Different nasopharynx and oropharynx microbiota imbalance in children with Mycoplasma pneumoniae or influenza virus infection

Background: The Mycoplasma pneumoniae(MP) and influenza virus are two common pathogens causing pediatric acute respiratory tract infection. Though emerging reports demonstrated imbalanced respiratory microbiota in respiratory infection, the respiratory microbiota differences between MP and influenza virus remained to be explored. 
Methods: We collected paired nasopharyngeal(NP) and oropharyngeal(OP) microbial samples from 165 children, including 40 patients with MP pneumonia, 66 patients with influenza virus infection and 59 age-matched healthy children. 
Results: The NP and OP microbial diversity decreased in MP infection and increased in influenza infection as compared to healthy children. The Staphylococcus dominated Mycoplasma pneumoniae pneumonia(MPP) patients’ NP microbiota while five representative patterns remained in influenza patients. In OP microbiota, Streptococcus significantly enriched in MPP group and decreased in Influenza group. Decision tree analysis indicated that Ralstonia and Acidobacteria could discriminate microbial samples in healthy (59/67), MP (35/38) and Influenza groups (55/60) with high accuracy. 
Conclusions: This study revealed that dominant bacterial structure in the airway was niche- and disease-specific. It could facilitate the stratification of respiratory microbial samples with different infectious agents.