16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria.

ABSTRACT:

Aims

Test the choice of 16S rRNA gene amplicon and data analysis method on the accuracy of identification of clinically important bacteria utilizing a benchtop sequencer.

Methods and results

Nine 16S rRNA amplicons were tested on an Ion Torrent PGM to identify 41 strains of clinical importance. The V1-V2 region identified 40 of 41 isolates to the species level. Three data analysis methods were tested, finding that the Ribosomal Database Project's SequenceMatch outperformed BLAST and the Ion Reporter Metagenomics analysis pipeline. Lastly, 16S rRNA gene sequencing mixtures of four species through a six log range of dilution showed species were identifiable even when present as 0·1% of the mixture.

Conclusions

Sequencing the V1-V2 16S rRNA gene region, made possible by

SUBMITTER: Watts GS 

PROVIDER: S-EPMC5765505 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature