Microbiome Core Facility

Expanding Access to Microbiome Science

To help propel research collaborations and improve access to microbiome research, the Sharpton lab manages a microbiome data generation and analysis core facility. This BLS-2 core lab specializes in the generation and analysis of 16S rRNA gene and metagenomic sequence data from microbial communities associated with stool, saliva, or animal tissues (including biopsies). We apply assays and procedures that are informed by our experience and defined best practices in the field, especially those developed as part of the Human Microbiome Project and the Earth Microbiome Project. We have processed 1000s of samples and published dozens of papers using these approaches.

Services

Our service offerings currently include:

  1. Community-wide DNA extraction. We apply techniques that produce high-quality and abundant DNA extracts while mitigating taxonomic bias. These techniques include the use of bead-beating approaches to lyse cells, which is necessary to recover DNA from spore-forming microbes.
  2. 16S rRNA gene sequencing libray preparation. Using degenerate PCR primers, we target and amplify subregions of the 16S rRNA locus from the diverse pool of 16S genes present in microbiome DNA samples. Our default approach is to target the V4 hypervariable region following Earth Microbiome Project protocols.
  3. Metagenomic DNA library prep. We can implement Nextera Flex and Seqwell kits for preparing community-wide DNA for metagenomic sequencing on an Illumnia platform.
  4. Management of DNA sequencing. We partner with collaborators, especially the Center for Genome Research and Biocomputing, to sequence prepared libraries. For 16S projects, we suggest the use of the Illumina MiSeq platform (v3 chemistry), the generation of paired-end reads, and a multiplexing depth of no fewer than 25,000 reads / sample (though needs vary based on project goals). For metagenomes, we suggest the use of the Illumnia HiSeq3000 or NextSeq, the generation of paired-end reads, and multiplexing depth of no fewer than 10M reads / sample (though needs vary based on project goals).
  5. Quality control and summarization of sequence data. We apply rigorous methods to remove spurrious sequences or bases, and in the case of metagenomes, host-DNA. We also bioinformatically process 16S and metagenomic data to produce summary tables of either taxon counts (16S or metagenomes) or gene family counts (metagenomes) using standard software techniques (e.g., dada2, HUMAnN2).
  6. Custom bioinformatic and data analytic analyses. We can conduct project-specific analyses, including assessment of how the diveristy or composition of the microbiome links to specific covariates, whether the relative abundance of specific taxa or gene families associates with specific covariates, or multi’omic integration.

We apply assays and procedures that are informed by our experience and defined best practices in the field, especially those developed as part of the Human Microbiome Project and the Earth Microbiome Project.

Pricing

Our services are defined through the Oregon State University fee book and are thus offered at cost. For specific inquries and service quotes, please contact Dr. Sharpton, as needs and thus costs will likely vary on a per project basis. We are happy to consider custom requests that differ from the approaches listed above.

For planning purposes, we summarize major service packages and their costs below.

16S RNA Gene Sequencing

We currently offer a fixed rate fee of $38 per sample (plus the cost of DNA sequencing) to generate and summarize 16S rRNA gene sequence data.

This service includes DNA extraction, V4 16S PCR-based library prep, and library quality control. We work with a third party vendor, typically the CGRB, to generate 16S sequences on an Illumnia MiSeq (typically ~$2,000). This service also includes quality control of the raw sequence data, identification of ASVs using dada2, and taxonomic annotation of the ASVs. The service provides clients with the outputs of these analyses alongside the raw fastq 16S sequence files.

Facilities

Our core lab benefits from access to cutting-edge facilties and equipment that ensure timely generation of high quality data as well as a biocomputing infastructure that we specifically developed for microbiome and metagenome analyses.

We increasingly leverage automated strategies to increase sample throughput. But due to our focus on data quality, we rigorously evaluate approaches prior to their implementation. For example, we recently acquired two OpenTrons OT-2 fluid handling robots to accelerate DNA extration and library prepration procedures thanks to a generous donation from the Pacific Northwest Center for Translational Environmental Health Research.

For a full description of our molecular biological and comptuational facilites, please view our current Facilities and Equipment descriptions.