Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

ABSTRACT: As new sequencing technologies become cheaper and older ones disappear, laboratories switch vendors and platforms. Validating the new setups is a crucial part of conducting rigorous scientific research. Here we report on the reliability and biases of performing bacterial 16S rRNA gene amplicon paired-end sequencing on the MiSeq Illumina platform. We designed a protocol using 50 barcode pairs to run samples in parallel and coded a pipeline to process the data. Sequencing the same sediment sample in 248 replicates as well as 70 samples from alkaline soda lakes, we evaluated the performance of the method with regards to estimates of alpha and beta diversity. Using different purification and DNA quantification procedures we always found up to 5-fold differences in the yield of sequences betwee

SUBMITTER: Sinclair L 

PROVIDER: S-EPMC4315398 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature