Enteropathway: the metabolic pathway database for the human gut microbiota

Abstract The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota i...

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Bibliographic Details
Published in:Briefings in bioinformatics 2024-07, Vol.25 (5)
Main Authors: Shiroma, Hirotsugu, Darzi, Youssef, Terajima, Etsuko, Nakagawa, Zenichi, Tsuchikura, Hirotaka, Tsukuda, Naoki, Moriya, Yuki, Okuda, Shujiro, Goto, Susumu, Yamada, Takuji
Format: Article
Language:English
Subjects:
Applications programs
Computational Biology - methods
Databases, Factual
Gastrointestinal Microbiome
Humans
Intestinal microflora
Metabolic Networks and Pathways
Metabolic pathways
Metabolism
Metabolites
Microbiota
Microorganisms
Modules
Problem Solving Protocol
Software
Statistical analysis
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Summary:Abstract The human gut microbiota produces diverse, extensive metabolites that have the potential to affect host physiology. Despite significant efforts to identify metabolic pathways for producing these microbial metabolites, a comprehensive metabolic pathway database for the human gut microbiota is still lacking. Here, we present Enteropathway, a metabolic pathway database that integrates 3269 compounds, 3677 reactions, and 876 modules that were obtained from 1012 manually curated scientific literature. Notably, 698 modules of these modules are new entries and cannot be found in any other databases. The database is accessible from a web application (https://enteropathway.org) that offers a metabolic diagram for graphical visualization of metabolic pathways, a customization interface, and an enrichment analysis feature for highlighting enriched modules on the metabolic diagram. Overall, Enteropathway is a comprehensive reference database that can complement widely used databases, and a tool for visual and statistical analysis in human gut microbiota studies and was designed to help researchers pinpoint new insights into the complex interplay between microbiota and host metabolism.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbae419