The metagenome-microbiome knowledge you want is all here (2023.7)

Welcome to click on the blue "metagenome" above to follow us!

Metagenome/microbiome is one of the most popular research fields in the world today. In order to strengthen the exchange and dissemination of metagenomics technology and results, and promote the development of the global Chinese microbiome field, young researchers from the Chinese Academy of Sciences created the "Metagenomics" public account, and the joint sea Colleagues at home and abroad jointly create a platform for pure dry goods technology and thought exchange in this field.

The public account is pushed daily, and the latest achievements, scientific research ideas, experiments and analysis techniques in the field of metagenomics are shared on weekdays. The theory is solid and practical; the weekend science and life columns are easy to read and watch movies. At present, 3100+ original articles are shared, 150,000+ small partners exchange and learn together here, and the cumulative reading exceeds 40 million+.

The public account co-founded a new high-level journal "iMeta" on metagenomics, microbiome and bioinformatics, an open access journal co-published by Wiley, Enterobacteriaceae Branch and hundreds of Chinese scientists in this field. The chief editor is Liu Shuangjiang, a researcher at the Institute of Microbiology, Chinese Academy of Sciences It is jointly held by Professor Fu Jingyuan from the University of Groningen in the Netherlands. The goal is to publish high-impact papers in the top 10% (IF > 15). For details, see: iMeta launch promotional video . Published the first monograph "Microbiome Protocol eBook" in this field, which was written by 352 colleagues in the field, free and open source, and continuously updated. For details, see "Microbiome Protocol eBook (Microbiome Protocol eBook) 1st Edition" jointly completed by 125 units .

Founded the world's first microbiome and bioinformatics journal, iMeta, a new high-level journal .

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Note: All blue words are links to articles, click to read the original text

iMeta—the top journal of microbiome and bioinformatics

• World premiere of iMeta's inaugural promotional video - Chinese version (with bilingual subtitles)

• Summarize 2022 and welcome 2023! iMeta's 2022 Best Review Selection

• iMeta | In 2022, 60 papers were published and cited 340 times, and it ended perfectly, because 2023 will be more exciting with you

• 2023 China Gut Conference｜iMeta special issue call for papers in progress!

• iMeta | Huang Yuan/Deng Yue/Su Zhanhao/Xin Fengjiao-Cardiovascular Disease and Gut Microbiome Special Issue Call for Papers

• 26 editorial board members of iMeta journals selected as 2022 Global Highly Cited Scholars

• iMeta Science Editor Recruitment Notice (Home Office, Flexible Work)

• iMeta is included in DOAJ database! (2022/10/17)

• How iMeta can be quickly retrieved in CNKI

• iMeta | Cited 500 times, published 85 articles, immediate index 5.88, 100 citations took 38 days (2023/2/26)

• iMeta | Cited 400 times, published 71 articles, immediate index 5.63, 100 citations took 36 days (2023/1/19)

• iMeta | Cited 300 times, published 60 articles, immediate index 5, 100 citations took 49 days (2022/12/14)

• iMeta | 200+ citations, immediate index 3.98, 54 days to 100 citations (2022/10/26)

• 3 articles of iMeta journals were included in PubMed

• Highlights of iMeta's inaugural publication-Explore the unknown, never stop (global youth editorial board's blessing)

• iMeta high starting point periodical inaugural meeting and academic seminar successfully held: promotional film, live video, report live playback

• Recruitment of young editorial board members of iMeta journals (positioning IF>15)

• iMeta | Yao Yanpo/Ju Feng/Cui Li/Niu ​​Ben presided over the Soil Environmental Biosafety and Health Special Issue Call for Papers

• iMeta | Lou Yilai/Mendes/Kudrin chaired the BRICS Soil Micro-Food Web Special Issue Call for Papers

• September 2022 Updated Scholarly Publishing Transparency and Best Practice Codes

• iMeta | Baidu authentication completed, search for "iMeta" directly to the homepage of the publisher and the submission link

• iMeta | International Standard Serial Number ISSN print version officially confirmed, double ISSN application completed

• iMeta wishes you a Happy Chinese New Year!

• iMeta | January 2023 Development Report

iMeta Highly Cited Papers

• Xinong Jiaoshuo/Wei Gehong et al.-Relationship between soil fungi and bacterial community construction in arid ecosystems

• Network Analysis Platform iNAP Graphic/Video Tutorial

Bioinformatics/Microbiome Journal Recommendations

• Bioinformatics/Microbiome Journal Recommended: mBio

• Recommended by bioinformatics/microbiome journals: mSystems

• Bioinformatics/microbiome journal recommendation: ISME Journal

• Bioinformatics/microbiome journal recommendation: Microbiome

• Bioinformatics/microbiome journal recommendation: Genome Biology

• Recommended by bioinformatics/microbiome journals: Genome Research

• Bioinformatics/microbiome journal recommendation: Nature Biotechnology

• Journal Alert: Is Microbiology Spectrum a 9-point journal? Maybe only 3 points this year

iMeta related information

• amazing! Articles published by iMeta were downloaded 104,215 times in 166 countries and regions! A maximum of 10,000+ person-times for a single article!

• iMeta | For every hundred citations, the immediate index is > 2 times for journals such as ISME and NAR

• iMeta | English new media Twitter (twitter) homepage has more than 1,000 followers (22/10/1)

• The number of followers on the iMeta public account exceeds 10,000

• iMeta | FSCapture report screen recording and video editing (video tutorial)

• iMeta | EndNote to adjust the perfect citation format tutorial

• Publons: a platform for article review and editorial certification

• How to submit a paper to iMeta Journal? ScholarOne Submission and Review System Author Use Tutorial

• Report video recording: Tencent meeting screen recording + portrait picture-in-picture special effects

• High-impact journal iMeta sets sail (microbiome & bioinformatics)

• iMeta is included in Scopus database!

• iMeta enters the ResearchGate academic social platform to help the international development of journals

• iMeta: Indexed by Google Scholar

• iMeta Journal Submission and Review System ScholarOne Officially Launched

• 12 editorial board members of iMeta journals were selected as Clarivate Analytics' 2021 Highly Cited Scholars

• iMeta Metagenome & Bioinformatics Journal - Background and Introduction

• iMeta journal consultant James M Tiedje was elected as a foreign academician of the Chinese Academy of Sciences

• Analysis of SCIE journals in mainland China: how many journals? How many posts? How much involution has been solved? where is the future

• Analysis of SCIE journals in the field of microbiology (40 in the UK and US, 0 in mainland China)

• How to solve the dilemma of 95% of SCI papers outflow in China

• Interview with Wiley Open Science Ambassador——Liu Yongxin

• iMeta's 2022 Best Method Selection

• iMeta's 2022 Best Research Selection

• iMeta's 2022 Best Review Selection

• iMeta's 2022 Best Graphic Abstract Selection

• Results of iMeta's 2022 "Best Review" Selection

• iMeta's 2022 "Best of Research" Selection Results

• iMeta's 2022 "Best Methods" Selection Results

iMeta latest article Chinese version + video

• iMeta | Ding Wubin from the Salk Institute develops a python package tutorial for visualizing multimodal genomics data

• iMeta | Zhang Weipeng Group of Ocean University of China reveals the mechanism of biofilm assembly on the surface of marine microplastics

• iMeta | Professor Li Wenjun's team from Sun Yat-Sen University describes the culture strategy of prokaryotic microorganisms in different extreme environments

• iMeta | Qi Suhua/Gu Bing/Luo Lan/Wang Liang-Reveal that maca-derived extracellular vesicles can promote the release of serotonin and improve depression through the brain-gut axis

• iMeta | University of Wisconsin Zhou Zhichao develops modular tools to study viromes

Volume 2 Issue 2 (2023.5)

• iMeta Journal Volume 2 Issue 2 Cover: The Gut Microbiome Song

• iMeta | Hu Yongfei Group of China Agricultural University reveals the developmental trajectory of chicken gut microbes and its relationship with host metabolism

• iMeta | Liu Zhihua from Southern Medical University reveals that high-salt diet induces synapse loss and memory impairment

• iMeta | Du Juan's team at Karolinska Institutet in Sweden reveals that the salivary flora of patients with cervical dysplasia is altered and affected by conization treatment

• iMeta | Citing 7000+, Hyprologis Chen Shifu released a new version of fastp, which can process FASTQ data faster and better

• iMeta | Huashan Hospital Affiliated to Fudan University Confirms the Existence of Intratumoral Bacteria in Adrenocortical Carcinoma and Correlates with Prognosis

• iMeta | Yang Ruifu Group of the Academy of Military Medical Sciences developed IMBEC technology for the isolation of pathogenic commensal bacteria in patients with colorectal cancer

• iMeta | Chu Haiyan Group, Nanjing Institute of Soil Science, Chinese Academy of Sciences develops a method for quantifying microbial community-level biological associations

• iMeta | Yang Cao Group of Huazhong University of Science and Technology reviewed the interaction between extracellular vesicles and microbiome: a new strategy for disease treatment

• iMeta | Han Xinhui's group from Northwest A&F University reveals the impact of precipitation changes on the complexity and multifunctionality of soil microbial networks

• iMeta | Zhang Yanqiong/Xu Haiyu/Zhou Xuezhong jointly developed ontology representation, enrichment analysis and similarity calculation evaluation based on SoFDA disease-syndrome-prescription association

• iMeta | Yao Wen Group of Henan Agricultural University develops an interactive web application for drawing Circos diagrams

• iMeta | Xiaoli Wu/Liwei Xie review Gut microbiota may serve as a common hub in the pathogenesis of schizophrenia and obesity

• iMeta | Yang Jun's team from the Institute of Urban Studies, Chinese Academy of Sciences reveals the impact of microbial migration in urban parks on biodiversity and ecological functions

• iMeta | The latest review of "interplastic" microbes from Wang Jie's group at China Agricultural University

• iMeta | University of Groningen Fu Jingyuan's group published a review on Nature's study on the spread of microbial strains

• iMeta | Xie Liwei and Ma Ying from Southern Medical University jointly discovered the changes in the structure of the intestinal microbial network in newborns

• iMeta | Research on Misuse of Reporter Score in Microbial Enrichment Analysis by Wu Dingfeng of Zhejiang University and Liu Lei of Tongji

• iMeta | Academician Yin Yulong/Zheng Dawei Yongjun and others reviewed the research progress of probiotic fermentation of Chinese herbal medicine

• iMeta | An Overview of Host-Derived Metabolic Molecules Regulating the Gut Microbiota

• iMeta | Zheng Jusheng's team at Westlake University: Cohort Study Plan for Gestational Diabetes Mellitus

Volume 2 Issue 1 (2023.2)

• iMeta Journal Volume 2 Issue 1 Officially Published Online

• iMeta Journal Volume 2 Issue 1 Cover Officially Published

• iMeta | Zhang Dong, a young researcher at Lanzhou University: Statistical analysis of molecular phylogenetics and phylogenetic trees using PhyloSuite

• iMeta | Cui Hanbin's team from the First Affiliated Hospital of Ningbo University reviewed the research progress of intestinal microbes and flora metabolites related to ischemic heart disease

• iMeta | 2022 iMeta Progress and Reviewer Acknowledgments

• iMeta | Zhou Shiliang's team from the Institute of Botany, Chinese Academy of Sciences and Liu Yanlei's team from Hebei Engineering University revealed the pattern of plant species diversity and its influencing factors in the eastern section of the modern Silk Road

• iMeta | Easy Amplicon: An easy-to-use, reproducible workflow for microbiome amplicon analysis

• iMeta | Li Xiangzhen/Yao Minjie develop microbial co-occurrence network comparison process

• iMeta | OmicStudio: a composable, instant-feedback bioinformatics cloud platform that generates high-quality, publication-quality graphs

• iMeta | The Cao Weidong Group of the Institute of Resource Planning, Academy of Agricultural Sciences reveals the role of planting and using leguminous green manure endogenously to drive soil authigenic nitrogen fixation

• iMeta | North Chinese Medicine Li Xiaojiaoyang Group Review Decoding the role of immune T cells-a new field for improving metabolism-related fatty liver disease

• iMeta | Yang Yuyi Group of Wuhan Botanical Garden, Chinese Academy of Sciences explores the differentiation strategy of plankton to cope with the intensification of algal blooms in urban lakes

• iMeta | Liu Yongqin's group at Lanzhou University reveals the impact of plant colonization on the dynamics of microbial communities at glacier fronts

• iMeta | Wei Zhong Group of Nanjing Agricultural University develops a high-throughput rapid detection platform for multi-pathogenic biological contamination

• iMeta | Xia Yu Group of SUSTech reviewed strategies and tools for second and third generation metagenomic analysis (Illumina & Nanopore)

• iMeta | Zheng Qingfei Group of The Ohio State University Publishes a Review of Multi-Omics Methods to Study the Tumor Microbiome

• iMeta | Team Liu Jian from Shandong University – Salinity stress weakens the Matthew effect in the microbial world

• iMeta｜Yangyu Liu Group of Harvard Medical School Reveals the Challenges of Ecological Dynamics to Microbe Traceability

• iMeta｜Jinan University Chen Jiali/Bai Weibin reviewed the interaction mechanism between high-fat diet-mediated intestinal bacteria disorder and chronic diseases

• iMeta | Liu Hongwei/Zhang Haiyang, Western Sydney University - Warm and dry environments select bacteria with smaller genomes

• iMeta｜Nanjing Medical University Liu Xingyin Group developed a new method for the absolute abundance of microorganisms (QMD)

• iMeta | Songzhe Fu from Dalian Ocean University and Qian Yang from Ghent University develop a workflow combining metagenomic sequencing and flow cytometry

• iMeta | Wang Yunqiang's group from the Institute of Earth Environment, Chinese Academy of Sciences analyzed the life history strategies of grassland soil microorganisms

• iMeta | Liu Qing Group of Xiangya Hospital-Pan-cancer Analysis Reveals Clinical and Molecular Characteristics of Copper Death Regulators

Volume 1 Issue 4 (2022.12)

• iMeta | Volume 1, Issue 4, 20 articles from 8 countries are officially released (2022.12)

• iMeta | Prokaryotic microorganism pan-genome and genome analysis platform IPGA

• iMeta | Wu Yonghong Group, Nanjing Institute of Soil Science, Chinese Academy of Sciences reveals geographical imprints and ecological functions of biotic and abiotic components of periplexus

• iMeta | mibPOPdb: Microbial degradation database developed by Zhang Houjin, Huazhong University of Science and Technology

• iMeta｜Liu Shuangjiang Group, Institute of Microbiology, Chinese Academy of Sciences released the resource library and strain-level metabolic profiles of human Lachnospiraceae strains

• iMeta | Jiang Jingzhe from the South China Sea Institute of the Academy of Water Sciences/Shi Mang from CUHK reveals a new type of RNA virus in oysters using the virome

• iMeta | Yangdong Group of China National Agricultural University reveals the regulation of dietary fiber chemical structure on gut microbes

• iMeta | Tongji University Zhu Ruixin's team targeted cornerstone strains to restore dysregulated butyrate-producing bacteria in non-alcoholic fatty liver

• iMeta | Cui Jie Group of Shanghai Pasteur Institute of Chinese Academy of Sciences summarizes the twenty-year research on the marine RNA virome

• iMeta | Du Yuzhou's team from Yangzhou University reveals the assembly mechanism of two insect gut microbial communities with the same food in the same domain

• iMeta | The latest article of ggtree from Yu Guangchuang Group of Southern Medical University - the data structure of phylogenetic tree storage and visualization

• iMeta | The Chu Haiyan Group of the Southern Institute of Soil Sciences, Chinese Academy of Sciences reveals the stabilizing effect of fungi on multi-kingdom communities in alpine timberlines

• iMeta | Zhongnong Ma Xi Group reviews the interaction between intestinal flora and stem cell nests to maintain intestinal homeostasis

• iMeta | Degas collaboration reveals genetic diversity and community composition of kudzu mycorrhizal fungi

• iMeta | Huake Ningkang and others have opened up the identification of traditional Chinese medicine components and network pharmacological analysis, helping the standardization, digitalization and internationalization of traditional Chinese medicine

• iMeta | Zhejiang University Jiangchao Group Review Environmental Exposure Group Panoramic Landscape

• iMeta | Zhang Yang Group of Chengdu University of Traditional Chinese Medicine develops a database of anti-coronavirus Chinese medicine and its mechanism and efficacy

• iMeta | MetaTrass, a high-quality metagenomic assembly tool based on co-labeled sequencing data from Fan Guangyi group of Qingdao Huada University

• iMeta | Ma Yonghui Group of Xiamen University explores the ethical cognition and attitude of bacteria donors towards intestinal bacteria transplantation

Volume 1 Issue 3 (2022.9)

• iMeta | Volume 1, Issue 3, 14 articles from 8 countries are officially released (2022.9)

• iMeta | Nannong Shen Qirong team releases microbial network analysis and visualization R package ggClusterNet  tutorial to calculate network stability

• iMeta | Gu Zuguang, German National Cancer Center, published a complex heat map (ComplexHeatmap) visualization method. Is this the shortest citation in the world?

• iMeta | Zhang Jiachao Group of Hainan University - Inflammatory Bowel Disease Prediction Model Based on SNV Gene Markers of Gut Microbiota

• iMeta | Dai Lei Group of Shenzhen Institute of Advanced Technology developed a strain analysis tool video tutorial that can simultaneously extract the composition and genetic composition of co-existing strains

• iMeta | Sangerbox: Interactive and integrated clinical bioinformatics analysis platform

• iMeta | Is short-read amplicon sequencing suitable for prediction of microbiome function?

