The Microbial Culture and Metabolomics Core features facilities and equipment for the aerobic and anaerobic culture of microbial species in both batch and continuous systems as well targeted metabolomics services. The core offers training and usage for all equipment as well as consultation towards experimental design and method development of microbial culture studies. Additionally, the core offers anaerobic culture services; working with the researcher, the core will purchase, receive, and revive strains from commercial culture collections (i.e., ATCC, DSMZ). The core will prepare glycerol stocks, liquid cultures, or gavage-ready suspensions for inoculation of animals with pure or define-mixed microbial communities.
This includes an anaerobic chamber (Type B, Coy Labs, Grass Lake, MI), a microaerobic chamber (0.1-20% with 0.1% resolution, Polymer, Coy Labs, Grass Lake, MI), a custom-built anaerobic degassing station, and various glassware in the range of 50 – 1000 mL. In addition, the core features an automated bioreactor (BioFlo 320, Eppendorf, Hauppauge, NY), which is capable of maintaining pH and dissolved oxygen levels at a given setpoint. This system can be operated in batch, fed-batch, or continuous modes and is compatible with the Eppendorf BioBlu Single-Use Vessels, which allows for operation of volumes between 0.32 – 40 L. The core also contains a laser phosphorimeter (PMOD 500, Oxygen Enterprises, LLC., Philadelphia, PA) for phosphorescent measurement of oxygen using OxyPhor G4.
Microaerobic Chamber (Coy Labs)
BioFlo 320 (Eppendorf) for batch, fed-batch, and continuous microbial culture studies
Targeted metabolomics involves the absolute quantification of a specific (targeted) set of metabolites.
The metabolomics branch of the core features a Waters Acquity uPLC System with a QDa single quadropole mass detector. This system is configured for bile acid, short chain fatty acid (SCFA), and amino acid analysis using an autosampler with a capacity of 192 samples. The core will process, extract, and analyze the following samples:
We require at least 25 mg of fecal material for amino acids and/or bile acid analysis, and at least 50 mg for SCFA analysis. For information on sample collection, aliquoting, storage, and transfer to the core, please contact elliotf [at] pennmedicine.upenn.edu (Elliot Friedman).
HPLC system (Waters) with single-quadropole mass detector for targeted metabolite analysis
List of Analytes
If you are interested in working with the Microbial Culture & Metabolomics Core, please visit our iLab storefront to learn more and to submit service requests.
Dr. Gary Wu
gdwu [at] mail.med.upenn.edu
Elliot Friedman, PhD
elliotf [at] mail.med.upenn.edu
938 BRB II/III
Cassidy Strange, BS