Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, 15 Shangxiadian Road, Fuzhou 350002, China.
Key Laboratory of Environmental and Applied Microbiology, CAS; Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, No.9, Section 4, Renmin South Road, Chengdu 610041, China.
FEMS Microbiol Ecol. 2021 Jan 26;97(2). doi: 10.1093/femsec/fiaa255.
A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput sequencing technique, especially amplicon-sequencing-based community data. After conducting the initial bioinformatic analysis of amplicon sequencing data, performing the subsequent statistics and data mining based on the operational taxonomic unit and taxonomic assignment tables is still complicated and time-consuming. To address this problem, we present an integrated R package-'microeco' as an analysis pipeline for treating microbial community and environmental data. This package was developed based on the R6 class system and combines a series of commonly used and advanced approaches in microbial community ecology research. The package includes classes for data preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta diversity analysis, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis. Each class is designed to provide a set of approaches that can be easily accessible to users. Compared with other R packages in the microbial ecology field, the microeco package is fast, flexible and modularized to use and provides powerful and convenient tools for researchers. The microeco package can be installed from CRAN (The Comprehensive R Archive Network) or github (https://github.com/ChiLiubio/microeco).
在微生物群落生态学研究中，使用高通量测序技术会产生大量的测序数据，特别是基于扩增子测序的群落数据。在对扩增子测序数据进行初步的生物信息学分析后，基于操作分类单元和分类分配表进行后续的统计和数据挖掘仍然很复杂和耗时。为了解决这个问题，我们提出了一个集成的 R 包-"microeco"，作为处理微生物群落和环境数据的分析管道。该软件包是基于 R6 类系统开发的，结合了微生物群落生态学研究中常用的和先进的一系列方法。该软件包包括用于数据预处理、分类丰度绘图、venn 图、alpha 多样性分析、beta 多样性分析、差异丰度检验和指示分类群分析、环境数据分析、零模型分析、网络分析和功能分析的类。每个类都设计为提供一组易于用户访问的方法。与微生物生态学领域的其他 R 包相比，microeco 包使用起来快速、灵活且模块化，并为研究人员提供了强大而方便的工具。microeco 包可以从 CRAN（综合 R 存档网络）或 github（https://github.com/ChiLiubio/microeco）安装。