• iMeta | Lin Yanbing/James M. Tiedje/Gu Jie et al reveal the regulatory effect of flora on the parasitic plant Liedang

• iMeta | Donnong Wu Fengzhi/Nan Nongwei Zhong revealed the mechanism of biochar inhibiting crop soil-borne diseases

• iMeta | Chen Chengjie/Xia Rui from South China Agricultural University released a simple method for constructing Circos diagrams with TBtools

• iMeta | Ye Mao/Shi Yu et al. review the dynamic shuttling and ecological function of intracellular and extracellular genes in the environmental microbiome

• iMeta | South China Normal University Zhang Wang's Group Reviews the Hidden Links Between the Human Lung Microbiome and Human Health and Disease

• iMeta | Li Ji Group of Zhongnong reveals the structure of tomato microbiome in long-term positioning experiment of organic agriculture

• iMeta | A comparative study of flow cytometric taxonomic communities and shotgun viral metagenomics in urban wastewater treatment plants in Singapore

Volume 1 Issue 2 (2022.6)

• iMeta | Volume 1 Issue 2 Officially Released Online (2022.6)

• iMeta | The Deng Ye Group of the Ecological Center of the Chinese Academy of Sciences released the microbiome network analysis platform iNAP

• iMeta | Kong Xiangqing's team from Nanjing Medical University created eHypertension, a prospective multi-omics longitudinal essential hypertension cohort

• iMeta | Majorbio Cloud: One-stop multi-omics data analysis platform

• iMeta | Chen Lianmin/Kong Xiangqing from Southern Medical University revealed the potential impact of intestinal bacteria on complex diseases from the perspective of genome function

• iMeta | Chen Feng Group of Peking University reviewed the standardization research of oral microbiome: from technology-driven to hypothesis-driven

• iMeta Cover | Metaproteomics analysis one-stop tool set iMetaLab Suite (Figeys Group, University of Ottawa, Canada) 1 hour video tutorial + PPT

• iMeta | Chen Feng/Chen Zhibin of Peking University published the experimental method of sampling various parts in oral microbiome research (Protocol)

• iMeta | Ding Xia, Nanchang University, et al.-Effects of aquaculture system on the microbiome and intestinal metabolome of soft-shelled soft-shelled turtles

• iMeta｜Zhong Yang Quanquan of Xigong University et al.-Response mechanism of root flora along environmental gradient

• iMeta | Shenzhen Advanced Institute Ma Yingfei group developed a method based on neural network analysis of intestinal flora

• iMeta | Zeng Zhenling/Xiong Wenguang, South China Agricultural University, etc.-Study on the coexistence of drug resistance genes between pet dogs and owners in the family

• iMeta | Nanopore Sequencing of SUSTech Xiayu Group Reveals Microorganisms Can Mitigate Greenhouse Gas Emissions from High Altitude Permafrost

Volume 1 Issue 1 (2022.3)

• iMeta | Volume 1 Issue 1 is officially released online (2022/3/28)

• iMeta | imageGP

• iMeta: Integrating meta-omics to re-understand life and environmental science

• iMeta | Wu Qinglong/Wang Mingfu/Liu Jinxin et al. - Looking at human adaptation to plateau diet from the perspective of intestinal flora

• iMeta | Applications of De Bruijn Diagrams in Microbiome Research

• iMeta | SUSTech's Song Yi group reviews the genetic basis of plants seeking help from the microbiome under adversity stress

• iMeta | Huazhong University of Science and Technology Ningkang Group Review Metagenome Quantitative Analysis for Protein Structure Prediction

• iMeta | 电子科大林昊组开发蛋白质赖氨酸乳酸化位点预测工具DeepKla

• iMeta | 青岛大学苏晓泉组开发跨平台可交互的微生物组分析平台

• iMeta | 西农韦革宏团队焦硕等-土壤真菌驱动细菌群落的构建

• iMeta | 哈佛刘洋彧等基于物种组合预测菌群结构的深度学习方法

• iMeta | 中科院李小方等膳食甘草促进小鼠镉解毒并调节肠道菌群代谢

• iMeta | 浙大倪艳组MetOrigin实现代谢物溯源和肠道微生物组与代谢组整合分析 视频教程

跟着iMeta学做图

• 冲击图展示菌群随盐度的变化

• 山峦图展示微生物丰度随盐度增加的动态变化

• 环境因子在地图上的可视化

• 如何用python画世界地图，并用不同的颜色展现每个国家的数据？

• ggplot2绘制相关性分析线面组合热图

• 双侧柱状图展示具有正负相关性的类型数量

• 跟着iMeta学做图｜用三元图展示微生物种群相对丰度

• 分面箱线图展示alpha多样性并用标注差异分析结果

• ggplot2包绘制棒棒糖图展示变量间的相关性

• 绘制基于非加权Unifrac距离的主坐标分析PCoA图

• ComplexHeatmap包绘制热图展示不同样本物种相对丰度

• 用ggClusterNet绘制共现网络（Co-occurrence Network）

• circlize绘制环状热图展示细菌功能聚类分析

• NMDS分析展示群落beta多样性

• 群落微生物与环境因子相关性分析

• circlize绘制和弦图展示样本物种相对丰度

• ggplot2绘制多个饼图展示菌群物种组成

• 微生物组共现网络（Co-occurrence Network）绘制

• ggplot2绘制曼哈顿图展现物种丰度差异

• 跟着iMeta学做图｜ComplexHeatmap绘制多样的热图

• 世界海拔地图

• 使用ImageGP绘图热图Heatmap

• 使用ImageGP绘图富集分析泡泡图

• 使用PMS分析微生物组(图文+视频)

• DeepKla预测赖氨酸乳酸化位点

ImageGP使用教程

• 分享高颜值免费在线绘图介绍和使用的一次视频直播

• Video Demo | How to interpret and draw a phylogenetic tree online with attribute annotations?

• Video demonstration | WGCNA weighted co-expression analysis online operation

• Video Demo | ImageGP Redraws WGCNA Trait Association Heatmap

• Video Demo | Online Differential Gene/Species Analysis

• Video demonstration | Draw a volcano map and mark the name of the gene

• Video Demo | BIC Maps Differential Gene Volcanoes Without Code

• Video demonstration | Click the mouse to draw GO/KEGG enrichment analysis bubble diagram online

• Video demonstration | Meta-gene map online drawing

• Video demo | High-value free online drawing tool function preview and help preview

• Video Demo | Easily Draw Paired Wiring Box Diagrams Online

• Simple and Powerful Online Drawing

• Simple and Powerful Online Drawing - Upgraded Version

• Simple and Powerful Online Drawing - 3rd Edition

• Online WGCNA analysis (directly generate interactive result report)

• Online differential gene analysis (supports automatic and specified batch correction)

• This tool can combine parameters to draw two kinds of single-cell Marker display graphs

• High-value free online SCI drawing tool adds upload function

• Several small tools have been added to ImageGP

• How to ensure that the same group of samples in the article have the same color in different subgraphs?

• Recommend a master of biometric analysis tools

• Video demo | New features | Enhanced online LEFSe analysis and visual identification of marker genes or species

• Venn network display enrichment analysis results

• Single gene set enrichment analysis bubble plot drawing

• Bubble diagram drawing and display of multiple gene set enrichment results

• No code to adjust the clustering heatmap branch order

• Gene expression heatmap clustering and adding row and column annotations

• Heatmap to draw a Happy May Day

• Draw a heat map easily

• Continuing from yesterday's article, mark the gene name on the volcano map

• Draw a volcano map and mark the name of the gene

• Draw gene expression boxplot without code

• What is a 45 degree sloped volcano map?

• Directly draw a "volcano map" inclined at 45 degrees online

• Online PCoA analysis and related statistical tests

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"Microbiome Data Analysis" monograph

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• 112.CMJ: Guidelines for Human Microbiome Research Design, Sample Collection, and Bioinformatics Analysis

• 121. Build a microbiome analysis platform with personal computer (Win/Mac)

• 122. Introduction to Linux system and Shell command line, embark on the road of data analysis

• 123. Introduction to R and Statistical Plotting

• 211.Alpha Diversity Boxplot (Sample Chapter, 11 Figure 2 Video)

• 212. Alpha Diversity Dilution Curve of Sample Size and Sequencing Depth

• 213. Venn Diagram and Set Diagram (Venn&Upset)

• 221. Beta diversity PCoA and NMDS sorting

• 222. Beta Diversity Restricted Sorting CPCoA/CCA/RDA/LDA

• 223. Principal Component Analysis PCA

• 231. Bacteria species composition stacked histogram, chord diagram, word cloud

• 245. The heat map shows the species and functional abundance or absence and distance matrix of the microbiome

• 246. The application of ternary graph and actual drawing

• 251. The Simplest Network Drawing Method in the Whole Network, Xiaobai Gospel Packet Learning Packet

• 252. Microbial Network Diagram Reflecting Differences Between Groups OTU Modules

• 341. Introduction to Microbiome Research Technology Based on High-throughput Sequencing

• 342. Experimental design of microbiome research based on high-throughput technology

• 343. General Ideas for Microbiome Research Writing

• Ju Feng Group of West Lake University: Analysis ideas and common tools of environmental macroviromics

• Ju Feng Group of West Lake University: Examples and new discoveries of metagenomics of environmental microorganisms

• Windows 10 installs the Linux subsystem Ubuntu 20.04LTS, easy to use bio-information software, and kills virtual machines efficiently

• Introduction and latest impact factors of journals in the field of metagenomics

Academic report recording, PPT sharing

• iMeta Tsinghua Report Video | Liu Yongxin - Metagenome Data Analysis and Science Communication (1h)

• 75-minute introduction to microbiome data analysis and interpretation of results—Liu Yongxin (Hefei, June 23, 2021)

• Youth Life Science Forum Report: Amplicon and Metagenome Data Analysis and Visualization Process—Liu Yongxin (Beijing 210606)

• Opportunities and Challenges of Metagenome Data Analysis—Liu Yongxin (Beijing, December 8, 2020)

• Liu Yongxin: 20 minutes to explain microbiome data analysis and visualization

• Nanjing Yuan Jun/Wen Tao ISME: Accurately Predict the Occurrence of Soil Fusarium Wilt Based on Big Data Integration

• Wang Jinfeng Gut of Beisheng Institute: Time-series microbiome data reproduces the dynamic process of biofilm assembly PPT+video

• Ju Feng, West Lake University: Environmental Microbial Metagenomics (report video + PPT, November 23)

• December 8, 2020 Report by Liu Yongxin, Chinese Academy of Sciences: Opportunities and Challenges of Metagenome Data Analysis

• Amplicon and metagenomic data analysis process and visualization scheme—Liu Yongxin (Nanjing, October 27, 2020)

Conferences, Special Issues, Recruitment

training meeting

• January 6-8, Clinical Genome/Exome Data Analysis Practical Technical Seminar

• February 17-20, Advanced Transcriptome Analysis and R Language Data Visualization

• July 21-23, Microbiome-Metagenomic Analysis

• April 8-10, National Symposium on Biosafety and Health of Soil Environment

• On May 20-22, the opening ceremony & plenary session will be a preview

• October 13-15, Microbiome - Amplicon 16S Analysis

• 冠军出炉！2022『猛犸杯』国际组学数据创新大赛圆满收官

• 5月19日,中国肠道大会宏基因组培训-刘永鑫/王军/戴磊连讲7小时

专刊征稿

• Agronomy|3.9分JCR1区征稿/37天见刊-宏基因组解析农业微生物组专刊(刘永鑫/于鹏)

• 程旭/王蒙岑/袁梦婷/李建刚/熊武客座主编Frontiers根际微生物组专刊征稿(IF>6)

• JoVE微生物组专刊征稿，写方法拍视频教程发SCI

人才招聘

• 深圳基因组所刘永鑫组招聘博士后4名(3年100万+文章奖励+项目绩效)

• 深圳基因组所刘永鑫组诚聘科研助理(生物信息本科/微生物组相关硕士)

• 深圳基因组所刘永鑫组诚聘副研究员

• 基因组所刘永鑫组招收客座研究生/海外联培博士(荷兰瓦大/澳州莫道克/比利时列日/爱尔兰都柏林)

• 基因组所食品科学中心贾耿介课题组诚聘博士后

• 生信人才，你的舞台——基因帮诚招英才！

• 南科大翟继先组招聘，博士生8万+，博后34万+

• 西奈山医学院房刚组招聘博后—宏基因组与表观基因组

• 林科院亚热带所袁志林组招聘博后—林木根际微生物

• 中山大学生科院骆观正教授课题组诚聘博士后及副研究员

广告合作

• 4 篇 NAR | 生物大数据时代，如何做好数据管理和再利用，发IF10+的数据库文章？

科研经验

• 用ChatGPT 帮我写段生物信息代码

• ChatGPT 给出的的代码不太完善，如何请他一步步改好？

• 代码看不懂？ChatGPT 帮你解释

• ChatGPT也有犯晕的时候

• 发表16篇Nature、14篇Science！这位顶尖学者告诉你论文十法

• PubMed插件：分区、影响因子和即时IF一目了然

• 我的博士之路（壮根美颜-康亚龙）：五年读博路，苦熬曙光明

• Nature ：读博之前应该知道的二十件事情

• 研究生如何走出“迷茫”？

• Science：“每周工作进展汇报”在博士培养中的作用

• 学术界职称与凡人修仙传等级对应关系

• 论文返修与校对的经验教训

• 如何制作高质量的图文摘要（Graphical Abstract）

• 谷歌学术上网和查文献、引用、作者和领域分析指南

• 研究生新生进入实验室后，如何成长？5点建议分享

• Academician Zhang Qifa's heartfelt words are worthy of every master's/doctor's careful reading!

• Sub-journal of Nature: Do you want to become a bioinformatician?

• Full template for SCI paper submission

• 10 heart-to-heart sharing by a SCI doctor - the "Tao" of macro-omics research

• Which level is higher between 985 assistant professors and Erben professors?

• Interview with Wang Hongwei, Dean of Tsinghua Life Sciences: Faced with these situations, we must have the courage to say "no"

• Ten tips from postdoc to PI

• Nature: 16 criteria for a good mentor

• Graduate students, advisors are not your nanny

• 7 Facts and 5 Proposals About Gut Microbiome Research

• This article tells the true meaning of getting along with graduate students and tutors

• 24 Abilities that Graduate Students Should Exercise

• Do you want to study for a Ph.D., and how to graduate smoothly and find an ideal job after a Ph.D.? Five most down-to-earth advice

• Nature: Four golden lessons for doctoral students, recommended by Yan Ning

• Why do I attend so many academic conferences and still get nothing?

• The ultimate trick - how to gain something at an academic conference?

• AI Learning Tutorial 1 Basic Graphic Drawing 2 Mode Figure 3 Typographic Drawing Coronavirus

• PPT drawing schematic video + text version - learn in one article

• How to ask questions gracefully

• My Bioinformatics Journey

• My struggles with the development of TBtools

• Public number search method Daquan

• The trilogy of scientific research team growth: 1 cloud note 2 cloud collaboration 3 official account

• Literature reading 1GeenMedical 2SCI-HUB

• Life letter programming template   Perl  Shell  R

• Program Learning of Bioinformatics

• Thesis Figures, the secret you must know

• A comprehensive analysis of the principle of chart color application

• Raw Data Upload NCBI SRA Tutorial

• China Nucleic Acid Database GSA Data Submission Guidelines Amplicon 16S Example Metagenome Example

• Guidelines for Submitting Microbiome Data from the National Microbiological Science Data Center: Submitting Article Attachments

• Endnote X8 cloud synchronization: read literature anytime with internet

• Excel drawing new height-EasyCharts

• There is only one iSlide between you and a PPT master

• Windows10 Remote Desktop Ubuntu

• Students who want to post high-scoring papers come here, here are 10-scoring magazines and editors to learn about!

• Why is the impact factor of the new publication Microbiome so high? Professor Jacques Ravel, editor-in-chief, will tell you

• SCI paper writing 1. Three-paragraph structure of the paper 2. Logical analysis of the introduction

• PDF editing processing Compressed PDF file size to meet upload requirements

software process

• Chen Chengjie, Xia Rui: Data analysis tool TBtools introduction and operation video + official account/community

• Graphpad drawing beginners biostatistics drawing advanced

• TBtools - Bio-information widget used by more than 10,000 people

• BIOM: Biological Observation Matrix - A Common Data Format for Microbiome Data

• STAMP——Statistical analysis of differences between microbiomes Concise tutorial Chinese help document

• FUNGuild: fungal functional annotation

• Online RaxML to build a phylogenetic tree

• MetaboAnalyst 4.0, an upgraded metabolomics research tool

• Genevestigator: Find gene expression in published studies

• psRobot: Plant Small RNA Analysis System  

• RepeatMasker: Genomic Repeat Sequence Annotation

• Genome Annotation 1 Repeated Sequence 2 Non-coding and Coding Gene 3 Functional Annotation Prokka

• Canoco5 draws beautiful DCA or CCA diagrams

• A script for complete analysis of bacterial genomes

• Theory and Basic Implementation Process of Structural Equation Modeling (SEM)

• What you need to know about using structural equation modeling (theory)

• Identification and handling of batch effects in high-throughput data

Software Basics Must-Learn Series

• Linux command screen—terminal switching, working environment saving, screen synchronization, network disconnection prevention

• Play fancy screenshots and screen recordings——FastStoneCapture User Guide

• Nature Method: Bioconda solves the trouble of biological software installation

• Conda software installation: virtual environment, software channel, accelerated solving, cross-server migration

• The software cannot be installed, it may be because the network speed is slow! Conda/R/pip/brew and other domestic mirrors

• Data quality control software - fastQC

• A powerful tool to integrate QC quality control results - MultiQC

• Extremely fast FASTQ file quality control + filtering + correction fastp

online software

• More and more magazines use webp to store images, this tool can convert them to PNG online

• What should I do if the picture quality is low? This site is great!

