Characterization of TMAO productivity from carnitine challenge facilitates personalized nutrition and microbiome signatures discovery

  • Wei-Kai Wu (Creator)
  • Suraphan Panyod (Contributor)
  • Po Yu Liu (Contributor)
  • Chieh Chang Chen (Contributor)
  • Hsien Li Kao (Contributor)
  • Hsiao Li Chuang (Contributor)
  • Y. H. Chen (Contributor)
  • Hsin-Bai Zou (Contributor)
  • Han Chun Kuo (Creator)
  • Ching Hua Kuo (Creator)
  • Ben Yang Liao (Contributor)
  • Tina H. T. Chiu (Creator)
  • Ching-Hu Chung (Contributor)
  • Angela Yu-Chen Lin (Creator)
  • Yi Chia Lee (Contributor)
  • Sen Lin Tang (Creator)
  • Jin Town Wang (Contributor)
  • Yu-Wei Wu (Creator)
  • Cheng Chih Hsu (Contributor)
  • Lee Yan Sheen (Contributor)
  • Alexander N. Orekhov (Creator)
  • Ming Shiang Wu (Creator)



Abstract The capability of gut microbiota in degrading foods and drugs administered orally can result in diversified efficacies and toxicity interpersonally and cause significant impact on human health. Production of atherogenic trimethylamine N-oxide (TMAO) from carnitine is a gut microbiota-directed pathway and varies widely among individuals. Here, we demonstrated a personalized TMAO formation and carnitine bioavailability from carnitine supplements by differentiating individual TMAO productivities with a recently developed oral carnitine challenge test (OCCT). By exploring gut microbiome in subjects characterized by TMAO producer phenotypes, we identified 39 operational taxonomy units that were highly correlated to TMAO productivity, including Emergencia timonensis, which has been recently discovered to convert γ-butyrobetaine to TMA in vitro. A microbiome-based random forest classifier was therefore constructed to predict the TMAO producer phenotype (AUROC = 0.81) which was then validated with an external cohort (AUROC = 0.80). A novel bacterium called Ihubacter massiliensis was also discovered to be a key microbe for TMA/TMAO production by using an OCCT-based humanized gnotobiotic mice model. Simply combining the presence of E. timonensis and I. massiliensis could account for 43% of high TMAO producers with 97% specificity. Collectively, this human gut microbiota phenotype-directed approach offers potential for developing precision medicine and provides insights into translational research. Video Abstract