Many years ago most scientists believed that simply mapping out all the human genes would allow us to predict how our bodies worked. “Cracking the DNA code” that makes up the human genome would usher in a new era of health and human advancement. It hasn’t happen yet for a number of reasons. One of the primary reasons is that science’s definition of “our genes” was too narrow. Extrapolation from a few examples of human physiology and phenotypic  function, as well as mutation rate caused by radiation, researchers estimated that 100,000 genes should make up the human genetic code. The thought was that specific genes would encode characteristics for everything from eye color to how you and ancient humans metabolized that cold pint. However, when the human genome was finish it turned out we only have about 20,000 “human” genes; we are barely more genetically complex than a fruit fly. To make matters even more humbling, the human genes on our DNA are actually outnumbered by “foreign” genes encoded by viral-like elements. From this viewpoint, most of the DNA in our genomes is really not ours. And when we expand our idea of “human” genes to include the DNA of our resident microbes, our human genetics start to look pretty paltry.
We have a vast reservoir of genetic material that has only recently been seriously considered. These extra genes largely are from the viruses and microbes that live in our guts. In fact, most of humanity’s genetic diversity comes from these symbionts . Basically, we are a walking ecosystem made up of microbial and human cells as well as viruses. There are actually more of them then there are of us: ten microbial cells and at least a 100 viruses for every human cell. These microbial and viral associates help us digest our food and change the way we develop. And at the end of our lives, these microbes will happily eat our bodies.
These close associations between microbes, viruses, and humans are not unique to our species. Every plant and animal on earth is actually a symbiosis of these and other components. This intricate system of many organisms working to form a whole whose function is much greater than its parts is called a holobiont. We often use this term interchangeably with “ecosystem” (and I will do so in this book); however, holobiont encompasses the idea of ecosystem more specifically. Though the idea of a holobiont has been around for a while, Lynn Margulis coined the term in 1993 to better describe that macro-species (including humans) universally live in close association with different biological entities (usually with micro-species like bacteria) in positive or negative ways or sometimes both depending on the day. This way of living is often called symbiosis. Margulis claimed that all individuals who participate in a particular symbiosis are bionts and the entire organism that is comprised of these bionts is a holobiont. Therefore, we humans aren’t merely human but a biont that contributes to a conglomerated human holobiont made up of many species from multiple kingdoms. We are walking worlds, teeming with diverse life.
If we think of this symbiosis on the artificial scale of a city, we can see how a holobiont can be a single functional entity with many individuals contributing to it. The city of San Francisco is a macro-biont that contains many micro-individuals (humans, animals, actual microbes, etc.) whose functions keep the city thriving. We—the human holobiont—are just like a city: a larger entity with defining characteristics that separate us from other larger entities, yet we are comprised of a myriad of smaller entities that contribute to our uniqueness. New York is not San Francisco—both cities have distinct personality and feel that seems connected to—yet bigger than—their inhabitants and location. In these cities, many individuals break up, through specialization, the big job of running a city, making the amount of work accomplished greater than the sum of the working parts. However, for either city, if you removed the human occupants, you would no longer have a city—the cities are dependent on the population of micro-entities within their larger structure. Without humans, these cities would be become lifeless and cease to be New York or San Francisco.
Having a symbiosis of diverse individuals that can utilize diverse sources of nutrient energy and fight deadly elements confers survival flexibility despite environmental flux. In 1906, San Francisco survived a massive earthquake and fire that destroyed most of its structures because its human bionts stayed and worked to reconstruct it. In 2005, New Orleans was attacked by a hurricane yet, years later, is once again becoming a metropolis because its micro-bionts adapted to the change. Holobionts are hardy like cities particularly because they are more than one part. The very functional diversity that makes up the holobiont protects it from being decimated by fluctuating environmental pressures.