All the metagenome-microbiome knowledge you want is here (2023.12)

Welcome to click on the blue “Metagenomic” button above to follow us!

Metagenomics/microbiome is one of the most popular research fields in scientific research 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 "Metagenomic" public account, and jointly Colleagues inside and outside work together to create a platform for exchange of pure technology and ideas in this field.

The public account is pushed every day, sharing the latest results, scientific research ideas, experiments and analysis techniques in the field of metagenomics on weekdays, with strong theoretical knowledge and strong practical skills; weekend science popularization and life columns make it easy to read articles and watch movies. Currently, 3,200+ original articles are shared, and 160,000+ friends communicate and learn together here, with a cumulative reading of over 40 million+.

The public account co-founded a new journal "iMeta" with a high starting point for metagenomics, microbiome and biological information. It is an open access journal co-published by Wili, the Enterobacteriaceae Branch and hundreds of Chinese scientists in this field. The editor-in-chief is Researcher Liu Shuangjiang from the Institute of Microbiology, Chinese Academy of Sciences, and Professor Fu Jingyuan from the University of Groningen in the Netherlands are jointly responsible. The goal is to publish the top 10% (IF > 15) of high-impact papers. For details, see: iMeta’s inaugural promotional video. Published the first monograph in this field, "Microbiome Experiment Manual", which was written with the participation of 352 colleagues in the field. It is free and open source and continuously updated. For details, see125 units jointly completed the "Microbiome Experiment Manual" (Microbiome Protocol eBook) 1st Edition》. Founded iMeta, the world’s first microbiome and bioinformatics journal with a high starting point.

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

Recommended articles

iMeta—top journal on microbiome and bioinformatics

• iMeta's inaugural promotional video is world premiere - Chinese version (bilingual subtitles)

• iMeta | Cited over 1,700 times, published 136 articles, immediate index 12.4, 100 citations took 16 days (2023/11/23)

• iMeta Journal Volume 2 Issue 2 Officially released online

• iMeta Journal Volume 2 Issue 1 is officially released online

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

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

• iMeta | Volume 1, Issue 2, officially released online (2022.6)

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

10000+

• 125 units jointly completed the first edition of "Microbiome Protocol eBook"

• Summary of the list of national outstanding youths and outstanding youths in 2023

• Professor from Tsinghua University: I have seen too many doctoral students suffer from mental breakdown, mental imbalance, physical breakdown, and achieve nothing!

• A letter written by Academician Zhang Qifa to his doctoral student: Working 12 hours a day is just a lower limit

• Master's degree, Nature works 100 hours a week | Tutor's heartfelt words: Graduate students engage in scientific research for 40 hours or less a week, how can they compete?

• Nature Review: Innovative methods for cultivating uncultured microorganisms

• What kind of copywriting geniuses do Beijingers have? I laughed to death at their anti-yang jokes.

• First: Don’t have any plans to take a vacation while working on your thesis; second, the instructor is rarely wrong; third...

• Shi Yigong: You can’t get a PhD without hundreds of hours of communication and training with your supervisor! Cultivating students depends on "influence through ears and eyes"

• Liu Yongxin: Want to learn microbiota bioinformatics analysis - 21 minutes to get you started

• Genetics: Microbiome Data Analysis Methods and Applications

• Nature: Microbial culture technology is developing rapidly, and everything will be solved in the future!

• USEARCH—the simplest and easiest to learn amplicon analysis process (general agent in China)

• Nature review: Rob Knight teaches you step-by-step analysis of bacterial flora data 2020 updated version

• A must-read for introductory microbiome + practical course on metagenomics

• Metagenomic Analysis Tutorial

• A complete collection of basic specifications for charts and graphs in academic papers

• A good article that all graduate students should read: The sun is warm and scientific research is quiet

• This is my graduate life

• Life on the human body: After watching this film, I want to remove the bacteria and parasites from my body

• Science: Scientists see with their own eyes the entire process of bacterial resistance

• Nature review: Nitrogen cycle network composed of microorganisms

• Nature rectifies the name of pets: cats and dogs are indispensable for good health of babies

• Can Nature be discovered through DNA extraction?

• If you mix the culture medium like this again, your bacteria will be poisoned!

