ArticleNature communications2023
Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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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.
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Who cites it
51 citing papers in PubMed, 72 citations in OpenAlex.
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- Antibiotic-Driven Gut Microbiome Dysbiosis: Resistome Dynamics, Metabolic Disruption, and Paths to Restoration.Antibiotics (Basel, Switzerland) · 2026Review
- Decoding the functional landscape and resistome profile of the gut microbiome in the Pangwala tribal community of India.BMC microbiology · 2026Article
- Goat gut microbiome as a reservoir for microorganism-encoded short peptides: regulation by host development age and nematode challenge.NPJ biofilms and microbiomes · 2026Article
- ComparativeFoods (Basel, Switzerland) · 2026Article
- Towards microbiome-informed strategies for predicting and preventing pregnancy complications.Reproduction & fertility · 2026Review
- Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.Foods (Basel, Switzerland) · 2026Review
- Cross hybridization Inference for Phylogenetic Resolution (CIPHR)-FISH enables microbiome imaging with strain level taxonomic resolution.bioRxiv : the preprint server for biology · 2026Article
- Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.Microbiome · 2026Article
- Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.Frontiers in microbiology · 2026Article
- Marmot gut microbiomes are stable against dietary variation.Oecologia · 2025Article
- Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.FEBS open bio · 2025Article
- Breastfeeding and the milk resistome shape the establishment and transmission of antibiotic resistance genes in the infant gut microbiome.Gut microbes · 2025Article
- Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism.Nature microbiology · 2025Article
- Modulatory effects of Boletus edulis on the gut microbiota in Atlantic salmon (Salmo salar) utilizing an artificial teleost gut model.Animal microbiome · 2025Article
- Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs.Nature communications · 2025Article
- Opportunities and Challenges of Multiomics for Discovery and Monitoring of Human Pathogens.Environment & health (Washington, D.C.) · 2025Review
- Metaproteomic Analysis to Assess the Impact of Storage Media on Human Gut Microbiome in Fecal Samples.Proteomics · 2025Article
- Dissecting microbial communities with single-cell transcriptome analysis.Science (New York, N.Y.) · 2025Review
Corrections and comments
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Authors and funding
12 authors at 2 institutions in 3 countries.
Funding
Abstract
Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.
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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.