Is 16S rRNA Sequencing Ready for Illumina Sequencer?
Claesson et al (2010) compared for the first time 16S rRNA metagenome sequencing on Roche GS FLX and Illumina GAIIx. Several tandem combinations of variable regions were targeted in microbial DNA extracted from fecal sample material and sequencing of the PCR amplicons was performed in a quarter segment of a full GS FLX run and a full lane of GAIIx with 2x 100 bp module.
Comparison revealed that taxonomic classification down to genus level is a lot worse for Illumina reads because of their shorter read length and higher error rate. Also the insight into rarely occurring species is far from increasing considerably in comparison to GS FLX sequencing, as it might have been expected because of the significantly higher coverage.
As the authors suggest a big step forward to increase classification efficiencies with Illumina technology is sequencing of fragments with insert sizes smaller than 200 bp. Following this strategy forward and reverse read which display poor quality at the read ends are overlapping and thus generate a consensus sequence with improved quality.
For sure respective studies are underway and we will continue to monitor the latest developments concerning this topic.