Is cheese actually good for your gut? The best (and worst) cheeses for your microbiome

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For years, cheese has been the dietary scapegoat. Too fatty. Too salty. Too indulgent. The sort of food you sheepishly enjoy in dim lighting with the fridge door ajar. But increasingly, this beloved dairy product is undergoing a quiet redemption arc – one fuelled not by fad diets or viral trends, but by something far more persuasive: gut science.

Cheese has been unfairly demonised for decades, mainly because of its saturated fat content. But that narrative is outdated,” says Professor Tim Spector, epidemiologist, author and co-founder of the ZOE health study.

“Recent science shows that saturated fats in whole foods like cheese don’t behave the same way as those in heavily processed foods. In fact, moderate cheese consumption doesn’t raise cholesterol in the way we once feared, and according to large epidemiology studies, appears pretty good for us, actually reducing heart disease risk.”

What’s more, cheese isn’t just harmless – it might be actively helpful. “Cheese is a fermented food, and many varieties contain live healthy bacteria – or what we now refer to as probiotics – which play a really important role in our gut health,” Spector explains. “So no, the old reputation isn’t deserved anymore. We should rethink cheese as a gut-friendly food when it’s the right kind, and part of a diverse, whole-food-rich diet.”

That caveat – “the right kind” – is crucial. Because not all cheeses are created equal. Some deliver microbial benefits that rival kefir or sauerkraut. Others are little more than creamy imposters, offering all the indulgence with none of the gut payoff. So, which cheeses deserve a regular spot on your cheeseboard – and which ones are better left in the supermarket plastic tray?

The gut-friendly hall of fame

The best cheeses for gut health tend to be those that are raw, unpasteurised, traditionally aged or made using live cultures. They’re often made with minimal processing and are rich in microbial diversity. Think farmhouse classics rather than shrink-wrapped singles.

“Not all cheeses are created equal. If you’re looking for potential gut health benefits, artisan cheeses – especially those that are raw or unpasteurised, or traditionally aged – tend to contain more diverse microbes. Most real cheeses contain some live microbes,” says Spector.

Blue cheeses, like Roquefort or Stilton, are prime examples. “You get a greater diversity in those like roquefort or stilton that have blue moulds injected,” he says. “Or aged dry cheeses like cheddars, Mrs Kirkham’s Lancashire or aged goudas, and some alpine-style cheeses like Comté or goat’s cheeses. In soft cheeses of high quality, you can virtually see the microbes growing and spreading at room temperature (like bries, and epoisses).”

Good news for cheddar lovers: this British staple isn’t just comforting, it’s also naturally low in lactose and packed with gut-friendly compounds (Getty/iStock)

UK cheese lovers are already on the right track. Brits consume around 12kg of cheese per person per year, and while Cheddar accounts for over half of household cheese sales, there’s growing interest in artisan, goat and even blue cheeses. (Stilton, incidentally, now has Protected Designation of Origin status, making it both patriotic and probiotic.)

Easy on the gut: what about lactose?

One of the most common concerns around cheese and digestion is lactose. While milk and some soft dairy products can cause bloating or discomfort in people with lactose intolerance, many cheeses – especially aged ones – are naturally low in lactose.

During the ageing process, bacteria break down much of the lactose in the cheese. Hard cheeses like cheddar, parmesan, comté and aged gouda typically contain only trace amounts, making them far more tolerable for those who struggle with dairy. Goat’s and sheep’s milk cheeses are also often easier to digest due to their slightly different fat and protein structure.

So if milk doesn’t sit well with you, don’t write off cheese altogether. Choosing the right variety could mean enjoying its flavour – and its gut benefits – without the digestive fallout.

The old reputation isn’t deserved anymore. We should rethink cheese as a gut-friendly food when it’s the right kind, and part of a diverse, whole-food-rich diet

Professor Tim Spector

How to eat cheese for your gut

There’s more to gut-friendly cheese than just buying the right block. What you eat with it matters too. The magic happens when you pair cheese with fibre-rich, plant-based foods that help feed the microbes you’re introducing.

Try teaming a wedge of mature cheddar with slices of apple or pear, layering goat’s cheese onto lentil or beetroot salads, or adding aged gruyère to a slice of wholegrain sourdough with a spoonful of sauerkraut. Even a ploughman’s lunch can be microbiome-supportive if you pile on the pickled onions and raw veg.

The goal? Synergy. You’re combining live cultures or postbiotic-rich cheese with the prebiotic fibre that nourishes your existing gut bacteria. And no, this doesn’t mean you can’t have a gooey baked camembert – just maybe serve it with roasted chicory or leeks instead of a family-sized baguette.

The ones that don’t count (sorry, pizza lovers)

As with many things in nutrition, processing is the problem. The more refined and stabilised a cheese is, the less it offers in terms of microbial value.

“Don’t expect any live microbes on cheap pizza cheeses, or those that have been frozen or in spray cans,” says Spector. That includes many shredded supermarket blends, pre-sliced sandwich fillers and processed cheese spreads – though he concedes that some of the latter “contain at least two to three species of microbes, so have some benefits”.

Still, if gut health is your goal, it’s worth prioritising quality over convenience. Fortunately, UK consumption of processed cheese is on the decline, hovering at just 0.8-1kg per person per year. A small slice, you might say, of the total dairy picture.

So what’s the science?

If you’re imagining a battalion of probiotic bacteria marching through your gut after a bite of brie, you wouldn’t be entirely wrong. But there’s more to the story than just live cultures.

Roquefort and stilton aren’t just for Christmas; their microbial diversity makes them some of the most gut-supportive cheeses you can eat (Getty/iStock)

“It’s not just about live probiotics,” Spector explains. “While some cheeses do contain beneficial live microbes, what’s exciting is that even dead bacteria and bacterial fragments – recently called postbiotics (I like zombie microbes) – support gut health. These can interact with our immune system or feed existing gut microbes, stimulating diversity or beneficial activity indirectly.”

Cheese also contains bioactive compounds produced during fermentation, such as peptides, short-chain fatty acids and lipids, which may influence the immune system and overall gut function. In other words, the benefits of cheese don’t die with the microbes.

Where cheese fits in

Should you swap your kefir for camembert? Not quite. While good cheese can certainly contribute to gut health, its impact depends on variety, quality and quantity.

“Cheese can be an excellent contributor to a gut-friendly diet, especially if it’s a raw or traditionally made variety that can house over 20 species,” says Spector. “But if we’re honest, the average budget cheeses’ impact on gut microbial diversity is probably modest compared to powerhouse fermented foods like kefir, kimchi, kombucha and sauerkraut, which are teeming with a wider range of live microbes.”

So think of cheese not as a probiotic powerhouse, but as a valuable team player. As Spector puts it: “Rather than thinking of cheese as a silver bullet, think of it as one part of a broader, diverse dietary approach that includes many minimally processed whole foods. And yes, that includes enjoying good cheese ideally with some fruits or sauerkraut – in moderation of course.”