Fungus. Fruit skin. Bugs. Bacteria. Even for open-minded readers like yourselves it is hard to write about wild fermentation without sounding unappetising. After decades of Dettol, pasteurisation and use-by dates, I'm now asking you to consider a practice that encourages the growth of microbes – and what's more, I'm asking you to put the result in your mouth. Never mind that this process is millennia old; that your grandmother or great-grandmother would have been as familiar with it as breathing – we've all grown up with parents and teachers who waged war against "germs" and other "nasties".

"The idea of creating a bacterial colony with more cells than people in the world, keeping it, using it to process food and eating it with the bacteria still live – that is a huge concept for people to get their head around," says Simon Poffley of The Fermentarium, a Walthamstow school dedicated to teaching the production of fermented foodstuffs. "There is still this deep-seated belief that if things are unpasteurised, they are unsafe."

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The reality is – well, that it's complicated. No one's denying the existence of pathogens or the role pasteurisation plays in eliminating them. But when it's effectively handled, natural fermentation is far from dangerous. "You create an environment which is inhospitable to pathogenic bacteria, and which allows the right bacteria to flourish," says Poffley – whether that's in the making of sauerkraut, a sourdough starter, cider or cheese. In the years since the Second World War our drive to manufacture food en masse has lead to the industrial production of microbial cultures for use in food and drink, and the pasteurisation of anything in which microbial action could naturally happen.

Within just a few generations, the idea that we could just let raw milk sour to make cheese, allow grapes to develop a white sheen of yeast before picking and pressing them, or rub cabbage leaves with salt and leave them to stew in their own juices without pasteurising the resulting sauerkraut became unfathomable, and that in turn has had serious consequences for the environment, our health and biodiversity in food.

Up until relatively recently humans interacted with nature on a far greater level

"Up until relatively recently humans interacted with nature on a far greater level," continues Poffley. "It was normal to eat a lot of different foods, with lots of bacteria, and our gut and microbiome will have been influenced by that." Today, the United Nations Food and Agricultural Organisation estimate that 90% of the world's calories are delivered by just 50 crops. 100 years ago, several thousand plants would have done the same. As our supply chains and diets converge across the world, local, heritage varieties of fruits, grains and vegetables are disappearing – and with them, a whole host of ancient methods of preservation. "I remember as a kid in the seventies it was common to make home-brewed ginger beer – something we teach now at The Fermentarium, along with elderflower wine, cider and so on." he muses. "The rise of mass-produced convenience food put an end to that. And I think that's one reason many people are turning back to more naturally fermented food and drink."

Of course, wild fermentation is only one part of the answer to this crisis of culinary homogeneity, but it's an important one for several reasons – not least of them flavour. Wild fermented food and drinks harness the multiple bacterial and yeast spores that exist naturally in our environment, as opposed to those cultivated in a laboratory. Their interaction with each other and with raw ingredients creates tastes that are peerless next to a can of supermarket ginger beer, say, or a loaf of sliced white bread made with just one strain of commercial baker's yeast. Where a viscous, bubbling tub of flour-and-water starter nurtures both wild yeast and lactobacilli bacteria that work in a symbiotic relationship to prove and leaven sourdough, the chemical-laden 'Chorleywood process' of producing bread all but removes the need for fermentation. The former takes eight hours and yields a stretchy dough with that distinctive tangy flavour; the latter's bland, pappy result takes little more than three.

"The longer it ferments, the more flavour you get," explains John Townshend of Kennington Bakery, a stalwart for sourdough in South London. "Lactic fermentation is what makes the bread sour. Lactobacilli break down the starches in the wheat, and the yeast metabolise the by-products." The lactobacilli thus form an acidic environment in which wild yeast, present on the wheat grains and in the atmosphere, thrive and release carbon dioxide – hence the big, blustery bubbles in your bread. Commercial baker's yeast, produced in large steel vats on a diet of beet sugar, is a different beast altogether. It doesn't grow naturally on wheat, and it doesn't work with lactobacilli so there's no lactic fermentation. "As a result, this yeast interacts with the gluten quite differently," says Townshend – and enzymes, emulsifiers and energy intensive processes must serve to compensate for the drastically reduced fermentation time. Long story short, the results are less flavoursome, less digestible and ultimately less sustainable than anything you'll find in Kennington Bakery.

"Clench your fist, and you've a million wild yeast and bacterial spores in there alone. They're everywhere," says Tom Oliver, of Oliver's Cider in Herefordshire. He's not in wild fermentation for the health benefits (though he reckons cider swiggers make for "less morose drinkers") so much as the flavour that comes with heritage varieties of cider apple, and wild cultures of yeasts. "Farmhouse cider making has relied on the action of wild yeast throughout the centuries. Why wouldn't you use something that was naturally available, and was generally accepted to give a better flavour profile?" The cost of purchasing commercial lab-grown yeast, the effort of preparing it for inoculation and the fact that wild yeast offers multiple varieties of yeast to commercial yeast's single strain makes it a no brainer. "'Pitched' – that is, bought and added – yeast is good for a fast fermentation and getting a specific, simple flavour profile, but multiple yeast fermentations and time will always produce a more complex drink."

