In praise of a little dirt: The cleanliness paradox

As the Tata Group CTO, I had the opportunity to work with Yale researchers on the gut microbiome, its influence on human health, and the role of prebiotics in shaping that delicate ecosystem. One research insight mentioned during those discussions has stayed with me. Microbiome-free baby mice (delivered by C-section and raised in sterile environments) show noticeably less stress when separated from their mothers. At first glance, that seems beneficial. Yet these same mice also exhibit muted emotional responses overall. Their world is quieter, but also curiously flattened. Without microbes, their physiology and behaviour shift in ways that are both measurable and profound.

Science was making a simple point: the microbiome matters, not just for digestion or immunity, but for how an organism experiences life itself. Over the past century, however, our relationship with microbes has narrowed to a single storyline: one where microbes are enemies to be eliminated. Clean water, sanitation, antibiotics, and vaccination transformed human health. Yet, in parallel, we have seen a rise in allergies, asthma, eczema, food intolerances, and autoimmune conditions. The contradiction is difficult to ignore. The cleaner we became, the more our immune systems seemed to struggle. This contradiction is now recognised globally as the cleanliness paradox: we removed the harmful microbes, but we also removed the good ones.

Birth, milk, and the critical hours: The earliest moments of life are also the most biologically instructive. A baby’s first major immune lesson begins not in the nursery but in the birth canal. During vaginal birth, the infant is coated with maternal microbes that seed the gut and start training the immune system. When birth occurs via caesarean section (which is often medically necessary), this microbial inheritance is bypassed. Large population studies around the world show that children born through C-section face a higher likelihood of developing asthma and allergies.

Breast milk continues this biological exchange. It is not simply nutrition but a carefully evolved communication system containing bacteria, complex sugars, and immune molecules. These sugars, known as human milk oligosaccharides, are not meant for the baby alone. They are intended to feed specific gut bacteria, which in turn guide the development of regulatory immune cells. Formula milk, despite many advances, cannot reproduce this living, dynamic ecosystem.

And then comes the wider world. The first three hours, days, and weeks matter enormously. Early microbial exposures, from skin, air, soil, and human contact, help the immune system understand what is harmless and what is harmful. Shielding infants too aggressively from microbial life does not protect them; it deprives them of teachers.

When clean becomes too clean: Modern urban lifestyles have pushed us into an era of extreme hygiene. Antibacterial soaps, surface sanitisers, routine antibiotic use, air-conditioned indoor childhoods, and limited contact with soil and animals have collectively reduced the microbial diversity surrounding children.

The result is visible. Peanut allergies, once rare in many parts of the world, have risen sharply. Grass and pollen allergies have become more intense. Food allergies in some countries have doubled in just a decade. Asthma diagnoses correlate strongly with early antibiotic exposure, especially repeated courses in the first year of life. Genes cannot explain this rapid shift. Microbial deprivation can.

A tale of two Bengaluru childhoods: Within Bengaluru, for example, the contrast between semi-urban communities and gated communities offers a microcosm of the cleanliness paradox.

In semi-urban communities, children still run barefoot on dusty fields, play with street dogs, climb trees, and return home wearing the day’s adventures on their skin. Their microbial exposures are rich, random, and evolutionarily familiar. This is truer in rural settings. However, the downside is the increased exposure to pathogens and groundwater contaminants, leading to acute and chronic health issues.

In gated communities, life is immaculate. Playgrounds are clean. Lawns are manicured. At home, surfaces are typically disinfected. Children spend more time indoors, and when they venture out, the environment is controlled and predictable. Ironically, in these cleaner environments, pollen and food allergies are more common. This is despite better nutrition, healthcare, and infrastructure. Their immune systems are not optimal.

The difference is not economic. It is microbial.

A sensible approach to dirt: This is not an argument for abandoning hygiene. Clean water, sanitation, and vaccines remain among humanity’s most outstanding achievements. The issue is not cleanliness but the loss of microbial diversity. A balanced approach allows for safe, meaningful microbial exposure.

A life scrubbed free of microbes may look orderly, but biologically, it is unbalanced. The immune system thrives on diversity, not deprivation. As counterintuitive as it seems, the road to better health for future generations may lie not in more disinfectants but in more contact with the living world. Sometimes, the simplest wisdom is also the oldest: a little dirt is good for you.

The writer is the former CTO of Tata Group and founder of AI company Myelin Foundry is driven to peel off known facts to discover unknown layers.

Disclaimer: The views expressed above are the author's own. They do not necessarily reflect the views of DH.