# Interpreting Microbiome Signatures with MicrobiomeNet

## TL;DR

MicrobiomeNet is a web platform that uses genome-scale models to explore the functions and interactions of microbes in the microbiome.

## Contribution

MicrobiomeNet introduces a comprehensive tool for analyzing microbiome signatures using metabolic models and microbial associations.

## Key findings

- MicrobiomeNet hosts 12,400 genome-scale metabolic models and 6 million microbial signatures.
- The platform enables users to explore metabolic interactions and associations among microbes.
- Protocols are provided for analyzing carbohydrate utilization and identifying gut microbes producing deoxycholic acid.

## Abstract

MicrobiomeNet (https://microbiomenet.com) is a web‐based platform developed to provide functional insights into microbiome signatures using genome‐scale metabolic models (GEMs). It currently hosts 12,400 GEMs and around 6 million microbial signatures. Users can start by searching microbes, metabolites, genes, or enzymes, and perform common tasks such as to characterize the metabolic capacity for a given microbe, to explore known microbial associations, as well as to understand potential metabolic interactions. This book chapter provides practical, step‐by‐step instructions for navigating MicrobiomeNet to obtain functional insights into individual microbes or microbial association networks. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Characterizing the Metabolic Profile of a Microbe of Interest

Basic Protocol 2: Elucidating Metabolic Interactions from Microbial Associations

Basic Protocol 3: Analyzing Carbohydrate‐Utilization Pathways to Explain Co‐Responsive Taxa

Basic Protocol 4: Identifying Novel Deoxycholic Acid‐Producing Gut Microbes

Basic Protocol 5: Assessing the Faecalibacterium prausnitzii–Coprococcus Relationship