Frequently Asked Questions

About Corebiome

Our founders, Dan Knights (CEO), Daryl Gohl (CSO), and Kenny Beckman (COO), are experts in the fields of microbiome science and high-throughput genomics; and they maintain positions at the University of Minnesota and at CoreBiome.

CoreBiome was built on intellectual property licensed from the founders’ labs in Computer Science, the BioTechnology Institute, and the Genomics Center at the University of Minnesota.

CoreBiome is a licensee of University of Minnesota (UMN) intellectual property; and was originally incorporated in July of 2016, as Micrometer, Inc.

CoreBiome received seed funding from angel investors and the UMN’s investment fund (Discovery Capital).

Following a short period operating within the UMN Genomics Center in early 2017, CoreBiome has been operating independently since June 2017, at its current location at the University Enterprise Labs (UEL) incubator.

As of January 2019, CoreBiome has been a wholly-owned subsidiary of OraSure, Inc., headquartered in Bethlehem, Pennsylvania.

CoreBiome pioneered the use of shallow shotgun next-generation sequencing as a superior (higher-resolution) alternative to amplicon-based (e.g., 16S) microbiome profiling.

Our initial proof-of-principle ​study​ established that affordable, relatively low-depth shotgun sequencing (e.g. 500,000-2,000,000 read depth per sample) was able to provide species-level resolution and gene content inference, providing many of the benefits of deep shotgun sequencing at a cost approaching that of amplicon-based methods.

CoreBiome’s proprietary analysis pipelines merge open-source informatics tools with shallow shotgun algorithms licensed from the University of Minnesota.

This intellectual property was licensed and commercialized as BoosterShot™.

CoreBiome is also at the ​leading edge of investigations into the sources of error​ that have stymied accurate microbiome profiling.

A ​systematic analysis of the molecular mechanisms that plague amplicon-based methods​, published in 2016, resulted in methods – implemented as CoreBiome’s BenchMark™ assay – that dramatically minimize both qualitative and quantitative biases.

BenchMark™ incorporates intellectual property (patent pending) derived from University of Minnesota research.

Lastly, CoreBiome is distinguished by its focus on “soup-to-nuts” quality control, which has been strengthened by our incorporation into the OraSure family of companies that includes DNA Genotek.

Every step of a next-generation sequencing microbiome experiment – including sample collection, nucleic acid extraction, library creation, sequencing, and informatics – ​is a potential source for error.

From the outset, CoreBiome’s founders have sought to eliminate biases and ensure quality control at all aspects of this workflow.

With the addition of DNA Genotek’s sample collection expertise (​OMNIGene for oral, gut and vaginal microbiome​) and our AWS-based Core Analysis data analysis engine, CoreBiome technologies provide comprehensive quality control.

Working with CoreBiome

CoreBiome’s customers include microbiome scientists in pure and applied fields from industry and academia.

We provide microbiome sequencing and analysis to power microbiome discovery and analysis in small start-ups and Fortune 500 companies, the labs of individual university researchers, and direct-to-consumer companies.

We serve researchers in pharmaceutical and agriculture R&D, environmental monitoring, cosmetics development, pet nutrition, direct-to-consumer testing, and other industries.

Our microbiome experts have extensive experience within academia and can provide valuable insights to help researchers get the data they need for publication.

We pride ourselves on the scientist-to-scientist relationship we have with our customers and strive to accelerate microbiome discovery by ensuring high-quality data and methods.

CoreBiome provides high-quality microbiome sequencing and analysis ​services​ that are affordable, reliable and scalable for commercial entities of all sizes.

We provide services for a wide range of applications in human health​, agriculture,​ and ​environmental monitoring​.

To get started working with CoreBiome, please ​contact us​ for a quote.

Whether you have samples in hand or are working on receiving funding, our team will work with you to define your project, goals, timelines, and deliverables.

Our sales team will initially work with you to determine the best ​services​ CoreBiome can offer and coordinate sample shipments.

Once samples are at CoreBiome, our ​services​ team will provide email updates for your samples as they move through the pipeline.

Cost and Turnaround Time

Project turnaround times can be adjusted to meet your needs.

Our standard turnaround times are six weeks for projects with less than 88 samples and three weeks for projects greater than 88 samples.

