ArticleMicrobiome2021
Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome.
Article in Microbiome, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed, 53 citations in OpenAlex.
- High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.Nature communications · 2026Article
- Integration of human microbiota (SIHUMIx) and zebrafish models reveals microbiome-mediated host responses to azoxystrobin.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
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- Less missing values-evaluation of proteomics workflows for the quantification of (small) proteins.microLife · 2026Article
- CoMPaseD: advanced planning of proteomic experiments aiming to identify small proteins.microLife · 2026Article
- Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends.Food science & nutrition · 2025Review
- Propensity for proto-gene emergence in bacteria.Genome biology · 2025Article
- De novo gene birth and the conundrum of ORFan genes in bacteria.Genome research · 2025Review
- Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.Nature communications · 2025Article
- A catalog of small proteins from the global microbiome.Nature communications · 2024Article
- Article
- Review
- Enzymatic machinery of wood-inhabiting fungi that degrade temperate tree species.The ISME journal · 2024Article
- Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.Microbiome research reports · 2024Article
- High-throughput screening of the effects of 90 xenobiotics on the simplified human gut microbiota model (SIHUMIx): a metaproteomic and metabolomic study.Frontiers in microbiology · 2024Article
- Hematology profile, digestive enzymes, thyroid hormones, productivity, and nitrogen balance of growing male rabbits supplemented with exogenous dietary lysozyme.Animal biotechnology · 2023Article
- Examining the functional space of gut microbiome-derived peptides.MicrobiologyOpen · 2023Article
- Computational exploration of the global microbiome for antibiotic discovery.bioRxiv : the preprint server for biology · 2023Article
- Detection of Known and Novel Small Proteins inAnalytical chemistry · 2023Article
- Review
Corrections and comments
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Authors and funding
14 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities.
resultsWe created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx.
conclusionsWe outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
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