Louis Pasteur transformed biology by proving that microorganisms cause fermentation and infectious disease. Before him, disease was blamed on vague “miasmas” or bad air. Pasteur showed that specific microbes could be identified, cultured, and linked to specific illnesses. This insight saved millions of lives and rightly made germ theory the foundation of modern medicine.
But his contemporary Claude Bernard, an equally towering figure, was asking a deeper physiological question. He did not deny the existence of germs. Instead, he asked: Why does the same germ cause disease in one person but not in another?
Bernard’s answer lay in what he called the “milieu intérieur”—the internal environment of the body. Temperature, blood chemistry, nutrition, hormones, immune balance, and metabolic health together create a living terrain. In a stable, resilient internal environment, Bernard argued, disease struggles to take hold. In a disturbed one, even ordinary microbes can become dangerous.
Pasteur and Bernard thus represented two complementary but competing visions of disease. Pasteur emphasised external agents; Bernard emphasised internal conditions. Public health, understandably, embraced Pasteur. Germs could be seen, measured, and fought. Bernard’s ideas were harder to operationalise, slower, and less dramatic—but far more foundational.
The famous deathbed remark attributed to Pasteur—“It is the soil”—symbolises a late realisation that germs alone do not explain illness. Microbes are ubiquitous; exposure is constant. Yet illness is selective. Tuberculosis infects many but sickens few. Cancerous mutations arise in everyone, but progress in some. Viruses enter countless bodies but devastate only a fraction. These patterns make sense only when the host environment is placed at the centre.
“The soil” refers to the body’s biological resilience: immune competence, metabolic stability, inflammatory tone, nutritional status, stress physiology, and repair capacity. Germs are sparks; the soil determines whether there is a fire. Antibiotics can kill bacteria, but they do not restore a weakened immune system. Surgery can remove a tumour, but it does not necessarily correct the terrain that allowed it to grow.
This debate still shapes medicine today. Acute care medicine—emergency rooms, infections, trauma—operates largely on Pasteur’s model and does so brilliantly. Chronic disease medicine, however, falters because diabetes, heart disease, autoimmune disorders, cancer, and neurodegeneration are not primarily germ-driven problems. They are diseases of internal imbalance, unfolding over years as the soil deteriorates.
Pasteur’s concession does not diminish germ theory; it completes it. Disease is not a simple invasion story. It is an interaction between agent and host, trigger and terrain. When medicine forgets the soil, it ends up endlessly chasing symptoms and suppressing microbes while the deeper conditions remain unchanged.
In that sense, Bernard’s insight—and Pasteur’s late acknowledgment—points toward a more mature vision of health:
Not merely fighting disease, but cultivating the conditions in which disease cannot easily arise.
That idea, more than a century old, is only now being rediscovered.