• The resurgence of this horrific infectious disease that was supposed to disappear is a man-made disaster

• Yixi-Zhao Liping-Big Tree Bacteria

• Order takeout for Physarum polycephalum, it really likes eating oyster mushrooms

• A feast of parasites may cure immune diseases caused by cleanliness

• NBT cover: Rice NRT1.1B gene regulates root microbiome to participate in nitrogen utilization

• Understand the role of intestinal flora in the human body

• Popular Science in Island Countries—The Great Leap Forward of Life

• What is the difference between 3-point and 30-point articles?

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

• The development history of sequencing, 150 years of ups and downs

• Nature Commentary: China has become a superpower, behind it is the power of science

• The National Academy of Sciences announces future agricultural development directions-bioinformatics and microbiome

• Microorganisms may be the breakthrough in the next agricultural revolution

5000+

• From the top scorer in the college entrance examination to the youngest doctoral supervisor at the Chinese Academy of Sciences! She is the first Chinese woman to win this international award!

• A common problem among many doctoral students is over-reliance on their supervisor!

• From a doctoral student at Fudan University to an associate professor at a 985 university, poverty makes people realize how difficult it is to get rid of low self-esteem.

• Collect quickly! English clichés commonly used when responding to reviewers’ comments

• Zhu Yongguan, Zhang Fusuo, et al.: Soil microbiome and soil health

• Zhu Yongguan: Progress and Prospects of Soil Microbiome in China

• In 2019, China’s natural microorganisms won the bid of 400 million yuan

• Will he win the Nobel Prize next time? Jeffrey Gordon, founder of the gut microbiome

• Eight superpowers of bacteria

• How does it feel to have a great mentor but a poor one yourself?

• All the knowledge you want about biophilia is here - Biochemistry Guide

• NBT: Experiment vs analysis, who has the greatest influence on the results?

• NC: 16S sequence prediction medium recipe

• Cell: A life of shared weal and woe between humans and intestinal flora

• 35 pictures to understand the magical relationship between the intestines and the brain

• In-depth and good article - Where is our future?

• Basic color matching methods for academic charts

• Guide you step-by-step to reproduce the diagram of the cover article of the microbiome

• 79 super microbial knowledge to help you give birth to a super baby

• Talking about the past and present life of 16S

• 16S+ Function Prediction Science: Corpse Degradation Process

• Nature: Metagenomic association analysis (1) (2)

• Nature sub-journal: How intestinal flora divide enterotypes

• One command to draw CNS map-ggpubr

3000+

• Simple and beautiful online biographical drawing tool imageGP 2.0 internal beta Sequence extraction ID, motif, translation, reverse complement

• NBT-4 35-point New Year articles focus on metagenomic research

• Understanding the microbiome in one article

• An article explaining how to conduct tumor microbiome research

• Evolutionary Tree Read in one article

• iTOL beautification 进阶  

• GraPhlAn evolutionary tree Species tree Cladogram official tutorial in Chinese Reproduce Nature article practice

• Evolview base Advanced

• Letter from student-biostar handbook

Monograph "Microbiome Data Analysis"

• Crowdfunding to write "Practical Microbiome Data Analysis and Visualization" - becoming the founder of the Encyclopedia of Metagenomics (Table of Contents)

• Editor's preface: original intention, plan, requirements, advantages, goals and prospects

• 111.Protein Cell: A practical guide to amplicon and metagenomic data analysis

• Protein Cell: Institute of Genomics Liu Yongxin/Nan Nong Yuan Jun released best practices for microbiome R language analysis

• 112.CMJ: Guidelines for human microbiome study design, sample collection, and bioinformatics analysis

• 121. Personal computer to build a microbiome analysis platform (Win/Mac)

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

• 123.Introduction to R and statistical plotting

• 211.Alpha Diversity Boxplot (sample chapter, 11 Figures 2 Video)

• 212. Alpha diversity dilution curve for sample size and sequencing depth

• 213. Venn diagram and set diagram (Venn&Upset)

• 221.Beta diversity PCoA and NMDS ranking

• 222.Beta diversity restriction ranking CPCoA/CCA/RDA/LDA

• 223. Principal Component Analysis PCA

• 231. Stacked histogram, chord diagram, word cloud of bacterial species composition

• 245. Heat map displays species and functional abundance or absence of microbiome, distance matrix

• 246. Application of ternary diagram and practical drawing

• 251. The simplest network drawing method on the entire Internet, Xiaobai Gospel Packet Learning Packet Association

• 252. Microbial network diagram reflecting the difference between groups OTU module

