In 1989, British epidemiologist David Strachan published a page-and-a-half paper in the British Medical Journal. He had studied health data on 17,414 British children all born in the same week in 1958, and noticed something odd: the more older siblings a child had, the less likely they were to suffer from hay fever. Strachan suggested microbes were involved — and inadvertently launched one of the most productive debates in modern immunology.
Strachan’s observation was counterintuitive. By the logic of the time, dirt meant disease. Hygiene meant health. But the data said something different: children who grew up in more “microbial” environments — with messy older siblings, in crowded nurseries, on farms — had lower rates of allergy and autoimmune disorders than children raised in sterile urban apartments.
Strachan called it the “hygiene hypothesis” — a term that immediately began to mislead. The point was not that we should wash less. The point was that an immune system deprived of normal microbial “education” in early childhood loses the ability to calibrate its responses properly.
Immunity — like any skill — requires practice. Without enough varied “training encounters” in childhood, it begins to treat harmless things as threats.
When the Berlin Wall fell in 1989, scientists gained a rare gift: the chance to compare two populations with nearly identical genetic backgrounds who had lived for forty years under different conditions.
West Germany — wealthier, cleaner, with more developed household hygiene. East Germany — with large, crowded nurseries, less sterile domestic environments, and more contact between children and soil and animals. Epidemiologists expected the East Germans to be less healthy. The picture was the reverse: allergic disease rates — bronchial asthma, hay fever, atopic dermatitis — were substantially higher in the West.
Subsequent research confirmed the finding. German paediatrician Erika von Mutius, who had taken on the project expecting to demonstrate the superiority of Western medicine, was surprised by her own results. She published them in The Lancet in 1992 and has since become one of the leading researchers in the field.
The hygiene hypothesis has grown more precise over time. Modern researchers prefer the term “old friends hypothesis,” introduced by British immunologist Graham Rook in 2003. The core idea: not just any microbes are beneficial for immune education — what matters are the organisms humanity has lived alongside for hundreds of thousands of years: soil bacteria, intestinal helminths, non-pathogenic mycobacteria.
These “old friends” stimulate the formation of regulatory T-cells (T-regs) — the key mediators of immune tolerance discussed in the immunity and pregnancy article. Without sufficient diversity of these organisms in early childhood, the T-reg system forms less effectively. The result: heightened reactivity — allergies, asthma, atopy, and in more severe cases, autoimmune disorders.
Birth is the first and perhaps most intensive microbial priming of a baby’s life. Passing through the birth canal, the newborn receives a founding population of bacteria from the mother — primarily Lactobacillus — which becomes the foundation of their gut microbiome for the first years of life.
In a caesarean section, this does not happen: the first bacteria the baby contacts are those from the skin of medical staff and the air of the operating theatre. This is not a disaster, but it is a different start. A 2019 meta-analysis (Huang et al., BMJ) drawing on data from more than 700,000 children found that C-section babies have a modestly elevated risk of asthma, obesity and immune disorders. The effect is small but statistically robust.
A similar story applies to antibiotics in the first two years of life. They save lives from real infections — that is their primary purpose. But broad-spectrum antibiotics destroy not only pathogens but also a large proportion of commensal flora. Several large cohort studies have documented an association between antibiotic courses in early childhood and elevated risk of allergic disease in school-age children.
The first 1,000 days — from conception to age two — are when the microbiome and the immune system shape each other. What happens during this window has long-term consequences.
In 2020, Finnish researchers from Tampere University conducted an unusual experiment. In several urban daycare centres in Helsinki, they replaced asphalt and gravel with turf, forest litter and peat-enriched sand. They then observed the children for a month.
The result, published in Science Advances: children who played on the new “forest” surfaces showed a significant increase in skin and gut microbiome diversity within 28 days. The ratio of regulatory to pro-inflammatory immune cells shifted toward a more tolerant profile. The children did not fall ill more often — counter to the intuitive fears of many parents.
This was a demonstration that the immune system remains plastic well into ages 3–5, and that even a modest increase in environmental microbial diversity produces a measurable physiological effect.
A future child’s microbiome begins to take shape even before birth — through the mother’s microbiome. The composition of her vaginal and gut flora influences the founding bacterial set the newborn will receive. This is not an argument for or against medically indicated caesarean section — but it is an argument for consciously caring for one’s own microbiome during the preparation for pregnancy.
Probiotic supplements during pregnancy — the data are mixed. Some studies show reduced atopy risk in children when mothers take Lactobacillus rhamnosus GG in the third trimester; others do not confirm the effect. A decision should be made with a clinician, not based on advertising.
“Vaginal seeding” after caesarean section — a growing practice but not yet a standard: safety and long-term effects are still being studied.
Hygiene has saved more lives than any other medical intervention in history. That is beyond question. But between “wash your hands before eating” and “sterilise everything around the child” there is an enormous distance. Thirty years of research has convincingly shown that moderate contact with microbial diversity in early childhood is not a risk — it is a requirement for normal immune development.
This does not mean deliberately exposing a child to infections. It means that forests, soil, animals, an unwashed carrot from the garden are not enemies. Your child’s immune system will very likely thank them for it.
We did not evolve in sterile conditions. Our immune system expects the world around it to be a little dirty.
The article on Immunity and Pregnancy (Learn section) covers T-reg cells and their role in carrying a pregnancy in greater depth. Module 3 (Biohacking & Preconception) includes a microbiome support protocol for the preconception period. Both are available free.
the concept that reduced microbial contact in early childhood raises risk of allergic and autoimmune disease. More precisely called the “old friends hypothesis.”
the collective community of all microorganisms living in symbiosis with a human host. The gut microbiome contains around 100 trillion cells and more than 1,000 bacterial species.
microorganisms living permanently in the human body without harm, and generally with benefit. Distinct from pathogens.
carbohydrates in breast milk that feed beneficial gut bacteria, primarily Bifidobacterium.
regulatory T-lymphocytes providing immune tolerance. Their normal development depends substantially on early-life microbial diversity.