knowing that there are millions of tiny microbes in those swirls, living off the sugars in the cells of the cabbage. Microbes will be plentiful in any cabbage you buy (whether organic or not) and they are specially adapted to that plant. They come in many types – those most likely to be successful are the group known as lactic acid producing bacteria (LAB for short) and are called Lactobacillus, Leuconostoc and Weissella ; other less well trained (adapted) ones are called Klebsiella, E. coli, Pseudomonas, Bacillus and Staphylococcus. You will usually find some yeasts called Saccharomyces, which also like beer, as well as Candida, which likes dark sweaty bits of our bodies. You will also find some moulds, like Aspergillus and Penicillium, and finally many tiny viruses called phages that are highly specialised killers of the lactic acid bacteria. Think of this motley crew as competing teams in a fermentation game show, where teams of microbes will compete for survival.
The first fermentation
Once chopped, you simply place the cabbage into a clean bowl with a generous pinch of sea salt (around 2 per cent of the weight of the cabbage) and start to massage the salt in with clean dry hands. You squeeze and massage your cabbage well, drawing out as much juice as possible. The salt causes the plant cells to lose their structure as the internal fluid leaks out under a process called osmosis. After a few minutes you should have a good amount of liquid at the bottom of your bowl, which will be full of natural sugar from the cabbage – an exciting fast-food treat for the microbes to help them grow and multiply. You transfer the floppy cabbage pieces with all their juices to a clean jar, packing it down with your fist, making sure the liquid covers the top of the cabbage. You might top the jar up with a little salty water if needed, add some herbs or spices such as caraway seeds or fennel, and any other shredded veg you want to use. Just a few extra slices of carrot gives the microbes more tasty carbohydrate
options to eat and speeds up the fermentation process. You then use the outer leaves of the cabbage to push down the mixture as hard as you can to compress it – this acts as a natural lid, keeping the air out.
We are surrounded by microbes. Earlier that day, if you were gardening or stroking your pet, some of the soil or pet microbes will have made your hands their home, even if you washed your hands. Your kitchen window is open, and the breeze carries in some extra microbes including natural yeast. These microbes too will now join the game show, competing with your tough cabbage microbes in a brutal survival contest to see which will give your fermented cabbage its unique composition. The first challenge is to see which microbe teams cope best without oxygen. Friendlier anaerobic bugs that can live without much oxygen are more likely to survive, while the oxygen-loving microbes, which include a few nastier characters (pathogens) that can cause health problems, will likely be killed off by the salt and the lack of oxygen in your fermenting jar. At the same time the salt, as well as punishing some microbes, offers survivors a reward by sucking out and releasing the sugars normally stored in the cabbage cells.
Now you pop your jar shut, reducing the oxygen inside, and know that many microbe competitors have now been eliminated, leaving more food for the survivors. All you do now is place your mixture into a cool, dark place and wait for the magic to happen. This process of ‘cold cooking’ isn’t really magic but simply an elimination contest of chemical-producing microbes. After just twenty-four hours, you’ll start to see bubbles forming at the top of the liquid – a clear sign that tiny microbes have reproduced and started feasting on the cabbage. Its fibres and polyphenols, as well as the sugary core, are a banquet for these bugs, and their appetite is insatiable. These tiny bubbles of carbon dioxide produced by specialised microbes (both yeast and a few bacteria) rise to the top and may need to be let out every few days to avoid too much pressure building up into a slow dribble of liquid or, worse, a ferment explosion. This is what’s affectionately referred to as ‘burping’ your ferments.
The survival contest isn’t quite over for the microbes, and there is still plenty of competition to get to the final prize. Some rivals
have quite enjoyed the lack of oxygen and the salty environment and, without the competition from their oxygen-loving colleagues, they have multiplied. But they are in for a shock. When they are without oxygen, other microbes start producing weak acids, such as lactic acid and acetic acid, which change the mixture into an acidic environment with pH levels below 4.5, which few species can handle. After about three days, only the specialist bacteria and yeasts are left. The aggressive microbes that can cause trouble, such as E. coli and Staphylococcus, have been eliminated, making the now fermented cabbage – or sauerkraut – safe to taste-test.