• 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: Environmental macroviromics analysis ideas and common tools

• Ju Feng Group of West Lake University: Metagenomics examples and new discoveries of environmental microorganisms

• Install the Linux subsystem Ubuntu 20.04LTS on Windows 10, easily use biometric software, and kill virtual machines in seconds

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

Academic report recording and PPT sharing

• Qitan | Introduction and market application of domestic third-generation sequencing technology (with video)

• iMeta Tsinghua report video | Liu Yongxin-metagenomic data analysis and scientific communication (1h)

• 75-minute introductory microbiome data analysis and result interpretation—Liu Yongxin (Hefei, June 23, 2021)

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

• Opportunities and challenges of metagenomic data analysis—Liu Yongxin (Beijing, December 8, 2020)

• Liu Yongxin: 20 minutes of practical microbiome data analysis and visualization

• Nanjing Yuan Jun/Wen Tao ISME: Accurate prediction of soil blight occurrence based on big data integration

• Wang Jinfeng Gut of Peking University of Science and Technology: 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)

• Report by Liu Yongxin of the Chinese Academy of Sciences on December 8, 2020: Opportunities and challenges of metagenomic data analysis

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

Conferences, special issues, recruitment

training meeting

• November 6-9, the 5th Bergey International Symposium on Systems Microbiology

• On November 10, the founding meeting of the Microbiome Professional Committee of the Chinese Society of Microbiology and the Microbiome and Health Academic Forum

• November 17-19, Clinical Genome/Exome Data Analysis Practical Technology Seminar

• November 24-27, Microbiome-Metagenomic Analysis

• December 15-17, Advanced Transcriptome Analysis and R Language Data Visualization

• April 12-14, Microbiome-Amplicon 16S Analysis

Call for papers for special issue

• Agronomy|3.9 points JCR1 area call for papers/37 days to publish - special issue on metagenomic analysis of agricultural microbiome (Liu Yongxin/Yu Peng)

• Cheng Xu/Wang Mengcen/Yuan Mengting/Li Jiangang/Xiong Wu Guest Editor-in-chief Frontiers Rhizosphere Microbiome Special Issue Call for Papers (IF>6)

• JoVE microbiome special issue calls for papers, write methods and make video tutorials to send to SCI

Recruitment

• Shenzhen Institute of Genomics Liu Yongxin’s group recruits 4 postdoctoral fellows (1 million in 3 years + article reward + project performance)

• The Liu Yongxin group of Shenzhen Institute of Genomics is looking for a scientific research assistant (undergraduate degree in bioinformatics/master degree in microbiome)

• Recruitment｜ Wang Xinjie Group of Shenzhen Institute of Genomics is recruiting postdoctoral fellows and doctoral students in 2024

• Shenzhen Institute of Genomics Liu Yongxin’s group is recruiting associate researchers

• Liu Yongxin's group at the Institute of Genomics is recruiting visiting graduate students/overseas joint training doctoral students (University of WMU in the Netherlands/Murdoch in Australia/Liège in Belgium/Dublin in Ireland)

• Gengjie Jia’s research group at the Food Science Center of the Institute of Genomics is looking for postdoctoral fellows

• Biotech talents, your stage - Gene Help is looking for talents!

• Southern University of Science and Technology Zhai Jixian's group is recruiting, with 80,000+ doctoral students and 340,000+ postdocs

• Fang Gang's group at Mount Sinai School of Medicine is recruiting postdocs—Metagenomic and Epigenome

• Yuan Zhilin's group at the Institute of Subtropical Tropical Sciences, Academy of Forestry, is recruiting postdocs - forest rhizosphere microorganisms

• The research group of Professor Luo Guanzheng of the Sun Yat-sen University Academy of Sciences is looking for postdoctoral fellows and associate researchers.

Advertising cooperation

• 4 articles NAR | In the era of biological big data, how to manage and reuse data well and publish IF10+ database articles?

Scientific research experience

• Use ChatGPT to help me write a biometric code

• The code provided by ChatGPT is not perfect. How can I ask him to improve it step by step?

• Can't understand the code? ChatGPT helps you explain

• ChatGPT also gets dizzy sometimes

• Published 16 Nature and 14 Science articles! This top scholar tells you ten ways to write a paper

• PubMed plug-in: Partitions, impact factors and instant IF are clear at a glance

• My path to a Ph.D. (Strong Roots and Beauty - Kang Yalong): Five years of studying for a Ph.D., hard work leads to a bright future

• Nature: Twenty things you should know before studying for a PhD

• How do graduate students get out of "confusion"?

