Evidence map›Paper›PMID 40983948›Full record

ArticleGenome biology2025

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

Haris Zafeiropoulos, Ermis Ioannis Michail Delopoulos, Andi Erega, Aline Schneider, Annelies Geirnaert, John Morris, Karoline Faust

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Haris ZafeiropoulosDepartment 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.
Ermis Ioannis Michail DelopoulosDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium.
Andi EregaInstitute of Food, Nutrition and Health, Laboratory of Food Biotechnology, ETH Zurich, Schmelzbergstrasse 7, Zurich, 8092, Switzerland.
Aline SchneiderInstitute of Food, Nutrition and Health, Laboratory of Food Biotechnology, ETH Zurich, Schmelzbergstrasse 7, Zurich, 8092, Switzerland.
Annelies GeirnaertInstitute of Food, Nutrition and Health, Laboratory of Food Biotechnology, ETH Zurich, Schmelzbergstrasse 7, Zurich, 8092, Switzerland.
John MorrisResource for Biocomputing, Visualization, and Informatics, University of California San Francisco, 16th Street, San Francisco, CA, 94143, USA.
Karoline FaustDepartment of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium. karoline.faust@kuleuven.be.

Funding

EMBO Scientific Exchange Grant 9017Horizon 2020 101000309
6 · The paper itself

Abstract

Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. Nodes, representing taxa, are enriched with phenotypic traits, while edges are enhanced with metabolic complementarities, highlighting potential cross-feeding relationships. microbetag's online version relies on microbetagDB, a database of 34,608 annotated representative genomes. microbetag can be applied to custom (metagenome-assembled) genomes via its stand-alone version. MGG, a Cytoscape app designed to support microbetag, offers a streamlined, user-friendly interface for network retrieval and visualization. microbetag effectively identified known metabolic interactions and serves as a robust hypothesis-generating tool.

Indexed as

Metabolic Networks and PathwaysMicrobiotaSoftwareDatabases, GeneticMetagenomeMolecular Sequence AnnotationData integrationEnrichment analysisMicrobial associationsPathway complementarityPhenotypic traitsSeed set

Identifiers

PMID40983948
PMCPMC12455805

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.