The Internal Ecosystem Crisis: How We're Killing Our Microbiome (2025)

Imagine this: While we're all busy fretting over the planet's vanishing rainforests and endangered species, a silent crisis is unfolding right inside our own bodies—one that could be just as devastating. But here's where it gets controversial... What if the key to reversing it isn't just about eating more yogurt or popping vitamins, but embracing a lifestyle that reconnects us with nature in ways that might make some folks squirm? Dive in as we explore how we're sabotaging our inner ecosystems—and the thrilling steps we can take to bring them back to life.

First off, let's catch up on the week's most pressing climate updates, and don't forget that the game-changing Cop30 summit is just around the corner in Belém, Brazil. Our dedicated team at The Guardian will be bringing you unparalleled on-the-ground reporting, including special editions of Down to Earth over the coming weeks where you'll get direct insights from our journalists.

Essential reads:

In focus:

Picture your body as a bustling, miniature universe, teeming with trillions of bacteria alongside smaller groups of fungi and viruses. These tiny inhabitants coexist in harmony, much like how animals, plants, water, and rocks interact in a vibrant forest. This intricate web is what scientists call the human microbiome—a personal ecosystem that's crucial for our well-being.

To beginners, the idea of microbes coating our skin, lining our guts, and populating other areas might sound a bit creepy at first. But think of it this way: just as we protect rainforests to sustain life on Earth, we must safeguard these internal communities to keep ourselves thriving. They play vital roles in digestion, immunity, and even mood regulation. For instance, if you're familiar with Tim Spector's work on gut health (https://www.theguardian.com/lifeandstyle/2022/may/15/go-with-your-gut-tim-spector-power-of-microbiome), know that the microbiome isn't confined to the digestive system. In the vagina, these microbes maintain an acidic environment to fend off harmful invaders, acting like a natural bodyguard. On the skin, they specialize in healing wounds, while over 100 types of fungi (https://www.nature.com/articles/nature12171) call our feet home—each person's mix is uniquely their own, influenced by factors like age and environment.

Dr. James Kinross, a surgeon and lecturer at Imperial College London, and author of 'Dark Matter: The New Science of the Microbiome,' compares the decline in our internal microbial diversity to an 'internal climate crisis.' He's pinpointed culprits like overreliance on medications—especially antibiotics—which wipe out good microbes along with the bad, plus diets heavy in ultra-processed foods and a growing disconnect from natural surroundings that deprives us of beneficial exposures.

But here's the part most people miss: Kinross emphasizes that simple, everyday changes can turn this around. 'It shifts our approach from the old-school medical mindset of eradicating all microbes to embrace a more balanced, nature-centric view that treats our bodies like ecosystems worth conserving,' he explains. And this is where things could get controversial—critics might argue that promoting 'letting in' microbes sounds risky in our germ-phobic world, but emerging science suggests it's a calculated reconnection.

Research is increasingly connecting two layers of biodiversity: the external world of soil, water, plants, and animals, and the internal realm within us. Humans evolved to swap microscopic organisms with our environment through touch, breath, and even ingestion. As Kinross notes, the field of microbiome study has gained serious traction. 'I used to talk to nearly empty rooms for two decades; now, they're packed,' he shares.

Urban living, however, has walled us off from nature, limiting our interactions with healthy microbes. City planners are innovating to bridge this gap (https://www.theguardian.com/environment/2025/oct/30/rich-lizards-luxury-effect-more-plants-wildlife-wealthier-suburbs-health-aoe), by integrating greenery, clean water features, and mature trees into urban spaces. Finland leads the charge with a pioneering initiative to amplify nature exposure in early childhood education. Forty-three daycare centers (https://www.biwe.fi/en/nationwide-research-on-the-rewilding-of-kindergarten-yards-vahvistu/) have received a combined €1 million (£880,000) to transform their outdoor areas, fostering children's contact with diverse microscopic life.

