ArticleNature communications2025
Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.
Article in Nature communications, 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
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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
7 citing papers in PubMed.
- Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.mSystems · 2026Article
- Review
- The Japanese gut microbiome: ecology, uniqueness, and impact on health and disease.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2026Review
- Expanded gut microbial genomes from Chinese populations reveal population-specific genomic features related to human physiological traits.Genome medicine · 2025Article
- Association of Gut Microbiota With Performance Level Among Iranian Professional and Semi-Professional Runners: A Cross-Sectional Study.Health science reports · 2025Article
- HiBC: a publicly available collection of bacterial strains isolated from the human gut.Nature communications · 2025Article
- Function-based selection of synthetic communities enables mechanistic microbiome studies.The ISME journal · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Microbes use a range of genetic codes and gene structures, yet these are often ignored during metagenomic analysis. This causes spurious protein predictions, preventing functional assignment which limits our understanding of ecosystems. To resolve this, we developed a lineage-specific gene prediction approach that uses the correct genetic code based on the taxonomic assignment of genetic fragments, removes incomplete protein predictions, and optimises prediction of small proteins. Applied to 9634 metagenomes and 3594 genomes from the human gut, this approach increased the landscape of captured expressed microbial proteins by 78.9%, including previously hidden functional groups. Optimised small protein prediction captured 3,772,658 small protein clusters, which form an improved microbial protein catalogue of the human gut (MiProGut). To enable the ecological study of a protein's prevalence and association with host parameters, we developed InvestiGUT, a tool which integrates both the protein sequences and sample metadata. Accurate prediction of proteins is critical to providing a functional understanding of microbiomes, enhancing our ability to study interactions between microbes and hosts.
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What Socratic 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 Socratic graph.