ReviewThe ISME journal2013
Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.
Review in The ISME journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
34 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.FEMS microbiology ecology · 2016Guideline
- From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.Microbiology and molecular biology reviews : MMBR · 2026Review
- Review
- Multi-omic stable isotope probing revealsISME communications · 2026Article
- Metaproteomics in the One Health framework for unraveling microbial effectors in microbiomes.Microbiome · 2025Review
- Metabolic Responses, Cell Recoverability, and Protein Signatures of Three Extremophiles: Sustained Life During Long-Term Subzero Incubations.Microorganisms · 2025Article
- Nanopore sequencing enables novel detection of deuterium incorporation in DNA.Computational and structural biotechnology journal · 2024Article
- Integrated analysis reveals important differences in the gut and oropharyngeal microbiota between children with mild and severe hand, foot, and mouth disease.Emerging microbes & infections · 2023Article
- Energetically exploiting lignocellulose-rich residues in anaerobic digestion technologies: from bioreactors to proteogenomics.Biotechnology for biofuels and bioproducts · 2023Article
- Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation.Water research X · 2023Article
- Unravelling metabolic cross-feeding in a yeast-bacteria community usingMolecular systems biology · 2023Article
- Daylight-driven carbon exchange through a vertically structured microbial community.Frontiers in microbiology · 2023Article
- Delineation of mechanistic approaches of rhizosphere microorganisms facilitated plant health and resilience under challenging conditions.3 Biotech · 2022Review
- Integrated Analysis of the Alterations in Gut Microbiota and Metabolites of Mice Induced After Long-Term Intervention With Different Antibiotics.Frontiers in microbiology · 2022Article
- Critical Assessment of MetaProteome Investigation (CAMPI): a multi-laboratory comparison of established workflows.Nature communications · 2021Article
- Dysbiosis of Gut Microbiota Promotes Hepatocellular Carcinoma Progression by Regulating the Immune Response.Journal of immunology research · 2021Observational
- The Lichens' Microbiota, Still a Mystery?Frontiers in microbiology · 2021Review
- PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.Frontiers in chemistry · 2021Article
- Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights.International journal of molecular sciences · 2020Review
- Rhizosphere microbiome: Engineering bacterial competitiveness for enhancing crop production.Journal of advanced research · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.
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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.