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TOPICAL COLLECTIONS

Analysis and Visualization Methods for Amplicon and Metagenomic Data of the Microbiome

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Guest Editors

Yong-Xin Liu

Yong-Xin Liu

Chinese Academy of Sciences, Institute of Genetics and Developmental Biology

Dr. Yong-Xin Liu obtained his undergraduate degree in Biotechnology (Microbiology), his master’s degree in Crop Genetics and Breeding from the Northeast Agricultural University, and his PhD in Bioinformatics from the University of Chinese Academy of Sciences, focusing on next-generation sequencing data analysis. He then completed a post-doctoral fellowship at the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (IGDB, CAS). For the last four years, Dr. Liu has been working as a bioinformatics analyst in IGDB, focusing on microbiome data analysis, method development, and the dissemination of bioinformatics knowledge. He has published twenty-five articles in different journals including Science, Nature Biotechnology, and Cell Host & Microbe. These articles have been cited over a thousand times. He participated in the development of QIIME 2 and was invited to write review articles about microbiome analysis, which were published in Protein & Cell, Current Opinion in Microbiology, and the Chinese Medical Journal. He is also the editor-in-chief of the WeChat subscription account “Meta-Genome”, which has been releasing over 1,800 essays on updates and news in the field of microbiome, analysis methods, and other bioinformatics knowledge. There are over 90,000 followers of the WeChat account, and the essays have been read more than 14 million times. Google Scholar https://scholar.google.com/citations?user=NoxNy_IAAAAJ

Tong Chen

Tong Chen

China Academy of Chinese Medical Sciences, National Resource Center for Chinese Materia Medica

Dr. Tong Chen obtained his bachelor’s degree in Life Sciences from Northeast Forestry University and his PhD in Bioinformatics from the University of Chinese Academy of Sciences, focusing on next-generation sequencing data analysis. For the last five years, Dr. Chen has been working as an assistant professor in CACMS, focusing on bioinformatics analysis and method and data platform development. At present, he has published papers in Cell Stem Cell, Nucleic Acids Research, etc. He was also invited to write reviews about microbiome analysis, which were published in Protein & Cell and the Chinese Medical Journal. He has established a new media platform (WeChat Offical Account) called "Bio-data" and served as its editor-in-chief. This new media platform has published over 700 original papers, analysis methods, and experiences of communications of bioinformatics. It has over 70,000 followers.

Maosheng Zheng

Maosheng Zheng

North China Electric Power University, College of Environmental Science and Engineering

Dr. Maosheng Zheng obtained his PhD in Environmental Engineering from Peking University, focusing on the field of wastewater treatment. He then has been engaged in teaching and research at the College of Environmental Science and Engineering, North China Electric Power University, with research interests in environmental microbiology, biological nitrogen removal technology, greenhouse gas emission, and control of wastewater treatment. Dr. Zheng has participated in more than 10 research projects, including National Natural Science Foundation of China, Beijing Natural Science Foundation, sub-project of Shanghai Committee of Science and Technology and so on. He has published 27 articles in SCI-indexed journals including Journal of Hazardous Materials, Bioresource Technology, Journal of Cleaner Production, etc. Furthermore, he has published one monograph (Nitrogen removal characteristics of aerobic denitrifying bacteria and their applications) in Springer Theses, which was nominated by Peking University as an outstanding PhD thesis.

Collection Overview

Advances in high-throughput sequencing have fostered developments in microbiome research, and massive microbiome datasets have been generated. Microbiome data analysis enables researchers to understand the interaction mechanisms between the microbiome and the host. However, the lack of tutorials for complex analysis and visualization makes it difficult for researchers to access this field.

This collection aims to provide researchers with easy-to-use methods for microbiome analysis and visualization. The scope of this collection covers tutorials for analysis software, database local and online usage, analysis pipelines, and statistical and visualization methods. The visualization methods include, but not limited to, alpha- and beta-diversities, taxonomic composition, difference comparisons, ordination, correlation, networks, and evolution. The statistical methods mainly include compositional analysis and machine learning.

Articles

Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks
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Divergence of Root Microbiota in Different Habitats based on Weighted Correlation Networks

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2021

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