2.3.1. Sequence screening and preparations for meta-analysis
We used Quantitative Insights into Microbial Ecology (QIIME2) version
2019.10 [18], for the meta-analysis. QIIME2
pipeline provides a start-to-finish workflow, beginning with
demultiplexing sequence reads and finishing with taxonomic and
phylogenetic profiles. The sequences from the individual study were
imported to QIIME2 using CasavaOneEight format, and the quality of the
sequences was checked by the default settings in QIIME2. Based on the
sequence quality, the sequence was trimmed, denoised, aligned and
checked for chimera using DADA2 (single and paired-ends sequence were
trimmed based on the length of primer used) [21].
The feature table and representative sequence of each file were merged
using QIIME2 feature merge table and merged representative sequences.