ArticleMicrobiome2020
Estimating relative biomasses of organisms in microbiota using "phylopeptidomics".
Article in Microbiome, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- MARLOWE: taxonomic characterization of unknown samples for forensics using de novo peptide identification.Scientific reports · 2026Article
- Unravelling the Potential of Fungal Division of Labour in the Laccase ProducerJournal of fungi (Basel, Switzerland) · 2025Article
- 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
- Wood decay under anoxia by the brown-rot fungus Fomitopsis pinicola.Nature communications · 2025Article
- MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics.Journal of proteome research · 2025Article
- Participation of gut microbiota and bacterial translocation in chronic systemic inflammation in recently diagnosed rheumatoid arthritis patients.Current research in microbial sciences · 2025Article
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- Universal Identification of Pathogenic Viruses by Liquid Chromatography Coupled with Tandem Mass Spectrometry Proteotyping.Molecular & cellular proteomics : MCP · 2024Article
- Oral microbial profiles of extrinsic black tooth stain in primary dentition: A literature review.Journal of dental sciences · 2024Review
- Article
- Exploring Andean High-Altitude Lake Extremophiles through Advanced Proteotyping.Journal of proteome research · 2024Article
- Human gut microbiome and metabolite dynamics under simulated microgravity.Gut microbes · 2023Article
- GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry.International journal of molecular sciences · 2023Article
- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).Journal of biomolecular techniques : JBT · 2023Article
- First Isolation and Characterization of Bacteria from the Core's Cooling Pool of an Operating Nuclear Reactor.Microorganisms · 2023Article
- Evaluation of the Limit of Detection of Bacteria by Tandem Mass Spectrometry Proteotyping and Phylopeptidomics.Microorganisms · 2023Article
- Deep Paleoproteotyping and Microtomography Revealed No Heart Defect nor Traces of Embalming in the Cardiac Relics of Blessed Pauline Jaricot.International journal of molecular sciences · 2023Article
- Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool.Frontiers in microbiology · 2023Article
- Metaproteomics to understand how microbiota function: The crystal ball predicts a promising future.Environmental microbiology · 2023Article
- Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is an important need for the development of fast and robust methods to quantify the diversity and temporal dynamics of microbial communities in complex environmental samples. Because tandem mass spectrometry allows rapid inspection of protein content, metaproteomics is increasingly used for the phenotypic analysis of microbiota across many fields, including biotechnology, environmental ecology, and medicine.
resultsHere, we present a new method for identifying the biomass contribution of any given organism based on a signature describing the number of peptide sequences shared with all other organisms, calculated by mathematical modeling and phylogenetic relationships. This so-called "phylopeptidomics" principle allows for the calculation of the relative ratios of peptide-specified taxa by the linear combination of such signatures applied to an experimental metaproteomic dataset. We illustrate its efficiency using artificial mixtures of two closely related pathogens of clinical interest, and with more complex microbiota models.
conclusionsThis approach paves the way to a new vision of taxonomic changes and accurate label-free quantitative metaproteomics for fine-tuned functional characterization. Video abstract.
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