Le monde bactérien est prédominant – l'humanité n'en constitue qu'une infime partie. La biomasse de ces organismes microscopiques dépasse de 35 fois celle de l'ensemble du règne animal. De la synthèse de notre ADN à la détermination des civilisations ayant survécu, ces acteurs invisibles ont profondément marqué le cours de l'histoire.
L'impact des maladies sur le destin de l'humanité
L'avènement de l'agriculture sédentaire, avec la domestication des plantes et des animaux, a involontairement engendré les conditions idéales pour l'émergence de pandémies. Les sociétés de chasseurs-cueilleurs, caractérisées par une faible densité de population et une mobilité élevée, étaient moins exposées aux maladies infectieuses.
Cependant, la transition vers des communautés agricoles plus denses a radicalement modifié le paysage épidémiologique, avec des conséquences inattendues pour l'évolution de l'humanité. (1)
An Epidemiological Revolution
The truly revolutionary upheaval of the Neolithic period wasn't agricultural - it was epidemiological. This may very well have been the most lethal period caused by infectious disease in human history. As Jonathan Kennedy points out in Pathogenesis, for the first time, our ancestors lived in dense settlements and in close proximity to a wide variety of animals - domesticated ones, as well as uninvited guests such as rats and fleas. This created ideal conditions for the emergence of zoonotic infectious diseases (2) which jump from animals to humans. And the increasingly crowded and unsanitary living conditions helped spread the pathogens from person to person. Infections that might have fizzled out in smaller, scattered hunter-gatherer groups now had a constant supply of new hosts. Early farming villages became epicenters of disease outbreaks.
A Lasting Impact
The numbers tell a sobering story. Studies show that 500-1,000 years after adopting agriculture, communities typically saw death rates spike dramatically. Population growth didn't just slow – it sometimes reversed. Consider this: between 10,000 BCE and 5,000 BCE, world population barely crept from 4 million to 5 million - a mere 25% increase over five millennia, when even modest growth should have doubled the population. The contrast with what followed is striking: over the next five thousand years, from 5,000 BCE to 1 AD, the world population exploded more than twentyfold, reaching over 100 million. (3)
Written in our DNA
Recent DNA evidence indicates that many contemporary infectious diseases originated in Neolithic pathogens - including plague, tuberculosis, hepatitis B, and measles. The archaeological record provides stark confirmation: Egyptian mummies bearing smallpox-like rashes, and ancient artwork depicting the telltale signs of polio - a rather grim but eloquent testimony to our species' early encounters with these diseases.
The first major waves of infectious diseases killed so many people that they left permanent marks in the human DNA. Studies of genes involved in human immunity reveal that most adaptations and mutations occurred in the last 12,000 to 6,000 years, which broadly corresponds to the adoption of agriculture and the spread of settlements. These farming communities, connected enough for diseases to become endemic childhood afflictions, essentially became evolutionary pressure cookers for human immunity.
It is a Bacterial World
Our ancestors' run in into pathogens and bacteria should not come as a surprise. After all we are all descendants of a single cell, bacterium-like organism - the so called Last Universal Common Ancestor (LUCA). The tree of life evolved from there, but in remarkably lopsided fashion - while there are an estimated 9 million species of animals, plants and fungi on earth, there are an estimated 1 trillion types of bacteria and the bacteria-like archaea. Complex life forms represent less than 0.001 percent of Earth's species - a humbling statistic. And all those bacteria add up: their total mass is 35 times that of all animals. Bacteria are, without question, clearly the dominant forms of life on earth.
Furthermore, Bacteria made the planet habitable for complex life. Some 2.5 billion years ago, when there was little to no free oxygen in the air and water, a new form of bacteria evolved to utilize photosynthesis. These microscopic pioneers proceeded to pump vast amounts of oxygen into the ocean and atmosphere over several hundred million years. Multicellular organisms only appear in the fossil record after this great oxygenation event. Even today, bacterial descendants in the form of phytoplankton account for at least half of the oxygen produced by living organisms. We owe our very existence to bacterial innovation!
