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Bai D, Chen T, Xun J, Ma C, Luo H, Yang H, Cao C, Cao X, Cui J, Deng Y, Deng Z, Dong W, Dong W, Du J, Fang Q, Fang W, Fang Y, Fu F, Fu M, Fu Y, Gao H, Ge J, Gong Q, Gu L, Guo P, Guo Y, Hai T, Liu H, He J, He Z, Hou H, Huang C, Ji S, Jiang C, Jiang G, Jiang L, Jin LN, Kan Y, Kang D, Kou J, Lam K, Li C, Li C, Li F, Li L, Li M, Li X, Li Y, Li Z, Liang J, Lin Y, Liu C, Liu D, Liu F, Liu J, Liu T, Liu T, Liu X, Liu Y, Liu B, Liu M, Lou W, Luan Y, Luo Y, Lv H, Ma T, Mai Z, Mo J, Niu D, Pan Z, Qi H, Shi Z, Song C, Sun F, Sun Y, Tian S, Wan X, Wang G, Wang H, Wang H, Wang H, Wang J, Wang J, Wang K, Wang L, Wang S, Wang X, Wang Y, Xiao Z, Xing H, Xu Y, Yan S, Yang L, Yang S, Yang Y, Yao X, Yousuf S, Yu H, Lei Y, Yuan Z, et alBai D, Chen T, Xun J, Ma C, Luo H, Yang H, Cao C, Cao X, Cui J, Deng Y, Deng Z, Dong W, Dong W, Du J, Fang Q, Fang W, Fang Y, Fu F, Fu M, Fu Y, Gao H, Ge J, Gong Q, Gu L, Guo P, Guo Y, Hai T, Liu H, He J, He Z, Hou H, Huang C, Ji S, Jiang C, Jiang G, Jiang L, Jin LN, Kan Y, Kang D, Kou J, Lam K, Li C, Li C, Li F, Li L, Li M, Li X, Li Y, Li Z, Liang J, Lin Y, Liu C, Liu D, Liu F, Liu J, Liu T, Liu T, Liu X, Liu Y, Liu B, Liu M, Lou W, Luan Y, Luo Y, Lv H, Ma T, Mai Z, Mo J, Niu D, Pan Z, Qi H, Shi Z, Song C, Sun F, Sun Y, Tian S, Wan X, Wang G, Wang H, Wang H, Wang H, Wang J, Wang J, Wang K, Wang L, Wang S, Wang X, Wang Y, Xiao Z, Xing H, Xu Y, Yan S, Yang L, Yang S, Yang Y, Yao X, Yousuf S, Yu H, Lei Y, Yuan Z, Zeng M, Zhang C, Zhang C, Zhang H, Zhang J, Zhang N, Zhang T, Zhang Y, Zhang Y, Zhang Z, Zhou M, Zhou Y, Zhu C, Zhu L, Zhu Y, Zhu Z, Zou H, Zuo A, Dong W, Wen T, Chen S, Li G, Gao Y, Liu Y. EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research. IMETA 2025; 4:e70001. [PMID: 40027489 PMCID: PMC11865343 DOI: 10.1002/imt2.70001] [Show More Authors] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Accepted: 01/22/2025] [Indexed: 03/05/2025]
Abstract
Shotgun metagenomics has become a pivotal technology in microbiome research, enabling in-depth analysis of microbial communities at both the high-resolution taxonomic and functional levels. This approach provides valuable insights of microbial diversity, interactions, and their roles in health and disease. However, the complexity of data processing and the need for reproducibility pose significant challenges to researchers. To address these challenges, we developed EasyMetagenome, a user-friendly pipeline that supports multiple analysis methods, including quality control and host removal, read-based, assembly-based, and binning, along with advanced genome analysis. The pipeline also features customizable settings, comprehensive data visualizations, and detailed parameter explanations, ensuring its adaptability across a wide range of data scenarios. Looking forward, we aim to refine the pipeline by addressing host contamination issues, optimizing workflows for third-generation sequencing data, and integrating emerging technologies like deep learning and network analysis, to further enhance microbiome insights and data accuracy. EasyMetageonome is freely available at https://github.com/YongxinLiu/EasyMetagenome.
