The Microbiome Protocols eBook initiative: Building a bridge to microbiome research

Yunyun Gao; Kai Peng; Defeng Bai; Xiao-Ye Bai; Yujing Bi; Anqi Chen; Baodong Chen; Feng Chen; Juan Chen; Lei Chen; Tong Chen; Wei Chen; Xu Cheng; Yanfen Cheng; Jie Cui; Jingjing Dai; Junbiao Dai; Zhaolai Dai; Ye Deng; Yi-Zhen Deng; Wei Ding; Zhencheng Fang; Wei Fu; Hanbing Gao; Shaohua Gu; Xue Guo; Xuguang Guo; Dongfei Han; Lele He; Yatao He; Hui-Yu Hou; Baolei Jia; Gengjie Jia; Shuo Jiao; Wei Jin; Feng Ju; Zhicheng Ju; Siyuan Kong; Canhui Lan; Bing Li; Da Li; Diyan Li; Jingdi Li; Meng Li; Qi Li; Qiang Li; Wen-Jun Li; Xiaofang Li; Xuemeng Li; Yahui Li; You-Gui Li; Zhibin Liang; Ning Ling; Fufeng Liu; Qing Liu; Shuang-Jiang Liu; Hongye Lu; Qi Lu; Guangwen Luo; Hao Luo; Yuheng Luo; Hujie Lyu; Chuang Ma; Liyuan Ma; Tengfei Ma; Jinfeng Ni; Ziqin Pang; Xiaojing Qiang; Yuan Qin; Qingyue Qu; Chao Ran; Shuqiang Ren; Haitao Shang; Luyang Song; Linyang Sun; Weimin Sun; Liping Tang; Jian Tian; Kai Wang; Mengzhi Wang; Ming-Ke Wang; Tao Wang; Xiao-Yan Wang; Yao Wang; Yiwen Wang; Youshan Wang; Hailei Wei; Hong Wei; Zhong Wei; Tao Wen; Jiqiu Wu; Linhuan Wu; Linkun Wu; Jiao Xi; Bo Xie; Guofang Xu; Jun Xu; Shanshan Xu; Qing Xue; Liping Yan; Haifei Yang; Jun Yang; Junbo Yang; Ruifu Yang; Yalin Yang; Ying-Jie Yang; Xiaofang Yao; Yanpo Yao; Salsabeel Yousuf; Ke Yu; Zhengrong Yuan; Zhilin Yuan; Dong Zhang; Tianyuan Zhang; Weipeng Zhang; Yunzeng Zhang; Zhaonan Zhang; Zhen Zhang; Zhi-Feng Zhang; Shengguo Zhao; Wei Zhao; Maosheng Zheng; Ziqiang Zheng; Xin Zhou; Yuanping Zhou; Zhigang Zhou; Mo Zhu; Yong-Guan Zhu; Haiyan Chu; Yang Bai; Yong-Xin Liu

doi:10.1002/imt2.182

The Microbiome Protocols eBook initiative: Building a bridge to microbiome research

Imeta. 2024 Mar 19;3(2):e182. doi: 10.1002/imt2.182. eCollection 2024 Apr.

Authors

Yunyun Gao¹, Kai Peng², Defeng Bai¹, Xiao-Ye Bai³, Yujing Bi⁴, Anqi Chen⁵, Baodong Chen⁶, Feng Chen⁷, Juan Chen⁸, Lei Chen⁹, Tong Chen¹⁰, Wei Chen¹¹, Xu Cheng¹, Yanfen Cheng¹², Jie Cui¹³, Jingjing Dai¹⁴, Junbiao Dai¹, Zhaolai Dai¹⁵, Ye Deng⁶, Yi-Zhen Deng¹⁶, Wei Ding¹⁷, Zhencheng Fang¹⁸, Wei Fu⁶, Hanbing Gao¹⁹, Shaohua Gu²⁰, Xue Guo⁶, Xuguang Guo²¹, Dongfei Han²², Lele He²³, Yatao He²⁴, Hui-Yu Hou¹, Baolei Jia²⁵, Gengjie Jia¹, Shuo Jiao²⁶, Wei Jin¹², Feng Ju²⁷, Zhicheng Ju²⁸, Siyuan Kong¹, Canhui Lan^{29

