Library preparation and sequencing of the amplicons were carried out at the Core Facility Molecular Biology, Centre for Medical Research at the Medical University Graz, Austria. In brief, DNA concentrations were normalised using a SequalPrep™ normalisation plate (Invitrogen), and each sample was indexed with a unique barcode sequence (8 cycles index PCR). After pooling of the indexed samples, a gel cut was carried out to purify the products of the index PCR. Sequencing was performed using the Illumina MiSeq device and MS-102-3003 MiSeq® Reagent Kit v3-600cycles (2 × 150 cycles). The obtained fastq data is available in the European Nucleotide Archive under the study accession number: PRJEB41618.
The fastq data analysis was performed using QIIME277 (link),78 (link). After quality filtering, the DADA2 algorithm79 (link) was used to denoise truncated reads and generate amplicon sequence variants (ASVs). Taxonomic classification80 (link) was based on the SILVA v132 database81 (link) and the obtained feature table and taxonomy file were used for further analysis (Supplementary Table4 ). The overlapping features from negative controls (DNA extraction and PCR negative controls) were manually subtracted or removed from both the bacterial and archaeal dataset. The reads classified as chloroplast and mitochondria were also removed.
The fastq data analysis was performed using QIIME277 (link),78 (link). After quality filtering, the DADA2 algorithm79 (link) was used to denoise truncated reads and generate amplicon sequence variants (ASVs). Taxonomic classification80 (link) was based on the SILVA v132 database81 (link) and the obtained feature table and taxonomy file were used for further analysis (Supplementary Table
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