Your purple cabbage has now turned a sunset pink and is softer in texture and tangier in flavour. The hundreds of different chemicals and fibres from the original plant have fuelled the survivor microbes to multiply furiously, producing even more acid and carbon dioxide bubbles. The winning microbes now call your jar home, creating hundreds of new chemicals, or metabolites, as a by-product of their demolition of the cabbage. Every microbe that breaks down fibre and uses polyphenols creates a so-called ‘postbiotic’ chemical, which never existed before this process began. Like a magician popping a bunny out of a hat, this is microbial wizardry at its finest and you have a front row seat. And this exact same process of fermentation, breaking down plants to make brand new chemicals, happens inside each and every one of us.
It’s time to taste your tangy sauerkraut after patiently waiting for it to reach just the right amount of crunch, sourness and complexity for you. I eat sauerkraut after between five and ten days depending on colour (red cabbage takes longer than white), plant combinations and room temperature, which all impact the speed of fermentation. This wonderful cocktail of microbes and metabolites, fibres and polyphenols then enters your internal gut universe to face further struggles for survival in the next round of the fermentation game show. Waiting for them are hundreds of trillions of microbes (mainly bacteria and viruses, but also fungi and parasites in our large intestine, and before them, just a few billion microbes in the lining of our small intestine). Each mouthful of fermented food not only adds newcomers to join our resident gut microbiome, it also helps
feed them with a delicious variety of fibres and polyphenols that have already been partly transformed or pre-digested by fermentation in the sauerkraut jar.
The difference between eating raw sliced red cabbage in a salad and fermented sauerkraut is huge – and this is all down to the power of the oldest form of cooking: fermentation. Let’s look at what happens to the kraut and its special team of acid-loving, oxygen-hating survivors as we take a bite, and they are once again forced to adapt to a new environment in the finals of the competition.
The second fermentation
In our mouths, mixing with our saliva, our competitors find themselves in a neutral, non-acidic environment. This isn’t a problem as they are only there a few seconds before passing on to the next challenge: the stomach. Here they are surrounded by gastric acid, which has a pH lower than 2 – much too low for comfort for the microbes. We used to assume that virtually all the billions of microbes (25 billion on a serving of sauerkraut) were instantly killed off by the stomach’s acid, but this was based on old data and cell culturing methods that ignored 99 per cent of microbe species. Some will die off in a few minutes, especially the ones from the outer parts of the kraut, but others may be protected within a layer of leaves where the acid can’t penetrate. Also, very small microbes, which were only recently discovered, may fly under stomach acid’s radar. Called ultramicrobacteria (UMB ) or ultra-small bacteria, they have a maximum size of 0.1 cubic micrometres (µm3) and some are as small as 0.009 µm3. To put this in perspective, a single E. coli bacteria could house 150 of these tiny lifeforms, and 150,000 would fit on the tip of a human hair. Aside from UMB , many standard-sized microbes can also suddenly shrink down as a temporary protection mechanism against changes in acidity or temperature, usually avoiding detection by even our current methods.
We know that a few selected bacteria love even these harsh conditions and live in our stomach permanently; for instance, a key natural
resident is Helicobacter pylori, which can cause ulcers and can usually be eliminated by a combination of three antibiotics. But, interestingly, probiotic microbes targeting the stomach lining can also reduce the severity of these ulcers, when the acidity has dropped. The acidity of our stomachs varies a lot and people with stomach infections (gastritis) or taking antacid drugs like PPI s (proton pump inhibitors) have reduced acidity, allowing many more good and bad microbes to survive. This can occasionally be good if the microbes come from probiotics, like our kraut, but they are more generally bad for us if they are pathogens, which increase our risk of gut infections.
So despite the cull of all the weaker, more exposed microbes, many of our merry band still hang on to pieces of cabbage and continue undaunted down to the duodenum and small intestine. Here, life gets somewhat easier in the more hospitable surrounding liquid and slimy gut layers. Our contestants will pass a few resident microbes in the small intestine tucked into the many crevices and hiding places of this vast structure, which, at 7 metres long and 200 metres squared, would nearly cover a tennis court if stretched out. We don’t yet know much about precisely what happens in the (badly named) small intestine, as it is very hard to access without cutting someone open. New smart capsules, which are designed to be swallowed, take a tiny biopsy as they enter this zone and get collected in the toilet the next day, but so far only a few of these expensive experiments have been conducted. So while we know that the main role of the small intestine is to absorb nutrients, we are still guessing what else goes on here. The current consensus is that the main interaction between the intestine’s residents and the fermented foods is signalling and sensing. The microbial residents, when detecting the cabbage visitors, signal to their friends and networks that fibre and polyphenols are on their way down to the colon (large intestine), which contains vast hordes of microbes.
