ArticleeLife2019
Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
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- From genomes to interventions: computational strategies transforming parasitology.Frontiers in veterinary science · 2026Review
- Genome-scale metabolic modeling ofmSystems · 2025Article
- Narrow-spectrum resource-utilizing bacteria drive the stability of synthetic communities through enhancing metabolic interactions.Nature communications · 2025Article
- Seed2LP: seed inference in metabolic networks for reverse ecology applications.Bioinformatics (Oxford, England) · 2025Article
- In silico encounters: harnessing metabolic modelling to understand plant-microbe interactions.FEMS microbiology reviews · 2025Review
- Structure and composition of early biofilms formed on dental implants are complex, diverse, subject-specific and dynamic.NPJ biofilms and microbiomes · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Using Genomics to Decipher the Enigmatic Properties and Survival Adaptation of Candidate Phyla Radiation.Microorganisms · 2023Review
- Teasing out missing reactions in genome-scale metabolic networks through hypergraph learning.Nature communications · 2023Article
- Functional comparison of metabolic networks across species.Nature communications · 2023Article
- Controlling the human microbiome.Cell systems · 2023Review
- Culture-based approaches to studying "microbial dark matter".Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome.Microbiome · 2022Article
- Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease.Clinical microbiology reviews · 2022Review
- Fusobacterium nucleatum Metabolically Integrates Commensals and Pathogens in Oral Biofilms.mSystems · 2022Article
- Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation.Cell host & microbe · 2021Article
- Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
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Authors and funding
3 authors.
Funding
Abstract
The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several
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