dynamic relationships that exist among and between host organisms and their associated microorganisms—only a tiny fraction of which act as pathogens.
A recent revolution in our collective understanding of microbes is that the vast majority of these organisms live in communities and lead intensely interactive lives, competing, cooperating, and forming associations with one another and with their living and nonliving host environments. As the earth’s first living inhabitants, communities4 of microorganisms have had several billion years to coevolve and adapt to one another and their environments, resulting in a world of spectacular diversity and interdependence. Indeed, microbial communities are intricately intertwined with all ecosystems on Earth—from the extreme environments of the human gut to deep-sea hydrothermal vents and the windswept plains of Antarctica.
This ecological view of microbial life has enormous potential for transforming our understanding of the world around us. Recent research on the communities of microorganisms that live in and on us (the human microbiome) suggests that many traits once assumed to be “human”—such as the digestion of certain foods or the ability to defend against disease—may result from human-microbe interactions (Dethlefsen et al., 2007; IOM, 2006). Such findings have dispelled the notion that “human beings are physiological islands, entirely capable of regulating [our] own internal workings” and replaced it with the notion of the human body as a complex ecosystem (Ackerman, 2012). This realization “promises to radically alter the principles and practices of medicine, public health, and basic science” (Relman, 2012).
Recognition of the ubiquity and importance of microbial communities not only advances an ecological view of microbial life but also raises intriguing questions about the formation of groups that behave collectively in ways that have consequences for their individual members. There is mounting evidence to suggest that molecular “conversations” take place among members of a broad spectrum of microbial communities, and also between a variety of microbes and host organisms. Having only recently become aware that such conversations exist at all, our ability to eavesdrop on them and to translate them into scientific knowledge can be described as rudimentary at best. Yet, there is the emerging sense that microbes interact in complex, diverse, and subtle ways that we have yet to fully appreciate, much less understand.
Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them,
4 For the purposes of this overview, and as suggested by speaker Joan Strassmann of Washington University at St. Louis, “microbial community” simply means “all the small forms of life occurring in the same place and time, where same implies a shared place, with some possibility they will encounter each other, or take resources the other might have used.”