adult male bronchoalveolar fluid
Library construction was performed by DNA-fragmentation, end-repair, add A-tailing, adapter-ligation, and PCR amplification. The prepared libraries were quantified using Agilent 2100, and sequenced on an Illumina Next Seq 500 platform (Illumina, Inc.). All raw reads with high-quality data were obtained from the machine and low quality and low-complexity reads were removed. Next, the clean reads were mapped onto the UCSC human hg 19 reference database and excluded. The remaining reads were then aligned with the current bacterial, virus, fungal and parasite databases (NCBI; http://ftp.ncbi.nlm.nih.gov/genomes). Data were then classified and arranged based on bacteria, fungi, viruses and parasites. The database used in this study included 1,428 bacterial species, 1,130 viral species, 73 fungal species and 48 parasite species related to human diseases.