His ciders express the area of Herefordshire in general, and of his cider house specifically: its style, locale and cleanliness. Heritage cider apples – "some people use eaters, but I prefer those specifically grown for cider" – and perry pears are grown in the county's traditional orchards, in an important show of support for hyper-local produce. "It all starts with the fruit – good farming practices, growing the right fruit, selecting fruit that's not rotten. That gives you the juice and the sugar, and wild yeast on the fruit skins," he explains. "After that, it's about your cider house, your processes and attention to detail: making sure things are clean and nothing's incubating bad bacteria, but avoiding anti-bacterial detergent. It's about letting nature harbour itself where it normally would."

It's about letting nature harbour itself where it normally would

Oliver's support for local heritage fruits and its farmers speaks to wider concerns about biodiversity, and echoes that of other 'wild fermenters'. The Wild Beer Company in Somerset use seasonal, locally grown or foraged fruits to inoculate various beer worts before fermentation. Burning Sky brewery in Sussex ferment their seasonal brews with the help of microbes derived from foraged rosehips (Saison Automne), hawthorns (Saison L'Hiver) and elderflower and gooseberries (Saison L'Eté). Davenport vineyard and winery has planted nine different grape varieties, some of them quite unusual, according to the varying microclimate and soil type of the vineyard. Here in London, meanwhile, chef Jamie Park at Adam Handling's Frog Hoxton is as renowned for his fixation with fermenting and preserving surplus and waste fruit and veg as he is for his run to a MasterChef final.

"Jamie is passionate about preservation," The Frog's manager George Hersey explains. "He will give his team a challenge on this or that surplus or waste product – say the trim of Chinese leaves – and they will have to imagine in six months how they will use it on the menu. At Christmas, we had fermented wild garlic with our turkey dish, because why buy in garlic bulbs when there's so much local wild stuff in spring?" Right now, they're pickling tiny wild onions turned up by their forager. "We'll keep them for six months. Kohlrabi, too. It reduces waste, and you can use them all year round, throughout the seasons." It isn't easy – not least because fermentation rarely features on student chefs' curriculums – but it's stood The Frog in good stead, with environmentally conscious diners Googling "sustainable restaurants" and "zero-waste places to eat" in growing numbers.

Today The Frog Hoxton's wine list is entirely organic and wild-fermented, and the beer list is not far behind. At the restaurant's adjoining beer shop and café Bean and Wheat, fermented foods on the menu were a relatively easy sell – "the health industry has played a significant role in making things like kimchi and miso [fermented beans] fashionable. It's kick-started a change in behaviour," says Hersey – but he believes attitudes toward wine and beer will soon follow suit. "Just as plastic went from this amazing thing to the devil in a relatively short time, I think people will wake up to the stuff that goes on in winemaking: the chemicals sprayed on the vines, the crap going into the environment, the stabilisers and preservatives going into the mixture." Isabelle Legeron, founder of RAW Wine Fair and a pioneer of natural wine in the UK, agrees: "We're not producing stuff to feed the planet, so I don't understand how we can let non-organic wine producers pollute the water, reduce biodiversity and damage the natural landscape without them having to pay."

Again, this is about flavour as much as it is the environmental and health concerns arising from the use of chemicals: many people think that wild-fermented wines have a more complex taste profile. "The thing about most conventional wines is they are made using almost identical methods, yeasts, fertilisers and grape varieties," says Will Davenport, natural winemaker and the eponymous founder of Davenport vineyard. "The soil is homogenised and, not surprisingly, the wines taste pretty much the same." By making their wines as naturally as possible – eschewing fungicides, focusing all their efforts into cultivating the best grapes and allowing the grape juice to ferment spontaneously in tanks – Davenport ensures his wine is like no other. "If you buy in yeast, you are getting a single strain that produces a particular character in the wine," he says. If you don't do that, you get a number of wild strains, each adding something, and no one else can make it." Davenport's trademark isn't clever labelling, but invisible microbes that are unique to his grapes and winery.

I think people will wake up to the stuff that goes on in winemaking: the chemicals sprayed on the vines, the crap going into the environment

This USP does not come easy. Sure, Davenport is "just doing what winemakers would have done 60 to 80 years ago" – but the wines back then were a mixed blessing. Those of quality demanded craftmanship and fastidious farming practices. Those that weren't as good – well, you've probably tasted something like them recently: cloudy, sharp, with a hint of toilet on the nose. "Natural wine has become popular, and when things are popular there are those who do bad versions," laments Hersey. "People have been jumping on the bandwagon, mass producing and rushing the process when it takes years to perfect them." To ferment with wild yeast, producers need to commit to the path of least resistance to Mother Nature: avoiding any chemicals that might inhibit the growth of yeast or bacteria in the vineyard and winery, and working with her to deliver not a classic chenin or pinot, but what Legeron describes as "the best possible expression of the land."

