ArticlePLoS computational biology2014
A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Seed2LP: seed inference in metabolic networks for reverse ecology applications.Bioinformatics (Oxford, England) · 2025Article
- Functional comparison of metabolic networks across species.Nature communications · 2023Article
- Metabolic adaptation to vitamin auxotrophy by leaf-associated bacteria.The ISME journal · 2022Article
- Computing optimal factories in metabolic networks with negative regulation.Bioinformatics (Oxford, England) · 2022Article
- Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome biology · 2021Review
- Formation, characterization and modeling of emergent synthetic microbial communities.Computational and structural biotechnology journal · 2021Article
- Immune recognition of putative alien microbial structures: Host-pathogen interactions in the age of space travel.PLoS pathogens · 2020Review
- Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.eLife · 2019Article
- The Cost of Metabolic Interactions in Symbioses between Insects and Bacteria with Reduced Genomes.mBio · 2018Article
- Development of Chemically Defined Media Reveals Citrate as Preferred Carbon Source forFrontiers in microbiology · 2018Article
- More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes.Microbiome · 2017Review
- Enumeration of minimal stoichiometric precursor sets in metabolic networks.Algorithms for molecular biology : AMB · 2016Article
- Harnessing the landscape of microbial culture media to predict new organism-media pairings.Nature communications · 2015Article
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Authors and funding
5 authors.
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Abstract
Understanding microbial nutritional requirements is a key challenge in microbiology. Here we leverage the recent availability of thousands of automatically generated genome-scale metabolic models to develop a predictor of microbial minimal medium requirements, which we apply to thousands of species to study the relationship between their nutritional requirements and their ecological and genomic traits. We first show that nutritional requirements are more similar among species that co-habit many ecological niches. We then reveal three fundamental characteristics of microbial fastidiousness (i.e., complex and specific nutritional requirements): (1) more fastidious microorganisms tend to be more ecologically limited; (2) fastidiousness is positively associated with smaller genomes and smaller metabolic networks; and (3) more fastidious species grow more slowly and have less ability to cooperate with other species than more metabolically versatile organisms. These associations reflect the adaptation of fastidious microorganisms to unique niches with few cohabitating species. They also explain how non-fastidious species inhabit many ecological niches with high abundance rates. Taken together, these results advance our understanding microbial nutrition on a large scale, by presenting new nutrition-related associations that govern the distribution of microorganisms in nature.
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