Metagenomic/16 Sequencing Services



The DNA Core Facility currently applies high-throughput DNA sequencing services to the study of complex bacterial communities through the targeting of the V4 hypervariable region of the 16S rRNA gene. Bacterial 16S ribosomal DNA amplicon libraries are constructed by amplification of the V4 hypervariable region of the 16s rRNA with primers flanked by Illumina standard adapter sequences. Universal primers (U515F/806R) previously developed in collaboration with the MU Metagenomics Center target the V4 region to generate amplicons (1,3); primer sequences are available at proBase (http://www.microbial-ecology.net/probebase/) (2). Barcoding allows for the pooling of up to 384 samples.

The Informatics Research Core Facility (IRCF) can provide an analysis of the data using the Qiime pipeline, http://qiime.org/. This will provide graphical and tabular summaries of the taxa and OTU´s identified and their relative proportional representations.

The DNA Core can also assist with the following methods:

  • Sequencing of the ITS regions for characterization of fungal communities
  • Targeting of other hyper-variable regions of the 16S gene
  • Whole genome shotgun sequencing for metagenome characterization

Contact Nathan Bivens with any questions or to initiate a project.

References

[1] Caporaso JG, Lauber CL, Walter WA, Berg-Lyons D, Losupone CA, Turnbaugh PJ, Fierer N, and Knight R. 2011. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. PNAS. 108: 4516-4522.

[2] Loy A, Maixner F, Wagner M, Horm M. 2007. proBase ? an online resource for rRNA-targeted oligonucleotide probes: new feartures 2007. Nucleic Acids Res. 35: D800-D804.

[3] Walters WA, Caporaso JG, Lauber CL,Berg-Lyons D, Fierer N, Knight R. PrimerProspector: de novo design and taxonomic analysis of barcoded PCR primers. Bioinformatics. 10.1093/bioinformatics/btr087 (2011).





Service Fees

.....Analysis Description.... USD
Amplicon Generation Fee (<24 samples) $168/ set of samples
Amplicon Generation Fee (24-48 samples) $235/ set of samples
Amplicon Generation Fee (96 samples) $368/ set of samples

*Contact the DNA Core for external rates



Sample Submission Guidelines
  • Requirements for a plate submission are for each sample to be submitted at a concentration of 3.51ng/ul in 10mM Tris-Cl buffer (pH 8.5, or EB buffer from Qiagen kit ) at a volume of 60ul.
  • The preferred 96-well plate for submitting DNA is from MedSupply Partners (877-633-7779, http://www.medsupplypartners.com/); catalog # 15-3590. The core recommends the use of adhesive sealing sheets from Thermo Scientific (cat. #AB-0558).