TrpNet is a comprehensive resource for researchers to visually explore, search, or predict tryptophan metabolism within the context of human and mouse gut microbiome. Its key features include
- Comprehensive transformations: TrpNet consolidates known bio-transformations of tryptophan metabolism into 130 reactions and 108 metabolites annotated with host or/and microbial origins.
- High-resolution mapping: TrpNet maps tryptophan metabolism across ~ 5270 microbes (at strain level, ~2100 belonging to human gut microbiome) based on literature review and genome-scale metabolic models.
- Dynamic network creation: TrpNet produces the tryptophan metabolism network for the selected combination of microbes (and host) for intuitive visualization and understanding.
- Predicting tryptophan metabolites: TrpNet can predict tryptophan metabolites from 16S rRNA abundance information using Bayesian logistic regression models trained on our database
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Motivation
The gut microbiome is a critical regulator of its host homeostasis through the production of various bioactive metabolites which can be best exemplified by tryptophan derived metabolites. Tryptophan is an essential amino acid that undergoes complex host-microbiome co-metabolism leading to the production of an array of important metabolites including ligands of the aryl hydrocarbon receptor (AhR) such as Indoleacetic acid (IAA), indolepropionate (IPA) and Kynurenine (KYN) which are involved in host biological processes covering neuro-transmission, inflammation, and the immune response.
However, the existing pathway databases are mainly focused on the host tryptophan pathway and are not able to provide the information on tryptophan degradation across gut microbiome. Besides, not all tryptophan transformation are captured by these databases. Therefore, a comprehensive resource that covers the know tryptophan transform reactions and address the microbial contributors for tryptophan metabolites is necessary.
Publication
Lu, Y., Chong, J., Shen, S., Chammas, JB., Chalifour, L., and Xia, J. TrpNet: Understanding Tryptophan Metabolism across Gut Microbiome Metabolites 2022, 12(1), 10