biostudies-arrayexpressYu Chenmixed samplehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15179Metagenome sequencing All specimens were collected and immediately stored in a -80 freezer. All BALF samples were subjected to MS. DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech). DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China). Bioinformatic pipeline analysis Low-quality and short (<35 bp) reads were removed from raw data using fastp [10]. Remaining reads were mapped to the human reference genome (hg19) using the Burrows-Wheeler method to remove sequences of human origin. Filtered reads were classified with RefSeq, downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/).biostudies-arrayexpressSample Collection - Bronchoalveolar lavage fluid (BALF) was collected and stored at -80°CSequencing - Low-quality and short (<35 bp) reads were removed from raw data using fastpNucleic Acid Extraction - DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech).Library Construction - DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China)OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - All specimens were collected and immediately stored in a -80 freezer. All BALF samples were subjected to MS. DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech). DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China). Bioinformatic pipeline analysis Low-quality and short (<35 bp) reads were removed from raw data using fastp [10]. Remaining reads were mapped to the human reference genome (hg19) using the Burrows-Wheeler method to remove sequences of human origin. Filtered reads were classified with RefSeq, downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsBGISEQ-500DNA-seqmixed sampleYu ChenfalseFour groups of distinct lung microbiota in pulmonary diseasesMetagenome sequencing All specimens were collected and immediately stored in a -80 freezer. All BALF samples were subjected to MS. DNA was extracted from BALF using the TIANamp Micro DNA kit (DP316, Tiangen Biotech). DNA libraries were constructed with the end-repair method and then sequenced on the BGI Sequencer platform (BGI Genomics, Shenzhen, China). Bioinformatic pipeline analysis Low-quality and short (<35 bp) reads were removed from raw data using fastp [10]. Remaining reads were mapped to the human reference genome (hg19) using the Burrows-Wheeler method to remove sequences of human origin. Filtered reads were classified with RefSeq, downloaded from NCBI (ftp://ftp.ncbi.nlm.nih.gov/genomes/).2026-06-30T00:00:00Z2026-06-30T01:00:55.03Z2025-05-29T10:54:16.185ZE-MTAB-15179ERP173003EFO_0002944EFO_0004170EFO_0002693EFO_0005518EFO_0003816EFO_0004184