Random Graphical Model of Microbiome Interactions in Related Environments

IF 16.4 1区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Veronica Vinciotti, Ernst C. Wit, Francisco Richter
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引用次数: 0

Abstract

The microbiome constitutes a complex microbial ecology of interacting components that regulates important pathways in the host. Most microbial communities at various body sites tend to share common substructures of interactions, while also showing diversity related to the needs of the local environment. The aim of this paper is to develop a method for inferring both the common core and the differences in such microbiota systems. The approach combines two elements: (i) a random graph model generating networks across environments, and capturing potential relatedness at the structural level, with (ii) a Gaussian copula graphical model for the inference of environment-specific networks from multivariate microbial data. We propose a Bayesian approach for the joint inference of microbiota systems from metagenomic data for a number of body sites. The analysis of human microbiome data shows how the proposed random graphical model is able to capture varying levels of structural similarity across the different body sites and how this is supported by their taxonomical classification. Beyond a stable core, the inferred microbiome systems show interesting differences between the body sites, as well as interpretable relationships between various classes of microbes.

Abstract Image

相关环境中微生物群相互作用的随机图形模型
微生物组是由相互作用的成分组成的复杂微生物生态,调节着宿主体内的重要通路。不同身体部位的大多数微生物群落往往具有共同的相互作用子结构,同时也表现出与当地环境需求相关的多样性。本文旨在开发一种方法,用于推断此类微生物群系统的共同核心和差异。该方法结合了两个要素:(i) 生成跨环境网络的随机图模型,并在结构层面捕捉潜在的相关性;(ii) 从多变量微生物数据推断特定环境网络的高斯共轭图模型。我们提出了一种贝叶斯方法,用于从多个身体部位的元基因组数据中联合推断微生物群系统。对人类微生物组数据的分析表明,所提出的随机图模型能够捕捉到不同身体部位的不同结构相似性水平,以及它们的分类学分类是如何支持这种相似性的。除了一个稳定的核心之外,推断出的微生物组系统还显示出不同身体部位之间的有趣差异,以及不同类别微生物之间的可解释关系。
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来源期刊
Accounts of Chemical Research
Accounts of Chemical Research 化学-化学综合
CiteScore
31.40
自引率
1.10%
发文量
312
审稿时长
2 months
期刊介绍: Accounts of Chemical Research presents short, concise and critical articles offering easy-to-read overviews of basic research and applications in all areas of chemistry and biochemistry. These short reviews focus on research from the author’s own laboratory and are designed to teach the reader about a research project. In addition, Accounts of Chemical Research publishes commentaries that give an informed opinion on a current research problem. Special Issues online are devoted to a single topic of unusual activity and significance. Accounts of Chemical Research replaces the traditional article abstract with an article "Conspectus." These entries synopsize the research affording the reader a closer look at the content and significance of an article. Through this provision of a more detailed description of the article contents, the Conspectus enhances the article's discoverability by search engines and the exposure for the research.
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