Apples with Oranges: Comparing the GS-FLX vs Ion Torrent Platforms for 16S Metagenomics Studies

Decreasing costs and faster turn-around times mean that next-generation platforms are more readily accessible to metagenomics researchers. We compared the suitability of the GS-FLX (XLR70) and Ion Torrent (314 with 100bp chemistry) to generate data sets that are suitable for 16S-based taxonomic metagenomics. Two marine samples (A and B) were prepared and run on both platforms, and the reads BLAST-aligned to a 16S database compiled from the GreenGenes dataset. Putative identities of the organisms present in the sample were obtained and sorted by the strength of their representation in the dataset. Sample diversity between the two samples on the 454 platform showed 95% similarity of the most highly represented organisms, while the PGM showed 85%. In addition, comparison of sample A between the 454 and PGM showed only 40% taxonomic similarity, with sample B showing 60%. These results suggest that the shorter reads produced by the ion torrent are currently not suited for 16S metagenomic analysis, which requires longer reads for accurate taxonomic identification. Ongoing improvements to the read lengths (>400bp) will result in the maturation of the PGM as a useful tool for microbial metagenomics.