Integrated analysis of microbiome and host transcriptome unveils correlations between lung microbiota and host immunity in bronchoalveolar lavage fluid of pneumocystis pneumonia patients

Objective: Studies have indicated that the lung microbiota of patients with pulmonary diseases is disrupted and impacts the immunity. Pneumocystis pneumonia (PCP), a severe opportunistic pulmonary infection, is predominately attributed to host immune status. Little is known about the microbiological and immune landscape of the lungs in these patients. We aimed to explore the interaction between the lung microbiota and host immunity in PCP through multi-omics analysis. Methods: We selected pulmonary infection patients admitted to Beijing You An Hospital, Capital Medical University, from January 1, 2022 to August 31, 2022 and underwent bronchoscopy. Participants were divided into PCP and non-PCP group. We investigated the lung microbiota (via 16S rRNA gene sequencing) and host immune (via RNA-sequencing) on bronchoalveolar lavage fluid samples. The datasets were analyzed individually using bioinformatics approaches. Additionally, we performed spearman correlation analysis to assess the correlation between the OUT abundance of differential species and the expression levels of the differentially expressed genes (DEGs) related to the MAPK signaling pathway.