ArticleEcology letters2022
Contribution of genome-scale metabolic modelling to niche theory.
Article in Ecology letters, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Metagenome-scale modeling to assess microbiome metabolic complementarity for precision microbiota transplantation therapies.Gut microbes · 2026Article
- Nutrient control enables metabolic reconstruction ofbioRxiv : the preprint server for biology · 2026Article
- Selecting methods for draft GEM generation in multicellular eukaryotes: a comparative analysis.BMC bioinformatics · 2026Article
- Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.bioRxiv : the preprint server for biology · 2026Article
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- Matters of life and death in computational cell biology.NPJ systems biology and applications · 2026Review
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- Article
- Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.Cell systems · 2025Article
- Unveiling the link between phytoplankton molecular physiology and biogeochemical cycling via genome-scale modeling.Science advances · 2025Article
- Article
- Quantitative principles of microbial metabolism shared across scales.Nature microbiology · 2024Review
- Structure and composition of microbial communities in the water column from Southern Gulf of Mexico and detection of putative hydrocarbon-degrading microorganisms.Environmental microbiology reports · 2024Article
- A benchmark of optimization solvers for genome-scale metabolic modeling of organisms and communities.mSystems · 2024Article
- Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.Frontiers in microbiology · 2023Article
- Contribution of genome-scale metabolic modelling to niche theory.Ecology letters · 2022Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Standard niche modelling is based on probabilistic inference from organismal occurrence data but does not benefit yet from genome-scale descriptions of these organisms. This study overcomes this shortcoming by proposing a new conceptual niche that resumes the whole metabolic capabilities of an organism. The so-called metabolic niche resumes well-known traits such as nutrient needs and their dependencies for survival. Despite the computational challenge, its implementation allows the detection of traits and the formal comparison of niches of different organisms, emphasising that the presence-absence of functional genes is not enough to approximate the phenotype. Further statistical exploration of an organism's niche sheds light on genes essential for the metabolic niche and their role in understanding various biological experiments, such as transcriptomics, paving the way for incorporating better genome-scale description in ecological studies.
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