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Systems biology illuminates alternative metabolic niches in the human gut microbiome
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SUMMARY
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.
Title: Systems biology illuminates alternative metabolic niches in the human gut microbiome
Description:
SUMMARY
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.
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