Microbiome


Overview

The Genomics Center 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 Genomics Center 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.

Method Options


The Genomics Center 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 Genomics Center, 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. The MoBio DNA extraction kit provides a high level of purity for successful amplification of the sample’s organism. Please see our extraction page for details on all our extraction options available at the Genomics Center.

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 Genomics Center and pricing is listed under the pricing tab. External customers should contact Trina Kuriger for additional information. If your data analysis needs 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.

For updates on our microbiome service and all our technologies, events, and services offered at the Genomics Center, subscribe to our quarterly newsletter.

Pricing

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Standard

Service Scale Unit UMN External
Optional Extraction for Stool, Soil, and Other Environmental Samples.        
Low scale 24-48 sample $20.91 $24.52
Standard scale. 49-96 sample $15.54 $18.36
High Scale. Plate of 96. 1-any plate $1,249.92 $1,483.20
Dual-indexing. 16S/18S/ITS.        
Standard scale. 1-384 sample $9.12 $10.49
High Scale. 385-any sample $6.98 $8.03
Expedited. Standard scale1. 1-384 sample $14.05 $16.15
Expedited. High scale.1 385-any sample $9.98 $11.48
Amplicon-indexing. 16S/18S/ITS. Expedited.1        
Standard Scale. 1-any sample $8.54 $10.14
MiSeq. Sequencing.        
250-bp PE. v2. 8 million reads. 1-any lane $1,786.25 $2,136.96
300-bp PE. v3. 16 million reads. 1-any lane $2,248.60 $2,690.07
2x300 PE. v3. Expedited.1 1-any lane $2945.86 $3,385.67
2x300 PE. v3. Stowaway.2 1-4 1/8 lane $322.14 $385.39
16S Analysis. Tiered Pricing.3        
Required base cost/project. 1 project No charge $140.80
Additional cost/sample. 1-384 sample No charge $3.74
Cost/sample after 384th. 385-any sample No charge $1.85
Notes
  1. Expedited service is only available on a per 96-well plate basis and dependent on MiSeq availability. This rate must be paired with the Expedited MiSeq 300-bp PE run. Turnaround is ≤ 7 calendar days from sample submission, including MiSeq sequencing.
  2. Stowaway provides shallow (≤ 2M reads), low-cost sequencing for small-scale projects. Up to four 1/8 lanes can be requested with run time typically every 3 weeks. Clients needing faster turnaround should consider the iSeq instrument.
  3. UMN researchers can receive no charge analysis through MSI.
Guidelines

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Submission

How to Order


Please contact micbiom@umn.edu for project specifications.

Once project details are finalized, complete appropriate submission form for submitting samples or submitting client-made libraries and email to micbiom@umn.edu.

Forms


Sample submission form

Samples can be dropped-off at one of our locations.


1-202 Nils Hasselmo Hall (Minneapolis campus)
1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)
20 Snyder Hall (St. Paul campus)

If shipping samples, the following address should be used.


Please send the tracking information to micbiom@umn.edu.

University of Minnesota Genomics Center
Attn: Corbin Dirkx
4Front / Building 4 Suite E445A
3510 Hopkins Place N.
Oakdale, MN 55128   

Deliverables

Data Release


There are four options for transferring data from the UMGC to clients: 1) delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, 2) download from a secure website, 3) download with Globus, or 4) shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.

1. MSI storage

Internal clients have their data released to MSI's Shared User Resource Facility Storage (SURFS). Delivered data will be located in the "data_delivery" folder in your group's folder on MSI's primary filesystem (home/GROUP/data_delivery/umgc). MSI does not charge for SURFS storage costs, but files expire and are removed one year after they've been delivered. Files should be copied to other MSI storage locations such as Tier2, Tier3, or your group's "shared" folder before they expire. 

2. Web download

Internal clients that opt-out of MSI storage and external clients can download their data from a secure website using either a web browser or a command-line download tool, complete instructions are provided in an email from the UMGC. The client’s data is available for download for 30 days, after which the data will be removed from the data download website and the client takes responsibility for storing the data.

3. Globus

Internal and External clients can use Globus to download their data. This is the recommended method for external clients to download large datasets.

4. Hard drive

External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client at a cost of $250 per hard drive.

Data Recovery


The UMGC archives most customer data for a year and some datasets are retained for 5 years or more. If you need a dataset re-delivered email a request to next-gen@umn.edu to initiate data recovery. The UMGC does not provide any guarantee that data can be successfully recovered from the archive.