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As soon as we are born, bacteria move in. They stake claims in our digestive and respiratory tracts, our teeth, our skin. They establish increasingly complex communities, like a forest that gradually takes over a clearing. By the time we’re a few years old, these communities have matured, and we carry them with us, more or less, for our entire lives. Our bodies harbor 100 trillion bacterial cells, outnumbering our human cells 10 to one. It’s easy to ignore this astonishing fact. Bacteria are tiny in comparison to human cells; they contribute just a few pounds to our weight and remain invisible to us.
It’s also been easy for science to overlook their role in our bodies and our health. Researchers have largely concerned themselves with bacteria’s negative role as pathogens: The devastating effects of a handful of infectious organisms have always seemed more urgent than what has been considered a benign and relatively unimportant relationship with “good” bacteria. In the intestine, the bacterial hub of the body that teems with trillions of microbes, they have traditionally been called “commensal” organisms — literally, eating at the same table. The moniker suggests that while we’ve known for decades that gut bacteria help digestion and prevent infections, they are little more than ever-present dinner guests.
But there’s a growing consensus among scientists that the relationship between us and our microbes is much more of a two-way street. With new technologies that allow scientists to better identify and study the organisms that live in and on us, we’ve become aware that bacteria, though tiny, are powerful chemical factories that fundamentally affect how the human body functions. They are not simply random squatters, but organized communities that evolve with us and are passed down from generation to generation. Through research that has blurred the boundary between medical and environmental microbiology, we’re beginning to understand that because the human body constitutes their environment, these microbial communities have been forced to adapt to changes in our diets, health, and lifestyle choices. Yet they, in turn, are also part of our environments, and our bodies have adapted to them. Our dinner guests, it seems, have shaped the very path of human evolution.
In October, researchers in several countries launched the International Human Microbiome Consortium, an effort to characterize the role of microbes in the human body. Just over a year ago, the National Institutes of Health also launched its own Human Microbiome Project. These new efforts represent a formal recognition of bacteria’s far-reaching influence, including their contributions to human health and certain illnesses. “This could be the basis of a whole new way of looking at disease,” said microbiologist Margaret McFall-Ngai at the 108th General Meeting of the American Society for Microbiology in Boston last June. But the emerging science of human-microbe symbiosis has an even greater implication. “Human beings are not really individuals; they’re communities of organisms,” says McFall-Ngai. It’s not just that our bodies serve as a habitat for other organisms; it’s also that we function with them as a collective. As the profound interrelationship between humans and microbes becomes more apparent, the distinction between host and hosted has become both less clear and less important — together we operate as a constantly evolving man-microbe kibbutz. Which raises a startling implication: If being Homo sapiens through and through implied a certain authority over our corporeal selves, we are now forced to relinquish some of that control to our inner-dwelling microbes. Ironically, the human ingenuity that drives us to understand more about ourselves is revealing that we’re much less “human” than we once thought.
To find a biological answer to the question “Who are we?” we might look to the human genome. Certainly, when the Human Genome Project first produced a draft of the 3 billion-base-pair sequence, it was touted as a blueprint for human life. Less than a decade later, however, most experts recognize that our genomes capture only a part of who we are. Researchers have become aware, for example, of the influence of epigenetic phenomena — imprinting, maternal effects, and gene silencing, among others — in determining how genetic material is ultimately expressed. Now comes the notion that the genomes of microbes within us must also be considered. Our bodies are, after all, composites of human and bacterial cells, with microbes together contributing at least 1,000 times more genes to the whole. As we discover more and more roles that microbes play, it has become impossible to ignore the contribution of bacteria to the pool of genes we define as ourselves. Indeed, several scientists have begun to refer to the human body as a “superorganism” whose complexity extends far beyond what is encoded in a single genome.
The physiology of a superorganism would likely look very different from traditional human physiology. There has been a great deal of research into the dynamics of communities among plants, insect colonies, and even in human society. What new insights could we gain by applying some of that knowledge to the workings of communities in our own bodies? Certain body functions could be the result of negotiations between several partners, and diseases the result of small changes in group dynamics — or of a breakdown in communication between symbiotic partners.
Recently, for instance, evidence has surfaced that obesity may well include a microbial component. In ongoing work that is part of the Human Microbiome Project, researchers in Jeffrey Gordon’s lab at the Washington University School of Medicine in St. Louis showed that lean and obese mice have different proportions of microbes in their digestive systems. Bacteria in the plumper rodents, it seemed, were better able to extract energy from food, because when these bacteria were transferred into lean mice, the mice gained weight. The same is apparently true for humans: In December Gordon’s team published findings that lean and obese twins — whether identical or fraternal — harbor strikingly different bacterial communities. And these bacteria, they discovered, are not just helping to process food directly; they actually influence whether that energy is ultimately stored as fat in the body.
Even confined in their designated body parts, microbes exert their effects by churning out chemical signals for our cells to receive. Jeremy Nicholson, a chemist at Imperial College of London, has become a champion of the idea that the extent of this microbial signaling goes vastly underappreciated. Nicholson had been looking at the metabolites in human blood and urine with the hope of developing personalized drugs when he found that our bodily fluids are filled with metabolites produced by our intestinal bacteria. He now believes that the influence of gut microbes ranges from the ways in which we metabolize drugs and food to the subtle workings of our brain chemistry.
Scientists originally expected that the communication between animals and their symbiotic bacteria would form its own molecular language. But McFall-Ngai, an expert on animal-microbe symbiosis, says that she and other scientists have instead found beneficial relationships involving some of the same chemical messages that had been discovered previously in pathogens. Many bacterial products that had been termed “virulence factors” or “toxins” turn out to not be inherently offensive signals; they are just part of the conversation between microbe and host. The difference between our interaction with harmful and helpful bacteria, she says, is not so much like separate languages as it is a change in tone: “It’s the difference between an argument and a civil conversation.” We are in constant communication with our microbes, and the messages are broadcast throughout the human body.
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