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Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

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microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic

Haris Zafeiropoulos¹, Ermis Ioannis Michail Delopoulos², Andi Erega³

¹Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. haris.zafeiropoulos@kuleuven.be.

|September 22, 2025

Summary

We developed microbetag, a software ecosystem for annotating microbial networks by enriching taxa with traits and edges with metabolic data. This tool enhances accuracy and aids in discovering microbial interactions.

Keywords:

Data integration Enrichment analysis Microbial associations Pathway complementarity Phenotypic traits Seed set

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Published on: January 22, 2018

Area of Science:

Microbiology
Bioinformatics
Systems Biology

Background:

Microbial co-occurrence network inference faces challenges with accuracy and tool limitations.
Existing methods often fail to capture complex microbial interactions effectively.

Purpose of the Study:

To introduce microbetag, a novel software ecosystem for comprehensive microbial network annotation.
To enhance the understanding of microbial communities by integrating phenotypic and metabolic data.

Main Methods:

Developed microbetag, a software ecosystem with online and stand-alone versions.
Integrated microbetagDB, a database of 34,608 annotated genomes.
Created MGG, a Cytoscape app for network visualization and retrieval.

Main Results:

microbetag enriches network nodes with taxa traits and edges with metabolic complementarities.
The tool successfully identified known metabolic interactions within microbial networks.
microbetag demonstrated utility as a hypothesis-generating tool for microbial ecology.

Conclusions:

microbetag offers a robust solution to improve microbial network analysis accuracy.
The software ecosystem facilitates the discovery of potential cross-feeding relationships.
microbetag and its associated tools provide a user-friendly platform for microbial network exploration.