Kimchi, kombucha, sauerkraut, miso and kefir – all fermented foods and drinks – have been around for centuries, but suddenly they are all the rage. The reason? They are supposedly packed full of gut-healthy microorganisms, and we are finally waking up to just how much the trillions of microorganisms that live in our guts (AKA the gut microbiome) contribute to our mental and physical health.

True, probiotic products such as Yakult – sweetened skimmed milk fermented with a single strain of friendly bacteria – have been shifting hefty units for some time: the global probiotic market, dominated by yoghurt drinks, was worth $45.6bn (£33bn) last year. But Yakult is fairly bland and sweet. Traditional and home-fermented delicacies are another, more pungent matter altogether: kombucha (a naturally fizzy cocktail of green tea and sugar) tastes vinegary; kimchi (vegetables fermented Korean-style) is sour and fiery; sauerkraut, which is fermented cabbage, whiffs of sulphur. All can intimidate palates used to highly processed western blandness.

Because of how they are prepared, they all contain microorganisms that boost the diversity of good bacteria, yeasts and fungi living in our guts. Harbouring a flourishing gut flora has been linked to lower obesity, fewer autoimmune conditions and digestion problems, longer lifespan, good brain function and happiness.

Some very big companies are beginning to take this on board. If you could never quite trust the mouldering kombucha you once nurtured in your airing cupboard, now you can buy some from Whole Foods instead. Step forward brands such as Eaten Alive, Bio-tiful – whose flavoured version of the fermented-milk drink kefir is now stocked in Sainsbury’s – and the Urban Fermentary, whose bacteria-riddled pickles and drinks come in appetising packaging. (It is unlikely, however, that mass-produced, pasturised ferments will contain as many of the desired microorganisms as those made using traditional methods, so it’s worth checking how a product was made before you buy.)

Take sauerkraut, the pickled cabbage beloved of central Europeans. Unlike the majority of supermarket-bought pickles, which are preserved in vinegar and have no “live” element, the cabbage in sauerkraut is massaged in salt until the juices are drawn out and the healthy microorganisms living on it produce lactic acid. This stops it going off, while adding a vinegary twang. The result, says Tim Spector, professor of genetic epidemiology at King’s College London, where he also directs the British Gut microbiome project, is “a really good combination of a pro- and prebiotic”. Spector’s 2015 book, The Diet Myth, revealed that much of what we eat is digested by our microbes, which in turn produce vitamins and unlock other nutrients for us (and are influential in many other ways). As with live yoghurt, the probiotics are the friendly bacteria food contains, whereas prebiotic is the word for substances that feed your gut flora. “The cabbage actually feeds other microbes in your gut, so I’m definitely a fan of kraut, kimchi, all those kind of things.”

But unless you are fermenting foods yourself, these products are not cheap – a 375g jar of sauerkraut from Eaten Alive will set you back £6. It’s good to know, therefore, that bog-standard live yoghurts aren’t a total waste of time. All yoghurt is fermented and the milk used to make products for sale is legally required to be pasteurised to kill off pathogens, after which a few strains of lab-produced friendly bacteria are added. “We’ve done some [not-yet-published] research ourselves,” says Spector, “showing that [this] yoghurt definitely does have an effect on the microbes.” The added bacteria aren’t the same as the ones that live in our guts, he says. “The [former] are moving through the body, but they can have an effect on your existing microbes and we also know they produce substances that are beneficial. So, in a way, they’re energising your gut microbes as they go through, producing some chemicals that look as if they’re good for weight loss as well.” However, he reserves the title of “super yoghurt” for kefir. “It has about five times as many microbes, with more diversity, and also has extra fungi in there and they’re all good.”

Illustration: Bratislav Milenkovic

Sourdough bread is extolled for its natural wild fermentation, harvesting diverse yeasts and Lactobacillus bacteria from the environment, but they then all perish in the oven. The main health benefits come from microbes having chomped away on lots of fibre, breaking down the gluten proteins, releasing tasty, mould-deterring acids, rendering the nutrients more digestible and lowering the glucose spike after consumption. “But if you make it yourself,” says Spector, “the extra microbes go on your hands and there’s increasing likelihood that people who make sourdough are potentially healthier because they have greater microbe diversity.”

