Processing pipeline of the sequencing data
Quality-based pre-processing and merging of paired-end reads for all the sequencing data files was as we described [For the 16S rRNA amplicon sequencing data, pre-processed joint reads were analysed following the SILVAngs pipeline [Processing and taxonomic assignment of the ITS2 reads was conducted in R (version 4.0.2) using the As expected, a significantly higher number of classified 16S and ITS reads in DNA extracts from the BALF specimens compared to the negative extraction controls was observed (Fig. S