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Although researchers have found that the microbiota changed during the lower respiratory tract (LRT) infection, little was known about the association between LRT microbiome and refractory pneumonia (RMPP). From June 28th, 2019 to March 23rd, 2020, we enrolled fifty-two children diagnosed with RMPP or non-refractory pneumonia (NRMPP), and characterized the structure and function of microbiota in the bronchoalveolar lavage fluid (BALF) by metagenomic next generation sequencing (mNGS). Based on Bray-Curtis distance between samples, samples