Metabolomic and lipidomic characterization of Oxalobacter formigenes strains HC1 and OxWR by UHPLC-HRMS

  • Casey A. Chamberlain
  • Marguerite Hatch
  • Timothy J. GarrettEmail author
Research Paper
Part of the following topical collections:
  1. Young Investigators in (Bio-)Analytical Chemistry


Diseases of oxalate, such as nephrolithiasis and primary hyperoxaluria, affect a significant portion of the US population and have limited treatment options. Oxalobacter formigenes, an obligate oxalotrophic bacterium in the mammalian intestine, has generated great interest as a potential probiotic or therapeutic treatment for oxalate-related conditions due to its ability to degrade both exogenous (dietary) and endogenous (metabolic) oxalate, lowering the risk of hyperoxaluria/hyperoxalemia. Although all oxalotrophs degrade dietary oxalate, Oxalobacter formigenes is the only species shown to initiate intestinal oxalate secretion to draw upon endogenous, circulating oxalate for consumption. Evidence suggests that Oxalobacter regulates oxalate transport proteins in the intestinal epithelium using an unidentified secreted bioactive compound, but the mechanism of this function remains elusive. It is essential to gain an understanding of the biochemical relationship between Oxalobacter and the host intestinal epithelium for this microbe to progress as a potential remedy for oxalate diseases. This investigation includes the first profiling of the metabolome and lipidome of Oxalobacter formigenes, specifically the human strain HC1 and rat strain OxWR, the only two strains shown thus far to initiate net intestinal oxalate secretion across native gut epithelia. This study was performed using untargeted and targeted metabolomics and lipidomics methodologies utilizing ultra-high-performance liquid chromatography-mass spectrometry. We report our findings that the metabolic profiles of these strains, although largely conserved, show significant differences in their expression of many compounds. Several strain-specific features were also detected. Discussed are trends in the whole metabolic profile as well as in individual features, both identified and unidentified.

Graphical abstract


Metabolomics Lipidomics Oxalobacter formigenes Mass spectrometry LC-MS Oxalate Nephrolithiasis Hyperoxaluria 









Coenzyme Q10






Formic acid








Oxidized phosphatidylethanolamine





















The authors would like to acknowledge Dr. Cory A. Leonard, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, for her assistance with sample generation for this experiment, including media preparation and cell culture, harvest, and lysis. Also to be acknowledged are Dr. Jeremy P. Koelmel, Department of Pathology, Immunology and Laboratory Medicine, University of Florida, and Vanessa Y. Rubio, Department of Chemistry, University of Florida, for their contributions with figure generation for the lipidomics analysis and graphical abstract, respectively.

Funding information

This work was funded by the National Institutes of Health grant 2R01DK088892-05A1.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Supplementary material

216_2019_1639_MOESM1_ESM.pdf (1.6 mb)
ESM 1 (PDF 1626 kb)
216_2019_1639_MOESM2_ESM.xlsx (14 kb)
ESM 2 (XLSX 13 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Casey A. Chamberlain
    • 1
  • Marguerite Hatch
    • 1
  • Timothy J. Garrett
    • 1
    Email author
  1. 1.Department of Pathology, Immunology and Laboratory MedicineUniversity of FloridaGainesvilleUSA

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