CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention
Journal article, 2021

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.

Systems biology

Gastrointestinal

Gut microbiota

Author

Jun Geng

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Boyang Ji

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Gang Li

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Felipe López-Isunza

Universidad Autonoma Metropolitana - Iztapalapa

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Novo Nordisk Foundation

Technical University of Denmark (DTU)

BioInnovation Institute

Proceedings of the National Academy of Sciences of the United States of America

0027-8424 (ISSN) 1091-6490 (eISSN)

Vol. 118 13 e2019336118

Areas of Advance

Health Engineering

Subject Categories

Bioinformatics (Computational Biology)

Bioinformatics and Systems Biology

Physical Geography

DOI

10.1073/pnas.2019336118

PubMed

33753486

More information

Latest update

5/26/2023