Background:
Community acquired pneumonia (CAP) is a heterogeneous disease with a variety of causative pathogens and is a leading cause of morbidity and mortality. The characteristics of the CAP lower respiratory microbiota, as well as its dynamics and association with disease progression, are largely unknown.
Methods:
In this study, 1068 time-series sputum samples from 350 CAP inpatients were sequenced for the V3-V4 region of 16S rRNA.
Results:
The respiratory tract microbiota of CAP patients was composed of a variety of commensal bacteria or dominated by a single opportunistic pathogen (Pseudomonas, Acinetobacter, Mycoplasma, and Enterobacteriaceae), with the former scenario being more frequently observed in non-severe cases. Besides, the microbiota in severe cases had a lower alpha diversity and being enriched with Enterobacteriaceae compared to the non-severe cases and healthy population. Two pathways involved in menaquinol and butyrate synthesis were predicted to be more abundant in non-severe cases. Moreover, there were greater changes in the microbiota of severe patients than those of mild cases after admission, and intubation was frequently followed by Acinetobacter expansion. Additionally, we found that the infection by different pathogens seems to lead to different alterations in the microbiota.  
Conclusion：
Despite that the respiratory microbiota of most CAP patients did not include a high abundance of known pathogens, the composition and dynamics of the microbiota were distinct between the severe and non-severe patients. Clarifying the relationship between respiratory microbiota and the development of CAP will facilitate our understanding of the etiology of pneumonia and the establishment of effective diagnostic tools and more efficient treatment.
 

微生物组；肺炎