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Affiliation(s)
- Defeng Bai
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Tong Chen
- 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 SciencesBeijingChina
| | - Jiani Xun
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Chuang Ma
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
- School of HorticultureAnhui Agricultural UniversityHefeiChina
| | - Hao Luo
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Haifei Yang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
- College of Life SciencesQingdao Agricultural UniversityQingdaoChina
| | - Chen Cao
- Key Laboratory for Bio‐Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingJiangsuChina
| | - Xiaofeng Cao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Jianzhou Cui
- Immunology Translational Research Programme, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Yuan‐Ping Deng
- Research Center for Parasites and Vectors, College of Veterinary MedicineHunan Agricultural UniversityChangshaHunanChina
| | - Zhaochao Deng
- Institute of Marine Biology and Pharmacology, Ocean CollegeZhejiang UniversityZhoushanZhejiangChina
| | - Wenxin Dong
- Agro‐Environmental Protection InstituteMinistry of Agriculture and Rural AffairsTianjinChina
| | - Wenxue Dong
- Key Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of MedicineXizang Minzu UniversityXianyangChina
| | - Juan Du
- Karolinska Institutet, Department of Microbiology, Tumor and Cell BiologyStockholmSweden
| | - Qunkai Fang
- College of EnvironmentZhejiang University of TechnologyHangzhouChina
| | - Wei Fang
- College of Environmental and Resource SciencesZhejiang Agriculture and Forestry UniversityHangzhouChina
| | - Yue Fang
- The College of ForestryBeijing Forestry UniversityBeijingChina
| | - Fangtian Fu
- Department of Bioinformatics, Hangzhou VicrobX Biotech Co., LtdHangzhouZhejiangChina
| | - Min Fu
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant ProtectionAnhui Agricultural UniversityHefeiChina
| | - Yi‐Tian Fu
- Xiangya School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - He Gao
- Institute of Microbiology,Guangdong Academy of SciencesGuangzhouGuangdongChina
| | - Jingping Ge
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life SciencesHeilongjiang UniversityHarbinChina
| | - Qinglong Gong
- College of Animal Science and TechnologyJilin Agricultural UniversityChangchunJilinChina
| | - Lunda Gu
- Sansure Biotech IncorporationChangshaHunanChina
| | - Peng Guo
- School of Food Science and BiologyHebei University of Science and TechnologyShijiazhuangHebeiChina
| | - Yuhao Guo
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life SciencesHeilongjiang UniversityHarbinChina
| | - Tang Hai
- School of Life SciencesShanxi Datong UniversityDatongChina
| | - Hao Liu
- Department of Health & Environmental SciencesXi'an Jiaotong‐Liverpool UniversitySuzhouJiangsuChina
| | - Jieqiang He
- College of HorticultureNorthwest A&F UniversityYanglingShaanxiChina
| | - Zi‐Yang He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of ScienceThe University of MelbourneVICAustralia
| | - Huiyu Hou
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Can Huang
- Graduate School of Frontier SciencesThe University of TokyoKashiwa‐shi, ChibaJapan
| | - Shuai Ji
- Institute of Biotechnology, Helsinki Institute of Life ScienceUniversity of HelsinkiHelsinkiFinland
| | | | - Gui‐Lai Jiang
- Suzhou Medical CollegeSoochow UniversitySuzhouJiangsuChina
| | - Lingjuan Jiang
- Biomarker Discovery and Validation Facility, Institute of Clinical Medicine, Peking Union Medical College HospitalBeijingChina
| | - Ling N. Jin
- Department of Civil and Environmental EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Yuhe Kan
- College of Biology and OceanographyWeifang UniversityWeifangShandongChina
| | - Da Kang
- College of Environmental Science and EngineeringBeijing University of TechnologyBeijingChina
| | - Jin Kou
- College of Environmental and Municipal EngineeringLanzhou Jiaotong UniversityLanzhouChina
| | - Ka‐Lung Lam