• Science: The role of "weekly work progress report" in doctoral training

• Correspondence between academic titles and levels of mortals

• Lessons learned from thesis revision and proofreading

• How to create high-quality graphic abstracts (Graphical Abstract)

• A guide to accessing Google Scholar and searching for literature, citations, authors, and field analysis

• How do new graduate students grow after entering the laboratory? 5 suggestions to share

• Academician Zhang Qifa’s heartfelt words are worth reading carefully by every master/doctoral student!

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

• SCI paper submission full process template

• 10 articles shared by SCI doctors—the "Tao" of macroomics research

• Which level is higher, 985 assistant professor or second-level professor?

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

• Ten tips for going from postdoc to PI

• Nature: 16 criteria for a good mentor

• Graduate student, your supervisor is not your nanny.

• 7 facts and 5 initiatives about gut microbiota research

• This article tells the true meaning of the relationship between graduate students and supervisors

• 24 abilities that graduate students should develop

• Should I study for a Ph.D., and how can I successfully graduate and find my ideal job after studying for a Ph.D.? The five most practical pieces of advice

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

• Why have I attended so many academic conferences and still gained nothing?

• The ultimate tip—how ​​to gain something at academic conferences?

• AI learning tutorial1Basic graphics drawing 2Pattern diagram 3Typesetting Draw coronavirus

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

• How to ask elegantly

• My path to bioinformatics

• My struggles with developing TBtools

• A complete list of public account search methods

• Trilogy of research team growth:1 Cloud Notes 2 Cloud Collaboration 3 Public Account a>

• References 1GeenMedical 2SCI-HUB

• Programming board  Perl  Shell  R

• Bioinformatics program learning

• Paper Figures, the secret you must know

• Comprehensive analysis of the principles of chart color application

• Tutorial on how to quickly upload raw data to NCBI SRA

• China Nucleic Acid Database GSA Data Submission Guide Amplicon 16S Example Metagenomic Example

• National Microbial Science Data Center Microbiome Data Convergence Guidelines: Article attachments can be submitted

• Endnote X8 cloud synchronization: read documents at any time with Internet access

• Excel drawing reaches new heights-EasyCharts

• The only difference between you and a PPT expert is iSlide

• Windows 10 Remote Desktop Ubuntu

• Students who want to publish high-scoring papers should come here. Here are 10-scoring magazines and editors to learn about!

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

• SCI paper writing1. Three-paragraph structure of the paper 2. Logical analysis of the introduction

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

software process

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

• Graphpad drawing for beginners Biostatistical drawing advanced

• TBtools - a biometric gadget used by more than 10,000 people

• BIOM: Biological Observation Matrix - a common data format for microbiome data

• STAMP - Statistical Analysis of Differences between Microbiome Concise Tutorial Chinese Help Document

• FUNGuild: fungal functional annotation

• Online RaxML construction of phylogenetic tree

• MetaboAnalyst 4.0, an upgrade of powerful tools for metabolomics research

• Genevestigator: Find genes expressed in published studies

• psRobot: Plant small RNA analysis system  

• RepeatMasker: Genomic repeat sequence annotation

• Genome annotation1 Repeated sequences 2 Non-coding and coding genes 3 Functional annotation Prokka

• Canoco5 draws beautiful DCA or CCA plots

• A complete bacterial genome analysis script

• The theory and basic implementation process of structural equation modeling (SEM)

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

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

Software basics must-learn series

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

• Play with fancy screenshots and screen recording—FastStoneCapture User Guide

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

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

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

• Data quality control software—fastQC

• A powerful tool for integrating 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 website is great!

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

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

• National Microbial Science Data Center launches free one-stop bioinformatics analysis cloud platform

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

• Microbiome Database: The one-stop environmental genomics data cloud platform has been updated!

