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Metabolomics Knowledge Center

The goal of the Stanford ChEM-H Metabolomics Knowledge Center is to provide scientific expertise and instrumentation for the measurement of metabolites.

Metabolism is the chemical outcome of living organisms interacting with their environment.  Understanding metabolism is therefore critical in many branches of biology, including drug discovery and disease pathology.  However, accurate and comprehensive techniques for measurement of metabolites can be a challenge for many researchers.   At the ChEM-H Metabolomics Knowledge Center, we provide scientific expertise and instrumentation for the measurement of metabolites to the ChEM-H and Stanford communities.  Our center leverages expertise in mass spectrometry & allied techniques to understand the biology of small molecules – both metabolites and xenobiotics – and to apply that understanding to advances in human health.

Metabolomics Knowledge Center in the News

A tale of cacao, birds and the ‘power of emerging model systems’

Working with Stanford ChEM-H's Metabolomics Knowledge Center, Stanford researchers traced the genetic process through which parakeets produce either yellow or blue feathers. This work provides insights that could help scientists uncover other biochemical pathways.

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Druglike molecules produced by gut bacteria can affect gut, immune health

Working with Stanford ChEM-H's Metabolomics Knowledge Center, Stanford ChEM-H faculty fellows Michael Fischbach and Justin Sonnenberg found that manipulating the gut microbe Clostridium sporogenes changed levels of molecules in the bloodstreams of mice and, in turn, affected their health.

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Recent Publications

A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont, Liou CS, Sirk SJ, Diaz CAC, Klein AP, Fischer CR, Higginbottom SK, Erez A, Donia MS, Sonnenburg JL, Sattely ES, Cell, 2020, 180, 717-728.

A pathogen-responsive gene cluster for the production of highly modified fatty acids in tomato, J.E. Jeon, J.-G. Kim, C.R. Fischer, C. Dufour-Schroif, K. Wemmer, M.B. Mudgett, E. Sattely, Cell, 2020, 180, 176-187.

Depletion of microbiome-derived molecules in the host using Clostridium genetics, C.-J. Guo, B. Allen, K. Hiam, D. Dodd, W. van Treuren, S. Higginbottom, C. Fischer, J. Sonnenburg, M. Spitzer, M. Fischbach, Science, 2019, 366, 6471.

Family-wide Annotation of Enzymatic Pathways by Parallel In Vivo Metabolomics, Kim JT, Li VL, Terrell SM, Fischer CR, Long JZ, Cell Chem Biol., 2019, 26, 1623-1629.

CRISPR-Cas9 screens identify regulators of antibody-drug conjugate toxicity, Tsui CK, Barfield RM, Fischer CR, Morgens DW, Li A, Smith BAH, Gray MA, Bertozzi CR, Rabuka D, Bassik MC, Nat Chem Biol., 2019, 15, 949-958.

D2O Labeling to measure active biosynthesis of natural products in medicinal plants, R.S. Nett, X. Guan, K. Smith, A.M. Faust, E.S. Sattely, C.R. Fischer, AIChE Journal, 2018, 64, 4319-4330.

HEx: A heterologous expression platform for the discovery of fungal natural products, C.J.B Harvey, M. Tang, U. Schlecht, J. Horecka, C.R. Fischer, H.-C. Lin, J. Li, B. Naughton, J. Cherry, M. Miranda, Y. F. Li, A.M. Chu, J.R. Hennessy, G.A. Vandova, D. Inglis, R.S. Aiyar, L.M. Steinmetz, R.W. Davis, M.H. Medema, E. Sattely, C. Khosla, R.P. St. Onge, Y. Tang, M.E. Hillenmeyer. Science Advances, 2018, 4, eaar5459.

N-hydroxy-pipecolic acid is a mobile metabolite that induces systemic disease resistance in Arabidopsis, Y.-C. Chen, E.C. Holmes, J. Rajniak, J.-G. Kim, S. Tang, C.R. Fischer, M.B. Mudgett, E.S. Sattely. Proceedings of the National Academy of Sciences, 2018, 115, E4920-E4929.

A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites, D. Dodd, M.H. Spitzer, W. van Treuren, B.D. Merrill, A.J. Hryckowian, S.K. Higginbottom, A. Le, T.M. Cowan, G.P. Nolan, M.A. Fischbach, J.L. Sonnenburg. Nature, 2017, 551, 648-652.

Genetic Mapping and Biochemical Basis of Yellow Feather Pigmentation in Budgerigars, T.F. Cooke, C.R. Fischer, P. Wu, T.-X. Jiang, K.T. Xie, J. Kuo, E. Doctorov, A. Zehnder, C. Khosla, C.-M. Chuong, C.D. Bustamante. Cell, 2017, 171, 427-439.

Heterologous expression of diverse propionyl-CoA carboxylases affects polyketide production in Escherichia coli, G.A. Vandova, R.V., O'Brien, B. Lowry, T.F. Robbins, C.R. Fischer, R.W. Davis, C. Khosla, C.J.B. Harvey, M.E. Hillenmeyer. The Journal of Antibiotics, 2017, 70, 859-863.