ArticleiMeta2025
EasyMetagenome: A user-friendly and flexible pipeline for shotgun metagenomic analysis in microbiome research.
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31citing papers in PubMed
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31 citing papers in PubMed.
- metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.Gut microbes · 2026Article
- Unraveling the coastal marine plastisphere archaeome.Nature communications · 2026Article
- Wekemo Bioincloud 2026: An AI-enabled platform for standardized multi-omics data analyses.iMeta · 2026Article
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- Beyond omics: From descriptive profiling to causal and scalable design of fermentation microbiomes.iMeta · 2026Article
- MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.bioRxiv : the preprint server for biology · 2026Article
- Omics-based decoding of molecular and metabolic crosstalk in the skin barrier ecosystem.Cell death and differentiation · 2026Review
- Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.Nutrients · 2026Article
- Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.Microbiome · 2026Article
- Insights into antibiotic resistomes from gut metagenome-assembled genomes of the free-range pigs.Microbiology spectrum · 2026Article
- Accu16S/AccuITS: Accurate and broadly applicable amplicon sequencing for absolute microbiome quantification.iMeta · 2026Article
- Microbiome eco-evolution of cultivated and wild rice species across the genus Oryza and its importance in supporting rice growth.Microbiome · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Review
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.Nucleic acids research · 2026Article
- A Brief Review of Microbial Omics: Methods and Perspectives.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Metagenomic analysis of ocular microbiome in aqueous humor from myopia, cataract, primary open angle glaucoma and Posner-Schlossman syndrome.International journal of ophthalmology · 2026Article
- Multi-Omics Insights into Microbial Community Dynamics and Functional Shifts During Double-Round Bottom Fermentation of Strong-Flavor Baijiu.Foods (Basel, Switzerland) · 2025Article
- High-resolution microbiome analysis of host-rich samples using 2bRAD-M without host depletion.NPJ biofilms and microbiomes · 2025Article
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Authors and funding
124 authors.
Defeng BaiGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0009-0005-7762-7199
Tong ChenState 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.ORCID 0000-0003-3134-3113
Jiani XunGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0009-0005-7406-1513
Chuang MaGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0009-0009-0035-0733
Hao LuoGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0009-0005-3391-8576
Haifei YangGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0009-0003-8204-5850
Chen CaoKey Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics Nanjing Medical University Nanjing Jiangsu China.
Xiaofeng CaoCenter for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment Tsinghua University Beijing China.ORCID https://orcid.org/0000-0003-2036-9748
Jianzhou CuiImmunology Translational Research Programme, Yong Loo Lin School of Medicine National University of Singapore Singapore Singapore.
Yuan-Ping DengResearch Center for Parasites and Vectors, College of Veterinary Medicine Hunan Agricultural University Changsha Hunan China.
Zhaochao DengInstitute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China.
Wenxin DongAgro-Environmental Protection Institute Ministry of Agriculture and Rural Affairs Tianjin China.
Wenxue DongKey Laboratory for Molecular Genetic Mechanisms and Intervention Research on High Altitude Disease of Tibet Autonomous Region, School of Medicine Xizang Minzu University Xianyang China.
Juan DuKarolinska Institutet, Department of Microbiology, Tumor and Cell Biology Stockholm Sweden.
Qunkai FangCollege of Environment Zhejiang University of Technology Hangzhou China.
Wei FangCollege of Environmental and Resource Sciences Zhejiang Agriculture and Forestry University Hangzhou China.
Yue FangThe College of Forestry Beijing Forestry University Beijing China.
Fangtian FuDepartment of Bioinformatics, Hangzhou VicrobX Biotech Co., Ltd Hangzhou Zhejiang China.
Min FuAnhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection Anhui Agricultural University Hefei China.
Yi-Tian FuXiangya School of Basic Medicine Central South University Changsha Hunan China.
He GaoInstitute of Microbiology,Guangdong Academy of Sciences Guangzhou Guangdong China.
Jingping GeEngineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life Sciences Heilongjiang University Harbin China.
Qinglong GongCollege of Animal Science and Technology Jilin Agricultural University Changchun Jilin China.
Lunda GuSansure Biotech Incorporation Changsha Hunan China.
Peng GuoSchool of Food Science and Biology Hebei University of Science and Technology Shijiazhuang Hebei China.
Yuhao GuoEngineering Research Center of Agricultural Microbiology Technology, Ministry of Education, School of Life Sciences Heilongjiang University Harbin China.
Tang HaiSchool of Life Sciences Shanxi Datong University Datong China.
Hao LiuDepartment of Health & Environmental Sciences Xi'an Jiaotong-Liverpool University Suzhou Jiangsu China.
