Microbial Culture and Metabolomics Core

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 as services for both targeted and untargeted metabolomics. 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.

Microbial Culture Facility

Click the dropdown arrow above to learn about our equipment and price structure.

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 Facility

Click the dropdown arrow for information on our metabolomic services.

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 fecal (human, murine, cow, canine), plasma (human, murine, cow, canine), and microbial culture 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 Elliot Friedman.

*Note: SCFA levels in healthy plasma samples are typically below the limit of detection. For more information, please contact 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


Discovery Metabolomics

Click the drop down arrown to learn more about untargeted metabolomic services offered through Metabolon.
A 5% discount is offered on Metabolon services obtained through the core.

Discovery metabolomics is a technology for obtaining a comprehensive picture of the metabolome and mapping metabolites to their key biochemical pathways. It helps answer a wide variety of research questions and gives crucial insight into the function of genes, the basis of disease, and how treatments work. Discovery metabolomics also identifies the associated biomarkers, making it an attractive tool for investigators across multiple applications.

For moreinformation regarding discovery metabolomics through Metabolon, please contact Paul Fogle at pfogle@metabolon.com or via phone at 919-599-8687.

For more information about microbiome research with Metabolon, please click here.


If you are interested in working with the Microbial Culture & Metabolomics Core, please fill out THIS FORM.

For more information regarding discovery metabolomics through Metabolon, please contact Paul Fogle at pfogle@metabolon.com or via phone at 919-599-8687.

For more information about microbiome research with Metabolon, please click here

Operational Information

Dr. Gary Wu

Core Director

Elliot Friedman, PhD
Technical Director

Cassidy Strange, BS
Technical Assistant

© The Trustees of the University of Pennsylvania | Site best viewed in a supported browser. | Site Design: PMACS Web Team.