• Recommend a one-stop drawing tool that may be the most complete Venn diagram

• High-value free online SCI drawing tool adds upload function

• The National Microbiological Science Data Center launched a free one-stop bioinformatics analysis cloud platform

• Online differential gene analysis (supports automatic and specified batch correction)

• Microbiome database: a one-stop environmental genomics data cloud platform has been updated!

AI Series Video Tutorials

• 1 Thesis vector text, line editing

• 2 Thesis graphic editing and typesetting

• 3 After typesetting, graphics export like this Tiff/PNG

• 4 Show Mesh Remove Clipping Mask and Background

• 6 Direct selection tool to delete whiteboard

• 7Magic Wand Tool Batch Operation

• 8 several shortcut keys

• 9 Placement and fine-tuning of graphs

• 10 Setting fonts and fine-tuning

• 11 Resizing Objects

• 12 Batch transform single objects selected at the same time

• 13 Select all points

Amplicon analysis

• "Microbiome Analysis" 2018 e-book worth 130 Euros

• Book series "Statistical Analysis of Microbiome Data with R Language" worth 1143 yuan

• Re-read "Quantitative Ecology: R Language Application"

• The 8 most important software or algorithms in the microbiome field in the past ten years

Amplicon Tutorial

• Symposium on Amplicon 16S Analysis——Background Introduction

• Amplicon Chart Interpretation - Understanding Article Ideas

• Amplicon analysis process - grasp the analysis details

• Amplicon Statistical Mapping - Impact High Score Articles

• 16S function prediction 0 overview   1KO pathway PICRUSt  2 element cycle FAPROTAX  3 phenotype bugbase 4KO pathway Tax4Fun Tax4Fun2

• PICRUSt2: OTU/ASV and other 16S sequences predict metagenomics at will, and the reference database is increased by 10 times. NBT article interpretation software is used

• CHM: FishTaco associates the function of the sample with the corresponding microorganism to obtain the driving factor of the functional change

• 水稻微生物组时间序列分析 1模式图与PCoA  2a相关分析 2b散点图拟合 3冲击图 4随机森林回归

• Nature Method：Rob Knight团队开发Striped UniFrac算法分析微生物组大数据

QIIME2教程(2021.2)

• NBT：QIIME 2可重复、交互式的微生物组分析平台

• 1简介和安装Introduction&Install

• 2插件工作流程概述Workflow

• 3老司机上路指南Experienced

• Genome Biology：人体各部位微生物组时间序列分析

• 4人体各部位微生物组分析Moving Pictures

• 5粪菌移植分析练习FMT

• Microbiome：粪菌移植改善自闭症

• 6沙漠土壤分析Atacama soil

• mSystems：干旱对土壤微生物组的影响

• 7帕金森小鼠教程Parkinson’s Mouse

• Cell：肠道菌群促进帕金森发生ParkinsonDisease

• 8差异丰度分析gneiss

• 9数据导入Importing data

• 10数据导出Exporting data

• 11元数据Metadata

• 12数据筛选Filtering data

• 13训练特征分类器Training feature classifiers

• 14数据评估和质控Evaluating and controlling

• 15样品分类和回归q2-sample-classifier

• 16纵向和成对样本比较q2-longitudinal

• 17鉴定和过滤嵌合体序列q2-vsearch

• 18序列双端合并read-joining

• 19使用q2-vsearch聚类OTUs

• 20实用程序Utilities

• 21进化树推断q2-phylogeny

• 22命令行界面q2cli

• 23图形界面q2studio

• 24Python命令行模式Artifact API

• 25可用和开发中插件AvailableFuturePlugins

• 26 Developing a new plug-in DevelopingPlugin

• 27 Semantic type Semantic

• 28CommunityCommunity

• 29 Reference Database DataResources

• 30 Supplementary Resources SupplementaryResources

• 31 Noun Glossary

• 32 How to write methods and cite Citing

Yishengxin - Amplicon Tutorial

• 01-Background introduction

• 02- Fungal primer selection

Webserver online analysis platform

• This Venn network is beautiful! Take you to draw in 3 minutes!

• NAR | Hu Shengwei/Ni Wei/Chen Tong-Animal macromicrobiome composition and function comprehensive database CRAMdb released

• Microbiome web tool MicrobiomeAnalyst - teach you zero-based microbiome data analysis and visualization Nature sub-journal: official website tutorial Chinese version, practical tutorial,  NAR: original text interpretation

• NAR: gcMeta - Global microbiome data storage and standardized analysis platform

• NAR: rrnDB-16S copy number correction database

• METAGENassist helps you handle the graphic needs of metagenomic analysis

• SILVAngs: 16S/18S online analysis 1  2

• Microbiome database (http://egcloud.cib.cn) officially launched

• MetaCoMET - an online tool for core microbiome analysis

Related software and database tutorials

• Amplicon Analysis Artifact USEARCH Introduction v11 New Functions v11 Command Encyclopedia OTU Table Extraction otutab_rare Core OTU Identification otutab_core

• Make a USEARCH version of the RDP database for amplicon species annotation

• Amplicon Analysis Artifact VSEARCH Analysis Process 2.8.1 Chinese Help Document

• Nature Methods: Fast and accurate microbial source traceability tool FEAST Phyloseq format uses actual combat original code actual combat

• SourceTracker—microbial source analysis

• Introduction to LEfSe analysis
  Simplify and beautify LEfSe analysis result graph LEFSe optimization result and color matching video tutorial

• DADA2 Chinese Tutorial v1.8

• Microbial Amplicon Database Encyclopedia

• NAR: UNITE ITS Database for Fungal Identification

• MER: Accuracy of amplifying fungal communities based on ITS region markers

• MIMOSA2: Integrated analysis based on microbiome and metabolome data

• Variance decomposition analysis (VPA): Quantifying the proportion of community variation explained by different environmental factors

• FungalTraits: The latest fungal phenotype database beyond FUNGuild

Metagenome analysis

• Microbiome common database domestic backup site

High-scoring article and book recommendations

• Understand the metagenomic analysis routine in one article

• Springer Publishes the Second Edition of the Latest Guidebook for "Metagenomics" Research

• Nature review: 20,000 words guide you to systematic introduction shotgun metagenomic experiment and analysis

• 1 Review, MetaPhlAn2, Kraken, MetaMaps, HUMAnN2, MEGAHIT, MetaWRAP, and the Macro-Epigene Group

• 2 Review, metaSPAdes, IDBA-UD, MetaQuast, Prokka, metaProdigal

• 3 Metagenome quantification, functional annotation and advanced analysis codes

Software Reviews and Introductions

• Cell: Comparison of 20 Metagenomics Species Classification Tools '

• Sub-journal of Nature: Liu Yangyu, Rob Knight, etc. evaluate different metagenomic species quantification methods and their impact on the results

• NBT: Mainstream high-throughput sequencers have released the results of human/bacterial/metagenomic sequencing evaluations, and MGI has performed well

• mSystems: What else can we do beyond shotgun metagenomic sequencing

• Qingdao Institute of Energy proposed a new algorithm DMS for microbiome similarity

• Method innovation: 8 new tools for metagenomic analysis

• MIntO: a modular integrated analysis tool for microbial metagenomes and metatranscriptomes

Tutorial Series

• 2016 Canadian Metagenome Analysis Tutorial

• 1 Introduction - Definitions, Methods and Databases

• 2 Amplicons - Microbial Community Diversity

• 3PICRUSt function prediction

• 4 Metagenome Species Composition and Binning

• 5 Metagenome functional database and pathways

• 6 Metatranscriptome pipeline and functional BBI: Eran Elinav group review using metatranscriptome in microbiome research

• 7 Mining Microbiome Biomarkers

• 4,500 yuan microbiome training materials

• Microbiome Assistant - the most easy-to-learn amplicon and metagenomic analysis workflow

• GigaScience: ASaiM is based on the Galaxy microbiome analysis framework

• Professor of Statistics Department of Stanford University takes you to play microbiome analysis

• Experience summary of more than 30 metagenomic analysis software

• Overview of microbiome data analysis tools | 16S+metagenome+macrovirome+macrotranscriptome

• Nature Protocols: a computational framework for integrated metagenomic, metabolomic and phenotypic analysis

There is a parameter analysis Read-based

• Use of MetaPhlAn2 quantitative article interpretation software for metagenomic species composition based on multi-marker genes

• Functional quantification of HUMAnN2 based on UniRef database 1 Article interpretation 2 Software tutorial 3 Parametric analysis process

• Kraken: Ultra-fast metagenomic sequence classification software using precise alignments

• The use of kraken 1/2 and Bracken in the classification of metagenomic sequences

• Kraken2: Metagenome Rapid Species Annotation Artifact

• Getting Started with Metagenome Annotation and Visualization Artifact MEGAN

Assembly-based without parameters

• 1 Background knowledge - Shell entry and local blast combat

• 2Data quality control fastqc, Trimmomatic, MultiQC, khmer

• 3 Assembling and splicing MEGAHIT (more, faster, better and less) and evaluating quast

• MEGAHIT: an ultra-fast single-node solution for very large complex metagenomic assembly via succinct de Bruijn graphs

• metaSPAdes: a novel multifunctional metagenomic assembly tool

• IDBA-UD: Assembling metagenomic and single-cell data with non-uniform coverage

• MetaQuast: Evaluating Metagenome Assemblies

• 4 Gene Annotation Prokka Prokka: Fast Prokaryotic Genome, Metagenome Gene Annotation Prodigal: Prokaryotic Gene Identification and Translation Start Site Identification  metaProdigal: Gene and Translation Start Site Prediction in Metagenome Sequences

• 5 based on Kmer comparison data set sourmash

• 6 No comparison to quickly estimate gene abundance Salmon Salmon no comparison to rapid metagenomic gene quantification

• 7bwa sequence alignment, samtools view, bedtools abundance statistics

• 8-bin metagenomic binning, MaxBin, MetaBin, VizBin

• 9 Visualization of assembly and binning results—Anvi'o

• 10 Draw a circle diagram - Circos installation and use

Species/function annotation database

• NAR: an integrated ecological and evolutionary framework for querying uncultured viral genomes IMG/VR v3

• NAR|IMG/VR v4: an expanded database of uncultured viral genomes within a broad framework of functional, taxonomic, and ecological metadata

• Briefings in Bioinformatics: Research progress in software and databases related to microbial genomics and functional genomics

• Bioinformatics | Sun Yanni Group of Hong Kong City University develops VirBot, a sequence detection tool for novel RNA viruses

• WebMGA: an ultrafast online tool for cluster annotation of genome sequences

species annotation

• TaxonKit: Small, efficient, and practical NCBI taxonomy data command-line tool JGG | TaxonKit: A practical and efficient NCBI taxonomy data toolkit

eggNOG

• EggNOG functional annotation database online and local use eggNOG 5 database introduction

KEGG

• He developed the encyclopedia of genetics, but his contributions are little known

• How to use KEGG online database

• KEGG functional annotation tool KofamKOALA installation and use

• kofamscan: Annotate the KEGG pathway based on the HMM model

CAZy sugar metabolism

• NAR-2018-dbCAN2 identifies metagenomic CAZYome carbohydrate-associated genes

CARD antibiotic resistance/resistance gene

• Microbiome: Antibiotic Resistance Metrics in Urban Beaches and Sewage

antiSMASH

• antiSMASH: Prediction of microbial secondary metabolite gene clusters  

• NAR: antiSMASH database 2 - secondary metabolite gene cluster prediction

• PPT sharing of research progress on antibiotic resistance genes

• List some databases related to the analysis of secondary metabolite gene clusters

• ARGfams: A Tool and Database Resource for Rapid Annotation of Antibiotic Resistance Genes in Environmental Samples and New Gene Discovery

Boxing/MAG Topics

• Nature sub-journal: Analysis process of mining prokaryotic genome in metagenomics

• Microbiome: Metagenome group box process MetaWRAP introduction installation and database deployment  practice and result interpretation

• NBT: Metagenome "Reading Cloud" 10X database construction + Athena algorithm assembly to obtain high-quality microbial genomes

• DAS Tools: Recovering Genomes from Metagenomes Using Deduplication, Aggregation, and Scoring Strategies

• One article to understand metagenomic binning

• GTDB: Genome taxonomy database, species annotation and phylogenetic tree construction tool GTDB-tk

• CheckM - Bacterial Genome/MAG Integrity and Contamination Rate Assessment

• MaxBin2 - an efficient binning tool

Statistical Analysis and Visualization

• Krona plots species or functional composition circles

• microbiomeViz: Draw Cladogram in lefse results

• Nmeth: DEMIC - predicting bacterial growth rates using metagenomic data

• curatedMD package for mining metagenomic public databases

microbial genome

• Get De Novo Sequencing Analysis of Bacterial Genomes in One Article

• EZBioCloud: 16S and Prokaryotic Genome Species Annotation and New Species Identification

• drep: rapid de-redundancy of microbial genomes - article interpretation + help documents + actual combat

• A sharp tool for microbial taxonomy research: model microbial genome database

• Nature sub-journal: complete classification of bacteria and archaea from domain to species

• NAR: The Institute of Microbiology, Chinese Academy of Sciences released the progress of the global model microbial genome sequencing project

• NC: Chen Yihua Group, Institute of Microbiology, Chinese Academy of Sciences, discovered a novel initiation mechanism for polyketides

• Micro classroom: MUMmer - cloud tool of National Microbiology Science Data Center

• Cai Lei's research group at the Institute of Microbiology, Chinese Academy of Sciences successfully assembled the largest chromosome-level fungal genome to date

Research Hotspots

absolute quantification

• Summary of Methods for Absolute Quantification of Bacteria

• How much do you know about the absolute quantitative study of microorganisms

Reference gene (group) set

latest articles

• NM: human gut archaeal genome set

• NBT: Human Gut Microbiome Reference Genome Collection Covering More than 200,000 Genomes

• NBT: 50,000 Genomes and 12,000 New Species of Earth's Microbial Genomes

• NBT: 4941 Metagenome Assembled Genomes (MAGs) of the Bovine Rumen Microbiome

High Score and Feature Mining

• Nature2019: A new blueprint for the human gut microbiome

• Cell2019: 150,000 human microbial genomes! Ultra-large-scale metagenomic study reveals thousands of new species of human microbes

• Cell2019: Altered Tara2.0 gene expression and community turnover shape the global ocean metatranscriptome

• Cell Sub-Journal 2019: Single genes in the human microbiome reference gene set

training group

• NBT: 1520 genomes of cultured bacteria from the human gut

• NG: How did microbes adapt to plants? Bacterial genomes adapted to plant traits

historical classic

• NC2018: Structure and function of the global citrus rhizosphere microbiome

• PNAS2016: Global biogeography of microbial functional characterization of soil nitrogen cycling

• NBT2014: A reference gene set of tens of millions of genes in the human microbiome

• Nature2010: Construction of human gut microbiome reference gene set based on metagenomic sequencing

virus group

• NAR | Ma Yingfei Group of Shenzhen Advanced Institute released a high-throughput preparation method for chassis phage

• NAR: vRhyme - a bioinformatics tool for sorting viral genomes from metagenomics

• Sub-journal of Nature: The Banfield group at the University of California, Berkeley found that large phages in some freshwater lakes may accelerate aerobic methane oxidation

• PhiSpy: identifying phages in bacterial genomes

• DBSCAN-SWA: one line command to find lysogenic phages

• What's hot: 3 stories overview the leaps and bounds in gut virome research

• Nature: Liang Guanxiang et al. discovered the mode of segmental parasitism of enterovirome in newborns

• Sub-journal of Cell: Human enterovirome is highly diverse, stable and individual-specific

• QB: Virus Sequence Recognition Based on Deep Learning

• Challenges in Virome Research - Related Emerging Technologies

• SCLS: Cui Jie's group at Institut Pasteur reveals the genetic diversity of RNA viruses in marine invertebrates

• eBioMedicine | Cui Jie's team applied single-cell transcriptome technology to highlight the potential function of human endogenous retroviruses in gallbladder cancer

• Front Microbiol | Yuan Lihong from Guangdong Pharmaceutical Sciences/Jiang Jingzhe from Nanhai Institute of Water Sciences-Discussion on the latest classification criteria for RNA viruses

Topic on Three Generation Sequencing

• AS: Wang Jun's research group at the Institute of Microbiology, Chinese Academy of Sciences established mtNGS and mtTGS, a new method for pathogen detection targeting RNA

• Sub-journal of Nature: DNA extraction and metagenomics analysis of three-generation sequencing

• NanoPlot: Three-generation nanopore sequencing data quality assessment

• NBT: Use of OPERA-MS article interpretation software for the second and third generation mixed assembly software of metagenomics

• Nature Method | MetaFlye, the third-generation long-read metagenomic assembly software

• Sub-journal of Nature: Drug resistance analysis software NanoOK RT for third-generation Nonopore sequencing data

• Sub-journal of Nature: Using MinION to rapidly analyze the intestinal flora profile of premature infants and identify antibiotic-resistant pathogenic bacteria

• Sub-journal of Nature: A new method for the detection of multiple DNA methylation types in bacteria and flora by three-generation Nanopore sequencing

• NBT Cover: Nanopore Metagenome Identifying Lower Respiratory Pathogens in 6 Hours

• Nanopore sequencing reveals the effects of freezing and thawing on changes in soil microbial communities

• 2019 Novel Coronavirus Nanopore Sequencing Standard Operating Procedure

• Medicine in Microecology: The Wang Jun group of the Institute of Microbiology published the Nanopore third-generation sequencing method for the human enterovirome

• Selected high-scoring articles on nanopore metagenomic sequencing

• Facing the trillion-level sequencing market, where does nanopore sequencing technology go?

multi-omics

• Nature Microbiology | A standardized approach to multi-omics reveals the diversity of microorganisms and metabolites in the Earth's microbiome

• Sub-journal of Nature | Shen Xiaotao et al. Precise health monitoring based on multi-omics data of trace blood samples

Novel Coronavirus Topics

• JGG: COVID-19 infection leads to persistent imbalance of upper respiratory tract and intestinal flora in children

• Gastroenterology: Changes in the gut microbiota of COVID-19 patients during hospitalization

• Cell: Asymptomatic new crown patient positive for 105 days

• CEJ: Transmission characteristics, possible containment strategies and research challenges of coronaviruses from the Zhao Yagan Formation of Xi'an University of Technology

• Chem. Eng. J. | Effects of salinity on anoxic-aerobic system performance, microbial community dynamics and co-occurrence networks during wastewater treatment

• The Innovation | Direct Etiological Evidence: Asymptomatic Patients Can Cause COVID-19 Transmission

Linux and Shell

• seqkit: Sequence combing artifact-statistics, format conversion, length screening, quality value conversion, translation, reverse complementarity, sampling, deduplication, sliding window, splitting, etc. 30 all-round functions

• Do you know the 21 special symbols whose meanings are not easy to search for in Linux commands?