Large projects beyond 1,000 samples may require additional time. Contact us ​with questions.

We are happy to work with you to get your data back when you need it. Our shortest processing time is one week from sample arrival. Please ​contact us​ for more details regarding cost for expedited orders.

Upon project completion, our billing department will reach out to you with an invoice for services rendered.

Ensuring Data Quality

Using proper sample collection and storage techniques is critical to ensuring high-quality samples and data.

For collection and storage, we recommend DNA Genotek’s ​products​ as a gold standard for many types of samples. When possible, we also recommend that CoreBiome carries out DNA extraction of your samples on site.

If extraction at CoreBiome is not possible, we highly recommend following guidelines for submitting DNA found ​here​.

Microbiome measurements are susceptible to error, bias, and contamination at essentially every stage of the data generation process.

Incorporation of appropriate experimental controls is essential to ensure the reliability and reproducibility of microbiome data.

For every microbiome sequencing project, CoreBiome includes both positive and negative controls on each DNA extraction plate as well as positive and negative controls on each library preparation plate.
These controls are carried through the full sequencing process and analyzed to ensure data quality.

CoreBiome also provides an extensive​ QC Dashboard​ with each analysis report.

CoreBiome’s services are based on optimized microbiome profiling methods described in peer-reviewed publications:

BoosterShot™

Evaluating the Information Content of Shallow Shotgun Metagenomics​ Hillmann, B., Al-Ghalith, G.A., Shields-Cutler, R., Zhu, Q., Gohl, D.M., Beckman, K.B., Knight, R., Knights, D. 2018. mSystems. 3(6) DOI:10.1128/mSystems.00069-18.

BenchMark™

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies​ Gohl, D.M., Vangay, P., Garbe, J., MacLean, A., Hauge, A., Becker, A., Gould, T.J., Clayton, J.B., Johnson, T.J., Hunter, R., Knights, D., Beckman, K.B. 2016.. doi:10.1038/nbt.3601.

Sample Collection, Shipment, and Storage

Yes.

Through CoreBiome’s sister company, ​DNA Genotek​, we offer OMNIgene® collection kits for oral, gut (stool/fecal), and vaginal microbiome.

These optimized and validated collection solutions provide ambient temperature homogenization and stabilization at the point-of-collection for a true snapshot of the microbiota with no cold chain required.

Learn more about these collection kits and request trial kits.

If you have questions about collecting other types of microbiome samples, ​contact DNA Genotek​.

CoreBiome stores primary samples at our facility for up to three months and is happy to return samples to clients after processing.

Please notify CoreBiome before sample submission, if you are planning on sample return.

We additionally ask clients to provide shipping and payment information for return of samples.

Yes, CoreBiome will archive the data for your project for one year with no additional charge.

Services

CoreBiome has experience working with a wide range of sample types, including human gut (fecal), vaginal, urine, skin, oral, saliva, and biopsy samples, as well as in vitro cultures, animal, plant, soil, built environment, and other environmental samples.

We have worked with a variety of collection formats including bulk samples, swabs, and samples collected in stabilization buffers or directly frozen.

If you have questions about whether your sample type is suitable for analysis or which collection method to use, please ​contact us​.

For BenchMark™ (16S rRNA gene or ITS sequencing) CoreBiome uses the Illumina MiSeq.

For BoosterShot™ and StrainView™, samples are sequenced on the Illumina NextSeq or Illumina NovaSeq, depending on required read depths and project needs.

Analysis

Yes, example reports for ​BoosterShot™,​ ​BenchMark™​, and ​StrainView™​ are available on our website.

Yes, see the DATA tab of our example report.

Yes, any metadata you wish to provide will be incorporated into the data visualizations provided back in your Core Analysis report.

You will be able to view sample stratification by any metadata provided in all of the returned alpha and beta diversity plots.

You can submit any metadata along with your samples using our submission forms.

Yes, we can carry out a wide variety of custom analyses though our ​CorePlus Analysis​, including hypothesis testing, longitudinal analysis, biomarker discovery, and machine learning approaches.

We are happy to work with you to create publication-ready data visualizations.

Schedule a consultation with our informatics team to define goals and deliverables for your project.

Ready to get started?