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Protein Cell    2021, Vol. 12 Issue (5) : 315-330    https://doi.org/10.1007/s13238-020-00724-8
REVIEW
A practical guide to amplicon and metagenomic analysis of microbiome data
Yong-Xin Liu1,2,3(), Yuan Qin1,2,3,4, Tong Chen5, Meiping Lu6, Xubo Qian6, Xiaoxuan Guo1,2,3, Yang Bai1,2,3,4()
1. State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
2. CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
3. CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
4. College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
5. National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
6. Department of Rheumatology Immunology & Allergy, Children’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province 310053, China
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Abstract

Advances in high-throughput sequencing (HTS) have fostered rapid developments in the field of microbiome research, and massive microbiome datasets are now being generated. However, the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field. Here, we systematically summarize the advantages and limitations of microbiome methods. Then, we recommend specific pipelines for amplicon and metagenomic analyses, and describe commonly-used software and databases, to help researchers select the appropriate tools. Furthermore, we introduce statistical and visualization methods suitable for microbiome analysis, including alpha- and betadiversity, taxonomic composition, difference comparisons, correlation, networks, machine learning, evolution, source tracing, and common visualization styles to help researchers make informed choices. Finally, a stepby-step reproducible analysis guide is introduced. We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the biological significance behind the data.
Keywords metagenome      marker genes      highthroughput sequencing      pipeline      reproducible analysis      visualization     
Corresponding Author(s): Yong-Xin Liu,Yang Bai   
Online First Date: 14 September 2020    Issue Date: 08 June 2021
 Cite this article:   
Yong-Xin Liu,Yuan Qin,Tong Chen, et al. A practical guide to amplicon and metagenomic analysis of microbiome data[J]. Protein Cell, 2021, 12(5): 315-330.
 URL:  
https://academic.hep.com.cn/pac/EN/10.1007/s13238-020-00724-8
https://academic.hep.com.cn/pac/EN/Y2021/V12/I5/315
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