Molecular Microbiology -- Core Facility

Lilan Ling (Core Facility Head)
Office phone:
212-639-8727
E-mail(s)
lingl@mskcc.org

The Molecular Microbiology Core Facility (MMCF) was founded in 2010 as part of the Lucille Castori Center for Microbes, Inflammation, and Cancer. Headed by immunologist Eric Pamer, the laboratory provides investigators with the ability to characterize the microbiota inhabiting various human and animal environments based on their 16S ribosomal RNA gene sequences.

In collaboration with the Genomics Core Laboratory, the MMCF performs high-throughput sequencing of the 16S RNA gene using next-generation 454 sequencing technology. The Roche 454 sequencing platforms deliver hundreds of thousands of high-quality sequences per run, which are used to characterize and determine the relative abundances of bacterial species present. The laboratory analyzes the microbiota of a wide variety of environments, such as the small and large intestines, feces, oral cavity, surface of the skin, and urogenital tract.

The laboratory provides full sample-processing services from DNA 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 each project. Analysis tools are available to classify bacterial sequences down to the genus level (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. Current studies involve characterization of the changes in the intestinal microbiota of patients undergoing hematopoetic stem cell transplantation and their correlation to development of graft versus host disease; the influence of TLR signaling on the communication between intestinal microbes and innate immune responses; and the impact of oral and fecal microbiota on the pathogenesis of rheumatoid arthritis.

Investigators wishing to take advantage of the lab's services are encouraged to contact the lab manager to discuss the individual needs of each project, including sample collection and approaches to sequence analysis.

Publications