ArticleBioinformatics (Oxford, England)2018
Scalable and exhaustive screening of metabolic functions carried out by microbial consortia.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Article
- Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food.NPJ biofilms and microbiomes · 2026Review
- Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivatedISME communications · 2026Article
- Modeling the emergent metabolic potential of soil microbiomes in Atacama landscapes.Environmental microbiome · 2025Article
- A defined microbial community reproduces attributes of fine flavour chocolate fermentation.Nature microbiology · 2025Article
- Tailoring a Functional Synthetic Microbial Community Alleviates Fusobacterium nucleatum-infected Colorectal Cancer via Ecological Control.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.mSphere · 2025Article
- Seed2LP: seed inference in metabolic networks for reverse ecology applications.Bioinformatics (Oxford, England) · 2025Article
- Rationally designed microbial communities in agri-food production systems: from research to market.ISME communications · 2025Article
- Designing function-specific minimal microbiomes from large microbial communities.NPJ systems biology and applications · 2024Article
- Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships.Plants (Basel, Switzerland) · 2024Review
- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction.Environmental microbiome · 2023Article
- Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities.bioRxiv : the preprint server for biology · 2023Article
- Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation.Molecular ecology · 2023Article
- Enhancing plant growth promoting rhizobacterial activities through consortium exposure: A review.Frontiers in bioengineering and biotechnology · 2023Review
- Multi-genome metabolic modeling predicts functional inter-dependencies in the Arabidopsis root microbiome.Microbiome · 2022Article
- Article
- Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species.eLife · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: The selection of species exhibiting metabolic behaviors of interest is a challenging step when switching from the investigation of a large microbiota to the study of functions effectiveness. Approaches based on a compartmentalized framework are not scalable. The output of scalable approaches based on a non-compartmentalized modeling may be so large that it has neither been explored nor handled so far. Results: We present the Miscoto tool to facilitate the selection of a community optimizing a desired function in a microbiome by reporting several possibilities which can be then sorted according to biological criteria. Communities are exhaustively identified using logical programming and by combining the non-compartmentalized and the compartmentalized frameworks. The benchmarking of 4.9 million metabolic functions associated with the Human Microbiome Project, shows that Miscoto is suited to screen and classify metabolic producibility in terms of feasibility, functional redundancy and cooperation processes involved. As an illustration of a host-microbial system, screening the Recon 2.2 human metabolism highlights the role of different consortia within a family of 773 intestinal bacteria. Availability and implementation: Miscoto source code, instructions for use and examples are available at: https://github.com/cfrioux/miscoto.
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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.