Second Genome Solutions provides a cost-effective, highly-parallel sequencing service utilizing the Illumina MiSeq® sequencing system for conducting 16S community analysis. Using primers designed to target specific variable regions of the 16S ribosomal RNA gene, this method allows classification of both known and unknown bacteria. This method also enables comparative analysis between the relative abundance of bacterial and archaeal species.

Laboratory Methods

Next-generation sequencing has emerged as a powerful tool for investigating microbial communities in large sample sets. Our laboratory method begins with purified genomic DNA. Primers are tailed with sequences to incorporate indexing barcodes, and samples are pooled into a single library for sequencing. Taxonomic profiling on the MiSeq system is cycled to generate paired 250-bp reads in our protocols. These longer read lengths provide high-quality full length-reads of the gene to ensure the most accurate classification available through sequencing technologies. Raw data is available in FAST-Q files.


From the team that developed the cutting-edge technologies and software for microbiome profiling and analyses such as QIIME, PhyloChip and PhyloSeq, Second Genome Solutions offers an up-to-date analyses using its proprietary 16S bioinformatic data analysis software package, SecondGenomeR. This software can quickly provide compelling insight to your microbiome investigation. The software package was developed exclusively for microbiome comparative analyses, multivariate statistical analyses, and is a powerful interpretation tool for research and discovery. The bioinformatic pipeline for Second Genome Solution's 16S Community Analysis Pipeline incorporates several stages:

  • Sequence processing
  • Sequencing depth
  • Normalization
  • Sample composition overview
  • Sample-to-sample distance metrics
  • Ordination and clustering
  • Microbiome significance testing