"It is a huge commitment," Legeron continues. "It is not about just 'wild yeast or commercial yeast': it's about changing practices. You have to farm better, and you have to harvest your grapes when they are fully ripe so they have that critical mass of yeast population. Also, because the wild yeast work more slowly, you have to allow for more time in the tank or bottle." You have to be farming organically: fungicides, herbicides and so on will eliminate the wild yeast population, so growers like Davenport use natural pest control or copper to reduce mould and mildew – and you have to check the wine constantly during fermentation, to ensure "nothing weird is happening," says Davenport. "You can recover it, by pumping that juice into a clean tank and letting it run for a while – and it will sort itself out eventually and produce something amazing. However, it will take another couple of months – sometimes even years."

"It's a craft, at the end of the day," says Hersey. "Anyone with money can make wine by controlling the vineyards with artificial fertilisers and pesticides, then adding sugar, commercial yeast and stabilisers to get the flavour you want. But to put your faith in nature: to treat the soil as a living thing, rely on organic and biodynamic methods to get the right juice and ferment it for as long as it takes, without the chemical intervention – that's craftmanship."

The same goes for beer, cheese, sauerkraut, bread or indeed anything best produced not by controlling nature, but on harnessing its potential to yield something flavoursome to eat or drink. Wild yeast and bacteria cultures exists all around us, Hersey points out – but it takes a craft brewer, a cheesemaker, a winemaker or baker to make something actually delicious out of it. "Anyone can paint a picture, but that doesn't necessarily make you an amazing artist."

For decades we have shoehorned nature into our rules and requirements. Now we're realising (or rather, rediscovering) how much it can offer if we step back a bit. It takes confidence – "you have to be confident that nature can deliver," warns Legeron – and no small about of determination to deal with draconian Environmental Agency standards ("they couldn't get their heads round Jamie's bubbling bucket of kombucha," sighs Hersey), but across the country the people working with fermentation are pushing the boundaries of what it can offer.

There are brewers like Wild Beer Co who, as well as fermenting on fruit skins, are opening their vats and exposing their wort to the ambient brewery air and the microbes nestled in its beams, barrels and corners – an ancient lambic way of brewing inspired by Belgium. And there are people like Nick Vadasz of Vadasz Deli, channelling his Hungarian grandmother through unpasteurised sauerkraut and pickle recipes that involve no more than salt, locally sourced vegetables and a thorough understanding of time, brine and temperature: "I always like the analogy of the uterus, and the baby growing within that amazing fluid. If you imagine the barrel is the mother, the lactic acid brine is keeping everything safe inside it, encouraging the growth of the right bacteria and preventing anything bad from happening."

There are cheesemakers like Bill Oglethorpe of Kappacasein in Bermondsey, who makes his own starter culture by incubating raw milk – one of only a handful of producers to do so in Britain. Raw milk has its own ecosystem of bacteria, bringing a richness and complexity beyond compare to milk which has been pasteurised then inoculated with lab-grown starter culture. "Back in the day there were no starter cultures – cheese was made by simply leaving the milk to sour. When starters were introduced, there was a lot of controversy and people thought it wouldn't work. Now people think you can't make milk without them," Oglethorpe smiles wryly.

Like Davenport's wine and Wild Beer's wort, this method requires constant vigilance – his milk is routinely checked, as is the starter – but such pains are rewarded. His Bermondsey Hard Pressed, a fruity, hazelnutty hard cheese aged for 12-18 months in maturing rooms under a railway arch, is the best mountain-style cheese this side of the Channel. "If you are making a very specific cheese you might want a starter tailored to do that, but the cheese I am making seems to work well with the naturally occurring bacteria in the milk that I get from my farmer. It's totally linked to the place."

Back in the day there were no starter cultures – cheese was made by simply leaving the milk to sour

The list goes on. In 2016, when I met Vadasz for the first time at Brockley Market, he observed "We don't really have sour taste in our heads here in the UK. Everything has to be sweet – and if it's sour you eat it when you're pregnant, or once a year with a cheese board." What a difference three years makes: to our experience, our attitude toward the environment – and to our appetite for new experiences and tastes.

"I think people are rediscovering authenticity of flavour," explains Legeron. "We are sick of stuff that all tastes the same, which is very controlled." The more complex, often sour yet deeply flavoursome tastes of wild fermented food and drink might still be challenging – "but so long as you have people who love the heritage and sheer rawness of it all, you'll convince customers," agrees Hersey, before opening his reservations plan. It's 6pm: service time, and if The Frog's bustling, enthusiastic dining room is anything to go by, it won't be long before words like 'pasteurisation' and 'commercial yeast' ring in our ears as a little, well, unappetising...