Fig. 1

Distinct respiratory microbiome in CAP patients compared with healthy controls. a Overview of the study design. Hospitalized CAP patients were enrolled, and longitudinal samples were collected for respiratory/gut microbiome and host response profiling. The host‒microbe interactions detected were validated in a mouse model. b Compared with healthy controls, CAP patients expressed lower microbial diversity at admission. c The reduced alpha diversity persisted throughout the entire disease course and even 4 months post discharge. d Principal coordinate analysis (PCoA) based on the Bray‒Curtis distance revealed significant differences in sputum microbiota composition among CAP patients, healthy controls, and follow-up samples. e-f Cooccurrence network of microbes in healthy controls (e) CAP patients (f) and follow-up samples (g). Each node represents a microbial species, and edges represent statistically significant co-occurrence relationships. Prominent genera in major modules are colored and annotated on the plot. The numbers of nodes (N) and normalized edges per sample (E/sample) are shown at the top of each panel