I Contain Multitudes

We Are All Ecosystems of Microbes

Baba the pangolin, looking like a living pine cone, sits calmly at the San Diego Zoo as scientist Rob Knight approaches with a cotton swab. By dabbing Baba’s nose, Knight captures millions of microscopic cells that call the pangolin home. This microscopic menagerie, known as the microbiome, exists on and inside every creature on Earth. We are all teeming with bacteria, fungi, and viruses that travel with us from birth, sharing every meal. We are never truly alone.

If Earth's history were a single calendar year, single-celled microbes would be the sole inhabitants from March to October, building the world we know by pumping oxygen into the atmosphere and enriching the soil. Humans would arrive in the final thirty minutes. Our own existence is owed to a breathtakingly improbable event two billion years ago when a bacterium merged with an archaeon, forming a permanent partnership. This union created the complex eukaryotic cell—the building block of every plant and animal. The trapped bacterium evolved into the mitochondrion, the power station that fueled the rise of all complex life. This merger is a "black hole" in biology, a one-off innovation that allowed life to break through a ceiling of simplicity.

We often view microbes as "germs," but this ignores the vast majority of our partners. We are roughly half-microbe by cell count, carrying around 39 trillion bacterial cells alongside our 30 trillion human ones. These partners function like a hidden organ, providing a genetic wealth 500 times greater than our own to help us digest food, synthesize vitamins, and educate our immune systems. Across the animal kingdom, these alliances grant extraordinary powers: the hoopoe bird paints its eggs with bacterial secretions to ward off infection, leafcutter ants use antibiotic-producing microbes to protect their gardens, and even the lethal poison of a pufferfish is a gift from its resident bacteria.

If these partners vanished, grazing animals like cows would starve without gut microbes to break down plant fibers, and deep-sea ecosystems would collapse. To a microbe, every body is an island, with distinct habitats like the dry deserts of the forearm and the humid jungles of the armpit. This internal biogeography challenges our definition of an individual. If our bodies are built with instructions from both human and microbial genes, the concept of a solitary "self" dissolves. We are walking archipelagos, social collectives that have succeeded through billions of years of intimate collaboration.