HTS data processing
The sequencing process provided 22 demultiplexed raw fastq files. For each file, the quality of raw data was assessed using FastQC tools (Andrews, 2010). Each set of paired ends reads were merged into a single sequence using the VSEARCH software (Rognes, Flouri, Nichols, Quince, & Mahé, 2016). The minimum length of the overlap region between the reads was at least 36 bp, and the overlap region should not include more than 3 mismatches and 5 ambiguous bases. Next, primers were trimmed off using the trim_oligos.pl software (Sáenz de Miera; not published). Then, poor quality sequencing reads were filtered out according to the following parameters: minimum length = 251 bp, maximum length = 272 bp and Phred quality score = 35 using VSEARCH (Rognes et al., 2016). Next, the identical sequences were dereplicated to obtain Independent Sequence Units (ISUs). Finally, the UCHIME algorithm of VSEARCH (Rognes et al., 2016) was used to remove chimeric sequences.