Fig. 2.
Conceptual model of the human microbiome and layered factors influencing health and disease. The human microbiome can be conceptualized as having nested layers spanning epidemiologic to microscopic levels of organization, each of which can influence health and clinical outcomes such as infection. Community, diet, and medical treatments are among the most significant extrinsic factors (A) impacting the composition and function of the microbiome. Acute and chronic medical conditions as well as sociodemographic differences produce additional diversity in the microbiomes of individual patients (B). Within an individual, the distribution of microbes varies at anatomic and tissue levels (C), adding a spatial context to the dynamics of infection for surgeries performed on various body regions. The function and regulation of these communities are further affected by interactions between microbes (D) and with the host (E). At the level of an individual organism (F), differences in gene content, antimicrobial resistance, and virulence factor expression are clinically important determinants of infection that can be characterized and targeted.