Microbes: Partners in Evolution
The last twenty years of studying microbes has allowed us to understand that microbes aren’t optional forms of life that live within us; they truly constitute part of who we are biologically. To get a better grasp on this, we must first understand that our partnership with microbes is as old as the first species of hominids (our ancestors), and that the evolutionary changes that hominids experienced were accompanied by changes in our microbiota, too. Throughout human history there have been only a few landmark evolutionary bursts (rapid evolutionary changes) that have marked the course of hominids. Interestingly, two of them can be clearly linked to changes in our intestinal physiology and thus with our microbiome.
As hunters and gatherers (a lifestyle that lasted about 2.5 million years), our ancestors had no permanent homes, living in temporary shelters with few possessions so they could easily move from one place to another. Depending on the geographic region they inhabited, early humans ate different mixtures of meats, roots, tubers, and fruits—whatever was in season. Then an extremely important event occurred that led to one of these evolutionary bursts: our ability to control fire and cook food. We completely take it for granted now, but cooking food made it safer to eat, as heat kills the disease-causing bacteria that thrive in decomposing meat. It also changes the chemistry of the food itself, making it much easier to digest and a lot richer in energy. This sudden increase in energy levels changed everything for humans. No longer did our ancestors have to spend hours chewing raw food in order to extract enough calories to sustain everyday life. Think of what our closest relatives in nature, apes, are almost always doing when see them in the zoo or on TV. If humans hadn’t developed a way to cook food we, too, would have to spend six hours chewing five kilos of raw food every day to get enough energy to survive, just like our primate cousins do.
The fossil records of humans from this period consist of bones and teeth, making it impossible to determine what type of microbiota lived in the intestines of ancient hunters and gatherers. However, anthropologists have been able to show that the change in lifestyle and diet that resulted from the advent of cooking had anatomical consequences involving the intestines. As energy intake increased, the intestines of our human ancestors shortened and, amazingly, their brains grew, too, increasing in size by about 20 percent. Given what we know today about the link between gut microbes and brain development, it is very likely that intestinal microbiota had a part in this “sudden” brain growth. Brain enlargement improved our capacity to hunt, communicate, and socialize. In other words, cooking made us smarter—it made us human.
Another evolutionary landmark occurred about eleven thousand years ago. Certain groups of humans realized, probably by chance, that fallen grains from the wild wheat stalks they collected would give rise to more wheat if planted. When humans learned to domesticate plants for food, they tossed away their nomadic ways for a settled lifestyle. Having crops nearby meant that previously small tribes of a few dozen humans could grow to a few hundred, which in turn gave rise to basic traits of civilization, such as trade, written language, and math. If it weren’t for farming, we would all still be picking berry after berry from bushes and walking miles every day. The emergence of agriculture coincides with the appearance of the first cities; inadvertently, agriculture built our modern social structures. This lifestyle change was so successful that farmers replaced foragers, and these days only a handful of people maintain a hunter-gatherer way of life.
As expected, the lifestyle associated with farming came with major dietary changes. Humans no longer ate small bites throughout the day with the occasional feast after a hunt since farmers had a steady and somewhat predictable supply of foods. So how did this affect our microbiota? By domesticating grains and consequently obtaining most of their daily calories from their new crops, the diet of farmers became less diverse. Based on what is currently known about the microbiota’s response to diet, their microbiota likely became less diverse, too. In fact, comparing the intestinal microbiota of the Hazda people of Tanzania, one of the few contemporary tribes that relies on foraging, to a modern farmer is like comparing a rain forest to a desert, in terms of biodiversity. Less diversity in our microbiota is associated with a number of human diseases, many of which we cover in later chapters.
Although farming has been around for only eleven thousand years (just 0.004 percent of human history!), physiological changes have also been linked to the agricultural diet, and some of these changes involve our resident microbes. The new diet brought with it cavities and other periodontal diseases, mediated by bacteria rarely found in foragers. Our teeth, jaws, and faces have grown smaller, too, probably because chewing was reduced on such a diet. Some evolutionary biologists believe that we lived a healthier lifestyle as foragers, and that humans traded in that healthier lifestyle for food security and more babies (not a bad deal, actually!). Certain nutritionists have extrapolated from this a recommendation that, in order to promote health, all modern humans should eat the way hunters and gatherers did, but this has been debunked by top evolutionary biologists based on the fact that humans have adapted genetically to the challenges that farming generated (see the Caveman Diet, page 30).
What these two major events in human history teach us is that changes in lifestyle are accompanied by changes in our microbiota, and that these microbial changes might affect our health for better (e.g., cooking food and decreasing infections) or worse (e.g., agriculture and less microbial diversity). Whether we like it or not, we are married to microbes for life, in sickness and in health, for richer or for poorer.
Bugs “R” Us
Our microbes are part of what make us human, but our current way of living and eating, especially in the Western world, has exerted further changes in our microbiota and in our biology. In the past hundred years, and especially the last thirty years, humans have learned to process foods to make them tastier, more digestible, and more shelf-stable than ever before. On top of this, our push to clean up our world in order to fight infectious diseases, including the use of antibiotics, has further shifted the composition and diversity of our microbial communities. Double-punching our microbiota like this has induced huge changes in our intestinal environments and, as we will learn in the following chapters, on many other aspects of our bodies’ normal functions.
In order to appreciate how the microbiota influences our health, it is important that we discuss certain basic biological concepts about our microbiota and the organ most of them call home, the human intestine. The human microbiota consists of bacteria, viruses, fungi, protozoa, and other forms of microscopic life. They inhabit our skin, oral and nasal cavities, eyes, lungs, urinary tract, and gastrointestinal tract—pretty much any surface that has exposure to the outside world. Another term that is frequently used is microbiome, which refers not only to the identity of all the microbes living within us, but also to what they do. A total of 1014 microbes are estimated to live in the human body and, as mentioned, the intestinal tract is the biggest reservoir of microbes, harboring approximately 1013 bacteria. It is this community that influences us, their host, the most. In fact, unless otherwise noted throughout this book, when we use the term microbiota, we are referring to the intestinal microbiota. Although bacteria are approximately twenty-five times smaller than human cells, they account for a significant amount of our weight. If we were to get rid of our microbiota we would lose around three pounds, or about the weight of our liver or brain! A single bowel movement is 60 percent bacteria numbering more than all the people on this globe, a deeply disturbing fact for germophobes.
For microbes, the gastrointestinal system is a fabulous place to live. It’s moist, full of nutrients, and sticky (allowing microbes to adhere to it), and in many sections it completely lacks oxygen. Although it seems counterintuitive that any life-form would favor a place without oxygen, an enormous number of bacterial species either prefer or require such a place, as this world evolved for billions of years without oxygen.