Ancient humans were as obsessed with their bodies as the average American, but they thought big. They saw how an eye could create a river. They determined that a rib held up the sky. They figured the sun and the moon were the heads of decapitated twin gods. They knew the body was everything, but their scale was large and attention directed outward. Instead, as we examine the human holobiont, we are learning to look small and inside ourselves. Rather than a rib holding up the sky, we see a tooth containing a continent of life—the GI tract, an entire world. Our bodies are a veritable ecosystem, a thriving metropolis where intrepid organisms can successfully eke out a niche and thrive on available nutrients, shaping our bodily processes much the way we shape the earth (agriculture and city building being two of the many ways we alter our planet). Our bodies are like urban worlds, packed with vibrant life with the gut serving as the center.

Early humans settled the Fertile Crescent around ten thousand years ago. Long before written records or even artifacts that would survive millennia, a hunter-gatherer group of people moved into this fertile area and, initially brought together by communal worship and play, finally proceeded to figure out how to shape the landscape to provide the maximum amount of energy for their bodily needs. Agriculture was born, and out of this settled group of humans, social structures began to evolve to reflect their new stationary life: civilization. All this excess energy from permanent crops allowed humans to build more and more complex communities that furthered even more intricate relationships. People began to form bigger and bigger groups. These turned into cities where individuals began to fill specific niches or roles so that no one human had to do everything. Culture and trade in the form of food, goods, and services thrived. Marketplaces teemed with specialized humans doing tasks to get food, often transforming it into other forms like preserving easily spoiled grain by fermenting it into beer. All this nutrient energy fueled the most important goal of any organism: sex—that is, transferring genes to the next generation.

The same story was being told in our own bodies. About the time the ancient Mesopotamians were figuring out that if you stick seeds in the ground and water them, food you don’t have to hunt and gather will grow, new communities of tiny organisms were finding our gastrointestinal (GI) tract to be quite the Fertile Crescent as well*. As the surplus of energy from agriculture allowed humans to form groups and culture, this same surplus snaked through human bodies like a river, providing a rich and relatively safe source of nutrients for thriving microbial and viral communities. With the dawn of agriculture came the dawn of a new type of human: one populated by a vast host of organisms—far outnumbering his own cells—that could process the products of agriculture and co-evolve with others in a limited space, often supplying the human metabolism with essential nutrients human cells couldn’t make themselves.

Despite the central roles that our guts play in our culture and daily lives, we are only now beginning to scientifically understand this amazingly complex system. Only in the last decade have the tools necessary for studying our (or any ecosystem’s, really) abundant viral and microbial communities become available. There has also been a philosophical shift in how scientists study ecosystems like the gut. This relatively new approach is called systems biology and differs from the more traditional reductionist approach. Colloquially, a systems approach is more holistic in nature, favoring the function of the whole rather than breaking it into isolated parts. System biology takes into account that the whole most likely will be far more than the sum of its parts.

*All animals have microbial and viral communities, and humans are no different. Long before the dawn of agriculture, we harbored microbial and viral populations in our guts; however, researchers now speculate that the current iteration of our internal occupants didn’t occur until about 10,000 years ago when we began to farm and live in more densely packed communities (Alex Mira, Ravindra Pushker, and Francisco Rodríguez-Valera, “The Neolithic Revolution of Bacterial Genomes,” Trends in Microbiology 14, no. 5 (May 1, 2006): 200–206, doi:10.1016/j.tim.2006.03.001.)

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