Next Article in Journal
Knockout of Arabidopsis thaliana VEP1, Encoding a PRISE (Progesterone 5β-Reductase/Iridoid Synthase-Like Enzyme), Leads to Metabolic Changes in Response to Exogenous Methyl Vinyl Ketone (MVK)
Next Article in Special Issue
A Checklist for Reproducible Computational Analysis in Clinical Metabolomics Research
Previous Article in Journal
Modelling Metabolic Shifts during Cardiomyocyte Differentiation, Iron Deficiency and Transferrin Rescue Using Human Pluripotent Stem Cells
Previous Article in Special Issue
MSCAT: A Machine Learning Assisted Catalog of Metabolomics Software Tools
 
 
Article

TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome

1
Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2T5, Canada
2
Institute of Parasitology, McGill University, Montreal, QC H3A 2T5, Canada
3
MGH Center for Translational Pain Research, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02215, USA
4
Department of Medicine, McGill University, Montreal, QC H3A 2T5, Canada
5
Lady Davis Institute for Medical Research, Montreal, QC H3T 1E2, Canada
*
Author to whom correspondence should be addressed.
Academic Editor: Hunter N. B. Moseley
Metabolites 2022, 12(1), 10; https://doi.org/10.3390/metabo12010010
Received: 23 November 2021 / Revised: 20 December 2021 / Accepted: 20 December 2021 / Published: 23 December 2021
(This article belongs to the Special Issue Advances in Computational Metabolomics)
Crosstalk between the gut microbiome and the host plays an important role in animal development and health. Small compounds are key mediators in this host–gut microbiome dialogue. For instance, tryptophan metabolites, generated by biotransformation of tryptophan through complex host–microbiome co-metabolism can trigger immune, metabolic, and neuronal effects at local and distant sites. However, the origin of tryptophan metabolites and the underlying tryptophan metabolic pathway(s) are not well characterized in the current literature. A large number of the microbial contributors of tryptophan metabolism remain unknown, and there is a growing interest in predicting tryptophan metabolites for a given microbiome. Here, we introduce TrpNet, a comprehensive database and analytics platform dedicated to tryptophan metabolism within the context of host (human and mouse) and gut microbiome interactions. TrpNet contains data on tryptophan metabolism involving 130 reactions, 108 metabolites and 91 enzymes across 1246 human gut bacterial species and 88 mouse gut bacterial species. Users can browse, search, and highlight the tryptophan metabolic pathway, as well as predict tryptophan metabolites on the basis of a given taxonomy profile using a Bayesian logistic regression model. We validated our approach using two gut microbiome metabolomics studies and demonstrated that TrpNet was able to better predict alterations in in indole derivatives compared to other established methods. View Full-Text
Keywords: tryptophan metabolism; gut microbiome; co-metabolism; genome-scale metabolic model; network; indole derivatives tryptophan metabolism; gut microbiome; co-metabolism; genome-scale metabolic model; network; indole derivatives
Show Figures

Graphical abstract

MDPI and ACS Style

Lu, Y.; Chong, J.; Shen, S.; Chammas, J.-B.; Chalifour, L.; Xia, J. TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome. Metabolites 2022, 12, 10. https://doi.org/10.3390/metabo12010010

AMA Style

Lu Y, Chong J, Shen S, Chammas J-B, Chalifour L, Xia J. TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome. Metabolites. 2022; 12(1):10. https://doi.org/10.3390/metabo12010010

Chicago/Turabian Style

Lu, Yao, Jasmine Chong, Shiqian Shen, Joey-Bahige Chammas, Lorraine Chalifour, and Jianguo Xia. 2022. "TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome" Metabolites 12, no. 1: 10. https://doi.org/10.3390/metabo12010010

Find Other Styles
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Access Map by Country/Region

1
Back to TopTop