Data from: Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array

With the increasing democratization of high-throughout sequencing (HTS)
technologies, along with the concomitant increase in sequence yield per
dollar, many researchers are exploring HTS for microbial community
ecology. Many elements of experimental design can drastically affect the
final observed community structure, notably the choice of primers for
amplification prior to sequencing. Some targeted microbes can fail to
amplify due to primer-targeted sequence divergence and be omitted from
obtained sequences, leading to differences among primer pairs in the
sequenced organisms even when targeting the same community. This potential
source of taxonomic bias in HTS makes it prudent to investigate how primer
choice will affect the sequenced community prior to investing in a costly
community-wide sequencing effort. Here we use Fluidigm’s micro-fluidic
Access Arrays (IFC) followed by Illumina® MiSeq Nano sequencing on a
culture-derived local mock community to demonstrate how this approach
allows for a low-cost combinatorial investigation of primer pairs and
experimental samples (up to 48 primer pairs and 48 samples) to determine
the most effective primers that maximize obtained communities whilst
minimizing taxonomic biases.