Microbiome
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 ITS 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.
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
- 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.
- 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.
- UMN researchers can receive no charge analysis through MSI.
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
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)
100 Westgate Drive (St. Paul off-campus at UEL)
If shipping samples, the following address should be used.
Please send the tracking information to micbiom@umn.edu.
University of Minnesota Genomics Center
312 Church Street NE
1-202 Nils Hasslemo Hall
Minneapolis, MN 55455
612-624-3177
Deliverables
Data Release
There are three options for transferring data from the UMGC to clients: delivery to the Minnesota Supercomputing Institute’s (MSI) high-performance file system, download from a secure website, or shipment on an external hard drive. Please indicate your data delivery preference when placing an order for sequencing.
MSI storage
Internal clients and external clients that opt-in to MSI storage have their data released to the client’s MSI group directory on the MSI high-performance filesystem (/home/GROUP/data_release/umgc), from where it can be analyzed using MSI’s high-performance computers or Galaxy system. The data is stored for five years in uncompressed format with read-only permissions to avoid accidental modification, and secure off-site tape backups of the data are maintained for disaster recovery. MSI will charge the client a storage fee for this service.
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.
Hard drive
External clients may have data shipped on a hard drive purchased by the UMGC and invoiced to the client.
Data Recovery
MSI storage
MSI guarantees storage of client data for five years, after which the data can be transferred to tape for long-term storage, contact MSI (help@msi.umn.edu) for more information.
Web download and hard drive
Data is typically recoverable for up to 5 years. If the external researcher should ever need the FASTQ files re-posted to the data download website or shipped on a hard drive within 5 years from data release, email next-gen@umn.edu to initiate data recovery. The client will be charged for the cost of recovering the data from tape archive. The UMGC does not provide any guarantee that data can be successfully recovered from tape archive.