- School of Life SciencesThe Chinese University of Hong KongShatin, Hong KongChina
| | - Changchao Li
- Department of Civil and Environmental EngineeringThe Hong Kong Polytechnic UniversityHong KongChina
| | - Chong Li
- Department of Renewable ResourcesUniversity of AlbertaEdmontonAlbertaCanada
| | - Fuyi Li
- School of Geographical SciencesNortheast Normal UniversityChangchunJilinChina
| | - Liwei Li
- Department of GastroenterologyThe Second Affiliated Hospital of Guangxi Medical UniversityNanningGuangxiChina
| | - Miao Li
- Synaura Biotechnology (Shanghai) Co., Ltd.ShanghaiChina
| | - Xin Li
- School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Ye Li
- Institute of Soil Science, Chinese Academy of SciencesNanjingJiangsuChina
| | - Zheng‐Tao Li
- School of Art and Archaeology of Zhejiang UniversityZhejiangChina
| | - Jing Liang
- College of Animal Science and TechnologyGuangxi UniversityNanningChina
| | - Yongxin Lin
- Fujian Provincial Key Laboratory for Subtropical Resources and EnvironmentFujian Normal UniversityFuzhouChina
| | - Changzhen Liu
- College of Energy and Environmental EngineeringHebei University of EngineeringHandanHebeiChina
| | | | - Fengqin Liu
- College of Life SciencesHenan Agricultural UniversityZhengzhouChina
| | - Jia Liu
- College of Life ScienceNankai UniversityTianjinChina
| | - Tianrui Liu
- Jiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical SciencesJiangxiChina
| | - Tingting Liu
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Xinyuan Liu
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefeiAnhuiChina
| | - Yaqun Liu
- School of Life Sciences and Food TechnologyHanshan Normal UniversityChaozhouChina
| | | | - Minghao Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Wenbo Lou
- College of Animal Science and TechnologyJilin Agricultural UniversityChangchunJilinChina
| | - Yaning Luan
- The College of ForestryBeijing Forestry UniversityBeijingChina
| | - Yuanyuan Luo
- State Key Laboratory of Tea Plant Biology and UtilizationAnhui Agricultural UniversityHefeiAnhuiChina
| | - Hujie Lv
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
- Department of Life Sciences, Imperial College of LondonLondonUK
| | - Tengfei Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro‐Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouGansuChina
| | - Zongjiong Mai
- Department of OncologyThe Fifth Affiliated Hospital of Sun Yat‐sen UniversityZhuhaiGuangdongChina
| | - Jiayuan Mo
- College of Animal Science and TechnologyGuangxi UniversityNanningChina
| | - Dongze Niu
- National‐Local Joint Engineering Research Center of Biomass Refining and High‐Quality Utilization, Institute of Urban and Rural MiningChangzhou UniversityChangzhouJiangsuChina
| | - Zhuo Pan
- Department of PathologyAffiliated Cancer Hospital of Zhengzhou UniversityZhengzhouChina
| | - Heyuan Qi
- Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Zhanyao Shi
- College of Water SciencesBeijing Normal UniversityBeijingChina
| | | | - Fuxiang Sun
- New Direction Biotechnology (Tianjin) Co., LtdTianjinChina
| | - Yan Sun
- College of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and ImpactHebei University of EngineeringHandanChina
| | - Sihui Tian
- Institute of Botany, Chinese Academy of SciencesBeijingChina
| | - Xiulin Wan
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Guoliang Wang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry SciencesBeijingChina
| | - Hongyang Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical SciencesJiangsuChina
| | - Hongyu Wang
- College of Animal ScienceAnhui Science and Technology UniversityChuzhouChina
| | - Huanhuan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Jing Wang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental SciencesBeijingChina
| | - Jun Wang
- China CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and PreventionBeijingChina
| | - Kang Wang
- College of Animal Science and TechnologyYangzhou UniversityYangzhouJiangsuChina
| | - Leli Wang
- Key Laboratory of Agro‐Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangshaChina
