ArticleNature communications2025
Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases.
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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- Decoding the cancer microbiome: multi-omics, AI, and translational opportunities.Genome biology · 2026Review
- Integrating multi-omics technologies to decipher microbiome functions.Nature communications · 2026Review
- Systematic evaluation of PASEF acquisition strategies in complex metaproteomes.Nature communications · 2026Article
- Prevention of Intestinal Inflammation and Gut Dysbiosis by Prebiotic Grape Seed Flour in Mice with DSS-Induced Colitis.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Article
- TIPs: a deep learning-guided proteogenomic framework to expand the landscape of transposable element-derived antigens with immunopeptidomics.Genome biology · 2026Article
- A Viral Mutation Profiling and Discovery Strategy for Sensitive Multiplex Detection of Viruses and Variants in Saliva by Proteomics.bioRxiv : the preprint server for biology · 2026Article
- Interspecies interactions drive bacterial proteome reorganization and emergent metabolism.Nature ecology & evolution · 2026Article
- A Framework for Database Search with AI Models in Mass Spectrometry-Based Proteomics.Journal of proteome research · 2026Review
- Wastewater metaproteomics: tracking microbial and human protein biomarkers.ISME communications · 2026Article
- Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.PloS one · 2026Article
- Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling.Gut microbes reports · 2026Review
- From Identification to Insight: Making Full Use of the Diagnostic Potential of MS/MS Proteotyping in Clinical Microbiology Using Efficient Bioinformatics.Journal of proteome research · 2025Review
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Authors and funding
14 authors.
Funding
Abstract
The functional characterization of host-gut microbiome interactions remains limited by the sensitivity of current metaproteomic approaches. Here, we present uMetaP, an ultra-sensitive workflow combining advanced LC-MS technologies with an FDR-validated de novo sequencing strategy, novoMP. uMetaP markedly expands functional coverage and improves the taxonomic detection limit of the gut dark metaproteome by 5000-fold, enabling precise detection and quantification of low-abundance microbial and host proteins. Applied to a mouse model of intestinal injury, uMetaP revealed host-microbiome functional networks underlying tissue damage, beyond genomic findings. Orthogonal validation using transcriptomic data from Crohn's disease patients confirmed key host protein alterations. Furthermore, we introduce the concept of a druggable metaproteome, mapping functional targets within the host and microbiota. By redefining the sensitivity limits of metaproteomics, uMetaP provides a highly valuable framework for advancing microbiome research and developing therapeutic strategies for microbiome-related diseases.
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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.