• Why ls can run directly under Linux, but your program needs to write ./dir1/dir2/bin/bwa

• This open source Linux tutorial created for Shengxin learning is really fragrant!

• A programming template worth having by students - Shell

• A Programming Template Worth Possessed by Shengxin-Perl

• Teach you how to build a bioinformation analysis platform

• Windows easily realizes the linux shell environment: gitforwindows special tutorial: this 40M small tool helps you process data under windows even more powerful

• Open win10 built-in Linux subroutine

• Basic use of Docker-Ubuntu18.04

• Linux minimalist statistical analysis tool datamash

• csvtk: table processing artifact - beautification, statistics, header table, merge, transpose, filter, sample, de-redundancy, columnar, subtotal and simple drawing

• The technology of batch renaming of files, you deserve it

• What should I do if I forgot to add nohup to a long-time program?

• Recommend 2 commands to quickly upload and download files between the local and the server

R Statistical Plotting

• This amazing website r-graph-gallery provides codes of various graphs for your reference!

R language basics

• These special symbols in R language that you want to know the meaning but don't know how to look up

• Use conda to manage R packages

• The Dictionary of Diagrams — A Dictionary of Visual Diagrams

• Programming template-R language script writing: the simplest statistics and graphics, package installation, command line parameter analysis, file reading, table and vector graphics output

• R Language Statistics Introduction Course Recommendation - Data Analysis for the Life Sciences in Biological Sciences

• Summary of the basic routines of data visualization

• Convert R graphs to Word, PPT, Excel, HTML, Latex, vector graphics, etc.

• <-Do you know the difference between the assignment symbol arrow and the equal sign in R =?

• 30 cases of data manipulation using dplyr

• Intersection intersect, union union, setdiff to find differences

• R package reshape2, easy to achieve long and wide data table conversion

• R's fastest and most efficient big data processing R package than dplyr: tidyfst

• String processing stringr package application basis in microbial ecology

• 1 data types (vectors, arrays, matrices, lists, and data frames)

• 2 The main functions required to read and write data, and interact with the external environment

• 3 Data Filtering - Extracting Subsets of Objects

• 4Mathematical operations on vectors and matrices

• 5 control structure

• 6 functions and scope

• 7 Know the loop function lapply and sapply

• 8 Decompose the data frame split and view the object str

• 9 Simulation—Random Numbers, Sampling, Linear Models

ggplot2 drawing basics

• Efficient and practical guide to ggplot2 (visual scripts, tools, routines, color matching)

• Super detailed pheatmap heat map drawing tutorial (more than 5000 words)

• ggplot2 geographic information visualization up and down

• 1 Getting to know ggplot2 to draw geometric objects

• The use of 2 layers - basic, labeling, annotation

• 3 Toolbox - error bars, weighted numbers, display data distribution

• 4 Grammatical Basics

• 5 Build an Image by Layers

• 6 Scales, axes and legends

• 7 Orientation - facets and coordinate systems

• 8 theme settings, storage export

• 9 Data Wrangling Techniques Needed for Drawing

• ggThemeAssist: Adjust the theme of ggplot2 with the mouse, no need to remember these codes anymore!

• You don't need to know programming, but you can use ggplot2 to draw paper-level graphs? esquisse

• ggplot version of the waffle bar

R language statistical drawing

• Implemented principal coordinates analysis (aPCoA) with corrected covariates using the aPCoA package to rule out the effects of confounding covariates

• MBE: ggtreeExtra - Drawing circular evolutionary trees with layer overlay method

• Analysis of multiple comparisons in one-way analysis of variance in R language

• Simple use of DESeq2/EdgeR for differential analysis

• Species abundance sorted stacked column chart and analysis of species differences among treatments

• ggplot2 version clustering tree + species abundance stacked map

• R language: quickly generate many colors with obvious differences

• 50 ggplot2 visualization examples

• R language conference: summary of metagenomic data analysis and visualization routines

• 28 practical drawing packages, there are always several suitable for you

• Heat map drawing of R language study notes

• Get the results of pheatmap heatmap clustering and normalization

• How to adjust the order of branches in the cluster heatmap according to your own wishes

• R doing linear regression

• Plot correlation coefficient matrix corrplot

• Correlation matrix visualization ggcorrplot

• Draw interactive graphic recharts

• Interactive Visualization CanvasXpress

• cluster analysis factoextra

• LDA analysis, graphing and adding confidence-ggord

• Solve scatterplot sample label overlap ggrepel

• Adding p-values ​​or significance markers to ggpubr

• One-click batch completion of difference statistics and visualization in R language

• Alpha diversity dilution curve rarefraction curve

• The method of connecting the components of the stacked histogram: highlighting the changes between groups

• Shock plot showing time series variation between groups ggalluvial

• Sankey diagram riverplot

• Classification stacked histogram sequence and adding appropriate bar labels

• Analysis of multi-group comparison of non-parametric test in R language and graphic art of faceting and grouping

• Microbial environmental factor analysis ggvegan

• Mantel tests of the R package vegan explore whether the species composition of the community is related to the environment

• Colorful evolutionary tree and heat map are more suitable for ggtree

• Multiple regression tree analysis mvpart

• Random Forest randomForest Classification Classification Regression Regression

• Weighted Gene Coexpression Network Analysis WGCNA

• SPIEC-EASI's microbial network construction example

• The circlize package draws circos-plot

• R language to build a cool online blog system

• Use the ComplexHeatmap package to draw personalized heatmaps

• R package circlize: Tired of using the histogram? Try a nice chord diagram

• Interpretation of Science combination chart: related corrplot+environmental factor connection

• gganimate draws animations to observe continuous change data

• Pathview package: Integrate expression profile data to visualize KEGG pathway

• ggcor: correlation coefficient matrix Science-level combination chart

• ggridges package: temporally dynamic choppy graphs

• gg.gap: Excellent perfect solution for ggplot order truncated axes gg.gap draws truncated graphs

• Map world China provinces

• Reproduce Science's main map Maptree by hand

• R-Based Implementation of Mixed Linear Models

• An example of Procrustes Analysis assessing species-environment/function associations

• R language draws a stacked column chart with a clustering tree

• R language perfectly reproduces the STAMP result graph

• Drawing of abundance distribution map of microbial community based on KEGG prediction function

• Frequency histogram and scatterplot SOP

• Path Analysis Diagram

microbiome R package

• Microbiome statistics and visualization - an introduction to phyloseq

• R package animalcules - one-click interactive exploration of microbiome data Microbiome: animalcules - an R package for interactive microbiome analysis and visualization

• FEMS: R package microeco for data mining of microbial community ecology

• microbiomeMarker: an R package that integrates multiple biomarker analysis tools

• EasyMicroPlot: an integrated R package for rapid microbial downstream analysis

network

• Development of network method and introduction of latest iDIRECT method

• R language visualization reproduction of the network diagram layout in the Nature sub-journal by Zhou Zhongji's team

• Science: Combination charting

• MetagenoNets: Online Metagenome Network Analysis Practical Tutorial NAR Article Interpretation

• Use network diagrams to display Venn diagram collections and Cytoscape operation videos

• Implementation of network graph in R-igraph

• Gephi easily draws super beautiful network diagrams

• Microbial Network Construction: MENA, LSA, SparCC and CoNet  

• SparCC's microbial network construction example

• Cytoscape: MCODE package implements network modularization analysis GIANT package analyzes Z and P-score of the network to make a network diagram with bar and pie nodes

• One article to learn R-based static and dynamic network drawing

• Introduction to Network Fundamentals for an Overview of Network Analysis

Experimental Design and Technology

• One article explains how to do research on plant endophytes

• Environmental DNA high-throughput sequencing problems and solutions to SOPs (Part 1: From sample to data)

• Cell Reports: Removal of host and extracellular DNA to improve microbial genome yield (sputum samples)

• Enrichment and detection methods of viruses in environmental samples

• Microbiome Sampling and DNA Extraction Recommendations

• 20 Common Culture Medium Formulas for Microorganisms

• Those "wonderful" animal models for microbiome research

• Sample Biological Repeat Data Selection 1 Necessity  2 How many replicates are needed? Sample size determination

• Example of sample naming considerations

• NBT: Minimal Information Standards and Sequencing Specifications for Amplicon and Other Sequencing (MIMARKS)

• NBT: Minimal Information Criteria for Uncultured Viral Genomes (MIUViG)

• Amplicon primer selection 16S structure 16S single V4 region is the best choice? Primer evaluation

• Identification and classification of marine culturable microorganisms

• How to take a stool sample

• How to get Rhizosphere/Rhizoplane

• Microbiome: Comparison of Methods for Samples Stored at Room Temperature

• NBT: High-throughput sequencing of full-length 16S and 18S rRNA

• Microbiome: Quantitative variation and biomass effects in 16S amplicon sequencing studies

• Microbiome: a novel approach to amplicon detection of unicellular eukaryotes and parasites in environmental samples

• Rob Knight: PCR does not need to do triplicate remixing!

• Effects of DNA Extraction Methods on the Results of Plankton Community Research

basic knowledge

• Audio Column - Metagenome Vocabulary - 001 Metagenome

• Nature review: Microbiota, metagenome, microbiome stupidly confused

• Microbiome: microbiome noun definition

• α-, β-, γ-diversity in community ecology

• 16S sequencing, if you don’t know the OTU, you are out!

• If the amplicon analysis still gathers OTU, it is really OUT

• Introduction and comparison of mainstream non-clustering methods dada2, deblur and unoise3

• Comparison of sorting methods PCA, PCoA, NMDS, CCA

• Principles of overall difference assessment between groups by Adonis and ANOSIM methods

• PCoA Distance Algorithm Encyclopedia

• Understanding PCA and PCoA

• Why is the negative binomial distribution in the statistical analysis of next-generation sequencing data?

• Basic knowledge of metagenomics

• Overview of Functional Gene Diversity Research

• Amplicon SCI Routine 1 Differences in Community Structure 2 Differences Between Groups 3 Summary

• Environmental factor association analysis - CCA or RDA

• The things behind the P value

• Easy to understand ten commonly used algorithms for machine learning

• An article to understand the application of random forest in micro-ecology

• The ROC curve you want to know

• Correlation Analysis: Spearman, Kendall, and Pearson

• Learning Whole Genome Sequencing Data Analysis 1 Sequencing Technology 2fasta&fastq

• An article to understand the development and application of Nanopore sequencing technology

• Wheat's lifetime vector illustration collection stickers - from seed germination to ripening

Literature Interpretation

*Interpretation by the author (the author of the paper personally tells the results of the article and the story behind it).

National Journal of Light

• mLife | Climate warming reshapes the seasonal dynamics of grassland soil microbial communities

• Fundamental Research: The mechanism of root exudates affecting carbon turnover by regulating soil microorganisms

• STTT | Jiang Jiandong/Cao Xuetao/Wang Yan- Oral administration of berberine c improves Parkinson's symptoms through intestinal flora

• SBIO | Xinongwei Gehong Group-Negative interactions between soybean soil bacterial phyla affect the dynamic changes and functions of the community

• GPB: The latest version of GAPIT 3 genome-wide association analysis and prediction software is released

• JIPB: A review by Baiyang group on root microbiome community construction and its contribution to plant fitness

Nature

• Nature｜Intestinal and oral microbiome research on human-to-human transmission

• Biosynthetic potential of the global marine microbiome

• Nature | Zhu Xuan/Chen Fuhe/Yuan Guoyong and others confirmed that coronavirus uses host caspase-6 to promote replication

• Nature | Mirusviruses link herpesviruses to giant viruses

• Nature: Environmental factors shape Dutch gut microbiome

• Nature: Lung microbiome regulates brain autoimmunity

• Nature | Jiangxi Agricultural University Huang Lusheng/Chen Congying and others reveal the mechanism of pig blood type genes regulating intestinal flora

• Nature | The "chemical equipment" of the "arms race" between plants and pathogenic bacteria He Zuhua's research group has made significant progress in the immunometabolism mechanism of broad-spectrum disease resistance in rice

• Nature: Li Meng Group of Shenzhen University reveals a new phylum of Asgardian archaea (Wukong archaea) and its relationship with eukaryotes

• Nature: Cheng Lei/Li Meng and others discovered a new carbon metabolism pathway of methanogenic archaea

• Nature | Biogeography of prokaryotic genes

• Nature: Isolation of an archaea located at the "junction" of prokaryotes and eukaryotes

• Nature: Study on the Spatial Distribution of Complex Bacteria

• Nature: Jeff Dangl's team reveals that the genus Glupiota maintains root growth in the microbiome

• Nature: Rob Knight's team discovers blood and tissue microbiomes can diagnose cancer

• Nature: He Shengyang and Xin Xiufang published the homeostasis mechanism of plant phyllosphere microbiome*

• Nature: Li Hai et al. revealed that intestinal flora participates in shaping the B lymphocyte antigen receptor repertoire

• Nature: Human placenta should really be sterile

• Nature: The Academy of Advanced Sciences, Chinese Academy of Sciences discovered an evolutionary stability strategy for the colonization of spatially expanding habitats

• 10 Nature special reports on the results and prospects of the Human Microbiome Project 2 (iHMP)

• Nature: "Microbiome and Inflammatory Bowel Disease" by iHMP

• Nature: "Microbiome and Prediabetes" by iHMP

• Nature: 25 milestones in human microbiome research

• Nature: The first systematic study on the influence of gut microbes on drug metabolism

• Nature: Development of the gut microbiome over time in young children in the TEDDY program

• Nature: Announcements from Bacteria—The Quorum Sensing Effect

• Nature: Skin microbiota-host interactions

• Nature: Fungi invade the pancreas from the gut to colonize and enrich Malassezia bacteria

• Nature: How gut bacteria influence the brain to help eliminate fear-related behaviors

• Nature: Microbial bile acid metabolites regulate the homeostasis of host gut-specific Treg cells

• Nature Topic: The present and future of gut microbiota research

• Nature: Discovery of acquired bacterial defense genes in human gut microbiota

• Nature: Relying on manganese oxidation to achieve chemoautotrophic growth of bacteria

• Nature review: research progress on gut microbiota and colorectal cancer

• Nature Sharing: How to write a highly cited review paper?

Scinece

• Science | Rewilding plant microbiomes—crop ancestral microbiomes may offer a way to improve sustainable food production

• Science｜Changing microbial communities can enhance tree tolerance to climate change

• Science | Giant bacteria found in mangroves challenge traditional idea of ​​nuclear-free membranes

• Science | Zheng Wenshan and others released Microbe-seq, a new technology for microbiome single-cell sequencing (comments by Wang Jun/Dai Lei/Chao Yanjie)

• Science: Quantitative analysis of eukaryotic DNA 6mA by Fang Gang Group of Mount Sinai School of Medicine in New York to analyze the influence of bacterial contamination

• Science point of view: There is little cooperation among different bacterial species—reasonable use of the ubiquitous competition among bacteria to replace antibiotics

• Science: Prenatal maternal infection promotes tissue-specific immunity and inflammation in offspring

• Science: Archaeal ammonia oxidation in an anaerobic world

• Science: How do legumes build "nitrogen fixation factories"? Murray's group has made important progress in the mechanism of root nodule symbiosis

• Science: The Xianghua/Li Ming Group of the Institute of Microbiology, Chinese Academy of Sciences revealed a new toxin-antitoxin RNA system that guards CRISPR-Cas

• Science: Arabidopsis thaliana triterpenoids specifically regulate the root microbiome* Expert comment

• Sciences: Use dietary fiber to "catch" 15 strains of bacteria that relieve diabetes! *

• Science review: Using the rhizosphere microbiome to improve crop drought resistance and yield

• Science: Gut flora adds another function, revealing your real age

• Science: Major role of nitrite-oxidizing bacteria in dark oceans

• Science: Another star flora can regulate intestinal immunity?

• Science: The nitrogen fix

• Science: Comparative Genomes Reveal Phenotypic Evolution Mechanism of Silverfin Fish Response to Fishing Behavior

• Science Comments|Just add one kind of bacteria, tomato not only resists salt stress but also increases yield by 65%!