AI series video tutorials

• 1Thesis vector text, line editing

• 2Thesis graphics editing and formatting

• 3. After typesetting, the graphics are exported to Tiff/PNG like this

• 4Show grid remove clipping mask and background

• 6 Directly select the tool to delete the whiteboard

• 7 Magic Wand Tool Batch Operation

• 8 several shortcut keys

• 9. Placement and fine-tuning of diagrams

• 10Set fonts and fine-tuning

• 11Resize objects

• 12 Batch transform single objects selected simultaneously

• 13Select all points

Amplicon analysis

• Microbiome Analysis 2018 e-book worth €130

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

• Read "Quantitative Ecology: R Language Application" again

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

Amplicon Tutorial

• Seminar on Amplicon 16S Analysis - Background Introduction

• Interpretation of Amplicon Charts-Understanding the Idea of ​​the Article

• Amplicon analysis process - grasp the details of analysis

• Amplicon Statistical Drawing-High Score Articles

• 16S ability skill 0 Overview   1KO passage PICRUSt  2 element circulation FAPROTAX  3 table type bugbase 4KO passage Tax4Fun Tax4Fun2

• PICRUSt2: OTU/ASV and other 16S sequences can predict metagenomes at will, and the reference database is increased by 10 timesNBT article interpretation Software usage Bioinformatics | Zhang Liangliang’s group at Case Western Reserve University released the analysis and visualization R package ggpicrust2 for the prediction function of PICRUSt2

• CHM: FishTaco connects sample functions with corresponding microorganisms to obtain the driving factors for functional changes.

• Time series analysis of rice microbiome 1 Pattern diagram and PCoA  2a Correlation analysis 2b Scatter plot Fitting 3 Impact Plot 4 Random Forest Regression

• Nature Method: Rob Knight's team develops Striped UniFrac algorithm to analyze microbiome big data

QIIME2 tutorial (2023.7)

• NBT: QIIME 2 reproducible, interactive microbiome analysis platform

• 1Introduction&Install

• 2Plug-in workflow overviewWorkflow

• 3 Experienced guide for experienced drivers on the road

• Genome Biology: Time series analysis of microbiomes in various parts of the human body

• 4 Microbiome analysis of various parts of the human body Moving Pictures

• 5 Fecal Microbiota Transplantation Analysis Practice FMT

• Microbiome: Fecal bacterial transplantation improves autism

• 6Desert soil analysisAtacama soil

• mSystems: Effects of drought on the soil microbiome

• 7 Parkinson’s Mouse Tutorial Parkinson’s Mouse

• Cell: Intestinal flora promotes Parkinson’s disease

• 8 Differential abundance analysis gneiss

• 9Importing data

• 10Data exportExporting data

• 11Metadata

• 12Data filteringFiltering data

• 13Training feature classifiersTraining feature classifiers

• 14Data evaluation and quality controlEvaluating and controlling

• 15 Sample Classification and Regression q2-sample-classifier

• 16 Longitudinal and paired sample comparisons q2-longitudinal

• 17Identification and filtering of chimeric sequences q2-vsearch

• 18 sequence paired-end merge read-joining

• 19 Clustering OTUs using q2-vsearch

• 20 Utilities

• 21Evolutionary tree inference q2-phylogeny

• 22Command line interface q2cli

• 23 Graphical interface q2studio

• 24Python command line mode Artifact API

• 25 available and under development pluginsAvailableFuturePlugins

• 26Developing new plug-insDevelopingPlugin

• 27Semantic typesSemantic

• 28CommunityCommunity

• 29Reference databaseDataResources

• 30SupplementaryResourcesSupplementaryResources

• 31 nounGlossary

• 32How to write methods and reference Citing

Yishengxin-Amplifier Tutorial

• 01-Background introduction

• 02-Fungal primer selection

Webserver online analysis platform

• This Venn network is beautiful! Take you through drawing in 3 minutes!

• NAR | Hu Shengwei/Ni Wei/Chen Tong-Comprehensive database of animal macromicrobiome composition and function CRAMdb released

• Microbiome web tool MicrobiomeAnalyst  NAR original text  Nature sub-journal laboratory guide Practical tutorial a> NAR|MicrobiomeAnalyst 2

• NAR: Sun Yanni's group at Hong Kong University develops tools for identifying plasmids in metagenomes

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

• NAR: rrnDB-16S copy number correction database

• METAGENassist helps you handle the graphics needs of metagenomic analysis

• SILVAngs:16S/18S line analysis1  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 features V11 command list< a i=4>OTU table draw otutab_rare Core OTU identification otutab_core

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

• Amplicon analysis tool VSEARCH Analysis process 2.8.1 Chinese help document

• Nature Methods: Fast and accurate microbial source tracing tool FEAST Practical use of Phyloseq format Original code practice