Our Viral Heritage
The story becomes even more intriguing when we consider viruses. These microscopic entities are truly ubiquitous, found wherever life exists - and they even outnumber bacteria. A liter of seawater contains over 1 billion virus particles! Some viruses, called retroviruses, insert their DNA into host cells. When this happens in reproductive cells, the viral DNA becomes a permanent part of the genetic legacy passed to future generations. Remarkably, 8% of the human genome is of retroviral origin. Some of these inherited viral elements proved surprisingly useful, contributing to crucial functions like memory formation and childbirth. It seems our genome is something of a collaborative effort. (4)
Human Dependence on Microbes
This deep connection with microbes continues today. Our bodies and brains function properly only through a complex partnership with microbes that evolved alongside us. Our bodies are literally teeming with microscopic life - the total human microbiome weighs about the same as our brain, between 1 and 2 kg. We outsource essential tasks to these microbes, taking advantage of their rapid adaptation abilities. The microbiome contains around 500 times more genes than the human body, reproduces extremely fast, and can transfer genes between species.
The skin microbiome, for instance, is crucial for health - maintaining skin barriers, keeping skin moisturized, removing dead cells, and supporting repair. Gut bacteria assist with digestion and produce essential vitamins and minerals - and surprisingly, they even influence our feelings and behavior in significant ways.
Farmers as Accidental Conquerors
A Weapon of Mass Destruction
This complex dance between humans and microbes took an unexpected turn as farming communities developed disease resistance. While infectious diseases initially devastated these settlements, they also set the stage for one of history's most significant plot twists. Over generations, survivors passed on their genetic resistance to their children. Through a brutal process of natural selection, farming communities developed increasing immunity to endemic diseases - an advantage gained at a terrible cost of countless lives over many generations.
This hard-won immunity became an unexpected weapon. As farming populations expanded into new territories, they carried more than seeds and plows – they brought their diseases with them. When they encountered populations that hadn't developed similar immunity, the results were catastrophic. Hunter-gatherer communities, having never experienced these diseases, had no biological defenses against them. What might have been a childhood illness in a farming village could wipe out entire communities of hunter-gatherers. Migration became conquest, often without a single battle being fought. This pattern would repeat itself throughout human history, with major implications for indigenous populations and power dynamics.
The Spanish conquest of the Americas is perhaps one of the most well-known examples – European diseases killed far more indigenous people than weapons ever did - and contributed mightily to a small band of conquistadors gaining control over the powerful Inca empire.
A Europe of Immigrants
Lesser known is the surprising story that played out in Europe during the neolithic era. Starting some 9,000 years ago farmers who originated from Anatolia (modern day Turkey) arrived in Europe and accomplished something remarkable: they almost completely replaced the hunter-gatherer populations that had inhabited the continent since the end of the ice age. Their genetic legacy persists today, accounting for a large proportion of the genome in Southern European countries like Italy, Spain, and Greece.
One Small Steppe for Herders...
But this was just the first act. A second major migration occurred 5,000 years ago, originating from what might seem an unlikely source: the Eurasian Steppe. This vast grassland had remained largely untouched by agriculture, too dry and water-scarce to support farming communities. Yet two innovations would transform this seeming backwater into the launching pad for massive population changes: the invention of the wheel and the domestication of horses. These technological advances proved revolutionary. Wheeled wagons enabled the transport of water and supplies across vast distances, suddenly making large swaths of the Steppe accessible to nomadic herders. Horses multiplied their effectiveness, allowing herders to manage far larger herds than possible on foot. Armed with these advantages, the steppe herders began pushing westward into Northern Europe.
What happened next puzzled archaeologists for decades. These nomadic herders, despite their relatively small numbers, managed to replace most of the existing farming populations
across Northern Europe. The mystery was finally solved through recent DNA analysis of Neolithic skeletons, which revealed evidence of the oldest known plague bacteria stretching from Scandinavia to Ukraine. Scientists traced the plague's origins to farming towns in Ukraine, from where it spread rapidly through trade networks, causing population crashes estimated at 60% across much of Northern Europe.
