ArticleCommunications biology2025
A systematic benchmark of integrative strategies for microbiome-metabolome data.
Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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.
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.
Who cites it
7 citing papers in PubMed.
- Antioxidant and Anti-Inflammatory Effects of InhaledPlants (Basel, Switzerland) · 2026Article
- Integrated Metagenomic and Untargeted Metabolomic Analyses Characterize Enramycin-Associated Colonic Microbial and Metabolic Changes in Weaned Rabbits.Animals : an open access journal from MDPI · 2026Article
- The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.Scientific reports · 2026Article
- Compost fermented with thermophilic Bacillaceae reduces heat stress-induced mortality in laying hens through gut microbial modulation.Animal microbiome · 2026Article
- Mechanisms and Applications of Gastrointestinal Microbiota-Metabolite Interactions in Ruminants: A Review.Microorganisms · 2025Review
- Spatial and functional differentiation of microbial biofilms in a traditional cheese ripening environment.Scientific reports · 2025Article
- The human microbiome in clinical translation: from bench to bedside.Frontiers in microbiology · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.
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What OpenQuestion holds
Registered trials
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.