Acin-Albiac Marta, Filannino Pasquale, Gobbetti Marco, Di Cagno Raffaella
Faculty of Science and Technology, Free University of Bolzano, Bolzano, Italy.
Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy.
Comput Struct Biotechnol J. 2020 Aug 18;18:2290-2299. doi: 10.1016/j.csbj.2020.08.010. eCollection 2020.
The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.
表型-基因型图谱是在环境压力下由详细的表型和基因型数据得出的一种投影。尽管微生物或微生物群落的表型组反映了一个基因组或一组基因组的功能表达，但代谢特性依赖于表型。表型组学有潜力革新功能基因组学。在这篇综述中，我们讨论了表型组学发展的原因和方式。我们描述了表型组学如何可能扩展我们对微生物群落组装及其功能的理解，然后我们概述了使用Omnilog平台在表型组研究中的新应用，以及对其目前用于研究食品加工过程中乳酸菌（LAB）代谢特性的应用的修订。LAB被提议作为一个合适的模型系统来分析和讨论这种新兴组学方法的实施和应用。我们引入了“表型转换”，作为一种新的表型微阵列方法来深入了解细菌生理学。提供了管理和分析所生成数据的方法和工具的概述。最后，对迄今为止开发的流程（包括最具创新性的流程）的优缺点进行了批判性分析。我们提出了一个最近存档的R流程，它允许自动分析Omnilog数据，整合最新方法并应用此处描述的新概念。
