文献类型： 外文期刊

作者： Bai, Defeng ¹ ; Chen, Tong ² ; Xun, Jiani ¹ ; Ma, Chuang ¹ ; Luo, Hao ¹ ; Yang, Haifei ¹ ; Cao, Chen ⁵ ; Cao, Xiaofeng ⁶ ; Cui, Jianzhou ⁷ ; Deng, Yuan-Ping ⁸ ; Deng, Zhaochao ⁹ ; Dong, Wenxin ¹⁰ ; Dong, Wenxue ¹¹ ; Du, Juan ¹² ; Fang, Qunkai ¹³ ; Fang, Wei ¹⁴ ; Fang, Yue ¹⁵ ; Fu, Fangtian ¹⁶ ; Fu, Min ¹⁷ ; Fu, Yi-Tian ¹⁸ ; Gao, He ¹⁹ ; Ge, Jingping ²⁰ ; Gong, Qinglong ²¹ ; Gu, Lunda ²² ; Guo, Peng ²³ ; Guo, Yuhao ²⁰ ; Hai, Tang ²⁴ ; Liu, Hao ²⁵ ; He, Jieqiang ²⁶ ; He, Zi-Yang ²⁷ ; Hou, Huiyu ¹ ; Huang, Can ²⁸ ; Ji, Shuai ²⁹ ; Jiang, ChangHai ³⁰ ; Jiang, Gui-Lai ³¹ ; Jiang, Lingjuan ³² ; Jin, Ling N. ³³ ; Kan, Yuhe ³⁴ ; Kang, Da ³⁵ ; Kou, Jin ³⁶ ; Lam, Ka-Lung ³⁷ ; Li, Changchao ³³ ; Li, Chong ³⁸ ; Li, Fuyi ³⁹ ; Li, Liwei ⁴⁰ ; Li, Miao ⁴¹ ; Li, Xin ⁴² ; Li, Ye ⁴³ ; Li, Zheng-Tao ⁴⁴ ; Liang, Jing ⁴⁵ ; Lin, Yongxin ⁴⁶ ; Liu, Changzhen ⁴⁷ ; Liu, Danni ⁴⁸ ; Liu, Fengqin ⁴⁹ ; Liu, Jia ⁵⁰ ; Liu, Tianrui ⁵¹ ; Liu, Tingting ⁵² ; Liu, Xinyuan ⁵³ ; Liu, Yaqun ⁵⁴ ; Liu, Bangyan ⁵⁵ ; Liu, Minghao ⁵⁶ ; Lou, Wenbo ²¹ ; Luan, Yaning ¹⁵ ; Luo, Yuanyuan ⁵³ ; Lv, Hujie ¹ ; Ma, Tengfei ⁵⁸ ; Mai, Zongjiong ⁵⁹ ; Mo, Jiayuan ⁴⁵ ; Niu, Dongze ⁶⁰ ; Pan, Zhuo ⁶¹ ; Qi, Heyuan ⁶² ; Shi, Zhanyao ⁶³ ; Song, Chunjiao ⁶⁴ ; Sun, Fuxiang ⁶⁵ ; Sun, Yan ⁶⁶ ; Tian, Sihui ⁶⁷ ; Wan, Xiulin ¹ ; Wang, Guoliang ⁶⁸ ; Wang, Hongyang ⁶⁹ ; Wang, Hongyu ⁷⁰ ; Wang, Huanhuan ⁷¹ ; Wang, Jing ⁷² ; Wang, Jun ⁷³ ; Wang, Kang ⁷⁴ ; Wang, Leli ⁷⁵ ; Wang, Shao-kun ⁷⁶ ; Wang, Xinlong ⁵² ; Wang, Yao ¹ ; Xiao, Zufei ⁷⁷ ; Xing, Huichun ⁷⁸ ; Xu, Yifan ⁷⁸ ; Yan, Shu-yan ⁷⁹ ; Yang, Li ²² ; Yang, Song ⁷⁸ ; Yang, Yuanming ⁸⁰ ; Yao, Xiaofang ⁷⁵ ; Yousuf, Salsabeel ¹ ; Yu, Hao ⁹ ; Lei, Yu ⁸¹ ; Yuan, Zhengrong ⁸² ; Zeng, Meiyin ¹ ; Zhang, Chunfang ⁹ ; Zhang, Chunge ⁸³ ; Zhang, Huimin ⁸⁴ ; Zhang, Jing ⁴⁸ ; Zhang, Na ⁸⁵ ; Zhang, Tianyuan ¹ ; Zhang, Yi-Bo ⁷⁹ ; Zhang, Yupeng ⁸⁶ ; Zhang, Zheng ⁸⁷ ; Zhou, Mingda ⁸⁸ ; Zhou, Yuanping ⁸⁹ ; Zhu, Chengshuai ⁴⁴ ; Zhu, Lin ⁹⁰ ; Zhu, Yue ⁹¹ ; Zhu, Zhihao ⁸⁹ ; Zou, Hongqin ⁹² ; Zuo, Anna ⁹³ ; Dong, Wenxuan ⁹⁴ ; Wen, Tao ⁹⁵ ; Chen, Shifu ⁴⁸ ; Li, Guoliang ⁹⁸ ; Gao, Yunyun ¹ ; Liu, Yong-Xin ¹ ;

