ReviewComputational and structural biotechnology journal2020
Inferring composition and function of the human gut microbiome in time and space: A review of genome-scale metabolic modelling tools.
Review in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Genome-scale metabolic modelling of human gut microbes to inform rational community design.Gut microbes · 2025Article
- Article
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- Article
- Modulatory effects of traditional Chinese medicines on gut microbiota and the microbiota-gut-x axis.Frontiers in pharmacology · 2024Review
- Mathematical reconstruction of the metabolic network in an in-vitro multiple myeloma model.PLoS computational biology · 2023Article
- Assumptions on decision making and environment can yield multiple steady states in microbial community models.BMC bioinformatics · 2023Article
- Article
- Toward modeling metabolic state from single-cell transcriptomics.Molecular metabolism · 2022Review
- Impact of Contaminants on Microbiota: Linking the Gut-Brain Axis with Neurotoxicity.International journal of environmental research and public health · 2022Review
- Modeling approaches for probing cross-feeding interactions in the human gut microbiome.Computational and structural biotechnology journal · 2022Review
- Metabolic Modeling to Interrogate Microbial Disease: A Tale for Experimentalists.Frontiers in molecular biosciences · 2021Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The human gut hosts a complex community of microorganisms that directly influences gastrointestinal physiology, playing a central role in human health. Because of its importance, the metabolic interplay between the gut microbiome and host metabolism has gained special interest. While there has been great progress in the field driven by metagenomics and experimental studies, the mechanisms underpinning microbial composition and interactions in the microbiome remain poorly understood. Genome-scale metabolic models are mathematical structures capable of describing the metabolic potential of microbial cells. They are thus suitable tools for probing the metabolic properties of microbial communities. In this review, we discuss the most recent and relevant genome-scale metabolic modelling tools for inferring the composition, interactions, and ultimately, biological function of the constituent species of a microbial community with special emphasis in the gut microbiota. Particular attention is given to constraint-based metabolic modelling methods as well as hybrid agent-based methods for capturing the interactions and behavior of the community in time and space. Finally, we discuss the challenges hindering comprehensive modelling of complex microbial communities and its application for the
Identifiers
What Socratic holds
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 Socratic graph.