Microbial Culture and Metabolomics Core

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)

Anaerobic Chamber

BioFlo 320 (Eppendorf) for batch, fed-batch, and continuous microbial culture studies

Price Structure

• Consultation: $40/hr
• General Consumables (e.g., pipette tips, plates, vials): can be provided by the Core at vendor cost
• Specific Consumables (e.g., antibiotics, bacterial strains): To be Provided by the Investigator
• Anaerobic Chamber
  • Fee-for-service projects (we do the work): $40/hr (hands on time)
  • Chamber usage (investigator performs the work): $30/hr (hands on time)
    • Note: Training (~30 minutes) is required before use of the equipment 
• Bioreactor
  • Initial Training (~1.5 hrs): $50
  • Usage: $100/day
  • Eppendorf BioBlu Single-Use Vessels (To be provided by the Investigator):
    • 1 L (Eppendorf 78903509): $350
    • 3 L (Eppendorf M1363-0119): $750

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:

• Human Plasma: Amino acids, bile acids
• Human Feces: Amino acids, bile acids, short chain fatty acids
• Mouse Plasma: Amino acids, bile acids
• Mouse Feces: Amino acids, bile acids
• Microbial Culture Supernatant: Amino acids, bile acids, short chain fatty acids

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

Price Structure

• Amino Acids: $40/sample
• Bile Acids: $40/sample
• Short Chain Fatty Acids: $40/sample
• All Three: $80/sample