Jieqiang HeCollege of Horticulture Northwest A&F University Yangling Shaanxi China.
Zi-Yang HeSchool of Agriculture, Food and Ecosystem Sciences, Faculty of Science The University of Melbourne VIC Australia.
Huiyu HouGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Can HuangGraduate School of Frontier Sciences The University of Tokyo Kashiwa-shi, Chiba Japan.
Shuai JiInstitute of Biotechnology, Helsinki Institute of Life Science University of Helsinki Helsinki Finland.
ChangHai JiangShanghai Maritime University Shanghai China.
Gui-Lai JiangSuzhou Medical College Soochow University Suzhou Jiangsu China.ORCID https://orcid.org/0009-0000-5441-9438
Lingjuan JiangBiomarker Discovery and Validation Facility, Institute of Clinical Medicine, Peking Union Medical College Hospital Beijing China.
Ling N JinDepartment of Civil and Environmental Engineering The Hong Kong Polytechnic University Hong Kong China.ORCID https://orcid.org/0000-0003-1267-7396
Yuhe KanCollege of Biology and Oceanography Weifang University Weifang Shandong China.
Da KangCollege of Environmental Science and Engineering Beijing University of Technology Beijing China.
Jin KouCollege of Environmental and Municipal Engineering Lanzhou Jiaotong University Lanzhou China.
Ka-Lung LamSchool of Life Sciences The Chinese University of Hong Kong Shatin, Hong Kong China.
Changchao LiDepartment of Civil and Environmental Engineering The Hong Kong Polytechnic University Hong Kong China.
Chong LiDepartment of Renewable Resources University of Alberta Edmonton Alberta Canada.ORCID https://orcid.org/0000-0001-9330-5396
Fuyi LiSchool of Geographical Sciences Northeast Normal University Changchun Jilin China.
Liwei LiDepartment of Gastroenterology The Second Affiliated Hospital of Guangxi Medical University Nanning Guangxi China.
Miao LiSynaura Biotechnology (Shanghai) Co., Ltd. Shanghai China.
Xin LiSchool of Public Health University of Michigan Ann Arbor Michigan USA.
Ye LiInstitute of Soil Science, Chinese Academy of Sciences Nanjing Jiangsu China.
Zheng-Tao LiSchool of Art and Archaeology of Zhejiang University Zhejiang China.
Jing LiangCollege of Animal Science and Technology Guangxi University Nanning China.
Yongxin LinFujian Provincial Key Laboratory for Subtropical Resources and Environment Fujian Normal University Fuzhou China.
Changzhen LiuCollege of Energy and Environmental Engineering Hebei University of Engineering Handan Hebei China.
Danni LiuHaploX Biotechnology Shenzhen China.
Fengqin LiuCollege of Life Sciences Henan Agricultural University Zhengzhou China.
Jia LiuCollege of Life Science Nankai University Tianjin China.
Tianrui LiuJiangxi Province Key Laboratory of Sustainable Utilization of Traditional Chinese Medicine Resources, Institute of Traditional Chinese Medicine Health Industry, China Academy of Chinese Medical Sciences Jiangxi China.
Tingting LiuBeijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital Capital Medical University Beijing China.
Xinyuan LiuState Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei Anhui China.
Yaqun LiuSchool of Life Sciences and Food Technology Hanshan Normal University Chaozhou China.
Bangyan LiuTsinghua University Beijing China.
Minghao LiuState Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences Beijing China.
Wenbo LouCollege of Animal Science and Technology Jilin Agricultural University Changchun Jilin China.
Yaning LuanThe College of Forestry Beijing Forestry University Beijing China.
Yuanyuan LuoState Key Laboratory of Tea Plant Biology and Utilization Anhui Agricultural University Hefei Anhui China.
Hujie LvGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Tengfei MaState Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Centre for Grassland Microbiome, College of Pastoral Agriculture Science and Technology Lanzhou University Lanzhou Gansu China.
Zongjiong MaiDepartment of Oncology The Fifth Affiliated Hospital of Sun Yat-sen University Zhuhai Guangdong China.
Jiayuan MoCollege of Animal Science and Technology Guangxi University Nanning China.
Dongze NiuNational-Local Joint Engineering Research Center of Biomass Refining and High-Quality Utilization, Institute of Urban and Rural Mining Changzhou University Changzhou Jiangsu China.
Zhuo PanDepartment of Pathology Affiliated Cancer Hospital of Zhengzhou University Zhengzhou China.
Heyuan QiInstitute of Microbiology, Chinese Academy of Sciences Beijing China.
Zhanyao ShiCollege of Water Sciences Beijing Normal University Beijing China.