I visited one such center near Helsinki, where they'd essentially transplanted a forest floor onto what was once a parking lot. Making mud pies with toddlers and chatting with researchers revealed how this bold experiment improved kids' health (https://www.theguardian.com/environment/2025/oct/29/soil-sandpit-children-dirty-bacteria-finnish-nurseries-research-microbes-biodiversity-aoe)—from stronger immune systems to better mental well-being. And you don't have to import an entire woodland to reap benefits.

A fascinating Finnish study (https://www.sciencedirect.com/science/article/pii/S0160412024002915?via%3Dihub) demonstrated that even four weeks of tending plants can enrich skin microbes and bolster immune responses. It wasn't the gardening itself that mattered most, but the direct contact with nutrient-rich, varied soils. For extra clarity, imagine soil as a microbial supermarket—diverse dirt means a wider selection of beneficial bugs to stock your body's shelves.

Indoor solutions like green walls in workplaces can also diversify skin ecosystems. Research on a wall by Finnish firm Naava, which circulates air through plant roots for purification (https://www.naava.io/news/science-backed-naava-green-wall-purifies-air), showed a boost in skin-friendly Lactobacillus bacteria within just two weeks (https://www.nature.com/articles/s41598-022-10432-4.epdf?sharing_token=2-Sauoos5TXAofqXvLXgZtRgN0jAjWel9jnR3ZoTv0M1FBZEggBCXnZMx2awfp3tB6DYnpA5CrypHVhAf4Wlk1HL24seZ8ui5rM6FpufL9ROImXbrsNRrcHG-GprFtndGp2MWonU1f6YwgtoW6yj55JJIGO5iXL7tx9Dh5AKI0I%3D), helping prevent infections. Another example: Studies indicate pet ownership can enhance human health (https://link.springer.com/article/10.1186/s40168-020-00895-w), especially if pets roam outdoors regularly to bring in microbes. Even household dust from beds isn't all bad, as it carries beneficial spores.

Kinross reminds us we're integral to nature, covered in countless helpful bacteria meant to be exchanged. People with bigger social circles often boast richer gut microbiomes (https://www.sciencedirect.com/science/article/pii/S2452231719300181?via%3Dihub)—think teenagers with their adventurous exposures, or seniors in care homes whose diversity surges (https://www.nature.com/articles/nature11319). 'In cities, we're stacked like sardines but truly isolated,' he says, suggesting shared meals as a microbe-swapping ritual. 'Every home has its own microbial signature; dining at a friend's exposes you to their kitchen's unique array on utensils and surfaces.' Deeper human connections benefit overall health, not just the microbiome, he adds.

After the gut, the mouth hosts the body's second-most varied ecosystem. A single kiss can transmit 80 million bacteria. 'Go ahead and kiss—it's great for your microbiome,' Kinross advises. 'Make it count with a proper, lingering one.' As holiday season approaches, maybe that's a fun reason to hang the mistletoe sooner. But wait, is encouraging more kissing in a post-pandemic world a controversial take? Some might see it as promoting risky behavior, while others view it as a natural way to foster microbial exchange.

Read more:

  • The human microbiome: why our microbes might hold the secret to better health (https://www.theguardian.com/news/2018/mar/26/the-human-microbiome-why-our-microbes-could-be-key-to-our-health)

  • The brain microbiome: could cracking its code ward off dementia? (https://www.theguardian.com/lifeandstyle/2024/dec/01/the-brain-microbiome-could-understanding-it-help-prevent-dementia)

  • How we're harming our microbiome—and why just kimchi won't fix it – video (https://www.theguardian.com/science/video/2025/jun/26/how-were-killing-our-microbiome-video)

What do you think? Is embracing 'dirty' activities like mud play or passionate kissing the future of health, or does it clash with our hygiene-obsessed culture? Do you agree that urbanization is crippling our microbiomes more than we realize? Share your thoughts in the comments—let's spark a conversation!

The Internal Ecosystem Crisis: How We're Killing Our Microbiome (2025)
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