• SourceTracker—Microbiological source analysis

• Introduction to LEfSe analysis
  Simplify and beautify the LEfSe analysis result graph LEFSe optimization results and color matching version Video tutorial< /span>

• DADA2 Chinese tutorial v1.8

• Microbial amplicon database

• NAR: UNITE fungal identification ITS database

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

• MIMOSA2: Integrated analysis based on microbiome and metabolome data

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

• FungalTraits: the latest fungal phenotype database beyond FUNGuild

• NBT | Rob Knight and others released Greengenes2 to achieve consistent amplicon and metagenomic results

metagenomic analysis

• Microbiome commonly used database domestic backup site

High-scoring article and book recommendations

• Understand metagenomic analysis routines in one article

• Springer publishes second edition of latest guidance on "metagenomics" research

• Nature review: 20,000 words to introduce you to the system of shotgun metagenomic experiments and analysis

• 1 Review, MetaPhlAn2, Kraken, MetaMaps, HUMAnN2, MEGAHIT, MetaWRAP, and Macroepigroup

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

• 3Metagenomic quantification, functional annotation and advanced analysis code

Software reviews and introductions

• Cell: Competition of 20 metagenomics species classification tools‘

• Nature sub-journal: Liu Yangyu, Rob Knight and others evaluate different metagenomic species quantification methods and their impact on the results

• NBT: The evaluation results of mainstream high-throughput sequencers in human/bacterial/metagenomic sequencing are released, and MGI performs well

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

• Qingdao Energy Institute proposes new microbiome similarity algorithm DMS

• Method innovation: 8 new tools for metagenomic analysis

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

Tutorial series

• 2016 Canadian Metagenomic Analysis Tutorial

• 1 Introduction - Definitions, Methods and Databases

• 2 Amplifier-Microbiome Diversity

• 3PICRUSt function prediction

• 4Metagenomic species composition and binning

• 5Metagenomic functional databases and pathways

• 6 Metatranscriptome Processes and Functions BBI: Eran Elinav Group Review Using Metatranscriptomes in Microbiome Research

• 7 Mining for Microbiome Biomarkers

• Microbiome training materials for $4,500

• Microbiome Assistant - the easiest to learn amplicon and metagenomic analysis process

• GigaScience: ASaiM based on Galaxy microbiome analysis framework

• Professor from the Department of Statistics at Stanford University takes you through microbiome analysis

• Experience summary of more than 30 metagenomic analysis softwarePart 1 Middle Part

• Review of microbiome data analysis tools | 16S + metagenome + metavirome + metatranscriptome

• Nature Protocols: A computational framework integrating metagenomic, metabolomic and phenotypic analysis

Read-based analysis with parameters

• MetaPhlAn2 Quantification of metagenomic species composition based on multi-marker genes Article interpretation Software usage

• HUMAnN2 functional quantification based on UniRef database1 Article interpretation 2 Software tutorial 3 Parametric analysis process

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

• Metagenomic sequence species classification: the use of kraken 1/2 and Bracken

• Kraken2: a rapid species annotation tool for metagenomic genomes

• Getting started with the metagenomic annotation and visualization tool MEGAN

No parameters Assembly-based

• 1 Background knowledge-Shell introduction and local blast practice

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

• 3 Assembling and splicing MEGAHIT (faster, more economical) and evaluation quast

• MEGAHIT: Ultra-fast single-node solution for very large and complex metagenome assembly via concise de Bruijn graphs

• metaSPAdes: a new versatile metagenomic assembly tool

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

• MetaQuast: Evaluating metagenomic splicing

• 4 Gene Annotation Prokka Prokka: Rapid prokaryotic genome and metagenomic gene annotation Prodigal: Prokaryotic gene identification and translation start site identification< /span>  metaProdigal: Gene and translation start site prediction from metagenomic sequences

• 5 Comparative dataset sourmash based on Kmer

• 6Salmon for fast estimation of gene abundance without alignment Salmon for rapid metagenomic gene quantification without alignment

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

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

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

• 10 Draw 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 an extensive functional, taxonomic, and ecological metadata framework

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

• Bioinformatics | Hong Kong City University student Yanni Sun’s group develops VirBot, a sequence detection tool for new RNA viruses

• WebMGA: an ultra-fast online tool for clustering and annotating genome sequences

species annotation

• TaxonKit: A compact, 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 an encyclopedia of genes, but few people know his contribution.

