Systems biology elucidates the distinctive metabolic niche filled by the human gut microbe Eggerthella lenta

Cecilia Noecker, Juan Sanchez, Jordan E. Bisanz, Veronica Escalante, Margaret Alexander, Kai Trepka, Almut Heinken, Yuanyuan Liu, Dylan Dodd, Ines Thiele, Brian C. DeFelice, Peter J. Turnbaugh

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. Our culture media formulations, atlas of metabolomics data, and genome-scale metabolic reconstructions form a freely available collection of resources to support further study of the biology of this prevalent gut bacterium.

Original languageEnglish (US)
Article numbere3002125
JournalPLoS biology
Issue number5
StatePublished - May 2023

All Science Journal Classification (ASJC) codes

  • General Neuroscience
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology
  • General Agricultural and Biological Sciences

Cite this