Molecular Microbiology

Eric G. Pamer (Facility Head)

Office phone


Office fax



The Molecular Microbiology Facility (MMF) is part of the Center for Microbes, Inflammation, and Cancer. The laboratory works with investigators to use next generation sequencing platforms to analyze the microbial composition of experimental samples obtained from mice or clinical samples obtained from patients. The laboratory performs DNA extraction and PCR amplification using bar-coded primers for bacterial 16S ribosomal RNA gene sequencing on the Illumina MiSeq platform. We amplify the V4-V5 region of the 16S rRNA gene and, depending on the sequencing depth required, can provide from several thousand to millions of sequences per sample. In addition to 16S sequencing, the lab performs shotgun metagenomic sequencing of fecal samples using the Illumina HiSeq platform. The laboratory works with investigators to analyze the microbiota of the small and large intestines, feces, saliva and oral mucosal surfaces and the urogenital tract.

The MMF provides sample-processing services from DNA extraction and library preparation and sequencing to sequence processing and data analysis. Microbial community data can be analyzed in a variety of ways, depending on the individual needs of the project. Analysis tools are available to classify bacterial sequences down to the genus level (and to the species level when possible) to determine both community membership and structure. Included in the analysis are tools for graphic visualization of the bacterial composition of individual samples and for visualizing differences between samples. The lab supports investigators pursuing both basic and clinical research interests. Ongoing studies are characterizing changes in the intestinal microbiota of patients undergoing cancer treatment and in experimental mice.