Microbiome

The UMN Genomics Center (UMGC) provides microbiome marker gene amplification and sequencing services, beginning from biological samples or from extracted DNA. We offer library prep for multiple marker genes, including bacterial 16S rRNA, fungal ITS1/ITS2, and eukaryotic 18S rRNA, using methods the UMGC developed, which in a report in Nature Biotechnology, were shown to provide more quantitatively accurate and qualitatively complete measurement of mock community reference standards than other commonly used protocols.

Marker-gene sequencing is typically carried out using the Illumina MiSeq platform, but deeper sequencing on the Illumina NextSeq for larger-scale projects, or for metagenomic and meta-transcriptomic methods is also available. For more information and to initiate a project, please contact our microbiome team.

Metagenomic Genome Assembly
It is now possible to assemble genomes directly from metagenomic samples using proximity ligation-based methods. Please see our library prep page for details.

Method Options

The UMGC offers two library prep methods for microbiome profiling: dual-indexing and amplicon-indexing. The dual-indexing method was developed in-house by Dr. Daryl Gohl and our microbiome team to reduce biases and errors resulting from amplicon-based methods. Our published method uses a two-step process in which the marker gene of interest is first amplified using a set of adapter-tailed primers, followed by addition of flow cell adapters and sample-specific indices by overlap extension.

Because of the improvements in quantification and accuracy, our “best practices” method is the most requested method in our microbiome service. Less commonly used, but still supported by the UMGC, is the amplicon-based approach – please contact our microbiome team for pricing using this method. Both methods support multiple marker gene variable regions for taxonomic profiling.

Extraction

Optional high-throughput extraction services are available using a “bead-beating” method that uses abrasive beads to break the cell walls of microbes in stool, soil, and other environmental samples. Qiagen's Powersoil Pro DNA extraction kit provides a high level of purity for the successful amplification of the sample’s organism. Please see our extraction page for details on all our extraction options available at the UMGC.

Sequencing

In addition to dedicated MiSeq runs, the UMGC offers a shared MiSeq service called Stowaway Sequencing (Stowaway-Seq). This service provides shared sequencing for researchers who need low-depth sequencing coverage. We do this by splitting a 2 x 300 bp PE flow cell into 8 “lanes” at ≤ 2M reads/lane, which users purchase on a first-come, first-served basis. Stowaway-Seq is most useful for targeted amplicon sequencing or small pilot projects to assess custom applications. 

Please see the UMGC Sequencer Home for the run schedule and additional information on our MiSeq Service page. 

Bioinformatics

Our bioinformatic service offers analysis of 16S and ITS1 data using a pipeline implemented the Qiime 1.9.1 analysis software. The analysis includes filtering raw fastq files for primer and adapter dimer sequences, removing contaminating host sequences and chimeric sequences, clustering sequences into OTUs using the Qiime open-reference OTU calling method with the greengenes 16S reference or UNITE ITS reference, 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.

These analysis services are provided free of charge to UMN groups by the Informatics Institute. Contact Trevor Gould for more information. 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. If your data analysis needs to go beyond what is supplied by the analysis pipeline contact the Research Informatics Solutions group at the Minnesota Supercomputing Institute for support.

Start a Project

Our microbiome team will help determine which options will best meet your project budget, turnaround, and experimental goals. We are an Illumina Certified Service Provider the for MiSeq platform and undergo rigorous annual certification to guarantee our clients receive the highest quality data using the most up-to-date sequencing workflows. To see if your next microbiome project would benefit from our published dual-indexing method and expert sequencing, contact us at micbiom@umn.edu.

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