Important collaborators with the resident microbes are newly discovered ‘neuropod’ cells in the gut lining, which are specialised at sensing what food is being ingested by the microbes and what chemicals are being produced. This means that, via a vast relay system, they can rapidly alert the brain – in milliseconds – about the good
and bad nutrients coming their way. These novel food sensors have a key role to play in our eating patterns and have changed the way we think about the relationship between our brain and gut. As well as having taste receptors and detecting tiny amounts of sugars, fats and proteins, specialised neuropod cells can detect microbes and their chemical metabolites such as short chain fatty acids (SCFA ).
A new idea is emerging that the main effect of fermented foods, or at least the probiotic microbe component, is the way the microbes act on the small intestine to influence and talk to the immune system. Although we lack hard evidence, this makes sense as this is the only place on the journey that the gut environment is not hostile to our food microbes and, importantly, they are not outnumbered a million to one by resident microbes that would out-compete them. Some diseases of the small intestine can be helped or sometimes cured by probiotics, so we know external microbes can work in this environment. So it makes sense that the food microbes travelling on their cabbage raft stop off at this friendly port to rest and reproduce. This allows them to expand in numbers, producing greater quantities of helpful chemicals that interact with both the neuropod cells and the immune cells on the gut lining.
So, as our friendly kraut package makes its way to the large intestine, our body has plenty of advance warning and is primed.
After a brief respite, our intrepid travellers – with somewhat boosted numbers – are pushed through the ileal valve by peristaltic waves driven by the extensive nerve connections into the dark depths of the colon or large intestine (which is actually shorter than the small intestine). Despite the advance warning signals, our travellers are in for a shock. Suddenly they are surrounded by a mass of colon microbes. Imagine a group of twenty football fans trying to stick together as they leave the stadium after an away game, when all they can see are cheering opposition supporters. The microbes try to hang on to the fermented cabbage life raft for dear life. If they fall off they will surely die, as they are used to living on acidic salty cabbage and have not adapted to live in the alkaline environment of our gut, unlike the hardy locals.
A lucky few microbes with access to undigested cabbage manage
to hang around hidden and unnoticed to reproduce and produce some healthy chemical by-products such as short chain fatty acids with anti-inflammatory effects. As in the small intestine, these are detected by the neuropod-sensing cells and the many immune cells in the gut lining and send calming signals to our immune system and our brain. We believe these long-travelled microbes send these healthy signals via chemicals that are both powerful and unique; in other words, these chemicals would not be created simply by having your resident microbes feast on boiled cabbage. This is the power of fermented food.
Soon after, the kraut life raft is completely devoured by the hungry resident microbes, who use the nutrients in the different fibres and are able to extract all the polyphenols for energy to reproduce and produce even more beneficial chemicals. After a couple of days of fighting against the million to one odds in our guts, nearly all our original kraut microbes and their descendants will have likely died off. Their dead bodies are unceremoniously discarded in our stool, along with the trillions of other short-lived resident microbes. About half our stools every day are made of tiny dead microbes, which gives you an idea of the sheer numbers involved as well as the fast pace of life in our guts.
Until recently we couldn’t seriously examine more than a fraction of microbes in a normal stool sample. But now, with genetic sequencing, we can estimate how many of our lactic-acid producing microbes in our ferment make it all the way to the toilet bowl. Regular consumers of fermented foods, whether it is simple yogurt, kimchi or kraut, have much higher levels of fermenting microbes in stool samples than non-eaters. Crucially, these numbers are much greater than the amount of microbes entering the gut, showing they have multiplied inside our bodies.
The old assumption was that all probiotic microbes (whether in food or capsules) that reached our stomachs, died off before they could be effective and have any real health benefit. But we now know that many of them survive the stomach and small intestine before they reach the colon, and countless clinical studies now show they can improve health. Another odd but compelling reason the
probiotic microbes may be helping us is the possibility that they have an afterlife. Even after dying on the journey, we now believe they can provide post-mortem health benefits through chemicals they produce or from proteins on their cell lining. So far these zombie microbes only appear to be helpful, not harmful. We will explore this wacky afterlife idea more later.