作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst, Genome Anal Lab, Minist Agr & Rural Affairs, Shenzhen, Guangdong, Peoples R China

2.China Acad Chinese Med Sci, Natl Resource Ctr Chinese Mat Med, State Key Lab Qual Ensurance & Sustainable Use Da, Beijing, Peoples R China

3.Anhui Agr Univ, Sch Hort, Hefei, Peoples R China

4.Qingdao Agr Univ, Coll Life Sci, Qingdao, Peoples R China

5.Nanjing Med Univ, Sch Biomed Engn & Informat, Key Lab Bio Elect Environm & Adv Med Theranost, Nanjing, Jiangsu, Peoples R China

6.Tsinghua Univ, Sch Environm, Ctr Water & Ecol, State Key Joint Lab Environm Simulat & Pollut Con, Beijing, Peoples R China

7.Natl Univ Singapore, Yong Loo Lin Sch Med, Immunol Translat Res Programme, Singapore, Singapore

8.Hunan Agr Univ, Coll Vet Med, Res Ctr Parasites & Vectors, Changsha, Hunan, Peoples R China

9.Zhejiang Univ, Inst Marine Biol & Pharmacol, Ocean Coll, Zhoushan, Zhejiang, Peoples R China

10.Minist Agr & Rural Affairs, Agroenvironm Protect Inst, Tianjin, Peoples R China

11.Xizang Minzu Univ, Key Lab Mol Genet Mech & Intervent Res High Altit, Sch Med, Xianyang, Peoples R China

12.Karolinska Inst, Dept Microbiol Tumor & Cell Biol, Stockholm, Sweden

13.Zhejiang Univ Technol, Coll Environm, Hangzhou, Peoples R China

14.Zhejiang Agr & Forestry Univ, Coll Environm & Resource Sci, Hangzhou, Peoples R China

15.Beijing Forestry Univ, Coll Forestry, Beijing, Peoples R China

16.Hangzhou VicrobX Biotech Co Ltd, Dept Bioinformat, Hangzhou, Zhejiang, Peoples R China

17.Anhui Agr Univ, Coll Plant Protect, Anhui Prov Key Lab Integrated Pest Management Cro, Hefei, Peoples R China

18.Cent South Univ, Xiangya Sch Basic Med, Changsha, Hunan, Peoples R China

19.Guangdong Acad Sci, Inst Microbiol, Guangzhou, Guangdong, Peoples R China

20.Heilongjiang Univ, Sch Life Sci, Engn Res Ctr Agr Microbiol Technol, Minist Educ, Harbin, Peoples R China

21.Jilin Agr Univ, Coll Anim Sci & Technol, Changchun, Jilin, Peoples R China

22.Sansure Biotech Incorp, Changsha, Hunan, Peoples R China

23.Hebei Univ Sci & Technol, Sch Food Sci & Biol, Shijiazhuang, Hebei, Peoples R China

24.Shanxi Datong Univ, Sch Life Sci, Datong, Peoples R China

25.Xian Jiaotong Liverpool Univ, Dept Environm Hlth Sci, Suzhou, Jiangsu, Peoples R China

26.Northwest A&F Univ, Coll Hort, Yangling, Shaanxi, Peoples R China

27.Univ Melbourne, School Agr Food & Ecosyst Sci, Fac Sci, Melbourne, Vic, Australia

