气候变化领域集成服务门户(CCPortal): CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention

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DOI	10.1073/pnas.2019336118
	CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention
	Geng J.; Ji B.; Li G.; López-Isunza F.; Nielsen J.
发表日期	2021
ISSN	00278424
卷号	118 期号:13
英文摘要	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. © 2021 National Academy of Sciences. All rights reserved.
英文关键词	Gastrointestinal; Gut microbiota; Systems biology
语种	英语
scopus关键词	analytic method; Article; bacterial growth; bacterial structures; biogeography; clinical effectiveness; cohort analysis; colon; computer simulation; controlled study; cross-sectional study; dietary intake; ecosystem; feces; genetic variability; human; in vivo study; infancy; intestine flora; mathematical model; metabolomics; metagenomics; microbial population dynamics; molecular pathology; nonhuman; population abundance; prediction; priority journal; quantitative analysis; spatiotemporal analysis; stomach mucus; treatment response; validation process
来源期刊	Proceedings of the National Academy of Sciences of the United States of America
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/180067
作者单位	Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden; Departamento de Ingeniería de Procesos e Hidráulica, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México, 09340, Mexico; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs, Lyngby, Denmark; Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, 412 96, Sweden; BioInnovation Institute, Copenhagen N, DK2200, Denmark
推荐引用方式 GB/T 7714	Geng J.,Ji B.,Li G.,et al. CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention[J],2021,118(13).
APA	Geng J.,Ji B.,Li G.,López-Isunza F.,&Nielsen J..(2021).CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention.Proceedings of the National Academy of Sciences of the United States of America,118(13).
MLA	Geng J.,et al."CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention".Proceedings of the National Academy of Sciences of the United States of America 118.13(2021).