30}, Bing Li³¹, Da Li³², Diyan Li³³, Jingdi Li³⁴, Meng Li³⁵, Qi Li³⁶, Qiang Li³⁷, Wen-Jun Li³⁸, Xiaofang Li³⁹, Xuemeng Li⁴⁰, Yahui Li¹, You-Gui Li⁴¹, Zhibin Liang⁴², Ning Ling⁴³, Fufeng Liu⁴⁴, Qing Liu³², Shuang-Jiang Liu³², Hongye Lu⁴⁵, Qi Lu⁴⁶, Guangwen Luo¹, Hao Luo¹, Yuheng Luo⁴⁷, Hujie Lyu⁴⁸, Chuang Ma⁴⁹, Liyuan Ma⁵⁰, Tengfei Ma⁴³, Jinfeng Ni⁵¹, Ziqin Pang⁵², Xiaojing Qiang⁵³, Yuan Qin⁵⁴, Qingyue Qu⁵⁵, Chao Ran⁵⁶, Shuqiang Ren¹, Haitao Shang⁵⁷, Luyang Song⁵⁸, Linyang Sun⁵⁹, Weimin Sun⁶⁰, Liping Tang⁵⁵, Jian Tian⁶¹, Kai Wang⁶², Mengzhi Wang⁶³, Ming-Ke Wang⁶⁴, Tao Wang³³, Xiao-Yan Wang⁶⁵, Yao Wang¹, Yiwen Wang¹, Youshan Wang⁶⁶, Hailei Wei⁶⁷, Hong Wei⁶⁸, Zhong Wei¹², Tao Wen¹², Jiqiu Wu⁶⁹, Linhuan Wu⁷⁰, Linkun Wu⁷¹, Jiao Xi⁷², Bo Xie⁷³, Guofang Xu⁷⁴, Jun Xu⁷⁵, Shanshan Xu⁷⁶, Qing Xue¹², Liping Yan⁷⁷, Haifei Yang⁷⁸, Jun Yang⁷⁹, Junbo Yang¹, Ruifu Yang⁴, Yalin Yang⁵⁶, Ying-Jie Yang⁸⁰, Xiaofang Yao⁸¹, Yanpo Yao⁸², Salsabeel Yousuf¹, Ke Yu⁸³, Zhengrong Yuan⁷⁷, Zhilin Yuan⁸⁴, Dong Zhang⁷⁷, Tianyuan Zhang^{1

85}, Weipeng Zhang¹⁷, Yunzeng Zhang⁶³, Zhaonan Zhang⁸⁶, Zhen Zhang⁵⁶, Zhi-Feng Zhang⁸⁷, Shengguo Zhao⁶¹, Wei Zhao⁸⁸, Maosheng Zheng⁸⁹, Ziqiang Zheng⁹⁰, Xin Zhou³², Yuanping Zhou⁴⁰, Zhigang Zhou⁵⁶, Mo Zhu⁹¹, Yong-Guan Zhu⁹², Haiyan Chu⁹³, Yang Bai⁹⁴, Yong-Xin Liu¹

