Palidis: fast discovery of novel insertion sequences

The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinfor-matics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this cata-logue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.

Automated summary

The diversity of microbial insertion sequences, which are important in generating diversity in microbial genomes, is currently not well represented in microbial databases. In this study, a bioinformatics pipeline called Palidis is introduced to rapidly identify insertion sequences in metagenomic data from mixed microbial communities. Applying Palidis to 264 human metagenomes reveals 879 unique insertion sequences, with 519 being previously unknown. Querying this catalogue against a large database of isolate genomes provides evidence of horizontal gene transfer events across bacterial classes. The development of the Insertion Sequence Catalogue will be continued to serve as a valuable resource for researchers studying insertion sequences in microbial genomes.