GitHub repository linked: sudu87/Microbial-ecology-of-the-transplanted-human-lung. This contains the code, bacterial culture collection and README.md. Linked to publication: https://doi.org/10.1038/s41467-021-22344-4 Description of datasets given below: All_BAL_samples_raw_fastqc: FastQC reports for raw sequencing data after merging all samples. All_BAL_samples_processed_fastqc: FastQC reports for trimmed and curated merged data. Supplementary_Data_1: Table of 16S rRNA amplicon sequencing information, such as OTU relative abundance and taxonomy, by sample, without negative controls. Supplementary_Data_2: Table of 16S rRNA amplicon sequencing information, such as OTU relative abundance and taxonomy, for each negative control. Supplementary_Data_3: Detailed table showing frequency of all OTUs detected across the 234 BALF samples in terms of their abundance and prevalence. Supplementary_Data_4: List of Lung microbiota culture collection (LuMiCol) isolates with detailed information about sample number, culture conditions, taxonomy. This is a non-curated list containing about 300 isolates of which 215 were used for analysis. Supplementary_Data_5: OTU-isolate match summary listing the isolates that match OTUs in their 16S rRNA gene sequence, and information about the number of representative isolates in LuMiCol, with at least one representative isolate name, prevalence, and preference in terms of oxygen condition and media. Supplementary_Data_6: Detailed input and output files from unsupervised machine learning approach used by Genocrunch to determine Partition around medoids (PAMs) i.e. pneumotypes. The zip file includes parameters files: json and text files and Silhouette plots. Supplementary_Data_7: Detailed metadata table associated with all patients and samples.