Novaseq 6000 of SalmoSim pyloric caecum: replicate 3 time point 14
Sequence analysis was performed with our bioinformatic pipeline as described previously with slight modifications [33]. First, quality filtering and trimming (> Q30 quality score) was performed on all the reads of the 16S rRNA V1 hypervariable region using Sickle version V1.2 software [39]. Second, read error correction was performed using the BayesHammer module within SPAdes V2.5.0 software to obtain high-quality assemblies [40]. Third, paired-end reads were merged (overlap length 50 bp) using PANDAseq v2.11 software with a simple_Bayesian read merging algorithm [41, 42]. After overlapping paired-end reads, merged reads were dereplicated, sorted, and filtered chimaeras using the GOLD SILVA reference dataset [43], and singletons were removed by using the VSEARCH version 2.3.4 tool [44]. Merged paired-end filtered reads were clustered in operational taxonomic units (OTUs) using the VSEARCH software at 97% identity followed by a decontamination step by mapping OTUs against the host (Salmo salar) reference genome (available on NCBI) DNA using the BWA aligner implemented in the DeconSeq v0.4.3 tool [45]. Taxonomic assignment of OTUs was achieved using the Nave Bayesian Classifier [46] implemented in the QIIME 2 platform using the SILVA 132 database [47, 48]. Phylogenetic trees of OTUs were generated using FastTree software after using MAFFT for multiple sequence alignment [49]. The resultant OTU table was converted to a biological observation matrix (BIOM) format for the post-OTU statistical analysis [50].