Of course, alcoholic drinks are fermented, too, and red wine in moderation is actively gut-friendly. This is partly to do with the polyphenols in red wine, which you may have already heard about in their capacity as antioxidants, but they have the added benefit of being rocket fuel for good bacteria. It seems to be the combination of alcohol and polyphenols that is especially good. “If you compare grape juice and wine and gin’s effects on the microbiome,” says Spector, “gin isn’t very good, but red wine is better than grape juice. So, alcohol plus the fruit is good.”

Not surprisingly, warns Spector, “microbes don’t cope very well if you drink too much, and liver damage also causes problems for your microbes”. But he does hypothesise that beer and cider in moderation “are probably also of some benefit”. The alcohol has killed off the fermenting microbes before you drink, but you still get the tasty and useful chemical byproducts from fermentation. “A lot of these things that are thought to be bad for you,” says Spector, “have so many polyphenols that they might be overcoming any potential downsides.” He also recommends a little polyphenol-packed coffee and dark chocolate.

If you were to view your microbiome as a garden, fibre would be your fertiliser. Spector reckons that most people need to double their intake. Foods containing the best fibre types for your microbes – AKA prebiotic foods – include artichokes, jerusalem artichokes, leeks, celery, chicory, onions and garlic. Variety is the top priority. “So, it’s not just focusing on one or two of these examples,” warns Spector. “Our latest research is showing that it’s not necessarily someone who calls themselves vegetarian who has the most healthy gut – it’s the person who eats more diversity of plants in a week. Having the same salad every day isn’t going to be as healthy as eating a rich diversity of food with occasional meat.” This could just as easily be a way of describing the Mediterranean diet, with its kaleidoscope of fruit, veg, nuts, grains and legumes.

Illustration: Bratislav Milenkovic

The exciting news for carb lovers is that you can render potatoes, rice and pasta more prebiotic by cooking and then cooling them and then either eating them cold or reheating them (be careful with rice, which can potentially harbour unhealthy bacteria). In her book Gut, gastroenterologist Giulia Enders writes that, as they cool, some of the starch crystallises, making it more resistant to human digestion, “so your potato salad or sushi rice reaches your microbes untouched”.

Fasting – a dietary habit as ancient as fermenting – is also beneficial to gut health. “When you’re not eating,” says Spector, “a whole different set of microbes comes and cleans up your gut wall, eating the sugars and things there, and that’s important in keeping a good immune balance.” We are not talking extreme abstention. In fact, animal studies have shown microbes nibbling through the gut’s protective lining if starved for too long. But intermittent fasting with low-calorie days, or simply leaving long gaps between meals, is beneficial for your gut microbes. You are even allowed to skip breakfast – Spector says it’s a myth that this makes you gain weight. “There are now at least six randomised control trials showing that. Skipping breakfast has generally been shown to be good for adults and helps you lose weight. Basically, in southern Europe, their breakfast is an espresso and a cigarette, if they’re lucky, and they don’t snack. Whereas we are told to always eat breakfast and continual snacking is encouraged.”

Junk food is the gut microbes’ nemesis. In the introduction to a new book, The Healthy Gut Handbook, by Justine Pattison, Spector writes that after he put his student son on a fast food diet (chicken nuggets, burgers, soft drinks etc) for 10 days, the boy had lost 40% of his microbe species and felt sick and lethargic. Emulsifiers, which keep texture consistent, are rife in heavily processed foods and, warns Spector, “it has been shown in a couple of studies in rodents that they cause disruption of the gut microbes, which react differently and produce funny chemicals, in a similar way to sweeteners. If you give animals lots of sweeteners, you get a reduction in diversity of the microbes and they produce abnormal chemicals – different metabolic signals which have been shown to be more likely to give you diabetes and make you put on weight.” There’s no hard evidence yet in humans, but Spector has seen enough to make him wary of regularly eating these additives.

Refined sugar is another culprit, although we don’t fully understand the reasons. One simple answer, he suggests, could be: “If you’re eating junk food, you’re having a surge of fat and sugar that are absorbed before they reach the gut microbes, so you’re starving the guys of fibre lower down. Then they send out signals that promote obesity.”

Make slow changes to avoid discomfort

If you are inspired to consume more fibre, Pattison offers a word of warning: “It’s best to start slowly” – especially if you have digestive problems – or you could end up with uncomfortable bloating and wind. Each gut is unique and one diet doesn’t fit all, so if you change your eating habits to no avail, try something else. You are on the right track, says Spector, “if you notice a change in your bowel habit. After a couple of days, your stools will get softer and you’ll be going more regularly. That’s a sign your microbes have changed for the better, and though they are working harder, they are happier.”