We offer the standard Illumina 16S rRNA Demonstrated Protocol with up to 384 samples per MiSeq v3 Reagent kit sequencing run for microbial taxonomic diversity. We also offer large scale 16S rRNA Metagenomics protocols such as the one published by Caporaso et al. (2011) with longer inline barcodes and higher plexity.
The 16S rRNA metagenomics protocol is very useful as a screening tool in a project where the sample size is large. Results are presented as relative percentage abundance per sample and these can be show as tables and graphs.
Whereas 16S, 18S and ITS metagenomics uses a targeted sequencing profile, the shotgun metagenomics workflow does not target a specific region. The entire microbial community DNA sample is sequenced and the data is analysed using a set of different software tools such as MG-Rast or Kraken. Shotgun metagenomics is more sensitive and will give reliable profiles down to isolate level depending of the sequencing coverage used. It identifies all types of microbes in the sample such as bacteria, fungi, virus, protozoa including the host.
An example workflow in a projects with large samples would typically start with 16S rRNA/ 18S SSU rRNA screening of large samples. This will identify interesting samples showing taxonomic profiles. The second stage where more accurate data with high resolution is require would typically shift to shotgun metagenomics.
This application provides microbial eukaryotic taxonomic profiling using primers that targets the 18S SSU rRNA and are based on those of Amaral-Zettler et al. (2009). The constructs are designed to be used with the Illumina platform. The protocol is based on the Illumina 16S rRNA Demonstrated Protocol.
At Agiomix, our lab uses standardized SOPs with QC gates after every stage in the workflow to ensure the integrity of the final result.