"Clipping of adapter and primer sequences was done using cutadapt (v4.1). Reads with ambiguous base-calls (Ns) were first removed to accurately map short adapter and primer sequences. Paired-end reads without an exact match to the forward and reverse adapter and primer sequence were removed. Further processing of the sequencing data was done with the DADA2 R package (v1.24.0) in R (v 4.2.2) according to (Callahan et al. 2016). As first quality control step, truncation was done with a quality score cut-off (truncQ=2). Additional filtering to eliminate reads containing any ambiguous base calls or reads with high expected errors (maxEE=2,2) was performed. Reads mapping to the Phix genome were discarded as well. After dereplication, further denoising using the Divisive Amplicon Denoising Algorithm (DADA) error estimation algorithm and the sample inference algorithm selfConsist (with nbases=1e8) was done. The obtained error rates were checked and monotonicity was enforced in the model fit to deal with binned quality scores. The loess function was reweighted (log10 transformation of total transition probabilities) whilst the span was adjusted to 2. Denoised reads inferred were subsequently merged. Finally, the amplicon sequence variant (ASV) table obtained after the removal of chimera was used for taxonomy assignment. This was done with the Naive Bayesian Classifier (with an 80% minimal bootstrap confidence threshold) and the DADA2 formatted Silva v132 and RDP trainset 16 reference taxonomy according to (Quast et al. 2013; Wang et al. 2007). "