ArticlePLoS computational biology2022
Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Systematic evaluation of PASEF acquisition strategies in complex metaproteomes.Nature communications · 2026Article
- Unlocking therapeutic impacts of the gut microbiota with computational tools.Current opinion in biotechnology · 2026Review
- Dynamic remodeling of the gut microbiome and host responses after myocardial infarction revealed by longitudinal metaproteomics.Frontiers in microbiology · 2026Article
- Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.Nature communications · 2025Article
- Metaproteomic Dataset on Semi-Diurnal Variability of the Bacterioplankton Communities During a Spring Phytoplankton Bloom in the North Sea.Proteomics · 2025Article
- Article
- The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies.World journal of microbiology & biotechnology · 2025Review
- Growth Performance, Carcass Quality and Gut Microbiome of Finishing Stage Pigs Fed Formulated Protein-Energy Nutrients Balanced Diet with Banana Agro-Waste Silage.Life (Basel, Switzerland) · 2025Article
- Article
- Proteomics as a complementary approach to measure norovirus infection in clinical samples.Virology · 2025Review
- Identification of microbial species and proteins associated with colorectal cancer by reanalyzing CPTAC proteomic datasets.Scientific reports · 2025Article
- FISH-FACS proteomics: enhanced label-free quantitative proteome analysis from low cell numbers of uncultured environmental microorganisms.ISME communications · 2025Article
- Wise Roles and Future Visionary Endeavors of Current Emperor: Advancing Dynamic Methods for Longitudinal Microbiome Meta-Omics Data in Personalized and Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Review
- The Influence of Protein Secretomes of Enterococcus durans on ex vivo Human Gut Microbiome.Probiotics and antimicrobial proteins · 2024Article
- The Landscape and Perspectives of the Human Gut Metaproteomics.Molecular & cellular proteomics : MCP · 2024Article
- Metaproteomic and Metagenomic-Coupled Approach to Investigate Microbial Response to Electrochemical Conditions in Microbial Fuel Cells.Microorganisms · 2023Article
- Integrating the serum proteomic and fecal metaproteomic to analyze the impacts of overweight/obesity on IBD: a pilot investigation.Clinical proteomics · 2023Article
- Gut Microbiome Proteomics in Food Allergies.International journal of molecular sciences · 2023Review
- The interplay between herbal medicines and gut microbiota in metabolic diseases.Frontiers in pharmacology · 2023Review
- Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics.Frontiers in microbiology · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Host-microbiome interactions and the microbial community have broad impact in human health and diseases. Most microbiome based studies are performed at the genome level based on next-generation sequencing techniques, but metaproteomics is emerging as a powerful technique to study microbiome functional activity by characterizing the complex and dynamic composition of microbial proteins. We conducted a large-scale survey of human gut microbiome metaproteomic data to identify generalist species that are ubiquitously expressed across all samples and specialists that are highly expressed in a small subset of samples associated with a certain phenotype. We were able to utilize the metaproteomic mass spectrometry data to reveal the protein landscapes of these species, which enables the characterization of the expression levels of proteins of different functions and underlying regulatory mechanisms, such as operons. Finally, we were able to recover a large number of open reading frames (ORFs) with spectral support, which were missed by de novo protein-coding gene predictors. We showed that a majority of the rescued ORFs overlapped with de novo predicted protein-coding genes, but on opposite strands or in different frames. Together, these demonstrate applications of metaproteomics for the characterization of important gut bacterial species.
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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.