Affiliations

¹ Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China.
² Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine Yangzhou University Yangzhou China.
³ Shenzhen Bay Laboratory Shenzhen China.
⁴ State Key Laboratory of Pathogen and Biosecurity Beijing Institute of Microbiology and Epidemiology Beijing China.
⁵ Bio-Protocol Editorial Office China Bio-Protocol Journal Beijing China.
⁶ Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing China.
⁷ School of Stomatology Peking University Beijing China.
⁸ Institute of Medicinal Plant Development Chinese Academy of Medical Sciences Beijing China.
⁹ Department of Vascular Surgery, Fu Xing Hospital Capital Medical University Beijing China.
¹⁰ State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica China Academy of Chinese Medical Sciences Beijing China.
¹¹ Institute of Hydroecology Ministry of Water Resources & Chinese Academy of Sciences Wuhan China.
¹² Nanjing Agricultural University Nanjing China.
¹³ The Institute of Infection and Health Research Fudan University Shanghai China.
¹⁴ Department of Medical Laboratory the Affiliated Huaian No.1 Hospital of Nanjing Medical University Huaian China.
¹⁵ China Agricultural University Beijing China.
¹⁶ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre South China Agricultural University Guangzhou China.
¹⁷ Ocean University of China Qingdao China.
¹⁸ Zhujiang Hospital Southern Medical University Guangzhou China.
¹⁹ Central South University Changsha China.
²⁰ Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies Peking University Beijing China.
²¹ Department of Clinical Laboratory Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology The Third Affiliated Hospital of Guangzhou Medical University Guangzhou China.
²² School of Environmental Science and Engineering Suzhou University of Science and Technology Suzhou China.
²³ Hunan University Changsha China.
²⁴ School of Medicine, Model Animal Research Center (MARC) Nanjing University Nanjing China.
²⁵ Xianghu Laboratory Hangzhou China.
²⁶ National Key Laboratory of Crop Improvement for Stress Tolerance and Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences Northwest A&F University Yangling China.
²⁷ Westlake University Hangzhou China.
²⁸ Department of Ocean Science The Hong Kong University of Science and Technology Hong Kong China.
²⁹ School of Life Science and Technology Wuhan Polytechnic University Wuhan China.
³⁰ R-Institute Co. Ltd. Beijing China.
³¹ Tsinghua Shenzhen International Graduate School Tsinghua University Shenzhen China.
³² Institute of Microbiology Chinese Academy of Sciences Beijing China.
³³ Antibiotics Research and Re-Evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy Chengdu University Chengdu China.
³⁴ University of Oxford Oxford UK.
³⁵ Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study Shenzhen University Shenzhen China.
³⁶ Institute of Applied Ecology Chinese Academy of Sciences Shenyang China.
³⁷ School of Food and Biological Engineering Chengdu University Chengdu China.
³⁸ School of Life Sciences Sun Yat-Sen University Guangzhou China.
³⁹ Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology Chinese Academy of Sciences Shijiazhuang China.
⁴⁰ Guangdong Medical University Dongguan China.
⁴¹ Zhejiang Academy of Agricultural Sciences Hangzhou China.
⁴² Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre South China Agricultural University Guangzhou China.
⁴³ State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Centre for Grassland Microbiome, College of Pastoral Agricultural Science and Technology Lanzhou University Lanzhou China.
⁴⁴ College of Biotechnology Tianjin University of Science & Technology Tianjin China.
⁴⁵ Zhejiang University Hangzhou China.
⁴⁶ Children's Hospital of Chongqing Medical University Chongqing China.
⁴⁷ Animal Nutrition Institute Sichuan Agricultural University Chengdu China.
⁴⁸ Imperial College of London London UK.
⁴⁹ Anhui Agricultural University Hefei China.
⁵⁰ China University of Geosciences Wuhan China.
⁵¹ State Key Laboratory of Microbial Technology, Microbial Technology Institute Shandong University Qingdao China.
⁵² College of Agriculture Fujian Agriculture and Forestry University Fuzhou China.
⁵³ Institute of Grassland Research Chinese Academy of Agricultural Sciences Hohhot China.
⁵⁴ Institute of Genetics and Developmental Biology Chinese Academy of Sciences Beijing China.
⁵⁵ Institute of Zoology Chinese Academy of Sciences Beijing China.
⁵⁶ Feed Research Institute Chinese Academy of Agricultural Sciences Beijing China.
⁵⁷ Shenzhen Medical Academy of Research and Translation Shenzhen China.
⁵⁸ Henan Agricultural University Henan China.
⁵⁹ Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland.
⁶⁰ Institute of Eco-Environmental and Soil Sciences Guangdong Academy of Sciences Guangzhou China.
⁶¹ State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences Chinese Academy of Agricultural Sciences Beijing China.
⁶² School of Marine Sciences Ningbo University Ningbo China.
⁶³ Yangzhou University Yangzhou China.
⁶⁴ Naval Medical Center of PLA Naval Medical University Shanghai China.
⁶⁵ School of Life Sciences Taizhou University Taizhou China.
⁶⁶ Institute of Plant Nutrition, Resources and Environment Beijing Academy of Agriculture and Forestry Sciences Beijing China.
⁶⁷ Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning Chinese Academy of Agricultural Sciences Beijing China.
⁶⁸ The First Affiliated Hospital Sun Yat-Sen University Guangzhou China.
⁶⁹ Department of Genetics, University Medical Center Groningen University of Groningen Groningen The Netherlands.
⁷⁰ Microbial Resource and Big Data Center, Institute of Microbiology Chinese Academy of Sciences Beijing China.
⁷¹ College of JunCao Science and Ecology Fujian Agriculture and Forestry University Fuzhou China.
⁷² College of Natural Resources and Environment Northwest A&F University Yangling China.
⁷³ School of Life Sciences Central China Normal University Wuhan China.
⁷⁴ Department of Civil and Environmental Engineering National University of Singapore Singapore Singapore.
⁷⁵ Department of Gastroenterology, Clinical Center of Immune-Mediated Digestive Diseases Peking University People's Hospital Beijing China.
⁷⁶ Hefei University of Technology Hefei China.
⁷⁷ Beijing Forestry University Beijing China.
⁷⁸ Qingdao Agriculture University Qingdao China.
⁷⁹ Key Laboratory of Urban Environment and Health, Institute of Urban Environment Chinese Academy of Sciences Xiamen China.
⁸⁰ Tobacco Research Institute Chinese Academy of Agricultural Sciences Qingdao China.
⁸¹ Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture Chinese Academy of Sciences Changsha China.
⁸² Agro-Environmental Protection Institute Ministry of Agriculture and Rural Affairs Tianjin China.
⁸³ School of Environment and Energy Peking University Shenzhen Graduate School Shenzhen China.
⁸⁴ State Key Laboratory of Tree Genetics and Breeding Chinese Academy of Forestry Beijing China.
⁸⁵ Wuhan Benagen Technology Co., Ltd. Wuhan China.
⁸⁶ Peking University Beijing China.
⁸⁷ Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) Guangzhou China.
⁸⁸ Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences Tianjin China.
⁸⁹ College of Environmental Science and Engineering North China Electric Power University Beijing China.
⁹⁰ College of Life Science and Technology Wuhan Polytechnic University Wuhan China.
⁹¹ College of Life Sciences Henan Normal University Xinxiang China.
⁹² Institute of Urban Environment Chinese Academy of Sciences Xiamen China.
⁹³ State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science Chinese Academy of Sciences Nanjing China.
⁹⁴ Peking-Tsinghua Center for Life Sciences, College of Life Sciences Peking University Beijing China.

Abstract

The Microbiome Protocols eBook (MPB) serves as a crucial bridge, filling gaps in microbiome protocols for both wet experiments and data analysis. The first edition, launched in 2020, featured 152 meticulously curated protocols, garnering widespread acclaim. We now extend a sincere invitation to researchers to participate in the upcoming 2nd version of MPB, contributing their valuable protocols to advance microbiome research.