One of the reasons fermented foods are better for us than just eating the raw form is that they are, in essence, double fermented. The first ferment is in the jar, which you can witness unfold with its new smells, bubbles and changes in colour, texture and flavour; the second you have to imagine – in the darkness of your bowels. That first ferment means that your resident gut microbes can skip all the boring prep work and get on with cooking their ideal meal, giving them all the nutrients they need. A simple example of this is the way the lactose (the sugar present in milk) is predigested by external microbes when you make yogurt, cheese or kefir, so our own gut microbes have much smaller bites of lactose to deal with and so are therefore much more effective in splitting it into tiny sugars that are easily absorbed. This is why many people with milk intolerance or lacking the lactase gene mutation (80 per cent of the planet’s population) can cope with eating fermented dairy but not drinking fresh milk.
It has been a long journey for the microbes, from the cabbage in the field, to the salt-loving kraut microbes in a jar, to the heroic martyrs in the intestine who deliver their chemicals and die off. I hope their voyage helps to show you their transformational power and the astonishing efforts they make to keep us healthy.
Meet the fermenters
The life of microbes is fast and furious; they can pack a lifetime into a sixty-minute action movie in which they are born, live, eat, fight, reproduce, excrete chemicals and die. But their legacy lives on, as the influence of their dead body parts or fluids can still be felt months later. Many microbes can enter a state of suspended animation as either shrunken versions of themselves or as larger spores with a thick coat, protected from the harsh environment (acid, heat or cold) until conditions improve again. Others we know little about are so small they pass through filters and are called ultramicrobacteria.
As many as 50 per cent of bacterial species are able to form spores and enter a form of hibernation that can last years. This is a cunning defence mechanism to protect them from hostile environments. In rare cases, these spores can cause problems for us such as food poisoning from a microbe in reheated white rice (Bacillus cereus ), which is difficult to kill off with heat or alcohol and comes back to life with gentle heat. Luckily spores are not normally something to worry about when fermenting though, and most LAB are not spore-forming.
The speed at which microbes proliferate, and so the speed at which fermentation occurs, depends on several factors including the acidity of the environment and, crucially, the temperature. Some microbes can reproduce and duplicate every thirty minutes inside the body, but fermenters are a bit slower. After a few hours to settle into their new surroundings, they can double every ninety minutes. This means that in twenty-four hours twelve to thirteen generations can be produced. So if you add 3 grams of kefir grains containing 300 million colonies to your milk (we quantify numbers of microbes in colony-forming units, or CFU s), this works out after twenty-four hours at about 2 trillion microbes and over 700 billion per millilitre,
which is pretty impressive. The number of microbes may be lower for most commercial kefirs and yogurts where microbes are added at the later stages of production, just before chilling. In comparison, most probiotic supplements only have 1–10 billion CFU per capsule. Eventually the microbes die off as they run out of nutrients or space or they are stopped by the conditions. They often auto-destruct by producing too many by-products, like increasing alcohol content (around 15 per cent is tops) or overdoing the acidity.
Until very recently we knew virtually nothing about how many food microbes there are and what role they play. A 2024 study, which was the culmination of five years of work from an EU consortium, finally answered some big questions and tripled the number of food microbes we know about. It created a food microbe database by sequencing bacterial genes from 2,533 different foods and comparing them to the genes in gut samples of 30,000 people. These ranged from alcohol to dairy, kombuchas and kefirs, fermented (sausages and salamis) and non-fermented meats, seeds, roots, fermented and non-fermented fish, and fermented and non-fermented vegetables and fruits. They also looked at 358 subtypes of probiotic foods (from kimchi to sourdough) and included some foods that had never been studied properly before like fermented seeds, fish (e.g. Korean skate), Mexican pulque (fermented agave), African palm wine and different meats. They found over 10,000 distinct bacterial genomes that grouped into 1,036 species groups, the largest and most common of which were the Bacillota (formerly and confusingly known as Firmicutes). Around half of these microbes were known and half novel, even in well-studied food, such as dairy and many cheeses. These results show just how much we are discovering and have yet to learn.
Around 40 per cent of the bacteria detected were picky and found in only one food, whereas around a quarter were found in multiple foods. In general the fermented foods contained microbes that appeared in multiple other fermented foods; in non-fermented foods these species were often quite specific to the food. Examples include Brochothrix in meat, which makes it rapidly go rotten and smell, but an exception was raw milk, which contained low levels of the microbes you find in yogurt, several strains of Lactobacillus and
Streptococcus thermophilus. Many of these microbes have never been detected outside of food, suggesting that they have adapted to live in these specific foods.