• Science: The microbiome "gold rush" discovers new antibacterial agents from the human body

• Science: Pathogens activate the disease-suppressive function of plant endophytic flora

• Science: A review of how gut flora affects social behavior

• Science: The microbiome is the source of host emerging phenotypes

• Science: Nitrogen fixation still occurs in an environment full of ammonium salts

• Science: High-resolution source tracking technology based on microbial barcode system

• Science: British Castrillo group reveals that the coordination of microbiota and root endothelium supports plant nutritional balance!

• Science review: Humans and microorganisms advance and retreat together

• Science: New pathways for plants and microbes: Interactions with symbiotic and pathogenic microbes drive plant evolution!

• Science: Big data reveals the diversity and functional landscape of wild animal gut microbiota

• Science: Global dryland grazing and ecosystem services

Cell

• Cell | Dietary sugar-induced microbial dysbiosis disrupts immune-mediated protection from metabolic syndrome

• Cell: Cheng Gong Group of Tsinghua University reveals that an odor volatile of skin flora promotes flavivirus-infected hosts to attract mosquitoes

• Cell review: Single-cell approaches in the study of the human microbiome

• Cell丨Understand the role of "intracellular bacteria" in breast cancer in tumor metastasis and colonization by Cai Shang's team at West Lake Laboratory

• Cell: Chunjun Guo's group at Cornell University develops gene editing tools for non-model gut bacteria

• Cell: Long-term genetic stability and individual specificity of human gut microbiota

• Cell: Tick genome and metagenomic data

• Cell: A Reverse Ecology Method for Defining Microbial Populations by Gene Flow Introduction to PopCOGenT

• Cell: Zhejiang University Zhang Xing/Zhu Yongqun revealed the structure, assembly and torque transmission mechanism of bacterial flagellar motor

• Cell: Zhou Jianmin from the Institute of Genetics and Development, Chinese Academy of Sciences was invited to review the latest progress in plant immune activation and signal transduction

• Cell: Soil Inheritance

• Cell: How plant roots allow beneficial microbes to colonize

• Cell review: human gut microbiota - from association to regulation

• Cell: Cross-kingdom interaction of root microorganisms promotes survival of Arabidopsis thaliana

• Cell: small genes open a new field of microbiome research-large-scale identification of small proteins encoded by microbial genomes

• Cell: Absolutely heterotrophic organisms transformed into fully autotrophic organisms

• Cell's second burst | Guangdong CDC/Yale University uses nanopore sequencing to reveal the epidemiological spread of the new coronavirus genome in China and the United States

Nature review

• Nature review | The application potential of gut microbiota in the prevention and treatment of cardiometabolic diseases

• Nature Food | Zhejiang University constructs a precise design strategy for the phyllosphere microbiome to promote sustainable food production

• Nature review: Soil structure and microbiome function in agroecosystems

• Nature review: priority effects in the formation of microbial communities

• Nature Review: Liang Guanxiang and others summarize the development of human viromics in the past 20 years

• Nature review: a paper reveals how the life and death process of soil microorganisms affects biogeochemistry

• Nature review: From soil to clinic - the impact of microbial secondary metabolites on antibiotic tolerance and resistance

• NRM: The role of gut microbes in human metabolic health and disease

• Shu Wensheng and Huang Linan Nature Review Microbial Diversity in Extreme Environments

• NRM: Human Microbial Culture and Culture-Omics

• NRM: Formation mechanism and control dynamics of cyanobacterial blooms

• NRM: Embracing the Unknown - Unraveling the Complexity of the Soil Microbiome

• NRM: Tracing the "root": the microbial ecology of the plant rhizosphere

• Driving effects of NRM key species on microbial community structure and function

• NRM: The Microbiome of Permafrost

• NRM: Intraspecific diversity: explaining strains in the microbiome

• Nature Review: A Guide to Physician's Microbiome Analysis

• NRM: Social networks of microbes - how auxotrophs shape complex communities

• NRM: Increasing crop yields? The crop microbiome is key

• NRM: Emerging culture techniques for uncultured microorganisms

• NRM: Microbial Aging and Lifespan

• NRM: Predictive Biology: Interpretation, Simulation and Applications of Microbial Complexity

• Nature review: Microbes and climate change

• Nature review: A century of research on bacteriophages

• NRGH: The role of priority effects in shaping the gut microbiome early in life

• NRG: Applications and challenges of clinical metagenomics

• NRM: Microorganisms evolve and transform along the parasitic-symbiotic continuum!

• NRM: Methods and resources for metagenomic sequencing to study drug resistance genes

• NRM: uniqueness and commonality of mycorrhizal symbiosis

• NRM: How to Get Your Ideal Microbiome

• NRM: general principles and best practices for engineering the microbiome

• NRG: Everything you want to know about RNA-seq is here

• NRG: Methods and resources for metagenomic sequencing to study drug resistance genes

• NRM: Plant-microbiome interactions: from community assembly to plant health up and down

Sub-journal of Nature

• Nat Med | Wang Zhang/Lin Lifeng/Guan Weijie/Sun Jiufeng revealed that environmental pollution exposure affects respiratory health indicators through respiratory flora disturbance

• Nature Biotechnology | High-throughput microbial culturomics with automation and machine learning to isolate microbiomes

• Nature Microbiol | Nannong Zhang Ruifu Group reveals the interaction mode of plant probiotics in rhizosphere colonization

• Nature Microbiology | Wang Mengcen of Zhejiang University and others discovered a new mechanism for microbiome to regulate plant disease resistance defense

• Nature Microbiology | Reconstructing host information in the human gut metagenome

• Nature Sub-Journal | Chu Haiyan Group - Soil Biodiversity and Urban Green Space Ecosystem Functions (Comments by Zhu Yongguan/Wei Gehong)

• Sub-journal of Nature | A new breakthrough of Dazhang Heping's team in Nei Nong - full-text interpretation of the human gut microbiome at high resolution

• NBT|gutSMASH predicts specialized primary metabolic pathways for human gut microbes

• Strain-specific effects of probiotics drive gut microbiome development in preterm infants Nature Microbiology

• Nature Medicine | Fu Jingyuan/Chen Lianmin evaluate the importance of intestinal flora, diet and genetics on human metabolism (comments by Wang Jun/Zheng Jusheng)

• NBT Cover: Rice NRT1.1B Gene Regulates Root Microbiome Participation in Nitrogen Utilization*

• Nature Microbiology | Chen Yun/Bai Yang/Yu Yunlong et al. Identification of highly effective strains against wheat head blight and their mechanism of action

• Nature Microbiology | Wang Zhang/Chen Rongchang/Zhou Hongwei-Respiratory microbiota-host interaction mechanism in chronic obstructive pulmonary disease

• Nature Microbiology | SeqCode: Nomenclature of prokaryotes based on sequence data description

• Nature Protocols: Bacterial Culture Group Approach - High-throughput Isolation, Culture and Identification of Root Bacteria

• Nature Microbiology | The Green Secret of Goat Poop

• NBT | Liu Yongqin/Luo Yingfeng et al released the genome and gene set of glacier microbiome

• Sub-journal of Nature | Carbon sequestration rate in groundwater is similar to carbon sequestration rate in oligotrophic marine system

• Nature Microbiology | Bacillus subtilis biofilm promotes growth and disease resistance in melons

• Nature Microbiology | Viral genomes from six deep-sea sediment species that infect Asgardian archaea

• Sub-journal of Nature | Mapping the interaction of plant phyllosphere flora to establish genotype-phenotype relationships

• Sub-journal of Nature | Zhou Zhong's team reveals that long-term climate warming leads to a decrease in grassland soil microbial diversity

• Nature Method | Evaluation of CAMI2 Metagenome Analysis Method

• NBT: Wang Jun and others use AI to "dig" antimicrobial peptides in the intestine with super high efficiency

• Sub-journal of Nature: Metagenome assembly genome realizes genealogy analysis

• Sub-journal of Nature: A collection of 189,680 DNA virus genomes from human gut flora

• NBT: Nannong Shen Qirong and Wei Zhong's team: Phage combination therapy for tomato bacterial wilt (with video)*

• NBT: Wang Yunhao, Ou Jianhui, etc. review nanopore sequencing technology

• Sub-journal of Nature | Zhai Bing et al. Dynamic changes of intestinal fungal flora and analysis of clinical outcomes in hematopoietic stem cell transplantation (recruiting postdoctoral fellows, research assistants)

• NBT Cover: Nanopore Genome Sequencing for Rapid Clinical Diagnosis of Bacterial Lower Respiratory Tract Infection

• NBT: MaPS-seq sequencing method reveals the spatial distribution of gut microbes

• NBT: Engineered bacterial symbionts of nematodes improve biocontrol potential against western corn rootworm

• NBT: Using blood metabolome to predict gut microbiome diversity

• NBT: Rob Knight's team publishes a new method for dimensionality reduction of microbiome data

• NBT: Harnessing cellular triglyceride storage to enhance polyketide potency in Streptomyces

• NBT: a new method for improved binning and assembly of metagenomics

• Nature Methods: CUHK Luo Guanzheng Group has made important progress in the field of RNA modification methodology

• Nature Geoscience: Who is behind the restrictions on non-symbiotic nitrogen fixation*

• Nature Medicine: "The Microbiome and Preterm Birth" by iHMP

• Nature Medicine: Dynamics of the gut virome and bacteriaome in infants early in life

• NEE: Physicists who don't want to be chemists are not good biologists

• NEE review: function and functional redundancy in microbial systems

• Nature Microbiology: The Banfield group at the University of California reveals the diversity of CPR bacteria and DPANN archaea and their interaction with hosts under low-temperature TEM

• Nature Microbiology: Fang Gang Group Reveals Bacterial Epigenetic Regulation of Clostridium difficile Sporulation*

• Nature Microbiology: Video Interpretation! Siderophore: the "secret weapon" in the defense of scarce resources in the crop rhizosphere

• Nature Microbiology: A method for phylogenetic analysis of microbiome data

• Nature Microbiology: The bacterial community of global sewage treatment plants revealed!

• Nature Microbiology: Wang Sibao group reveals the molecular mechanism of antimalarial antimalarial bacteria in Anopheles mosquito gut

• Nature Microbiology Review: Diversity, Ecological Functions and Evolutionary History of Archaea

• [ Nature Microbiology: A standardized approach to species classification of archaeal genomes

• Nature Climate Change: Zhou Zhong's team reveals that climate warming enhances the complexity and stability of microbial networks

• Nature Plants: Host preference of symbiotic bacteria in plant root microbiomes

• Nature Plants: The core microbiome in sustainable agricultural ecosystems

• Nature Plants: University of British Columbia reveals a new mechanism for plants to shape the rhizosphere microbiome

• Sub-journal of Nature: Sundaresan Group - Sustained disruption of microbiome composition after long-term drought in rice (comments by Song Yi)

• Nature Plants: Root microbes can remotely improve plant responses to aboveground environmental stresses

• Nature Plants: Guo Huishan's research group at the Institute of Microbiology, Chinese Academy of Sciences reveals a new mechanism for soil-borne pathogens to evade host immunity

• Nature Plants: The Kenichi Tsuda group of Huazhong Agricultural University used in situ bacterial transcription and proteomics in plants to identify pathogenic protein of host immune attack

• Nature Plants: Sino-German cooperation discovers the key biological mechanism of mutual benefit between maize root system and rhizosphere beneficial microorganisms

• Nature Plants: Zhejiang University Wangmengchen group reveals new functions of endophytic bacteria in rice seeds for disease resistance

• Nature Plants: Wang Xuelu's team from Henan University reveals the evolution and molecular mechanism of compatibility between soybean and rhizobia

• Nature Protocols: He Shengyang's group established a standardized growth system for Arabidopsis microbiome research!

• Nature Food review: The Jizheng Group of the University of Melbourne reviews the potential of indigenous plant microbiomes for sustainable agriculture!

• NEE: Function and functional redundancy in microbial systems

• Nature Methods | Long-read metagenomic sequencing helps build a complete microbial tree of life

Nautre Communications

• NC | Dai Lei Group of Advanced Institute of Chinese Academy of Sciences develops SEER-FISH imaging technology to analyze the spatial structure of microbiome

• Nat. Commun | Zhang Weipeng Group of Ocean University of China reveals the main bacterial groups and their mechanisms of sulfur oxidation in marine biofilm communities

• NC | Ma Yingfei Group of Shenzhen Advanced Institute of Chinese Academy of Sciences Reveals the Diversity of Human Intestinal Archaeal Viruses

• NC | Cai Lei Group of Chinese Academy of Sciences reveals that transboundary synthetic flora enhance tomato resistance to Fusarium wilt

• NC | Harvard Medical School Liu Yangyu's group MAG analyzes the role of the human microbiome in COVID-19

• NC | Yang Gaowen's group from the College of Grassland Science and Technology of China Agricultural University reveals the positive effect of multi-factor interference on reducing soil microbial diversity

• NC | Dong Xiyang and others found a large number of nitrogen-fixing microorganisms in deep-sea cold seep sediments (video interpretation)

• NC | Tao Liang Group of West Lake University-TMPRSS2 "assists" virus infection and mediates host invasion of Clostridium sordellii hemorrhagic toxin

• NC | Gut cells and lactic acid bacteria work together to protect against Candida infection

• NC | Cheng Shulin/Chen Luonan/Zhang Chenhong-The improvement of exercise intervention on fatty liver and the relationship between intestinal flora network

• NC: Zhang Tong's team at the University of Hong Kong - Omics-based risk assessment framework for drug resistance genes

• NC: Hao Haiping and Zheng Xiao from China Pharmaceutical Sciences found that diet-microbe interaction relieves intestinal damage

• NC: Speakman Group, Institute of Genetics and Development-Brown fat is the key to improving blood sugar in germ-free mice

• NC: Metagenomic and metaproteomic analysis reveals soil microbial degradation of polyphenols

• NC: Wang Guanhong, Institute of Zoology, Chinese Academy of Sciences, etc. reviewed gene technology to prevent and control mosquito-borne diseases

• NC: Wang Jinfeng and others reveal the impact of vaginal flora ectopy on uterine health

• NC: Zhongnong Xuling/UC Berkeley Coleman-Derr-The Interaction Mechanism of Plants and Rhizosphere Microorganisms under Drought (Post-PhD Recruitment)

• NC: Ecology of inorganic sulfur accessory metabolizer genes in bacteriophages

• NC: Zhang Xiaohua's team at Haida University discovered a new mechanism for microbial resistance to high pressure in the Mariana Trench

• NC: Bacteria Construction—Random v. Determinism, Drought Stress, Host Screening, Unified Dynamics (Comments by Guo Liangdong and Yang Jun)*

• NC: The team of Nannong Shen Qirong and Zhang Ruifu reveals the deterministic bacterial assembly process inspired by diversity to limit community function

• NC: You think you are eating grass, but in fact you are still eating soil (Zhu Feng, Institute of Genetic Development)

• NC: Restoring bacterial diversity may reduce drug resistance

• NC: Diversity of honeybee gut microbes

• NC: In response to drought, bacteria collapse and fungi are still stable (Pure network analysis published in the sub-journal of Nature)

• NC: Jia Zhongjun Formation of Nantu Institute - Microbial Mechanism of Methane Oxidation in Paddy Fields

• NC: Shenyang Institute of Ecology reveals the important role of pathogenic fungi and insects in the coexistence of woody plant species in temperate forests

• NC: Machine learning approach expands all members of the anti-CRISPR protein family

• NC: Immune repertoire high-throughput analysis tool: IGoR - more precise analysis of immune repertoire

• NC: Scientists from the Institute of Microbiology built a mouse gut microbial resource bank

• NC: Nannong team decodes and reconstructs microbial quorum sensing system

• NC: Effects of Global Change Factors on Soil Microbial Diversity and Function

• NC: Cable bacteria reduce methane emissions from rice-growing soils

• NC: Computational framework iGDA for reconstruction of strain-level metagenomic sequences by three-generation sequencing

• NC: Wei Liu/Yufeng Pan found that gut microbes can affect the aggressive behavior of Drosophila

npj journals

• npj | Zhang Demin's team from Ningbo University reveals the regulation mechanism of the bacterial community in the shrimp biofloc culture system

• npj | Dehua Wang/Xueying Zhang et al reveal the mechanism of desert rodents tolerating high salt through the "microbiota-gut-kidney" axis

• South China Normal University Wang Zhang, Guangdong Provincial Hospital of Traditional Chinese Medicine Huang Qingchun, Huang Runyue and others revealed the characteristics of intestinal flora in patients with gout

• Global emergence properties of bacterial communities induce drought resistance in Arabidopsis npj Microbiomes

Science and Advance Series

• Science Advances | Wang Gaofeng Group of the Plastic Surgery Department of Nanfang Hospital reveals that symbiotic microorganisms in the skin promote hair follicle regeneration

• SA: Yang Yuanhe Group of the Institute of Botany Reveals the Key Regulatory Effects of Mineral Protection and Microbial Attributes on Permafrost Carbon Dynamics

• SA | Absolute Quantification Technology of Tianhao Accu16S Bacteria Helps Discover the Mechanism of “Gut-Bone Axis” Regulating Osteonecrosis

• Science sub-journal: Co-adaptation of host genome and microbiome under long-term insecticide-induced selection

• SA: Nannong Shen Qirong's team's Science sub-journal reveals that early tomato microbiome function determines adult health*

• SA: Impaired detoxification function of gut microbiota in autism patients revealed by class pair analysis

• AS: Xihu Zheng Jusheng/Ju Feng-Accumulation of specific drug resistance genes in the human gut may lead to increased risk of diabetes

• AS | CUHK Ding Tao/Tian Guobao et al reveal that differential input of oral flora shapes two lung types associated with health status

Why are there so few Science sub-journals? Because the volume of journals and articles is the smallest, which is an order of magnitude less than the Nature sub-journals.