| | - Shao‐kun Wang
- Institute of Ecological Conservation and Restoration, Chinese Academy of ForestryBeijingChina
| | - Xinlong Wang
- Beijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Yao Wang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Zufei Xiao
- State Key Laboratory for Ecological Security of Regions and Cities, Institute of Urban Environment, Chinese Academy of SciencesXiamenChina
| | - Huichun Xing
- Center of Liver Diseases Division 3, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Yifan Xu
- Center of Liver Diseases Division 3, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Shu‐yan Yan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Invasive Alien Species Control of Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Li Yang
- Sansure Biotech IncorporationChangshaHunanChina
| | - Song Yang
- Center of Liver Diseases Division 3, Beijing Ditan HospitalCapital Medical UniversityBeijingChina
| | - Yuanming Yang
- Guangzhou University of Chinese MedicineGuangzhouChina
| | - Xiaofang Yao
- Key Laboratory of Agro‐Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of SciencesChangshaChina
| | - Salsabeel Yousuf
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Hao Yu
- Institute of Marine Biology and Pharmacology, Ocean CollegeZhejiang UniversityZhoushanZhejiangChina
| | - Yu Lei
- Key Laboratory of Livestock BiologyNorthwest A&F UniversityYanglingShaanxiChina
| | - Zhengrong Yuan
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Meiyin Zeng
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Chunfang Zhang
- Institute of Marine Biology and Pharmacology, Ocean CollegeZhejiang UniversityZhoushanZhejiangChina
| | - Chunge Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Huimin Zhang
- School of Food Science and TechnologyShihezi UniversityShiheziXinjiangChina
| | | | - Na Zhang
- College of Biochemical EngineeringBeijing Union UniversityBeijingChina
| | - Tianyuan Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Yi‐Bo Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Key Laboratory of Invasive Alien Species Control of Ministry of Agriculture and Rural Affairs, Institute of Plant Protection, Chinese Academy of Agricultural SciencesBeijingChina
| | - Yupeng Zhang
- College of Resources and Environmental SciencesHenan Agricultural UniversityZhengzhouChina
| | - Zheng Zhang
- Tea Research Institute, Chinese Academy of Agricultural SciencesHangzhouZhejiangChina
| | - Mingda Zhou
- College of Environmental Science and EngineeringTongji UniversityShanghaiChina
| | - Yuanping Zhou
- Zhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic MedicineGuangdong Medical UniversityZhanjiangGuangdongChina
| | - Chengshuai Zhu
- School of Art and Archaeology of Zhejiang UniversityZhejiangChina
| | - Lin Zhu
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of TechnologyHarbinChina
| | - Yue Zhu
- School of Ecology, Environment and ResourcesGuangdong University of TechnologyGuangzhouGuangdongChina
| | - Zhihao Zhu
- Zhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic MedicineGuangdong Medical UniversityZhanjiangGuangdongChina
| | - Hongqin Zou
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural SciencesBeijingChina
| | - Anna Zuo
- School of Traditional Chinese MedicineSouthern Medical UniversityGuangzhouGuangdongChina
| | - Wenxuan Dong
- Department of Animal SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Tao Wen
- College of Resource and Environmental SciencesNanjing Agricultural UniversityNanjingJiangsuChina
| | - Shifu Chen
- HaploX BiotechnologyShenzhenChina
- LifeX Institute, School of Medical TechnologyGannan Medical UniversityGanzhouChina
- Faculty of Data ScienceCity University of MacauMacauChina
| | - Guoliang Li
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of ForestryJiangxi Agricultural UniversityNanchangJiangxiChina
| | - Yunyun Gao
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Yong‐Xin Liu
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhenGuangdongChina
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