ArticleProceedings of the National Academy of Sciences of the United States of America2021
CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Leveraging genome-scale metabolic models to understand aerobic methanotrophs.The ISME journal · 2024Pooled it
- The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.Gut microbes reports · 2026Review
- Constraint-Based Metabolic Modeling Approach for Microbial Communities.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Modeling for understanding and engineering metabolism.QRB discovery · 2025Article
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- DyMMM-LEAPS: An ML-based framework for modulating evenness and stability in synthetic microbial communities.Biophysical journal · 2024Article
- A mechanistic modelling approach of the host-microbiota interactions to investigate beneficial symbiotic resilience in the human gut.Journal of the Royal Society, Interface · 2024Article
- Article
- Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.Microbial biotechnology · 2024Review
- Gut microecology: effective targets for natural products to modulate uric acid metabolism.Frontiers in pharmacology · 2024Review
- Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis.The ISME journal · 2023Article
- Towards applications of genome-scale metabolic model-based approaches in designing synthetic microbial communities.Quantitative biology (Beijing, China) · 2023Review
- Current Perspectives on Gastrointestinal Models to Assess Probiotic-Pathogen Interactions.Frontiers in microbiology · 2022Review
- Modeling approaches for probing cross-feeding interactions in the human gut microbiome.Computational and structural biotechnology journal · 2022Review
- Systems Biology of Gut Microbiota-Human Receptor Interactions: Toward Anti-inflammatory Probiotics.Frontiers in microbiology · 2022Article
- Article
- Metagenome-Scale Metabolic Network Suggests Folate Produced byMicroorganisms · 2021Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Microbial variations in the human gut are harbored in temporal and spatial heterogeneity, and quantitative prediction of spatiotemporal dynamic changes in the gut microbiota is imperative for development of tailored microbiome-directed therapeutics treatments, e.g. precision nutrition. Given the high-degree complexity of microbial variations, subject to the dynamic interactions among host, microbial, and environmental factors, identifying how microbiota colonize in the gut represents an important challenge. Here we present COmputing the DYnamics of microbiota (CODY), a multiscale framework that integrates species-level modeling of microbial dynamics and ecosystem-level interactions into a mathematical model that characterizes spatial-specific in vivo microbial residence in the colon as impacted by host physiology. The framework quantifies spatiotemporal resolution of microbial variations on species-level abundance profiles across site-specific colon regions and in feces, independent of a priori knowledge. We demonstrated the effectiveness of CODY using cross-sectional data from two longitudinal metagenomics studies-the microbiota development during early infancy and during short-term diet intervention of obese adults. For each cohort, CODY correctly predicts the microbial variations in response to diet intervention, as validated by available metagenomics and metabolomics data. Model simulations provide insight into the biogeographical heterogeneity among lumen, mucus, and feces, which provides insight into how host physical forces and spatial structure are shaping microbial structure and functionality.
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