• Guide to using KEGG online database

• Installation and use of KEGG functional annotation tool KofamKOALA

• kofamscan: annotating KEGG pathways based on HMM model

CAZy glucose metabolism

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

CARD antibiotic resistance/drug resistance genes

• Microbiome: Study of the antibiotic resistanceome in urban beaches and sewage

antiSMASH

• NAR | antiSMASH 7.0: New and improved detection, regulation, chemical structure and visual predictions

• antiSMASH: prediction of microbial secondary metabolite gene clusters  

• NAR: antiSMASH database 2—Secondary metabolite gene cluster prediction

• PPT sharing on research progress of antibiotic resistance genes

• List some databases related to analyzing secondary metabolite gene clusters

• ARGfams: a tool and database resource suitable for rapid annotation of antibiotic resistance genes and discovery of new genes in environmental samples

Binning/MAG topic

• Nature sub-journal: Analysis process for mining prokaryotic genomes in metagenomes

• Microbiome: Metagenome binning process MetaWRAP Introduction Installation and database deployment  Practical combat and result interpretation< /span>

• NBT: Metagenomic "reading cloud" 10X library construction + Athena algorithm assembly to obtain high-quality microbial genomes

• DAS Tools: Recovering genomes from metagenomes using strategies for deduplication, aggregation, and scoring

• Understanding metagenomic binning in one article

• GTDB: Genome classification database, species annotation and evolutionary tree construction tool GTDB-tk

• CheckM - Bacterial genome/MAG completeness and contamination rate assessment

• MaxBin2 - an efficient binning tool

Statistical analysis and visualization

• Krona draws species or functional circle diagrams

• microbiomeViz: draw Cladogram in lefse results

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

• curatedMD package mines public metagenomic databases

microbial genome

• Complete De Novo sequencing analysis of bacterial genomes in one article

• EZBioCloud: 16S and prokaryotic genome species annotation and identification of new species

• drep: Rapid de-redundancy of microbial genomes - article interpretation + help documentation + practical combat

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

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

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

• NC: Chen Yihua’s group at the Institute of Microbiology, Chinese Academy of Sciences discovered a novel starting mechanism for polyketides

• Micro Classroom: MUMmer - National Microbial Science Data Center Cloud Tool

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

Research hotspots

genome set

latest articles

• NM: Human intestinal archaeal genome set

• NBT: Human gut microbial reference genome set covering more than 200,000 genomes

• NBT: A collection of 50,000 genomes and 12,000 new species of Earth’s microbial genomes

• NBT: 4941 metagenomic assembled genomes (MAGs) of the bovine rumen microbiome

High scores and feature mining

• Nature2019: A new blueprint for human intestinal flora

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

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

• Cell sub-issue 2019: Single genes in the human microbiome reference gene set

training group

• NC | BGI releases large-scale human intestinal culturable bacterial genome map

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

• NG: How do microorganisms adapt to plants? Bacterial genomes adapt to plant characteristics

historical classic

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

• PNAS2016: Global biogeography of functional characteristics of soil nitrogen cycling microorganisms

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

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

Special Topics on Third Generation Sequencing

• Nat. Methods | Harvard Li Heng's group develops third-generation HiFi metagenome assembly software—hifiasm-meta

• Nanopore R10.4.1 full-length 16s rRNA sequencing study

• AS: Wang Jun’s research group at the Institute of Microbiology, Chinese Academy of Sciences established new RNA-targeting pathogen detection methods mtNGS and mtTGS

• Nature sub-journal: DNA extraction and metagenomic analysis for third-generation sequencing

• NanoPlot: third-generation nanopore sequencing data quality assessment

• NBT: Interpretation of the second and third generation metagenomic hybrid assembly software OPERA-MS article Software usage

• Nature method | third-generation long-read metagenome assembly software metaFlye

• Nature sub-journal: NanoOK RT, third-generation Nonopore sequencing data drug resistance analysis software

• Nature sub-journal: Using MinION to quickly analyze the intestinal flora spectrum of premature infants and identify antibiotic-resistant pathogenic bacteria

• Nature sub-journal: A new method for detecting multiple DNA methylation types of bacteria and flora using third-generation Nanopore sequencing

• NBT cover: Nanopore metagenomic identification of lower respiratory tract pathogens in 6 hours

