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.

中文翻译：

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微生物组与感染专集

生物科学的最新发展很少能像微生物组研究的萌芽领域那样深刻或有影响力。在过去的十年中，微生物组参与了许多关键的生物过程，包括免疫系统发育、新陈代谢和行为。然而，研究人员仍在努力定义什么是健康的微生物组 (1)。微生物群落在个体之间存在差异，在物种水平上几乎没有重叠 (2)，因此几乎不可能通过列举微生物物种或对其基因进行编目来定义健康的微生物组 (3, 4)。我们无法将不断增加的微生物群测量深度转化为稳态框架，这可能是因为微生物群包含微生物群及其宿主环境 (5, 6)，但后者很少包含在分析中。换句话说，决定哪些微生物策略将在体内成功的环境因素需要与微生物群测量一起考虑，以了解什么构成了健康的微生物组 (7)。这些环境因素包括选择栖息地斑块中微生物生长和生存所需的表型特征的饮食和宿主功能 (8)。识别这些宿主功能的一种方法是研究粘膜病原体，因为它们的毒力因子针对所述宿主功能以改变栖息地特征，通常以促进病原体生长为目标 (9)。这一特性使病原体成为微生物组研究的绝佳工具 (10)。在这个关于微生物组和感染的特别收藏中，