28.Univ Tokyo, Grad Sch Frontier Sci, Kashiwa, Chiba, Japan

29.Univ Helsinki, Inst Biotechnol, Helsinki Inst Life Sci, Helsinki, Finland

30.Shanghai Maritime Univ, Shanghai, Peoples R China

31.Soochow Univ, Suzhou Med Coll, Suzhou, Jiangsu, Peoples R China

32.Peking Union Med Coll Hosp, Inst Clin Med, Biomarker Discovery & Validat Facil, Beijing, Peoples R China

33.Hong Kong Polytech Univ, Dept Civil & Environm Engn, Hong Kong, Peoples R China

34.Weifang Univ, Coll Biol & Oceanog, Weifang, Shandong, Peoples R China

35.Beijing Univ Technol, Coll Environm Sci & Engn, Beijing, Peoples R China

36.Lanzhou Jiaotong Univ, Coll Environm & Municipal Engn, Lanzhou, Peoples R China

37.Chinese Univ Hong Kong, Sch Life Sci, Shatin, Hong Kong, Peoples R China

38.Univ Alberta, Dept Renewable Resources, Edmonton, AB, Canada

39.Northeast Normal Univ, Sch Geog Sci, Changchun, Jilin, Peoples R China

40.Guangxi Med Univ, Dept Gastroenterol, Affiliated Hosp 2, Nanning, Guangxi, Peoples R China

41.Synaura Biotechnol Shanghai Co Ltd, Shanghai, Peoples R China

42.Univ Michigan, Sch Publ Hlth, Ann Arbor, MI USA

43.Chinese Acad Sci, Inst Soil Sci, Nanjing, Jiangsu, Peoples R China

44.Zhejiang Univ, Sch Art & Archaeol, Hangzhou, Zhejiang, Peoples R China

45.Guangxi Univ, Coll Anim Sci & Technol, Nanning, Peoples R China

46.Fujian Normal Univ, Fujian Prov Key Lab Subtrop Resources & Environm, Fuzhou, Peoples R China

47.Hebei Univ Engn, Coll Energy & Environm Engn, Handan, Hebei, Peoples R China

48.HaploX Biotechnol, Shenzhen, Peoples R China

49.Henan Agr Univ, Coll Life Sci, Zhengzhou, Peoples R China

50.Nankai Univ, Coll Life Sci, Tianjin, Peoples R China

51.China Acad Chinese Med Sci, Jiangxi Prov Key Lab Sustainable Utilizat Tradit, Inst Tradit Chinese Med Hlth Ind, Beijing, Jiangxi, Peoples R China

52.Capital Med Univ, Beijing Ditan Hosp, Inst Infect Dis, Beijing Key Lab Emerging Infect Dis, Beijing, Peoples R China

53.Anhui Agr Univ, State Key Lab Tea Plant Biol & Utilizat, Hefei, Anhui, Peoples R China

54.Hanshan Normal Univ, Sch Life Sci & Food Technol, Chaozhou, Peoples R China

55.Tsinghua Univ, Beijing, Peoples R China

56.Chinese Acad Sci, Inst Microbiol, State Key Lab Microbial Resources, Beijing, Peoples R China

57.Imperial Coll London, Dept Life Sci, London, England

58.Lanzhou Univ, Coll Pastoral Agr Sci & Technol, Ctr Grassland Microbiome, State Key Lab Herbage Improvement & Grassland Agr, Lanzhou, Gansu, Peoples R China

59.Sun Yat Sen Univ, Dept Oncol, Affiliated Hosp 5, Zhuhai, Guangdong, Peoples R China

60.Changzhou Univ, Inst Urban & Rural Min, Natl Local Joint Engn Res Ctr Biomass Refining &, Changzhou, Jiangsu, Peoples R China

61.Zhengzhou Univ, Dept Pathol, Affiliated Canc Hosp, Zhengzhou, Peoples R China

62.Chinese Acad Sci, Inst Microbiol, Beijing, Peoples R China

63.Beijing Normal Univ, Coll Water Sci, Beijing, Peoples R China

64.Deyang Peoples Hosp, Deyang, Sichuan, Peoples R China

65.New Direct Biotechnol Tianjin Co Ltd, Tianjin, Peoples R China

66.Hebei Univ Engn, Coll Energy & Environm Engn, Hebei Key Lab Air Pollut Cause & Impact, Handan, Peoples R China

