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MetaCore Onsite Training: A biomarker-assisted systems biology approach to explore host-microbiome-drug interactions

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Gut microbiota can impact drug therapy, or be impacted by drugs, through direct and indirect mechanisms1. Last year, Wo Hao and colleagues reported in Nature Medicine that the most frequently used drug for type 2 diabetic patients, metformin, alters the gut microbiome contributing to the therapeutic effects of the drug2. Herein, we devised a biomarker-assisted approach to study the metabolic processes impacted by metformin using drug monitoring biomarkers (Fig.1). Metabolomic, genomic and proteomic biomarkers for monitoring or predicting treatment efficacy of metformin, probiotics, and antibiotics, were mined from Clarivate Analytics Integrity database and used to enrich metabolic processes and pathway maps in MetaCore. Preliminary results indicated that common metabolomic biomarkers used for monitoring or predicting treatment efficacy of metformin, probiotics, and antibiotics, led to the enrichment of amino acid metabolic pathways with particular emphasis on L-ornithine and arginine pathways. It is known that amino acids, such as arginine, tryptophan and asparagine, are particularly important microbial nutrients that are central to the host–microbiome-drug interactions and further analysis is underway to understand the implications of disturbing these pathways on the microbiota and on metformin’s clinical response.

 At the end of this session we will be able to answer the following key questions:

  • How can I upload Metabolic, genomic and proteomic data into MetaCore to study?
  • How can I use one-click analysis to do enrichments in metabolic networks?
  • How can I compare genomics, proteomics and metabolomics data in MetaCore?
  • How can I save and manage important findings from pathway maps and process networks


  1. Spanogiannopoulos, P, et al. Nature Reviews Microbiology 14, 237 – 287, 2016.
  2. Wu, H, et al. Nature Medicine 23 (7),850 – 858, 201

Thursday, April 26, 2018
1:00pm - 3:00pm
C-103 - SHM 333 Cedar St, New Haven CT 06520
Medical School

Event Organizer

Profile photo of Rolando Garcia-Milian
Rolando Garcia-Milian