Chunjiao SongDeyang People's Hospital Deyang Sichuan China.
Fuxiang SunNew Direction Biotechnology (Tianjin) Co., Ltd Tianjin China.
Yan SunCollege of Energy and Environmental Engineering, Hebei Key Laboratory of Air Pollution Cause and Impact Hebei University of Engineering Handan China.
Sihui TianInstitute of Botany, Chinese Academy of Sciences Beijing China.
Xiulin WanGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Guoliang WangInstitute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences Beijing China.
Hongyang WangNational Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences Jiangsu China.ORCID 0009-0009-2271-4411
Hongyu WangCollege of Animal Science Anhui Science and Technology University Chuzhou China.
Huanhuan WangState Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences Beijing China.
Jing WangState Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences Beijing China.
Jun WangChina CDC Key Laboratory of Environment and Population Health, National Institute of Environmental Health, Chinese Center for Disease Control and Prevention Beijing China.
Kang WangCollege of Animal Science and Technology Yangzhou University Yangzhou Jiangsu China.
Leli WangKey Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha China.
Shao-Kun WangInstitute of Ecological Conservation and Restoration, Chinese Academy of Forestry Beijing China.
Xinlong WangBeijing Key Laboratory of Emerging Infectious Diseases, Institute of Infectious Diseases, Beijing Ditan Hospital Capital Medical University Beijing China.
Yao WangGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Zufei XiaoState Key Laboratory for Ecological Security of Regions and Cities, Institute of Urban Environment, Chinese Academy of Sciences Xiamen China.
Huichun XingCenter of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China.
Yifan XuCenter of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China.
Shu-Yan YanState 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 Sciences Beijing China.
Li YangSansure Biotech Incorporation Changsha Hunan China.
Song YangCenter of Liver Diseases Division 3, Beijing Ditan Hospital Capital Medical University Beijing China.
Yuanming YangGuangzhou University of Chinese Medicine Guangzhou China.
Xiaofang YaoKey Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences Changsha China.
Salsabeel YousufGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Hao YuInstitute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China.
Yu LeiKey Laboratory of Livestock Biology Northwest A&F University Yangling Shaanxi China.
Zhengrong YuanCollege of Biological Sciences and Technology Beijing Forestry University Beijing China.ORCID 0000-0002-5175-0675
Meiyin ZengGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Chunfang ZhangInstitute of Marine Biology and Pharmacology, Ocean College Zhejiang University Zhoushan Zhejiang China.
Chunge ZhangCAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences Beijing China.
Huimin ZhangSchool of Food Science and Technology Shihezi University Shihezi Xinjiang China.
Jing ZhangHaploX Biotechnology Shenzhen China.
Na ZhangCollege of Biochemical Engineering Beijing Union University Beijing China.
Tianyuan ZhangGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.
Yi-Bo ZhangState 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 Sciences Beijing China.
Yupeng ZhangCollege of Resources and Environmental Sciences Henan Agricultural University Zhengzhou China.
Zheng ZhangTea Research Institute, Chinese Academy of Agricultural Sciences Hangzhou Zhejiang China.
Mingda ZhouCollege of Environmental Science and Engineering Tongji University Shanghai China.
Yuanping ZhouZhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic Medicine Guangdong Medical University Zhanjiang Guangdong China.
Chengshuai ZhuSchool of Art and Archaeology of Zhejiang University Zhejiang China.
Lin ZhuState Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology Harbin China.
Yue ZhuSchool of Ecology, Environment and Resources Guangdong University of Technology Guangzhou Guangdong China.
Zhihao ZhuZhanjiang Key Laboratory of Human Microecology and Clinical Translation Research, the Marine Biomedical Research Institute, College of Basic Medicine Guangdong Medical University Zhanjiang Guangdong China.
Hongqin ZouInstitute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences Beijing China.
Anna ZuoSchool of Traditional Chinese Medicine Southern Medical University Guangzhou Guangdong China.
Wenxuan DongDepartment of Animal Sciences Purdue University West Lafayette Indiana USA.
Tao WenCollege of Resource and Environmental Sciences Nanjing Agricultural University Nanjing Jiangsu China.ORCID 0000-0003-0102-0487
Shifu ChenHaploX Biotechnology Shenzhen China.ORCID 0000-0001-5799-653X
Guoliang LiJiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry Jiangxi Agricultural University Nanchang Jiangxi China.ORCID 0000-0002-0599-5356
Yunyun GaoGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0000-0003-3389-9385
Yong-Xin LiuGenome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen Guangdong China.ORCID 0000-0003-1832-9835
Funding
No grant is acknowledged in the PubMed record.
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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