The DNA Core Facility applies high-throughput DNA sequencing to the study of complex bacterial and fungal communities. Several methods are employed:
- Targeted sequencing of the ITS regions for characterization of fungal communities
- Targeted sequencing of hyper-variable regions of the 16S gene
- Whole genome shotgun sequencing
Our facility has extensive experience performing 16S sequencing. 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 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.
Source: Ericsson, Aaron C., et al. "Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice." PloS one 10.2 (2015): e0116704.
Contact Nathan Bivens with any questions or to initiate a project.
 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.
 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.
 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).