ReviewPLoS computational biology2023
Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.
Review in PLoS computational biology, 2023. 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.
- Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.Probiotics and antimicrobial proteins · 2026Review
- Plant Immunometabolism: Metabolic Reprogramming Linking Developmental Signaling and Defense Metabolites.International journal of molecular sciences · 2026Review
- Improved flux profiling in genome-scale modeling of human cell metabolism.Cell reports methods · 2026Article
- Gempipe: a tool for drafting, curating, and analyzing pan and multi-strain genome-scale metabolic models.mSystems · 2026Article
- Quantifying and comparing causal patterns in stochastic chemical reaction networks.NPJ systems biology and applications · 2026Article
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- Tools and Technologies for Studying Cancer Metabolism.Cancer treatment and research · 2026Review
- Integrating metagenome-scale metabolic models and metabolomics to explore candidate biochemical interactions in cultivatedISME communications · 2026Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Genome-Scale Metabolic Models in Fungal Pathogens: Past, Present, and Future.International journal of molecular sciences · 2024Review
- Systematic elucidation of independently modulated genes in Lactiplantibacillus plantarum reveals a trade-off between secondary and primary metabolism.Microbial biotechnology · 2024Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In microorganisms, different from primary metabolism for cellular growth, secondary metabolism is for ecological interactions and stress responses and an important source of natural products widely used in various areas such as pharmaceutics and food additives. With advancements of sequencing technologies and bioinformatics tools, a large number of biosynthetic gene clusters of secondary metabolites have been discovered from microbial genomes. However, due to challenges from the difficulty of genome-scale pathway reconstruction and the limitation of conventional flux balance analysis (FBA) on secondary metabolism, the quantitative modeling of secondary metabolism is poorly established, in contrast to that of primary metabolism. This review first discusses current efforts on the reconstruction of secondary metabolic pathways in genome-scale metabolic models (GSMMs), as well as related FBA-based modeling techniques. Additionally, potential extensions of FBA are suggested to improve the prediction accuracy of secondary metabolite production. As this review posits, biosynthetic pathway reconstruction for various secondary metabolites will become automated and a modeling framework capturing secondary metabolism onset will enhance the predictive power. Expectedly, an improved FBA-based modeling workflow will facilitate quantitative study of secondary metabolism and in silico design of engineering strategies for natural product production.
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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.