Microbiome Sequencing

Optional high-throughput DNA extraction services are available using a bead-beating method, which employs abrasive beads to efficiently lyse microbial cell walls in stool, soil, and other environmental samples. The Qiagen PowerSoil Pro DNA extraction kit ensures high-purity DNA suitable for successful organism amplification. For extraction options and pricing, please visit our extraction services page.

Dual-indexing Method: Developed in-house by Dr. Daryl Gohl and the microbiome team, dual-indexing minimizes biases and errors associated with amplicon-based methods. This published approach uses a two-step process: first, amplifying the target marker gene with adapter-tailed primers, followed by the addition of flow cell adapters and sample-specific indices via overlap extension. Because of the improvements in quantification and accuracy, our “best practices” method is the most requested method.

Amplicon-indexing Method: Less commonly used, but still supported by the UMGC, is the amplicon-based approach. Please contact us for pricing using this method.

Dedicated Sequencing Runs: The Element AVITI24 is now the preferred platform for 16S/18S/ITS sequencing, offering faster, higher-quality, and more affordable sequencing. Benchmarking by the UMGC shows its performance is comparable to Illumina for 16S V4V5, though mid-project transitions are not recommended.

Shared Sequencing Runs: The UMGC's Stowaway Sequencing service offers shared AVITI24 sequencing for low-depth coverage, dividing a 2×300 bp Medium flow cell into four lanes (≤ 25M reads/lane). Ideal for targeted amplicon sequencing or small pilot projects, lanes are available on a first-come, first-served basis. 

See the Element AVITI24 pricing tab for rates. 

Our bioinformatic service offers analysis of 16S and ITS1 data using a pipeline implemented with the Qiime2 analysis software. The analysis includes filtering raw fastq files for primer and adapter dimer sequences, denoised using dada2, and calculating alpha and beta diversity metrics. These analysis results are summarized in a report, which includes a series of quality-control plots, interactive 3D PCA plots, taxonomy summary plots, and data summary tables.

Analysis is offered to external customers by the UMGC and pricing is listed under the pricing tab. External customers should contact Trina Kuriger for additional information. Analysis for UMN customers is available from the Minnesota Supercomputing Institute's Research Informatics group. Contact Trevor Gould for more information.