The variety of different species was also tested. The study actually found more diversity of microbe species on regular unpasteurised food compared with fermented food; this is because the process of fermentation rapidly eliminates the non-adapted microbes. The highest diversity of microbes was seen in fish samples (which explains the unique rotting fish smells due to the many chemicals produced). Unknown or novel species were found in nearly all foods, with the highest recorded numbers in fermented tea (kombucha) and Mexican fermented agave (pulque). Only twenty-five microbes (twenty-three bacteria and two yeasts) determined the tastes of most food categories and were more important than geography. Strangely there was considerable overlap of microbes living in kombucha, coffee and fermented (pu-erh) teas.
While hardly any food microbes were found in human saliva samples, around half were found in stool samples, suggesting that they can survive in our intestines, at least for a short while. In infants, 56 per cent of the total gut microbe species are shared with those in food, with a key microbe Bifidobacterium longum (found in breast milk) dominating, but as the gut microbe population increases in diversity, this decreases rapidly to 8 per cent in older kids and down to an average of 3 per cent in adults. This partly reflects an increasingly diverse diet – not just dependent on milk – but also our increased interactions with the wider world and the people and animals that inhabit it. This 3 per cent figure emphasises that the trillions of microbes in your gut can come from many different non-food sources, including the air, soil, animals and other humans. It also shows that the microbes we do share with food punch above their weight in their health benefits. As we saw earlier, the fermenting microbes are also likely to have a much bigger impact on the small intestine where (if we could measure them well) they would likely form a larger percentage.
But whatever the composition of your gut, you can acquire novel or extra microbes by eating different foods, whether fermented or
not. A great example is a specialist microbe found in algae (Vibrio EJY 3). When you eat fish that feed on this algae, you also ingest these microbes, which colonise your gut. Then, through a process called horizontal gene transfer, these microbes share DNA with gut bacteria already dwelling in your colon. This genetic game of give and take means that genes coding for enzymes that digest the seaweed get passed around, allowing your existing gut microbes (and you) to access all the nutrients and health benefits of seaweed when you eat it. This is what happens to people living on the coast in Japan, as their gut microbiomes evolve to benefit from the abundant and cheap seaweed around them, which they eat raw. People living elsewhere who occasionally eat sushi are unlikely to have the right seaweeddigesting microbes in their guts to extract all the best nutrients from the tough polysaccharides in raw seaweed. Our guts, depending on where we live, are also full of another unlikely passenger, brewer’s yeast (Saccharomyces cerevisiae ), probably because so many foods we eat regularly contain it.
We found another interesting microbe that is easy to pick up when studying a 30,000-person subset of the ZOE database of over 250,000 people with our Italian colleagues. We published our findings in the prestigious journal Nature Microbiology. The microbe Lawsonibacter is found in coffee and is present in high levels in the guts of coffee drinkers but not in tea drinkers. What we discovered is that although newborn infants lack this microbe, just a kiss from a coffee-drinking parent can colonise the gut in low levels. The microbe then waits patiently in a corner of our guts in small amounts for the day when it can feast on fragments of coffee. People in countries that never drink coffee had very low amounts of Lawsonibacter ; this means that even if you never eat or drink a particular food or beverage, if it is consumed by those close to you, some of its microbes can make their way to your gut. This is another reason diverse food cultures are a positive thing.
Many of the microbes living in or on our food are just there for the ride and may not be involved in fermenting or transforming the food, but others have evolved these special skills. There are hundreds
of these potential fermenters, ranging across a wide spectrum from bacteria to fungi and viruses. These fermenting microbes play a crucial, invisible role in transforming our food and our health. Despite their obscure-sounding scientific names, we need to start seeing them as our friends. So let’s take a moment to get to know some of these different types of microbes and how they work.
LAB (lactic acid forming bacteria) and other bacteria
Lactobacillus Lacto means milk in Latin and bacillus means a rod, so its name is a clue that this important group (with twenty-five subsets) of rod-shaped bacteria loves milk, feeding off the lactose sugar component. It’s also one of the LAB that are key for fermented foods as they convert sugars to acids and keep the Ph low (high acidity), thereby preventing spoilage by other microbes. They prefer dark unoxygenated spaces but can tolerate air, so they are called aerotolerant anaerobes. They prefer warm temperatures and tend to go to sleep in your fridge. They are fussy eaters and only feed off certain types of sugars called hexoses, but luckily there are plenty of these sugars available to them. Well-known subtypes include L. acidophilus (acid loving), L. delbrueckii, L. casei and L. paracasei (cheese loving), L. rhamnosus and L. gasseri and they are present in many ferments, such as yogurt, kefir, sourdough, sauerkraut, tempeh (fermented soy) and kimchi. They are used as probiotics and often form part of the starter culture for fermented foods. (Starter cultures are a mix of microbes and medium, i.e. food that the microbes enjoy, like seeds or grains. These well-established microbial communities kick off the fermentation process.)