The steppe herders' timing, it turned out, was impeccable - whether by luck or strategy. They encountered a landscape largely emptied by disease, with surviving communities too weakened to resist effectively. This demographic replacement was so complete that today, steppe herder DNA remains the largest source of ancestry in Northern Europe. Perhaps even more remarkably, these herders likely brought with them the Indo-European languages now spoken by several billion people worldwide.
The Original Invisible Hand
While economists speak of market forces shaping human behavior, a far more fundamental unseen force has been directing the course of civilization. What began as an accidental byproduct of agricultural settlement became history's first and most persistent invisible hand, silently determining which societies would flourish and which would fall. (5) (6)
The story of civilization's spread wasn't just about superior technology or military might. It was also - perhaps primarily - about invisible armies of microbes, inherited immunity, and the cruel lottery of survival. Our microscopic companions have impacted our physical evolution as well as our social structures, cultures, and economic systems. Our relationship with microorganisms continues to shape human destiny in profound and often unexpected ways - something we seemed to have forgotten about, until the recent COVID pandemic caught us unawares.
As we grapple with new infectious diseases in the 21st century, understanding our co-evolution with microbes can help us move towards a more balanced and resilient future, using these organisms for progress and innovation.
Postscript: The mirror bacteria that could end life as we know it
Our complex dance with microbes continues to evolve in surprising ways. In December 2024, over 35 leading scientists warned about a new frontier in microbial research: mirror bacteria. These theoretical organisms would be built using right-handed amino acids—the mirror image of all life on Earth, which uses left-handed amino acids exclusively. Initially thought to be a fascinating but harmless scientific pursuit, deeper research revealed a disturbing possibility: such mirror organisms could become an unprecedented invasive species, potentially triggering catastrophic ecosystem collapse.
The concern? While mirror bacteria could find enough nutrients to thrive and spread globally, our immune systems—evolved over millions of years to detect and fight normal bacteria—might be blind to these mirror invaders. Every plant and animal on Earth could be vulnerable to a new pathogen that nothing has evolved to fight.
Yet this story offers hope. Unlike many historical encounters between humans and microbes, we've identified this risk before it materialized. Scientists, including those who pioneered the research, are now calling for a halt to mirror bacteria development. As we continue our ancient partnership with microbes, perhaps we're finally learning to look before we leap.
(1) Much of this article borrows ideas and materials from three books: McNeill, William. Plagues and Peoples (1976) which remains a reference to this day, the more recent Kennedy, Jonathan. Pathogenesis. A History of the World in Eight Plagues (2023), and Scott, C. James. Against the Grain (2017).
(2) More than 60% of pathogens that can infect humans are zoonotic, that is to say that they originate in animals. And more than 70% of emerging pathogens originate in animals. Zoonotic Diseases: Etiology, Impact, and Control - PMC (nih.gov)
(3) Repeated plague infections across six generations of Neolithic Farmers | Nature and New research traces origins of zoonotic disease to the Neolithic period (rvc.ac.uk)
(4) Animals first evolved to reproduce by laying eggs. Between 100 and 200 million years ago a shrew-like creature first developed the capacity to gestate her young inside her body. This was made possible by the placenta, a remarkable temporary organ that enables nutrients to go from mother to baby, and CO2 and waste to travel in the other direction, without triggering the mother's immune system. Scientists believe a crucial function of the placenta was acquired by retrovirus which are able to attach to cells while circumventing an immune system response. Without this virus infection, mammals may have continued to reproduce by laying eggs!
(5) Did you notice anything wrong with the picture of the invisible hand? It has 6 fingers ... even after all this time Midjourney AI still draws some hands with 6 fingers :( I like the picture though, so I kept it!!
(6) A recent medical paper draws further parallels between microbiological communities and economic markets and discusses the profound interplay between microbial ecosystems and human health and behavior. Economic microbiology: exploring microbes as agents in economic systems - PMC