ArticleNature communications2023
Top-down identification of keystone taxa in the microbiome.
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 36 papers.
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Who cites it
36 citing papers in PubMed.
- Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.Current research in microbial sciences · 2026Article
- Deciphering microbial community dynamics using cross-sectional data-informed NeuralODE.Microbiome · 2026Article
- Patterns of Soil Microbial Diversity, Assembly, and Co-Occurrence Along a Natural Salinity Gradient in an Inland Saline-Alkali Wetland.Microorganisms · 2026Article
- The precisely regulated keystone taxa facilitate microbial mineralization of soil organic phosphorus via niche partitioning.NPJ biofilms and microbiomes · 2026Article
- Longitudinal dynamics of gut microbiota and mycobiota in pneumonia-derived sepsis: evidence of taxonomic stability and trans-kingdom network reorganization.Gut pathogens · 2026Article
- Research advances in the identification of gut keystone bacteria and formulation of suitable dietary intervention strategies for restoring gut homeostasis.NPJ biofilms and microbiomes · 2026Review
- Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.Foods (Basel, Switzerland) · 2026Review
- Keystone concept revisited: insights into microbial community dynamics and control.Nature reviews. Microbiology · 2026Review
- Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy.Foods (Basel, Switzerland) · 2026Review
- Root-derived low molecular weight organic acids modulate keystone microbial taxa impacting plant phosphorus acquisition.Journal of advanced research · 2026Article
- KeySDL: sparse dictionary learning for keystone microbe identification from steady-state observations using a dynamical-systems model.BioData mining · 2026Article
- A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.World journal of microbiology & biotechnology · 2025Review
- Potentiators empower synthetic microbiomes as silent guardians against co-contamination.Nature communications · 2025Article
- Deciphering gut microbial impact in coronary artery disease through multimodal computational approaches.BMC microbiology · 2025Article
- Alterations in Gut Microbial Co-Abundance Networks in Metabolic Syndrome: A Population-Based Cross-Sectional Study.Microorganisms · 2025Article
- Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut.Gut microbes · 2025Review
- Arbuscular Mycorrhizal Fungi as Core Engineers in Synthetic Microbial Communities: Boosting Plant Growth and Soil Health for Sustainable Agriculture.Journal of fungi (Basel, Switzerland) · 2025Review
- Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.Microbiology spectrum · 2025Article
- Targeted Intervention Strategies for Maternal-Offspring Transmission of Christensenellaceae in Pigs via a Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Genetic Characterisation of the Bacterial Microbiota Associating With a Strain of Epichloë Fungal Endophyte of Perennial Ryegrass and the Interaction With Its Paenibacillus Members.Environmental microbiology reports · 2025Article
Corrections and comments
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Authors and funding
2 authors.
Funding
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Abstract
Keystone taxa in ecological communities are native taxa that play an especially important role in the stability of their ecosystem. However, we still lack an effective framework for identifying these taxa from the available high-throughput sequencing without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. In addition, while most microbial interaction models assume pair-wise relationships, it is yet unclear whether pair-wise interactions dominate the system, or whether higher-order interactions are relevant. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the taxa. Our method does not assume a priori knowledge of pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real high-throughput sequencing of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystone species with correlated occurrence. The keystone analysis of single-time-point cross-sectional data is also later verified by the evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.
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