ArticleFrontiers in microbiology2021
Distinct Human Gut Microbial Taxonomic Signatures Uncovered With Different Sample Processing and Microbial Cell Disruption Methods for Metaproteomic Analysis.
Article in Frontiers in microbiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Metaproteomic portrait of the healthy human gut microbiota.NPJ biofilms and microbiomes · 2024Pooled it
- Postbiotics and Paraprobiotics as Next-Generation Gut Microbiome Modulators in Sustainable Aquaculture Health.Antibiotics (Basel, Switzerland) · 2026Review
- Cryptosporidium spp. infection drives distinct alterations in the faecal extracellular vesicles metaproteome of calves.Journal of animal science and biotechnology · 2026Article
- Microbial Omics.Progress in molecular and subcellular biology · 2026Review
- Omics and Multiomics-Based Diagnostics for Invasive Candidiasis: Toward Precision Medicine.Molecular & cellular proteomics : MCP · 2025Review
- Comparing and optimizing protein extraction methods with different lysis buffers for the analyses of human fecal microbiome via metaproteomics approach.Journal of microbiological methods · 2025Article
- Human gut microbiota analysis of cystic fibrosis infants using metaproteomics.Microbiology resource announcements · 2024Article
- Benchmarking low- and high-throughput protein cleanup and digestion methods for human fecal metaproteomics.mSystems · 2024Article
- Article
- Roles of the gut microbiota in human neurodevelopment and adult brain disorders.Frontiers in neuroscience · 2024Review
- GroEL-Proteotyping of Bacterial Communities Using Tandem Mass Spectrometry.International journal of molecular sciences · 2023Article
- Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis.Microbiology spectrum · 2022Article
- Functional and Taxonomic Traits of the Gut Microbiota in Type 1 Diabetes Children at the Onset: A Metaproteomic Study.International journal of molecular sciences · 2022Article
- Microbiomics Revealed the Disturbance of Intestinal Balance in Rabbits with Diarrhea Caused by Stopping the Use of an Antibiotic Diet.Microorganisms · 2022Article
- Intestinal Inflammation and Alterations in the Gut Microbiota in Cystic Fibrosis: A Review of the Current Evidence, Pathophysiology and Future Directions.Journal of clinical medicine · 2022Review
- Distinct Human Gut Microbial Taxonomic Signatures Uncovered With Different Sample Processing and Microbial Cell Disruption Methods for Metaproteomic Analysis.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The use of metaproteomics for studying the human gut microbiota can shed light on the taxonomic profile and the functional role of the microbial community. Nevertheless, methods for extracting proteins from stool samples continue to evolve, in the pursuit of optimal protocols for moistening and dispersing the stool sample and for disrupting microbial cells, which are two critical steps for ensuring good protein recovery. Here, we evaluated different stool sample processing (SSP) and microbial cell disruption methods (CDMs). The combination of a longer disintegration period of the stool sample in a tube rotator with sonication increased the overall number of identified peptides and proteins. Proteobacteria, Bacteroidetes, Planctomycetes, and Euryarchaeota identification was favored by mechanical cell disruption with glass beads. In contrast, the relative abundance of Firmicutes, Actinobacteria, and Fusobacteria was improved when sonication was performed before bead beating. Tenericutes and Apicomplexa identification was enhanced by moistening the stool samples during processing and by disrupting cells with medium-sized glass beads combined with or without sonication. Human protein identifications were affected by sonication. To test the reproducibility of these gut metaproteomic analyses, we examined samples from six healthy individuals using a protocol that had shown a good taxonomic diversity and identification of proteins from Proteobacteria and humans. We also detected proteins involved in microbial functions relevant to the host and related mostly to specific taxa, such as B12 biosynthesis and short chain fatty acid (SCFA) production carried out mainly by members in the
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