AnnotIEM: novel tool for microbiome species-level annotation of 16S gene based microbial sequencing

Identification of microbial species is essential for the generation of meaningful results from microbiome analysis. However, correct annotation of 16S microbial sequences remains a challenge, especially down to the species-level, because most available databases of 16S sequences are not well curated. AnnotIEM is a new tool for species-level annotation of sequences derived from 16S rRNA gene sequencing. AnnotIEM’s novel hit-selection algorithm combines top-hit and majority-hit alignment results from multiple databases. Benchmarking using in-vitro and in-silico mock community control datasets showed that AnnotIEM’s annotation precision on species-level (median=0.83) is significantly (p<0.0001) better than any currently available annotation tool. Benchmarking using a number of real-world environmental microbiome studies demonstrated that AnnotIEM gives higher fraction (58-68%) of species-level annotated sequences, as compared to any other currently available tool. In conclusion, AnnotIEM significantly improves bacterial annotation, which can greatly enhance the results of any microbiome study, and could be potentially used also for other organisms.