Cell Sub-journal

• Cell Host & Microbe | Wang Zhang reveals the molecular mechanism of respiratory microbiota disorder promoting lung function decline in chronic obstructive pulmonary disease

• Cell Sub-Journal | Ma Yingfei/Dai Lei-Phage Culture Group Analysis of Intestinal Dark Matter (Comments by Tong Yigang/Cui Jie/Guo Chunjun)

• Cell Sub-Journal | Gong Shenhai/Chen Peng/Zhao Xiaoshan/Zeng Zhenhua from Southern Medical University found that intestinal bacterial metabolites can alleviate drug-induced liver injury caused by acetaminophen overdose

• Cell Sub-Journal: Tsinghua Liang Guanxiang Group reviews the process of human virome from origin to maturity and the corresponding regulatory mechanism

• Microbiota-derived acetate promotes metabolic adaptations of the brain's innate immune system during health and disease

• Cell Host | Zhang Qunye/Wang Zhe/Zhang Cheng-Intestinal microbiota imbalance aggravates abdominal aortic aneurysm

• Sub-Journal of Cell: Sticking to you-bacterial auxin-mediated bacterial colonization of plant roots

• CHM: Zhou Jianmin's group from the Institute of Genetics and Development, Chinese Academy of Sciences discovered plant natural products that specifically target the pathogenicity of pathogenic bacteria and clarified the mechanism of action*

• CHM: Microbial-derived bacteriocins target host against diarrhea in early-weaned piglets

• CHM Review: Site Characterization of the Oral Microbiota: Microscale Habitat and Ecological Niches

• CHM Review - Establishing Causality: Opportunities for Synthetic Microbiota in Plant Microbiome Research

• CHM: Modularity of rhizobia microbial communities and their evolutionary relationship with symbiotic rhizobia

• CHM: Virome diversity in adult monozygotic twins is associated with gut microbiome diversity

• CHM: Li Jianfeng Group of Sun Yat-Sen University reveals that plants use bacteria to acquire fungal resistance

• CM: It was found that 60% of non-alcoholic fatty liver is related to intestinal bacteria, and the alcohol in the body of carriers can reach 4-6 times that of healthy people

• CM: Jiang Changtao's group at Peking University found that HIF-2α regulates fat thermogenesis through intestinal flora

• Cell Metab | Liu Xingyin's group revealed a new mechanism of anti-tumor immunity of gut microbes and their metabolite indole-3-lactic acid

• Breakthroughs and bottlenecks in TiMM microbiome research

• Cell Reports: Luo Guanzheng of CUHK + Ji Quanjiang of ShanghaiTech University - CRISPR-guided bacterial targeted genetic screening system

• Cell Reports: The Wei Fuwen Group of the Institute of Zoology, Chinese Academy of Sciences analyzed the function of seasonal changes in the intestinal flora of giant pandas

• Cell Reports | Peking University Wu Xiaolei/Nie Yong Group Metabolic Division Microbial Community Assembly Mechanism

Gut

• Gut | Huake Ningkang group uses transfer learning to overcome regional effects to achieve cross-regional disease diagnosis of microbial characteristics (video)

• Gut | China Pharmaceutical University Zhou Wei and other teams have made new progress in the research on the mechanism of intestinal flora driving rheumatoid arthritis and the intervention of traditional Chinese medicine

• Gut: Liu Xingyin/Wang Yichao/Cao Aihua and others reveal the developmental trajectory map of intestinal flora in children with autism (comments by Zhao Fangqing)

• Gut: Fecal virome transplantation alleviates symptoms associated with type 2 diabetes and obesity in mice

• Gut: Human body's initial microbial origins and reproductive health* Healthy pregnancy is critical for the child

• Gut: The stability and dynamic changes of the human oral flora

• Gut-2018- Identification of Gut Biomarkers for Early Liver Cancer

• Gut Microbes | Chen Gang/Wang Yi/Yang Jinhuan/He Qikuan/Characteristic flora characterized by multiple ecological niches as biomarkers for the diagnosis of liver cancer patients

PNAS

• PNAS | Species invasion changes microbial community phenology in a twenty-year freshwater time series

• PNAS | Academician Zhu Yongguan's team single-cell Raman combined with targeted metagenomics reveals soil active antibiotic resistance group

• PNAS: Drought delays establishment of sorghum root microbiome and enriches Gram-positive bacteria

• PNAS: Distinctiveness of human skin microbes and phylogenetic symbiosis in mammals

• PNAS: Asking about the stochastic and deterministic process of microbial community succession-who controls the ups and downs

Microbiome

• Microbiome | Wu Xiaolei/Nie Yong Group of Peking University: Artificial Neural Network Predicts the Composition of Activated Sludge Microbial Community

• Microbiome | Xinongwei Gehong reveals the response and detoxification of rhizosphere bacteria to licorice allelopathy

• Microbiome | Chen Yihua/Shenzhen Bay Tang Xiaoyu-Human-associated bacteria adopt an unusual pathway to synthesize 3-acetylated tetramers in order to adapt to the environment

• Microbiome | Xinongwei Gehong team reveals that plant domestication shapes wheat rhizosphere microbiome assembly and metabolic function

• Microbiome | Chinese Academy of Sciences/Academy of Agricultural Sciences/Zhejiang University analyzed the microbial-mediated nitrogen fixation function of plant aerial root mucus and the mechanism of homeostasis maintenance

• Microbiome | Fu Yunhe Group of Jilin University reveals a new mechanism of "rumen/gut-derived mastitis"

• Microbiome | Chinese Academy of Agricultural Sciences Wang Jiaqi/Zhao Shengguo: Construction of microsphere in situ culture method to achieve isolation of important urea-decomposing bacteria in bovine rumen

• Microbiome | Jiang Jingzhe's team from the South China Sea Institute of Water Sciences reveals the huge virus diversity in filter-feeding oysters

• Microbiome | Professor Hu Shengwei's team from Shihezi University reveals the composition and function of the horse gut microbiome

• Microbiome | The Shao Zongze Formation of the Third Institute of Oceanography reveals the diversity of viruses in deep-sea hydrothermal areas and their interactions with hosts

• Microbiome | Fu Yunhe Group of Jilin University reveals the new mechanism of "gut-derived mastitis"

• Microbiome | Agricultural Microbiome Resource Team Reveals the Vertical Transmission Mechanism of Endogenous Core Microbiome in Rice Seeds

• Microbiome | Zhou Zhichao developed METABOLIC, a functional analysis software based on microbial genomes (video)

• Mirobiome | Sun Weimin's team from the Soil Institute of Guangdong Academy of Sciences: Nitrogen-fixing endophytes can improve the ecological adaptability of Chinese miscanthus

• Microbiome: Academician Shen Qirong's team reveals the formation mechanism of soil-borne wilt rhizosphere microbial community

• Microbiome | Academician Chen Songlin of the Yellow Sea Institute/Hua Ke Ningkang et al.-The mechanism of gut microbiota in the formation of anti-vibriosis traits in Longli fish (semi-smooth tongue sole)

• Microbiome | Academician Yin Yulong's team Yin Jia's group has made important achievements in the field of porcine probiotics research

• Microbiome | Northeast Agricultural University Shi Baoming/Meng Qingwei and others revealed that host-microbe interaction mediates porcine enteritis immunity

• Microbiome | Chinese Academy of Agricultural Sciences Wang Jiaqi + Zhao Shengguo: Opportunities and challenges for metagenomics to guide the isolation and culture of uncultured microorganisms

• Microbiome: miniature eukaryotic intestinal parasites in sewage treatment plants: diversity, activity and removal

• Microbiome: Hong Kong Polytechnic Li Xiangdong Group - Hospital-sourced inhalable drug resistance genes and host communities, clinical associations and environmental risks

• Microbiome: Cai Lei's Group at the Institute of Microbiology, Chinese Academy of Sciences reveals that diseases affect plant microbiome community construction and functional adaptation

• Microbiome: Xinongwei Gehong team simplified synthetic flora to prevent Astragalus root rot by activating ISR

• Microbiome: Mobile resistanceomes of the human gut and pathogenic bacteria drive the growth of antibiotic resistance in the environment

• Microbiome: Zhang Jiachao and Rob Knight from Hainan University revealed the law of adaptive evolution of probiotics in the host intestine

• Microbiome：城环所杨军组-小幅盐度变化改变了城市水库微型真核浮游生物群落的构建过程和网络稳定性

• Microbiome：浙大马忠华团队-生防细菌抑制病原真菌新机制

• Microbiome：微生物所刘双江组建立人肠道微生物资源库（hGMB）

• Microbiome | 中科院张惠明团队揭示RNA介导的DNA甲基化影响植物根部微生物群落

• Microbiome：南土所梁玉婷组-稻田土壤产甲烷菌的共存模式

• Microbiome: 乡村环境微生物组成及功能基因或对呼吸道及过敏疾病具有保护性

• Microbiome：中国人群宿主遗传、肠道菌群与复杂疾病的关系

• Microbiome：地球上有多大比例的原核生物已经被测序了基因组？

• Microbiome: 微生物组的定义重新审视:旧概念和新挑战

• Microbiome：Kraken2进行16S物种注释又快又准，秒杀QIIME2

• Microbiome：捕食性细菌新类群-慢生单胞菌目细菌独特的生境适应性

• Microbiome：微生物群落在深海热液硫化烟囱体由活跃转换为非活跃状态过程中的演替模式

• Microbiome：华中农大谢卡斌组利用CRISPR系统减少16S rRNA基因测序宿主污染*

• Microbiome：南土所孙波组揭示间作重塑根际微生物组并促进生长的机制

• Microbiome：南京农大团队在粘细菌捕食的生态学功能方面取得重要进展

• Microbiome：中外合作揭示微生物群落降解复杂微生物聚合物的酶(视频导读)

• Microbiome：环境过滤驱动农田生态系统土壤古菌独特的空间分布*

• Microbiome：土壤微生物驱动退耕还林系统土壤剖面的养分循环*

• Microbiome：40年施肥处理后固氮菌及氮固定受抑制 新闻稿:南土所褚海燕组揭示长期施肥抑制根际微生物固氮的作用机制*

• Microbiome：根系分泌物驱动土壤记忆抵御植物病原菌*

• Microbiome：马铃薯疮痂病与土壤微生物组关系新进展*

• Microbiome: Are the microorganisms obtained from the so-called "enrichment culture" really "enriched"? *

• Microbiome: Chicken Gut Microbial Metagene Collection (Comments by Zhang Heping, Wei Hong, Qin Nan)*

• Microbiome: Application of multi-dimensional meta-omics method to synergistically reveal inter-bacterial interactions of complex bacterial communities on target substrate metabolism*

• Microbiome: Using Nanopore high-throughput sequencing technology to analyze the mobile resistance genome of sewage treatment system*

• Microbiome: stochastic processes dominate microeukaryotic plankton community building in subtropical rivers*

• Microbiome: Amplicon 16S analysis of the cycad microbiome*

• Microbiome: Wei Zhong's group reveals that rhizosphere protozoa community is a key factor in determining plant health*

• Microbiome: Skin and Gut Microbes of Wild Mammals in Response to Nuclear Contamination

• The Microbiome: The Journey of Microbes Between Plant Generations

• Microbiome: Nannong Zhang Ruifu's team reveals that grazing causes grassland microbiome changes to drive soil organic carbon transformation and productivity improvement

• Microbiome: The Institute of Genetics and Development of the Chinese Academy of Sciences reveals the wheat root microbiome under the combined effects of plant development and nitrogen fertilizer

• Microbiome: Resilience of soil microbial communities to organic and inorganic soil amendments and bacterial invasion

• Microbiome: NGLess language realizes the process of rapid and repeatable analysis of metagenomics NG-meta-profiler

• Microbiome: The first "social relationship" network of earth microorganisms is drawn in Zhejiang University!

• Microbiome: Re-discussing the Effect of Amplicon Function Prediction Analysis (Picrust)

• Microbiome: species-level classification using 16S rRNA gene dataset

• Microbime: Standard setting in the field of microbiomics

• Microbiome: domestication of rice seeds eco-evolutionarily shapes rice seed bacterial and fungal communities

• Microbiome: biogeographic patterns of planktonic and benthic diatoms in the Yangtze River

• Microbiome: ecological center Zhang Limei group - plant developmental stages drive the divergence of ecological roles of the maize microbiome

• Microbiome: Metagenomes reveal characteristics of resistance in tundra, temperate steppe and tropical soils

NAME

• ISME | Phage-mediated lysis strongly promotes growth of amino acid auxotrophic bacteria

• ISME | Professor Hu Feng's team from South Agricultural University revealed the mechanism of benzo[a]pyrene stress affecting the ecological adaptation strategy of earthworm gut virome

• ISME | 西湖鞠峰组-污水处理厂中粘细菌的活跃捕食特性和多样性与全球分布规律

• ISME | 西农韦革宏团队在沙漠“肥岛”微生物群落的环境适应策略研究中取得重要进展

• 解密根际有益菌VOCs消减土壤青枯菌生物障碍的生存-致病权衡机制

• ISME Comm | 机器学习和深度学习在微生物组研究中的应用

• ISME | 西农姜雨/牧医所黄火清等发布肠道原虫基因组集，颠覆百年认知

• ISME：表层蓝藻下沉至1000米深海固氮

• ISME | 浙大黄健华/陈学新等揭示寄生蜂调控寄主营养代谢的新机制

• ISME | 拟南芥次生代谢物调控微生物组介导的线虫入侵

• ISME | 沈其荣团队韦中组-土壤生物障碍发生的根际微生物组诊断

• ISME | 热液微生物群落揭示了喷口区的生物地理学和嗜热性的进化历史

• ISME | 沈其荣团队在有机肥驱动原生生物与芽孢杆菌互作防控土传病害取得进展

• ISME：林科院袁志林等-冷杉优势真菌共生发育的基因家族趋同演化及平衡选择机制

• ISME：胡锋/朱永官等揭示土壤噬菌体-宿主菌协同应对有机氯农药胁迫机制

• ISME：南农张瑞福组揭示芽孢杆菌通过代谢互作刺激常驻根际微生物促进植物生长！

• ISME：南农韦中等消减土壤青枯菌生物障碍新策略

• ISME：微生物网络构建与分析面临的挑战

• ISME：土壤微生物对硫的短期及长期利用的决定因素-基于13C,15N,14C和35S多同位素标记结果

• ISME：西农沈锡辉+韦革宏+王瑶揭示细菌铁获取和外膜囊泡招募新机制

• ISME：根系招募特异型菌群增强植物对盐胁迫的抗性

• ISME：中国林科院亚林所袁志林组揭示盐碱地根系深色有隔内生真菌种群基因岛的正向选择机制

• ISME：南土所梁玉婷组-不同气候条件下微生物代谢及残体介导施肥对土壤有机碳的影响

• ISME：中大李文均组在放线菌生命暗物质的生态功能与进化上取得进展

• ISME：昆士兰大学郭建华组-人造甜味剂会促进细菌耐药性的传播

• ISME：多组学揭示低氧环境下的汞甲基化细菌

• ISME：中科院微生物所揭示细菌利用光能新机制！

• ISME: 中科院南京土壤所褚海燕组揭示关键菌群的生物多样性决定作物产量

• ISME: 北大吴晓磊组发现囊泡为细菌利用环境血红素提供全新途径

• ISME：南农沈其荣团队基于大数据准确预测土壤的枯萎病发生 纯生信发ISME

• ISME: 近海沉积物中古菌群落的时空动态：群落构建机制和共现关系

• ISME：海洋氨氧化古菌的营养能量策略决定其生物地理学分布格局(秦玮组招聘博士/博后)

• ISME：中科院动物所张知彬组揭示肠道微生物介导了降雨变化对布氏田鼠种群的上行效应*

• ISME：群落构建过程的平衡介导农田土壤微生物群落物种共存*

• ISME：污水厂抗性组受细菌组成和基因交换驱动且出水中抗性表达活跃*

• ISME：城环所杨军组揭示水库蓝藻影响真核浮游生物的群落演替和物种共存*

• ISME：宿主性别可以决定肠道微生物对寄生虫感染的响应*

• ISME：整合分析揭示塑料圈微生物组的全球多样性

• ISME：二型糖尿病患者中与牙周炎相关的龈下菌群

• ISME：华中农大李霞组发现大豆根际微生物组变化与根瘤菌共生效率的关系

• ISME：病原菌介导植物根际有益微生物群落组装

• ISME：菌根真菌菌丝分泌物中的果糖作为信号激发解磷细菌活化植酸

• ISME：微生物生态学中的挑战：建立对于群落功能与动态的预测性认识

• ISME：高手开杠-‘1%的微生物可培养’到底为哪般？

• ISME：相关分析在微生物生态学中的应用与误用

• ISME：沈农栾军波组揭示水平转移基因的功能

• ISME：二氧化碳和氮水平对植物根表菌群和功能的影响

• ISME：比较基因组学揭示蓝藻进化和生境适应性特征

• ISME Commun: 华中农业大学在菌群收敛机制方面取得新进展

• ISME Comm | COVID-19疫情期间和之后河流浮游生物群落的干扰和恢复

Genome Biology/Research

• GB：香港城市大学孙燕妮组发表高准确度病毒株识别工具VirStrain

• GB：赵方庆组揭示生命早期肠道菌群演变规律及决定因素

• GB：MITRE利用微生物组时间序列数据推断与宿主状态变化相关的特征

• GB: Xu Jian/Wang Shi/Huang Shi are responsible for the development of a new method for microbiome sequencing 2bRAD-M

