Special Collection on the Microbiome and Infection

EDITORIAL

Few recent developments in the biological sciences have been as profound or impactful as the budding field of microbiome research. In the past decade, the microbiome has been implicated in many key biological processes, including immune system development, metabolism, and behavior. However, researchers are still struggling to define what constitutes a healthy microbiome (1). Microbial communities differ between individuals, exhibiting little overlap on the species level (2), thus making it all but impossible to define a healthy microbiome by itemizing microbial species or cataloguing their genes (3, 4). Our inability to translate an ever-increasing depth of microbiota measurements into a framework for homeostasis might be rooted in the fact that the microbiome encompasses the microbiota and its host environment (5, 6), but the latter is rarely included in the analysis. In other words, environmental factors that determine which microbial strategies will be successful in the body need to be considered alongside microbiota measurements to understand what constitutes a healthy microbiome (7). These environmental factors include the diet and host functions that select for phenotypic characteristics required for microbial growth and survival in a habitat patch (8). One way to identify these host functions is to study mucosal pathogens, because their virulence factors target said host functions to alter habitat characteristics, often with the goal to promote pathogen growth (9). This property makes pathogens excellent tools for microbiome research (10). In this special collection on the microbiome and infection, we showcase this exciting new area of research with a series of articles exploring the interface between the host and its microbial ecosystem.

Our special issue is kicked off by three insightful minireviews on how the metabolism of the gut microbiota impacts cancer therapy (11), susceptibility to respiratory infection (12), and the pathogenesis of ulcerative colitis (13). A research article by David O’Dwyer and coworkers demonstrates that cohousing exerts a more dominant influence over the gut microbiota composition in mice than their genetic status of Toll-like receptor signaling (14). The remaining research articles describe investigations of how infection alters the microbiota composition or the functionality of the microbiome. Using a mouse model, Melanie Gareau and coworkers present evidence that enteropathogenic Escherichia coli infection in childhood can result in a lasting impairment of the gut brain axis (11). Francois Trottein’s group reveals that viral respiratory tract infection alters the gut microbiota composition to impair short-chain fatty acid production, thereby rendering mice more susceptible to enteric Salmonella infection (15). The laboratory of Ryan Hunter introduces the concept that the microbiota composition of the respiratory mucosa modulates the virulence of Staphylococcus aureus during upper airway infection in mice (16). In two back-to-back research articles, Jeffrey Whitey’s group uses a zebra fish model to show that Vibrio cholerae infection alters the gut microbiota composition (17), which is partly dependent on the pathogen deploying a type VI secretion system (18). Finally, Ana Weil and her team demonstrate that the gut microbiota influences the human immune response to an oral cholera vaccine (19). Collectively, these articles showcase the various approaches available for using pathogens to interrogate microbiome function in animal models and in humans.

We hope that you will enjoy reading this cutting-edge work on host microbiota interaction and consider submitting your future work in this field of study to Infection and Immunity.

The views expressed in this Editorial do not necessarily reflect the views of the journal or of ASM.