Challenges of Comparing Marine Microbiome Community Composition Data Provided by Different Commercial Laboratories and Classification Databases

In the high-throughput sequencing (HTS) era, a metabarcoding technique based on bacterial V3–V4 hypervariable region of 16S rRNA analysis requires sophisticated bioinformatics pipelines and validated methods that allow researchers to compare their data with confidence. Many commercial laboratories conduct extensive HTS analyses; however, there is no available information whether results generated by these vendors are consistent. our study, we compared obtained for same marine microbiome community sample three laboratories. Additionally, as control determine differences between two databases, also performed “mock community” defined number microbial species. We assessed impact choice commonly used i.e., Greengenes SILVA, downstream analysis, including taxonomic classification assignment. demonstrated final depend laboratory conducting reference database ribosomal sequences. Our findings showed produced ASVs (amplicon sequence variants) ranged from 137 564. Different putative endosymbionts could be identified, correspond applied database. The presented might particular interest who plan perform using marker gene, identification endosymbionts, serve guide choosing optimum pipeline obtain most accurate reproducible data.