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Microbial Culture and Metabolomics Core

Overview of Services

The metabolomics portion of the core performs targeted metabolomics analyses of amino, bile, and short chain fatty acids in a number of sample matrices (see below). The microbial culture portion of the core features a range of microbial culture facilities and services. Facilities include two vinyl Type B anaerobic chambers (Coy Labs), a rigid microaerobic chamber (Coy Labs), two Epoch2 plate readers (Biotek), an Eppendorf BioFlo 320 fermenter/bioreactor/cultivar, a custom built minibioreactor array (48 15-mL reactors), and an oxygen phosphorimeter. The core can provide a number of culture services, including the quantification of bacterial load in research samples, isolation of strains from animal/human samples, characterization of strains, and preparation of strains for in vitro or in vivo studies, among others. Please submit a request to discuss your microbial culture project.


Metabolomics Guidelines

Turn-around time for samples ranges from 4-8 weeks but depends on the sample queue at the time of submission and the number of samples submitted.


Amino Acids

Bile Acids


Plasma – Human




Plasma – Mouse




Feces – Human




Feces – Mouse




Bacterial Culture Supernatant





  • Amino Acids: Alanine, Arginine, Aspartic Acid, Cystine, Glutamic Acid, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Theronine, Tyrosine, Valine, Taurine, HydroxyProline, Asparagine, Glutamine, GABA (γ-Aminobutyric acid), Tryptophan, Ornithine, AABA (α-Aminobutyric acid), HydroxyLysine
  • Bile Acids: Cholic Acid, Glycocholic Acid, Taurocholic Acid, Chenodeoxycholic Acid, Glycochenodeoxycholic Acid, Taurochenodeoxycholic Acid, Deoxycholic Acid, Glycodeoxycholic Acid, Taurodeoxycholic Acid, Lithocholic Acid, Glycolithocholic Acid, Taurolithocholic Acid, Muricholic Acids (α-, β-, γ-, ω-; mouse samples only)
  • Short Chain Fatty Acids: Acetic Acid, Propionic Acid, Isobutyric Acid, Butyric Acid, Isovaleric Acid, Valeric Acid, Isocaproic Acid, Caproic Acid, Heptanoic Acid

Sample Requirements

  1. Human Stool – One Eppendorf vial for bile and/or amino acid analysis with 100-150 mg stool frozen neat. One Eppendorf vial for SCFA analysis with 100-150 mg stool frozen neat. Exact weight for each sample must be included in the sample manifest.
  2. Mouse Stool – One Eppendorf vial for bile and/or amino acid analysis with 25-100 mg stool frozen neat. Exact weight for each sample must be included in the sample manifest.
  3. Plasma (Mouse or Human) – One vial with at least: 25 uL for amino acid analysis and 25 uL for bile acid analysis (i.e., 50 uL if both amino and bile acids are to be analyzed).
  4. Bile or Gastric Aspirate (Mouse or Human) – One vial with at least 25 uL for bile acid analysis.
  5. Bacterial Culture or Mammalian Cell Culture Supernatant – One vial for bile and/or amino acids with at least 50 uL of filter sterilized supernatant. One vial for SCFA analysis with at least 100 uL filter sterilized supernatant.

Please submit an electronic sample manifest containing a unique sample identifier for each aliquot, the sample type (e.g., stool, plasma), the sample weight (mg) or volume (uL), and what analysis you would like performed (i.e., AA, AA/BA, BA, SCFA).


Analysis Academic Industry
Amino acids $50 $75
Bile acids $50 $75
SCFA $50 $75
Any two classes $100 $150
Any three classes $100 $225


Please acknowledge/cite the "Microbial Culture & Metabolomics Core of the PennCHOP Microbiome Program and the Center for Molecular Studies in Digestive and Liver Diseases (NIH P30DK050306)" when publishing your results. This is vitally important for the continued operation of the core.


Gary Wu, MD | Director

Elliot Friedman, PhD | Technical Director


9th Floor BRB II/III

421 Curie Blvd

Philadelphia, PA 19104


Name Role Phone Email Location
Elliot Friedman, PhD
Technical Director