ArticleNature communications2020
Mapping the bacterial metabolic niche space.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.Microbiology spectrum · 2026Article
- Genome-guided characterization ofMicrobiology spectrum · 2026Article
- A horizontal connectivity mode in coastal oceans: transport overrides stratification to govern microbiome network stability.Applied and environmental microbiology · 2026Article
- A bacterial ecocline in Klebsiella pneumoniae may explain its backboned phylogeny.PLoS biology · 2026Article
- Revealing interactions between microbes, metabolites, and dietary compounds using genome-scale analysis.Microbiome · 2026Article
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Microbial cohorts: bringing ecological meaning to the modularity concept of co-occurrence networks.ISME communications · 2026Article
- Inhibition ofMicroorganisms · 2025Article
- Experimental mapping of bacterial fitness landscapes reveals eco-evolutionary fingerprints.Scientific reports · 2025Article
- Applying ecological principles to microbiome engineering.Nature microbiology · 2025Review
- Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.Cell systems · 2025Article
- Hidden Allies: Decoding the Core Endohyphal Bacteriome of Aspergillus fumigatus.Environmental microbiology reports · 2025Article
- Trait-Based Life History Strategies Shape Bacterial Niche Breadth.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Systematic representation and optimization enable the inverse design of cross-species regulatory sequences in bacteria.Nature communications · 2025Article
- Ecological strategies of bacteria shape inherent phage diversity in Atlantic salmon gut microbiomes.The ISME journal · 2025Article
- Bridging Ecology and Microbiomes: Applying Ecological Theories in Host-associated Microbial Ecosystems.Current clinical microbiology reports · 2025Review
- Mobility census for monitoring rapid urban development.Journal of the Royal Society, Interface · 2024Article
- Unsupervised pattern and outlier detection for pedestrian trajectories using diffusion maps.Physica A · 2024Article
- Deterministic and stochastic processes generating alternative states of microbiomes.ISME communications · 2024Article
- Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes.ISME communications · 2024Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rise in the availability of bacterial genomes defines a need for synthesis: abstracting from individual taxa, to see larger patterns of bacterial lifestyles across systems. A key concept for such synthesis in ecology is the niche, the set of capabilities that enables a population's persistence and defines its impact on the environment. The set of possible niches forms the niche space, a conceptual space delineating ways in which persistence in a system is possible. Here we use manifold learning to map the space of metabolic networks representing thousands of bacterial genera. The results suggest a metabolic niche space comprising a collection of discrete clusters and branching manifolds, which constitute strategies spanning life in different habitats and hosts. We further demonstrate that communities from similar ecosystem types map to characteristic regions of this functional coordinate system, permitting coarse-graining of microbiomes in terms of ecological niches that may be filled.
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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.