ArticleISME communications2024
Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.
Article in ISME communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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.
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Who cites it
8 citing papers in PubMed.
- Article
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Navigating multi-omic integration methods for human microbiome research.Nature microbiology · 2026Review
- Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.Microbiome · 2026Article
- Article
- Protein Structural Phylogenetics.Genome biology and evolution · 2025Review
- The microbiologist's guide to metaproteomics.iMeta · 2025Review
- Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed
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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.