ArticleProteomes2019
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.
Article in Proteomes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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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
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 65 citations in OpenAlex.
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Comparative performance of Scribe and database search engines in metaproteomic profiling of a ground-truth microbiome dataset.Journal of proteomics · 2026Article
- Identification and applications of disease-associated differential human and bacterial proteins with metaproteomic evidence.Health information science and systems · 2025Article
- A core human gut microbe,mBio · 2025Article
- Phylogenetic tree-based amino acid sequence generation for proteomics data analysis of unknown species.Computational and structural biotechnology journal · 2025Article
- Insights into human respiratory microbiome under dysbiosis and its analysis tool.Frontiers in microbiomes · 2025Review
- Article
- The Landscape and Perspectives of the Human Gut Metaproteomics.Molecular & cellular proteomics : MCP · 2024Article
- Article
- Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia.Scientific reports · 2024Article
- A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.Frontiers in microbiology · 2024Review
- The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020).Journal of biomolecular techniques : JBT · 2023Article
- Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome.mSystems · 2023Article
- Fecal Proteome Profile in Dogs Suffering from Different Hepatobiliary Disorders and Comparison with Controls.Animals : an open access journal from MDPI · 2023Article
- Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics.Computational and structural biotechnology journal · 2023Review
- A bibliometric analysis of the global impact of metaproteomics research.Frontiers in microbiology · 2023Article
- Reanalysis of ProteomicsDB Using an Accurate, Sensitive, and Scalable False Discovery Rate Estimation Approach for Protein Groups.Molecular & cellular proteomics : MCP · 2022Article
- Lactobacillus supports Clostridiales to restrict gut colonization by multidrug-resistant Enterobacteriaceae.Nature communications · 2022Article
- Article
- Metaproteomics as a tool for studying the protein landscape of human-gut bacterial species.PLoS computational biology · 2022Article
Corrections and comments
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Authors and funding
18 authors at 8 institutions in 5 countries.
Funding
Abstract
The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.
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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.