Ion Torrent NGS-based simple and intuitive solutions for microbiome research

Here I review the applications of Ion Torrent NGS technology in the field of microbiome research and some recent publications about it. With Ion Torrent 16S rRNA next generation sequencing, there are two common methods. The first one is custom targeted sequencing for one or two hypervariable regions, and the second method is Ion 16S Metagenomics kit sequencing for seven hypervariable regions (V2, 3, 4, 6, 7, 8 and 9). The Ion 16S Metagenomics kit is designed for rapid and comprehensive analyses for bacterial community research.

With these two methods, the products of PCR amplicons can be sequenced Ion Torrent NGS system (Ion GeneStudio S5 System) and analyzed using metagenomics workflow in the Ion Reporter software (Cloud computing service or local server). Microbiome researches based on Ion Torrent NGS using these methods have been introduced in various publications including intestinal, skin, oral microbiomes with humans or other animals, and forensic investigations.

Thermo Fisher has also released another very new and interesting kit for species-level microbiome profiling of microbial diversity in the human gut microbiome. This Ion AmpliSeq Microbiome Health Research Kit targets 8 out of the 9 hypervariable regions for increased resolution, and specific amplicons for 73 key bacterial species with immuno-oncology as well as autoimmune diseases and gut-related disorders. This new kit can be a very useful solution between simple 16S rRNA gene amplicon-based sequencing and very expensive and complicated shotgun metagenome sequencing.