67.Chinese Acad Sci, Inst Bot, Beijing, Peoples R China

68.Beijing Acad Agr & Forestry Sci, Inst Biotechnol, Beijing, Peoples R China

69.China Acad Chinese Med Sci, Natl Resource Ctr Chinese Mat Med, Beijing, Jiangsu, Peoples R China

70.Anhui Sci & Technol Univ, Coll Anim Sci, Chuzhou, Peoples R China

71.Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Beijing, Peoples R China

72.Chinese Res Inst Environm Sci, State Key Lab Environm Criteria & Risk Assessment, Beijing, Peoples R China

73.Natl Inst Environm Hlth, Chinese Ctr Dis Control & Prevent, China CDC Key Lab Environm & Populat Hlth, Beijing, Peoples R China

74.Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou, Jiangsu, Peoples R China

75.Chinese Acad Sci, Inst Subtrop Agr, Key Lab Agro Ecol Processes Subtrop Region, Changsha, Peoples R China

76.Chinese Acad Forestry, Inst Ecol Conservat & Restorat, Beijing, Peoples R China

77.Chinese Acad Sci, Inst Urban Environm, State Key Lab Ecol Secur Reg & Cities, Xiamen, Peoples R China

78.Capital Med Univ, Beijing Ditan Hosp, Ctr Liver Dis Div, Beijing, Peoples R China

79.Chinese Acad Agr Sci, Inst Plant Protect, State Key Lab Biol Plant Dis & Insect Pests, Key Lab Invas Alien Species Control,Minist Agr &, Beijing, Peoples R China

80.Guangzhou Univ Chinese Med, Guangzhou, Peoples R China

81.Northwest A&F Univ, Key Lab Livestock Biol, Yangling, Shaanxi, Peoples R China

82.Beijing Forestry Univ, Coll Biol Sci & Technol, Beijing, Peoples R China

83.Chinese Acad Sci, Inst Microbiol, CAS Key Lab Pathogen Microbiol & Immunol, Beijing, Peoples R China

84.Shihezi Univ, Sch Food Sci & Technol, Shihezi, Xinjiang, Peoples R China

85.Beijing Union Univ, Coll Biochem Engn, Beijing, Peoples R China

86.Henan Agr Univ, Coll Resources & Environm Sci, Zhengzhou, Peoples R China

87.Chinese Acad Agr Sci, Tea Res Inst, Hangzhou, Zhejiang, Peoples R China

88.Tongji Univ, Coll Environm Sci & Engn, Shanghai, Peoples R China

89.Guangdong Med Univ, Marine Biomed Res Inst, Coll Basic Med, Zhanjiang Key Lab Human Microecol & Clin Translat, Zhanjiang, Guangdong, Peoples R China

90.Harbin Inst Technol, Sch Environm, State Key Lab Urban Water Resource & Environm, Harbin, Peoples R China

91.Guangdong Univ Technol, Sch Ecol Environm & Resources, Guangzhou, Guangdong, Peoples R China

92.Chinese Acad Agr Sci, Inst Agr Resources & Reg Planning, Beijing, Peoples R China

93.Southern Med Univ, Sch Tradit Chinese Med, Guangzhou, Guangdong, Peoples R China

94.Purdue Univ, Dept Anim Sci, W Lafayette, IN USA

95.Nanjing Agr Univ, Coll Resource & Environm Sci, Nanjing, Jiangsu, Peoples R China

96.Gannan Med Univ, LifeX Inst, Sch Med Technol, Ganzhou, Peoples R China

97.City Univ Macau, Fac Data Sci, Macau, Peoples R China

98.Jiangxi Agr Univ, Coll Forestry, Jiangxi Prov Key Lab Conservat Biol, Nanchang, Jiangxi, Peoples R China

关键词： metagenome; microbiome; microbiota; pipeline; visualization

期刊名称：IMETA （ 影响因子：33.2； 五年影响因子：33.2 ）

ISSN： 2770-5986

年卷期： 2025 年 4 卷 1 期

页码：

收录情况： SCI

摘要： 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.