• Genome Research | Shanghai Institute of Immunology Chen Lei's team develops spatial metatranscriptome sequencing technology

• GR | SUSTech Xiayu Group-Nanopore Selective Sequencing Enrichment of Rare/Unknown Genomes in Microbiome

Cell Research

• Cover of Cell Research | Liu Zhihua's group reveals that intestinal flora can promote insulin secretion*

• Cell Research: Huanong Analyzes Soldier Fly Genome Map and Gut Microbiome Degradation Law

Protein & Cell

• Protein & Cell | Liu Yongxin Group, Institute of Genomics, Chinese Academy of Agricultural Sciences reviews the past, present and future of microbiome research

• Protein Cell | Luo Guanzheng/Liang Puping/He Chuan-CROss-seq technology systematically identifies the off-target effects of multiple CRISPR tools

• Protein & Cell: Gut Microbes in Cardiovascular Diseases and Their Potential Therapeutic Applications

• PC: The role of gut microbiota and its metabolites in metabolic diseases

• PC: Chen Feng et al. Discuss how oral flora affects the whole body*

• PC: A Comprehensive Summary of Effects on Microbiota for Drug Efficacy and Toxicity*

Molecular Plant/New Phyto/Plant Comm

• MP | Dongnong Wufengzhi/Nannongweizhong-Root exudate-mediated plant-specific interactions shape the rhizosphere microbiome's ability to suppress disease

• MP: Wang Ertao's group and collaborators reveal the co-evolutionary mechanism of arbuscular mycorrhizal symbiosis and root nodule symbiosis*

• MP Review: Systems Biology of Plant-Microbe Interactions

• MP: Microbial transboundary balance maintains plant health

• MP: Guo Huishan's group from the Institute of Microbiology, Chinese Academy of Sciences and Duan Chengguo's group from the Shanghai Plant Stress Center, Chinese Academy of Sciences collaborated to reveal a new mechanism of dynamic regulation of rape growth and immunity

• New Phytologist: Shen Qirong's team and Yuan Jun's team deciphered the formation mechanism of disease-suppressive soil under the invasion of fungal pathogens

• New Phytologist | Sun Bo/Liang Yuting Group of South Institute of Soil Sciences, Chinese Academy of Sciences reveals microbial strategies to promote crop growth in low-fertility soils

• New Phytologist: Sun Bo/Liang Yuting group of Nanjing Institute of Soil Science, Chinese Academy of Sciences revealed the coupling relationship between underground microorganisms and aboveground plant spatial turnover rate

• New Phyto | Shen Qirong's team, Li Rong et al. analyzed the mechanism by which the rhizosphere flora of bio-organic fertilizers cultivated disease-suppressive soils to resist the invasion of pathogenic bacteria

• New Phytologist | Zhongnong Feng Gu group reveals that the core microbiome of the mycelium helps AM fungi to mineralize organophosphate

• Plant Com: Introduction to HA-QAP Technology for Absolute Quantitative Detection of Host Microbiome * Full Text Interpretation

Bioinformatics/GPB/BiB

• GPB: The important impact of agricultural production activities on water body micro-ecology

• GPB: The mechanism of inulin's effect on improving glucose and lipid metabolism disorders

• GPB: Identification and mechanism study of key active ingredients of Gegen Qinlian decoction regulating intestinal flora in treating diabetes

• GPB: MicroPhenoDB quantifies associations between metagenomics and pathogenic microorganisms, core genes, and human disease phenotypes

• BiB: Wang Xiujie/Pei Xiaobing collaborated to develop single-cell omics cell marker gene identification algorithm COSG

• BiB | Jiang Jingzhe/Yuan Lihong/Sun Yanni teamworked to develop a bioinformation tool that can be used for rapid virus classification

• BiB: University of Electronic Science and Technology of China Zou Quan Group builds a disease prediction model and microbial biomarker discovery platform based on the balance of intestinal flora

• BiB | Wang Yiwen Group of Shenzhen Institute of Genomics, Academy of Agricultural Sciences proposed a multivariate algorithm framework for removing batch effects in microbiome data

• Bioinformatics: Liu Fu Group of Jilin University - Deep Learning to Identify Short Viral Sequence Virtifier from Metagenome Sequence

• Bioinformatics | Shen Wei/Hu Peng/Ren Hong's team developed KMCP, a metagenomic species composition analysis software that takes into account both prokaryotes and viruses

• Bioinformatics & BIB｜Sun Yanni Group of Hong Kong City University is a website for identifying and analyzing phage sequences in metagenomic data

American Society for Microbiology mSystems/mBio/AEM

• mSystems | Zhongnong Wangjie Group reveals the mechanism affecting the microbial community in the "plastic world" of soil

• mSystems | Dong Xiuzhu Group of Institute of Microbiology, Chinese Academy of Sciences found that bacteria and archaea co-metabolize betaine to produce methane

• mBio | Shanda Du Zongjun/Mu Dashuai found that sulfate-reducing bacteria drive microbial community assembly in marine sediments through niche modification

• mBio | Sun Bo/Liang Yuting Group of Nanjing Institute of Soil Science, Chinese Academy of Sciences reveals the impact of cross-boundary interactions on N2O emissions from rice fields

• mBio: Xinong Wei Gehong/Jiao Shuo et al. reveal that random assembly process promotes diversity and multifunctionality of rare species (recruitment attached)

• Academician James M. Tiedje: Microbes and Climate Change——A New Chapter for Future Research

• MS: Ding Tao/Wu Zhongdao, Sun Yat-Sen University-A new mechanism of gut microbiota regulating the fitness of the schistosomiasis transmission medium Biumbilical snail

• mSystems: Mysterious benthic virus communities and their ecological functions in the extreme environment of the "Fourth Pole of the Earth" Mariana Trench

• mSystems: Biogeochemistry enters the age of viruses - a diverse approach to studying viruses and biogeochemical cycles

• mSystems: Huazhong Agricultural University Hao Xiuli group found different responses of rare/abundant microbial groups to cadmium-contaminated soil amendments!

• mSystems: Qingda Su Xiaoquan explained the Beta diversity of the microbiome-from global comparison to local comparison

• mSystem: Bacteria-fungi interactions in the West Nongweger macrogroup affect microbial diversity-soil nutrient cycling

• mSystems: Su Xiaoquan, Xu Jian, etc. released the global microbiome structure and function search platform 2.0

• mSystems: Su Xiaoquan, Xu Jian - Global Microbiome Transformation Network Based on Big Data Engine

• mSystems: South China Agricultural University reveals the rice SST gene regulates the synergistic salt tolerance mechanism of rhizosphere microorganisms

• mSystems: Wang Dehua's group at the Institute of Zoology, Chinese Academy of Sciences reveals the mechanism by which the intestinal flora of wild animals improves survival at low temperature

• mSystems: Chu Haiyan Group of Nanjing Soil Institute was invited to publish a review of microbial biogeography (official video introduction)

• mSystems: The Chu Haiyan Formation of the Southern Land Research Institute reveals that the spatial ratio of the season has a greater impact on the soil microbial community at a large spatial scale

• mSystems: Soil stoichiometry affects soil C, N, and P cycling microbial abundance and its resistance to global change

• mSystems: Xu Zhenjiang's team at Nanchang University found that microbes predict age skin more accurately than gut

• mSystems: It can be seen from the siderophore to see the overall situation of the interaction of rhizosphere flora!

• mSystems: Relative abundance will distort the actual abundance. Is the absolute abundance obtained by combining 16S amplicon sequencing and total bacterial qPCR reliable?

• mBio: reproducibility, reproducibility, stability and universality of microbiome research

• AEM: Find him thousands of Baidu, use SIP to not get lost-identify the diversity and metabolic potential of arsenic oxidizing bacteria in sewage treatment units

• AEM: Nanlin Fanben et al. - Plant rhizosphere growth-promoting bacteria control soybean blight

• MS｜Xie Liwei's group found that mixed probiotic preparations and their metabolites can relieve colitis

• MS | Beihang He Zilong and other pan-genome studies on the driving factors of genome plasticity in Staphylococcus aureus

• MS|Plasmer: an accurate and sensitive bacterial plasmid prediction tool based on shared k-mers and genomic features and machine learning

Frontier series

• FiM | Family-level taxonomy of caudate bacteriophages: evaluation of current taxonomic tools using the latest ICTV taxonomy

• Frontiers in Immunology | Ludong University researched and analyzed the mechanism of combined virulence factors of Edwardsiella piscicida-induced hippocampal enteritis

• FiPS | Beilin Wu Rongling/He Xiaoqing-Network mapping reveals the interaction mechanism between Arabidopsis and phyllosphere microbiome

• FiM | The Dairy Innovation Team of the Institute of Animal Husbandry and Medical Research Established a Targeted Metaproteomics Method for Rumen Microbial Urease

• FiM: Southwest Minda Zhu Ying et al. - Research on gut microbiota promotes ex situ conservation of crested ibis

• FiPS review: research progress on the interaction between plant secondary metabolites and microbiome

• FiM: The intestinal flora of giant pandas may not be specialized in the ability to ferment cellulose

MDPI

• Agronomy | Sino-Nonglin Yanbing group biological agent combined with corn rotation to reduce sunflower rowang parasitism

SoilSBB/SEL/Geoderma

• EJSS: Liang Yuting Group of South Institute of Land Research - Habitat determines the relationship between bacteria, resistance genes and mobile elements in soil plant systems

• Geoderma: Liang Yuting Group of Nantu Institute of Soil Science - Coexistence Mechanism of Antibiotic Resistance Genes and Metal Resistance Genes in Manure-applied Soils

• SBB: Liang Yuting, Sun Bo, et al. Trans-climatic soil translocation of Nantu Institute reveals the environmental filtering effect of climate warming and fertilization on the increase of soil nitrogen-fixing microorganisms

• SEL Bombshell: Rediscovering mycorrhizae: Are mycorrhizae really as important as commonly believed?

• SEL | Plants recruit Pseudomonas spp. through root exudates to help resist aboveground pathogen infection

• SBB: Microbial community construction and biodiversity in oil-contaminated soils*

• SBB: Warming masks the effects of different forms of nitrogen on grassland microbial communities on the Qinghai-Tibet Plateau*

• SEL: Strive to become a "Cell" in the field of soil ecology

• SBB: Coexistence and assembly of nitrogen-fixing communities in pH-dominated soils of Chu Haiyan Formation of South Institute of Soil Sciences

• SBB: What exactly determines the characteristics of soil microbial communities

• SBB: Possible contribution of alternative nitrogenases to asymbiotic nitrogen fixation

Current Opinion Series

• COM: Application of recombinant flora system in root microbiome research*

• COM: Application of Next Generation Microbiome Technologies in Crop Production - Limitations and Need for Knowledge-Based Solutions

• COM: Beyond pathogens - the interplay of the microbiome and the plant immune system

• COM: Root-Soil-Microbe Interactions

• COB: Recycling in nature - Anaerobic microbial communities drive the degradation of natural biomass

• COPB: Current Review: Zhongnong Song Chunxu and others build a beautiful home for plant beneficial microbiome

Communications Biology

Nature Publishing's new open source journal, the goal is to undertake excellent articles rejected by Nature Communications. This year, it won the first impact factor, and it is expected to stabilize at around 8 points in 2-3 years (the average level of Nature Communications and Scientific Reports).

• CB: Qian Haifeng Group of Zhejiang University of Technology and others found that Pleurotus algae blooms promote the transmission and transfer of resistance genes

• CB: Liang Yuting Group of Nantu Institute - High stability and metabolic capacity of bacterial community promotes rapid reduction of easily decomposable carbon in soil

• CB: China Agricultural University Hu Yongfei group constructs an integrated chicken gut microbiome reference gene and genome set

EnvironmentEST/EM/EP/EI/JHM/STE

• STE | Yangda University/Institute of Genomics-Qicarbon Nanopore Long-read Metagenome Analyzes the New Mechanism of Highly Prevalent Drug Resistance Genes in Laying Hen Feces

• EST Cover: High-throughput sequencing of micron-scale single particles by Xia Yu's team at Southern University of Science and Technology reveals electron-mediated microbial interactions in high-temperature anaerobic digestion systems

• EST: Ju Feng Group of West Lake University-Pathogens in sewage plants and indigenous denitrifying bacteria are active expressers of multiple antibiotic resistance genes

• EST | Academician Zhu Yongguan's team from the Institute of Urban Environmental Protection has made progress in the study of the soil food web transmission of antibiotic resistance genes

• STOTEN | Zhu Yongguan's team reviewed complete ammonia oxidation - a more convenient microbial ammonia oxidation process

• EST | Peking University Zhu Huaiqiu group reveals the relationship between atmospheric microbes and human activities and their impact on human health

• Shenyang Institute of Ecology has made new progress in conservation tillage to promote sustainable agricultural development

• JHM: Ecological response mechanism of protozoa to soil erosion by acid mine wastewater

• JHM: China Science and Technology University Sheng Guoping Group Reveals that Vermicomposting Reduces the Spread of Antimicrobial Resistance Gene ARG in Sludge

• JHM | Huake Ningkang Group has made many achievements in the field of microbial-mediated interaction between the environment and humans

• EST: Sun Weimin's team from Guangdong Institute of Ecology published two parts of tailings microecological investigation

• EST: Li Fangbai's team reveals microbial-mediated arsenic oxidation coupled with nitric acid reduction

• EI: The Chu Haiyan group of Nantu Institute found that the core flora of agricultural soil microorganisms can improve soil ecological functions

• EI: Potential health hazards of metformin chlorinated by-products in drinking water by Wu Lianfeng & Ju Feng's team at West Lake University

• EI: Tian Da Wang Can + Queensland Guo Jianhua revealed that bioaerosol is an important transmission route of drug resistance genes in pig farms

• EP: The team of Sun Weimin, Guangdong Institute of Eco-Environmental Technology: The response mechanism of terraced soil microorganisms to the erosion of different acidic mine wastewater*

• EM: Born to be bacteria, self-improvement-the ecological adaptation mechanism of acidophilus in heavy metal-polluted soil

• EM: Soil pH and temperature regulate the construction of abundant and rare bacterial communities in agroecosystems

• EM: Differentiation strategies of soil rare and abundant microbial taxa under different climatic conditions

• STE: Environmental microbiota metabolites protect against inflammatory symptoms

• STE: South China Agricultural University Zeng Zhenling/Xiong Wenguang-Pig manure mediates the spread of antibiotic resistance genes to farm workers and the surrounding environment

• STE: Hu Songnian Group of Institute of Microbiology, Chinese Academy of Sciences Reveals the Biodiversity of ICU Environmental Bacteria within a Year

• Improving Microbial Literacy of Society: The Imperative!

Journal of Genetics and Genomics

• JGG | Zhai Qixiao Group of Jiangnan University Analyzes the Species Dependence of the In vitro Immunostimulatory Activity of Intestinal Probiotics

• JGG | The team of Wang Jun, Institute of Microbiology, Chinese Academy of Sciences, found that the mesenteric lymphatic system may be the second pathway of the gut-liver axis

• JGG: Su Xiaoquan's team from Qingdao University uses conditional pathogen index to assess environmental microbial risk

• JGG: Special Issue on Microbiome (Zhao Fangqing, Bai Yang, Zhang Zhigang, Wang Jun, Zheng Jusheng, Wei Hong, Shen Wei, Liu Yongxin, etc.)

• JGG: Study on host-microbe gene diversity and microcosmic co-evolution among multi-ethnic groups in my country

• JGG: Peking University Chen Feng + Chen Ning revealed the regulation of multiple factors on intestinal flora in vitamin A-deficient mice

• JGG: EVenn: Easily draw 5 Venn diagrams and Venn networks online in 3 minutes

• JGG: Research on Gut Microbes Helps Pangolin Captive Protection

• JGG: Gut bacteria aggravate small molecular weight carrageenan-induced rectal inflammation

• JGG: Wang Jun, Institute of Microbiology-A review of the research progress of innate immune cells in gastrointestinal diseases

• JGG: Jiang Xingpeng Group of Central China Normal University - Microbiome Association Test Method for Different Sparse Level Signals

• JGG: Zhao Fangqing, Zhao Xiang and others developed a new technology for macro-transcriptional library sequencing that efficiently captures RNA virus genomes

• JGG: Baiyang Group and Cao Xiaofeng Group of Institute of Genetics and Development-Rice Histone Methylation Regulates Root Core Bacteria

• JGG: Zhao Fangqing's group reviews the research progress of the microbiota-gut-brain axis and autism spectrum disorders

• JGG: Oral microbiome helps identify gestational diabetes

• JGG: Gut flora is closely related to the risk of severe COVID-19

• JGG: Microbiome Special Issue Call for Papers

• Genetics: Advances in Pan-Genome Research in Bacteria, Fungi, Animals and Plants

• JGG｜Ruan Jue Group, Institute of Genomics, Chinese Academy of Agricultural Sciences developed GAEP, a software for comprehensively evaluating the quality of genome assembly

Chinese science

• SCLS: Time-series analysis of the rice microbiome*

• SCLS: Arabidopsis siseterpenoids regulate the root microbiome*

• SCLS | Shen Qirong's team and Yuan Jun's group-Soil plant system affects the composition of gut microbes and feeding preferences of herbivores

• SCLS | Academician Zhu Yongguan et al. - Phage Technology Suppresses the Risk of Antibiotic Resistance and Hides the Pandemic

• SCLS: The Fang Rongxiang/Zhang Lili team from the Institute of Microbiology developed specific 16S primers for plant endophytic bacteria

• From "microbiome" to "microbiome": behind the change of translation of microbiome should be a complete change in research ideas and methods

• Science in China: Research on Plant Immunity and Green Prevention and Control of Diseases and Pests: Progress, Opportunities and Challenges

• Science Bulletin: Construction and application of synthetic microbial communities

• Science Bulletin: Cui Jie's group published the results of comparative viromic analysis of deep and shallow sea molluscs

• Science Bulletin | The latest developments in gut microbiota and coronary heart disease research

food

• Cai Lei and others from the Institute of Microbiology successfully carried out traceability of soybean origin and quarantine screening of pathogenic fungi using microbiome technology

review

• JAFC cover | Academician Shen Qirong's team reviewed the regulation of the rhizosphere microbiome to ensure plant health

• Trends in Plant Science | Plant Microbiome Dysbiosis and the Anna Karenina Principle

• Trends Plant Sci | Academician Zhu Yongguan and others reviewed the biological nitrogen fixation of plant leaves

• Trends Microbiol | Wang Guanhong's team reviewed the aseptic and bacterium-limited techniques in the study of host-microbial interactions

• TiM | Jia Baolei from Chung-Ang University and others reviewed the mechanism of gut microbiome-mediated reduction in cholesterol levels

• Annual Review丨Wang Ertao Group of the Chinese Academy of Sciences publishes a review on mycorrhizal symbiosis

• TiG: Wang Guanhong and Jackson Champer review commensal bacteria and gene drive technology to control mosquito-borne diseases

• TiP: New roles of pathogen-secreted host mimics in plant disease development reviewed by Hu Dafeng Group!