Lactococcus have a similar role and profile to Lactobacillus but grow in chains rather than rods. They also produce lactic acid, only eat glucose products and are commonly used in dairy fermentation. Many have lacto in their name as a clue, but there are many others, such as Pediococcus, Aerococcus and Weissella and Leuconostoc that have similar acid-producing properties.
Leuconostoc are chain-forming but are more adaptable and able to eat different foods, so they can live off a greater variety of plants, such as cabbage and milks. They also help make kombucha when they form part of the SCOBY colony (more about this later). They are useful to the process but can sometimes make your sourdough starter rather smelly, but the stench is generally short-lived – as the acid-producing bacteria grow in number, acid-sensitive Leuconostoc will be killed off.
Streptococcus thermophilus is a commonly known lactic acid producer, often used to make commercial yogurt. It is well adapted for poor oxygen environments, where it can hang around waiting for its moment. It is really fussy about temperatures though, and its superpowers come to life at warm temperatures of 35–42°C. It works well in a buddy system with its mate L. delbrueckii. Together, they have a non-aggression pact and swap nutrients such as folic acid. Many microbes produce vitamins like folic acid or vitamin K and use these as energy to trade with their friendly neighbours, as well as making some of these vitamins available for their hosts (that’s us).
What happens when an LAB such as Lactobacillus meets a glass of milk, for example when we make kefir or yogurt? As the bacteria floats around in the milk it will absorb (swallow) a small globule of the lactose sugar; once inside, it will digest it with an enzyme into its component sugars: glucose and galactose. It then uses the glucose and (sometimes the galactose) as an energy source to rapidly grow and reproduce and in doing so it releases lactic acid as a by-product. This causes a build-up of acid inside the cell, which it releases into the milk, slowly making it more acidic. This discourages any other less adapted microbes from feasting on the same milk.
Acetobacter aceti is the bacterium discovered by Louis Pasteur, which turns wine (ethanol) into vinegar (acetic acid). It is part of the Acetobacter genus that all produce acetic acid. Unlike the LAB they depend on oxygen and live off a variety of sugars they can ferment, such as flowers, honey, fruits and in soil. Also unlike the LAB they are quite mobile, can quickly form layers and have adapted a resistance to acid
so they can continue to live in the vinegar they produce. When the microbe Acetobacter annoyingly floats into an open bottle of red wine that you forgot about, it ingests the alcohol and, using two of its enzymes, converts it to acetaldehyde and then to acetic acid as a byproduct. It then excretes the acetic acid into the wine and this slowly converts it to vinegar. Acetobacter needs oxygen to work, which is why you can store an open bottle of red wine for a few days if you use a vacuum pump to deprive the microbes of oxygen, or if you store it in the fridge, which buys you more time as the drop in temperature slows down any microbe activity. As well as vinegar production it is used in many industrial processes including biofuels.
Bacillus is a rod-shaped bacterium that is a bit of an all-rounder – it can live with and without oxygen and, as an omnivore, it can eat carbohydrates, proteins and sometimes fats. It is tough too; when in trouble, it forms spores by folding over itself, cleverly doubling its cell wall. This makes it resistant to heat and cold, allowing it to persist for decades or centuries. Its main use is transforming the taste and texture of food. It can break down the tough proteins of soybeans to produce the soft, slimy and smelly natto with its distinctive flavours and provides extra vitamins like vitamin K2.
Bifidobacteria are branch-shaped static bugs that don’t like oxygen and eat carbs. They are the commonest microbe in the infant gut, enjoying body temperature and digesting breast milk oligosaccharides that help the baby to thrive. They are versatile and can produce both lactic acid and acetic acid in small amounts. They are also good team players, cooperating with many different species, such as the Lactobacilli and Streptococci in a range of fermented dairy foods to enhance flavour as well as health benefits.
Propionibacterium is an example of a real specialist fermenter. It is key to Swiss (and alpine) cheese-making and makes the holes in Emmental cheese. It relies on other microbes surrounding it to produce lactic acid, which it feeds off; in turn it produces propionic acid and acetic acid to aid fermentation. When well fed, it also eats fats