The city world in our gut is not a primitive culture. Rather it is a sophisticated conglomeration of a myriad of species that have all coevolved to live together (perhaps not in perfect harmony but in functional unity). In the past, the colon was considered an organ merely for absorbing water from indigestible material that makes up feces^[1]; however, now we know that the lower intestine is the site of many complex interactions between microbes, viruses, food, and our human cells. In particular, in the colon, one of the most important metabolic processes occurs: the microbial community ferments hard to digest food into simpler products that can be both used by microbes and absorbed by human cells. The fantastical microbial high-rises that cover every spare millimeter of the mucus layer provide a physical layer of defense from any roving microbial hordes that are looking to harm our human holobiont.

However, our human cells know better than to trust the microbial immigrants. In their quest for dominance over mucosal turf or nutrient energy, a microbe can potentially harm the human locals. All the leftovers from the small intestine—all that cellulose and indigestible sugar—enter the lower intestine, making the chaos of energy processing by microbes (usually in fermentative processes) so heated that human immune cells like dendrites and macrophages actively patrol the host side of the epithelial barrier to keep order, regularly taking samples of the mucus content by thrusting feelers through the tight junctions between human epithelial cells.  These sampling sessions tell our human system whether or not we have been attacked by a nasty foreign object or are happily cohabitating with our microbial colonists. Our immune system makes sure that every microbial inhabitant has the proper identification^[2] to live in the colon.  And microbes earn their keep and pay their rent in part by producing about 5-15% of the Calories our bodies can access as well as other vital molecules.

Though everything is related, we will most often focus on the colon in this book. The colon is the vibrant part of our holobiont. It is constantly changing in a cacophony of colors, smells, and inhabitants. It is here that we find life and death in epic proportions as every individual strives to out-compete its neighbor for energy and survive just long enough to pass on its genetic legacy. The microbes and viruses—yes, even our human cells—here will do anything to ensure this process works in their favor.

^[1] As well as its dangling appendage—the appendix, described as a useless vestigial structure from days gone by. However, we are learning that like the colon, the appendix is very important for gut health. It is now thought that the appendix serves as a fallout shelter of sorts, protecting microbes from the ravages of antibiotics and disease. Thus, the appendix can serve as reservoir of microbes to repopulate lost gut communities. The research on these concepts is very preliminary.

^[2] Our human cells learn which microbes are friendly or are foes by looking at the lipopolysaccharide (LPS) chains that dangle off the cells of every microbe. These LPS are often heavily modified and unique to that particular microbe.