• Liu Shuangjiang: Research on the impact of microorganisms on economic and social development

• Nearly 9 points of Shengxin magazine published a Venn diagram tool competition

• Microbiome big data: how to mine and utilize it?

• TM Review: Contamination in low microbial biomass microbiome research: issues and recommendations

• Chu Haiyan Group of Nantu Institute reviewed the technology and method of microbiology and its application

• TM: Microbial Rare Biosphere Community Assembly Process

• TM: Do intraspecific variations in rDNA copy number affect microbial community analysis?

• TM: Microbial Invasion: Processes, Patterns and Mechanisms

• TiM: Tsinghua Yang Yunfeng - Emerging Models of Microbial Functional Traits

• BA: Research progress of rhizosphere microbiome to improve plant salt tolerance*

• FEMS review: How to make sense of the "balls of yarn" in microbial networks

• TEE Review: Plant-Soil Feedback (PSF): A Bridge Between Natural and Agricultural Sciences

• MER: Systematic Understanding of Meta-Omics Experiments and Analysis

• Freshwater: Molecular Microbial Ecology for the 21st Century

• ARM: Ecology and evolution of the plant microbiome

• Ecology&Evolution|Microbial functional diversity from concept to application

• BA Review: The Biotechnological Potential and Applications of Microbial Communities

other

• Clin Nutr | Zhejiang University Children's Hospital-Chen Jie/Ni Yan revealed the effect of total enteral nutrition on intestinal flora and bile acid metabolism in children with Crohn's disease

• J Infect (IF 38) | Jia Baolei from Chung-Ang University and others revealed that Streptococcus, which encodes the lantibiotic in the human oral microbiome, is a potential risk factor for liver disease

• Ann Rheum Dis | Huake Han Jinxiang/Ningkang and others discovered the role of microbial dysbiosis and metabolic disorders in rheumatoid arthritis

• EM | Qiu Tianlei from the Institute of Biology, Beijing Academy of Agriculture and Forestry Sciences revealed the host distribution characteristics of ARGs in livestock manure and compost

• Clinical Chemistry | Zhang Jianzhong/Xu Jian develop single-cell precision diagnosis and treatment technology for Helicobacter pylori

• PBJ | Ningkang group of Huazhong University of Science and Technology reveals the regulation mode of licorice root transcriptome-microbial community-secondary metabolites

• PBJ | A review of the interaction between plant functional genes and rhizosphere microorganisms published by South China Agricultural University and Northeast Institute of Geography, Chinese Academy of Sciences

• NAR: RiboDetector, a powerful tool for identifying and removing rRNA sequences from sequencing data

• Microbiome data reveal the distribution and storage dynamics of rice toxin-producing fungi in China

• BFS: Liang Yuting Group of Nantu Institute of Soil Research reviewed the theory of microbial coexistence that promotes the health of soil plant ecosystems

• CUHK Li Wenjun's team made progress in the study of the biogeographic distribution pattern of nitrogen cycle functional genes

• IJMS: The Dairy Innovation Team of the Animal Husbandry and Medical Institute has made new progress in the development of new urease inhibitors for rumen microorganisms

• ME: Environmental DNA (eDNA) metabarcoding is transforming the way we survey plant and animal communities

• ESTL: Guo Jianhua and other novel multiplex amplicon sequencing methods can realize accurate quantification and virus traceability of SARS-CoV-2 RNA in sewage

• Aquaculture: The team of Xie Fengxing from Tianjin Academy of Agricultural Sciences reveals the correlation between the predicted function of the flora and the actual metabolic characteristics

• Water Research: Chu Haiyan Formation of Nantu Institute reveals significant divergence of bacterial communities in glacier source water and sediments

• Water Res | The Zhang Huajun/Zhang Demin Group of Ningbo University reveals the characteristics and mechanism of rapid recovery of microbial communities after seawater disinfection by bleaching powder

• Water Research | Xiayu Group of SUSTech Reveals Micron-scale Spatial Heterogeneity and Conserved Interactions of Anammox Bacteria

• Water Research | SUSTech Xia Yu et al. - Nanopore Metagenome Reveals Drug-Resistant Bacteria/Gene Characteristics and Drug-Resistance Gene Enrichment Mechanism in Sewage Receiving Water

• WR | The key to the stable occurrence of drug-resistant genes in source water: pathogenic bacteria as the "source" and community-building dominant bacteria as the "sink"

• Engineering: Wang Jun and Zhang Invention Group published research on in situ reconstruction of human intestinal flora and circadian rhythm

• EBioMedicine: Zheng Jusheng Group of West Lake University - The relationship between dairy product intake, intestinal microecology and cardiometabolic health

• PCE: Nannong Zhang Ruifu Group reveals a new strategy for microbial fertilizer strain Bacillus to respond to plant immune defense and achieve rhizosphere colonization

• [Xinjiang Cotton] Synthetic biology drives the fourth industrial revolution, and biotechnology promotes the healthy and green development of Xinjiang cotton

• Journal of Soil Science: Academician Zhang Fusuo and others put forward a new concept of rhizosphere life community

• GEB: Liang Yuting Formation, Southern Institute of Soil Sciences, Chinese Academy of Sciences - Latitudinal Distribution Characteristics of Paddy Soil β Diversity at the Continental Scale

• JGG: Oral microbiome helps identify gestational diabetes

• Diabetes Care: Machine learning reveals the characteristics of intestinal flora affecting type 2 diabetes

• Arthritis Rheumatology: Zhang Xuan + Wang Jun published the changes of intestinal flora in patients with systemic lupus erythematosus

• Horticulture Research: The manuscript of the model map of the win-win cooperation in the plant world

• FEMS: The Microbial World of Arsenic and Antimony Contaminated Soil Profiles

• FEMS: Sun Weimin's group from Guangdong Institute of Ecology uses DNA-SIP metagenomics to reveal antimony-oxidizing microorganisms and their metabolic pathways

• CSBJ review: Challenges and opportunities for microbiome data mining methods

• GCB: Ecological Center Deng Ye Group - Warming Changes Microbial Interactions

• GCB: Farmland soil-rich fungi are more adaptable than rare fungi (one interpretation + main picture reproduction)

• GCB: Weinong Wei Gehong's team - the complexity of soil multi-trophic level network enhances the connection between biodiversity and multifunctionality of farmland system

• GCB: Feng Youzhi Group of Southern Land Research Institute reveals that temperature nonlinearly controls the geographical distribution of soil saprophytic fungi worldwide

• GCB | Liu Yurong Group of Huazhong Agricultural University has made a series of new progress in the field of soil carbon turnover under altitude gradient

• GEB: The phylogenetic conservation of the ecological niche published by Jiao Shuo et al. determines the geographical pattern of soil archaea

• Su Xiaoquan Group of Qingdao University-Microbiome 16S Amplicon Function Correction Algorithm Meta-Apo

• BMC Biology: Sun Yanni Group of City University of Hong Kong published a tool for predicting virus hosts with high accuracy

• BMC Biology | Li Mingkun Group of Beijing Institute of Genomics, Chinese Academy of Sciences established a metagenomics research method for micro samples

• BMC: Characterization of the gut microbiota in children with juvenile arthritis*

• WR: The expression characteristics of host-specific markers in microbial contamination source apportionment in China*

• Water Research: SUSTech Summer Rain + Tang Yuanyuan-Typhoon’s Impact on Shenzhen’s Coastal Microplastics and Microplastic Circles

• WR: The Yang Jun Group of the Urban Ring Research Institute reveals that the construction of planktonic beetle communities in subtropical reservoirs is more strongly affected by stochastic processes than deterministic processes

• Science Bulletin: Wang Ertao's group from the Shanghai Institute of Plant Physiology published an "amplification-selection" assembly model of plant rhizosphere microbial communities based on absolute quantitative abundance*

• JCP: Research on the mechanism of N ₂ O and NO generation and community function in the process of biological aerated filter for coking wastewater treatment *

• Fungal Diversity: 70 authors jointly revised the classification system of the Basidiomycota of the fungal kingdom

• PCE: Root exudates from Nannong Shen Qirong's team drive soil-microbe-nutrient feedback in response to plant growth

• PB: Efficient biological nitrogen fixation supported by maize aerial root exudates

• EL: Who said that high N content will not fix nitrogen (in this study, "the more the better")

• EL: Nitrogen fixation capacity depends primarily on species taxonomy rather than soil nutrients

• BT: Key extracellular enzymes trigger efficient composting coupled to bacterial community succession

• BT: Material transformation, microbial community composition and metabolic function succession during composting of soybean hulls

• Viruses: Viral metagenomics reveals Malayan pangolins are infected by Sendai virus and coronavirus

• The Gaocheng-Guo Liangdong group of the Institute of Microbiology (recruitment attached) has made progress in the study of mycorrhizal adaptation strategies

• NewPhy.-Unveiling the dominant species

• New Phytologist: Wang Jianjun and others review the mountain microbiome and ecosystem function under global change

• Gut Microbes: Liu Xingyin's team at Southern Medical University reveals that gut microbes are associated with autism*

• Gut Microbes: Liu Xingyin Group of Southern Medical University-Gene variants in autism are associated with changes in gut microbiota, metabolites and cytokines

• Gut Microbes | Metagenome-based discovery of a large number of new microbial genomes in the gut of macaques

• China Microbiome Project—Crop Microbiome*  

• Journal of Applied Ecology: Comparison of Molecular Ecological Networks of Soil Fungi in Different Latitudes of Farmland in Black Soil Region of Northeast China*

• EID: Application of metagenomic sequencing to the identification of emerging diarrheal viruses*

• Current Biology: Duan Shoufu from Bai Fengyan's group at the Institute of Microbiology reveals a new mechanism for Saccharomyces cerevisiae to adapt to the environment through the reverse evolution of the gene network*

• Are Chinese people more susceptible to the new coronavirus? *

• Heredity: From heritability to enterobacteria: Concept and research progress

• Heredity: Mitochondrial Genome Assembly Strategies and Software Applications in the Genome Era

• NAR: A RiboFR-Seq method for linking 16S rRNA to metagenomics

• NAR: Zhejiang University Chen Yun/Ma Zhonghua team revealed a new mechanism of pathogenic fungal histone H3K27 methylation recognition

• IBD: Changes in the fungal flora of patients with ulcerative colitis after 5-aminosalicylic acid treatment

Journal introduction

• mLife, a comprehensive English journal of microbiology, was selected as a new journal with a high starting point

• The Innovation | Video introduction of high-quality English journals hosted by the Youth Promotion Association of the Chinese Academy of Sciences, positioning IF 20+ international top journals

• Applied and Environmental Microbiology (AEM)

• Soil Biology and Biochemistry(SBB)

• Bioresource Technology

• FEMS Microbiology Ecology

• Overview of non-top journals in the field of microbiology

• GPB editorial department recruitment notice 2019 Impact Factor breaks 7; CiteScore breaks 10

Popular science video - entertaining and entertaining

• Nature Comments丨Beyond your imagination, the droplets from a sneeze can fly so far! Wearing a mask to prevent new pneumonia is very necessary!

• One person posts two Science articles a day, with a video revealing: How do plants win the fight against germs?

• Gut—Liu Yangyu-Building an ecological network of intestinal flora

• CCTV9 let the dead body speak - secret forensic files

• Into Science: Bacillus subtilis replaces antibiotic addition in animal husbandry

• Into Science: A New Theory of the Weeder

• NHK recreates the magic cells of human life

• NHK understands the role of intestinal flora in the human body

• NHK Life Great Leap Forward

• The dark battle of the BBC human body's secret cell

• BBC Human Body Mystery Inside.the.Human.Body

• NGC Human Body Travel Inside.the.Living.Body

• NGC Womb Diary Womb  

• Talk show "Marry a Wife as a Female Doctor" Sequel "Marry a Wife Don't Marry a Female Doctor" The Confessions of a Female Doctor of Biology at Peking University, Hilarious and Tears

• Panoramic animation of the earth's 5,000-year change——After watching it, I sighed: the whole world is quiet

• Why Northeast Rice Is So Delicious

• Why is the human body temperature 37 degrees?

• A brief history of dragons

• Infrastructure Madness: Coatings for Isolating Anaerobic Bacteria in Hard Core Technology

• The rise of China in the eyes of Americans, let you understand the truth of the US trade war against China in 15 minutes!

• 89-year-old Tu Youyou once again shocked the world! Video about malaria, artemisinin and the story behind it

• Intestine · Dao | Qiu Xiu: Soup/burning incense affects the health of mothers and babies? See how the huge birth queue is revealed!

• Intestine and Dao | Zhu Yuanfang: Disinfection during birth inspection may accidentally injure the microbiome, and the 6 major measures will promote the microbiota to continue

• Intestinal tract | Ma Xiong: 20 years of research on autoimmune liver disease, striving for the gold medal of research doctor!

• Wang Jinfeng: 7 key words for the transmission of mother-to-child flora

Popular Science Graphics

original

• The poop you flushed away is becoming the savior of many gastrointestinal patients

• It turns out that this is how probiotics get rid of pathogenic bacteria

• CNS issued a series of endorsements, it turns out that ginger is so amazing

• Shocking anti-cancer drug from a small pharmaceutical factory with dozens of people

• Mouthwash increases diabetes, high blood pressure risk

• NEJM | Probiotic LGG is ineffective in treating gastroenteritis, Immunity|LGG promotes bone growth

• Gut, IJC and other 4 articles focused on - eating too much red meat is really bad for the body, pointing to cardiovascular disease, breast cancer, diverticulitis

• Oral flora keeps you on the same page—and a toothache as well as a heart attack

• Some dental care tips you may have overlooked

• Chinese New Year, drink less wine, drink more tea - green tea is not as simple as you think

• Crop domestication and human life

Comic science

• A picture to understand丨2019 Novel Coronavirus, what do you need to know?

• Legal drug that kills the most

• N abnormal manifestations of adult allergies

• Every Nature paper you read is published like this!

• Nature reviewed a manuscript, but was involved in a Nobel Prize case!

• Origin, Evolution, Creation, Exploration - A Time Journey Through 13.8 Billion Years

• In the 22nd hour of being infected with AIDS, I completed self-help

• AIDS Symphonic Poetry

• infected with AIDS

• A brief history of life

• Syphilis Rhapsody

• climate makes history

• Who is the son of tomorrow, anaerobic king or aerobic king?

• Mad Digestive Journey - An Introduction to the Digestive System

• Physics that Biologists Need to Know

• Fungi are actually crooked animals

• What are those people who don't reply to WeChat, thinking?

• "I paid, why should I say thank you?

other

• Disease enters the mouth: How soil microbiota influences gut health

• Nature sub-journal review: How will the microbiome develop after 2020?

• Regulating microorganisms to improve soil, can biological agents open a new chapter in agriculture?

• Rao Yi's thoughts on promotion or departure

• "Accidentally" Became a Boss: The Rob Knight Legend

• A new approach to personalized treatment of colon cancer—an organoid-based Cas9 screening platform | Cell Press Youth Promotion Association review

• Unbeknownst to Most, the Human Genome Is Decaying

• Postdoctoral fellow at Harvard Dental School: Teach you the basics of oral health care: brushing your teeth

• Postdoctoral fellow at Harvard Dental School: Teach you the basics of oral health care: dental floss

• Nature: Is Your Gut Bacteria Inherited From Your Parents Or Acquired?

• Cell: Taking probiotics for PK antibiotics? The consequences are so serious

• How difficult is it to publish a paper in Cell, Science, and Nature?

• How can I run without getting tired? Nature Medicine reveals microbiome boosts athletic performance

• Do you know how hard bacteria work for your happiness?

• Intestinal flora helps you get out of the singles, if you love TA, invite TA to eat together

• 56 pictures show you what bacteria look like

• Nature: Is caesarean section good? ——The Perspective of Gut Microbiota

• An overview of the development of bioRxiv preprints in the biological field

• The impact of microbes on human society

• Oral flora want to break through? This method has unlimited potential

written in the back

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