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

• 2019 Novel Coronavirus Nanopore Sequencing Standard Operating Procedures

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

• Selected articles with high scores in nanopore metagenomic sequencing

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

cancer microbiome

• Cancer Cell | Rutgers University reveals link between tumor microbiome, pancreatic cancer cell programming and immunity

Virome

• NAR | Ma Yingfei's group at Shenzhen Advanced Institute releases a high-throughput preparation method for chassis phage

• NAR: vRhyme - a biometric tool for sorting viral genomes in metagenomes

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

• PhiSpy: Identifying bacteriophages in bacterial genomes

• DBSCAN-SWA: Find lysogenic phages with one line of command

• Hot Topics: 3 Stories Overview Rapid Advances in Enterovirome Research

• Nature: Liang Guanxiang and others discovered the segmented parasitism pattern of enterovirome in newborns

• Cell sub-journal: The human intestinal virome is highly diverse, stable and individual-specific

• QB: Virus sequence identification based on deep learning

• Challenges in virome research - related emerging technologies

• SCLS: Institut Pasteur's Cui Jie group reveals genetic diversity of marine invertebrate RNA viruses

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

• eBioMedicine | Wang Hui’s group at Peking University People’s Hospital conducted a large-scale clinical study on rapid identification of lower respiratory tract infection pathogens using nanopore sequencing

• Front Microbiol | Yuan Lihong of Guangdong Pharmacy/Jiang Jingzhe of Nanhai Institute of Water Resources-Discussion on the latest classification standards of RNA viruses

multi-omics

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

• Nature sub-journal | Shen Xiaotao and others Precise health monitoring based on multi-omics data from trace blood samples

absolute quantification

• Summary of methods for absolute quantification of bacteria

• How much do you know about absolute quantitative research on microorganisms?

Linux and Shell

• XShell-easy-to-use ssh access server terminal usage tutorial

• seqkit: Sequence sorting artifact - statistics, format conversion, length filtering, quality value conversion, translation, reverse complementation, sampling, deduplication, sliding window, splitting and other 30 functions

• Do you know all the 21 special symbols in Linux commands whose meanings are difficult to search?

• htop | Linux process management tool usage tutorial

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

• This open source Linux tutorial created for student learning is really cool!

• A programming template worth having for beginners-Shell

• A programming template worth having for beginners - Perl

• Teach you step by step how to build a biometric analysis platform

• Windows easily implements the Linux shell environment: gitforwindows Special tutorial: This 40M small tool helps you process data under Windows with even more power

• Enable built-in Linux subroutines in win10

• Basic use of Docker-Ubuntu18.04

• linux minimalist statistical analysis tool datamash

• csvtk: table processing artifact - beautification, statistics, header tables, merging, transposing, filtering, sampling, de-redundancy, sorting, classification and summary and simple drawing

• The technology of batch renaming of files is worth having

• What should I do if a long-running program runs without adding nohup?

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

R statistical plotting

• This amazing website r-graph-gallery provides various graph codes 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

• Diagram Dictionary—a dictionary of visual diagrams

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

• Recommended introductory courses in R language statistics—Data Analysis for the Life Sciences

• Summary of basic routines for data visualization

• Convert R graphics 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 examples of data manipulation using dplyr

• Intersect, union, find differences setdiff

• R package reshape2 makes it easy to convert long and wide data tables

• The fastest big data processing R package in R and the most efficient than dplyr: tidyfst

• The application basis of string processing stringr package in microbial ecology

• 1Data type (vector, array, matrix, list and data frame)

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

• 3 Data filtering - extracting a subset of objects

• 4 Mathematical operations on vectors and matrices

• 5Control structure

• 6 Functions and Scope

• 7 Understand the loop functions lapply and sapply

• 8 Explode data frame split and view object str

• 9Simulation—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 5,000 words)

• ggplot2 geographical information visualization upper lower

• 1 First introduction to ggplot2 for drawing geometric objects

• 2 Use of layers—basics, labeling, and annotation

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

• 4 Grammar Basics

• 5Building images through layers

• 6Scales, axes and legends

• 7 Positioning - Facets and Coordinate Systems

• 8Theme settings, storage and export

• 9 Data sorting techniques required for drawing

• ggThemeAssist: Use the mouse to adjust the ggplot2 theme, no need to remember these codes anymore!

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

• ggplot version of waffle chart

R language statistical drawing

• Use the aPCoA package to implement covariate-corrected principal coordinate analysis (aPCoA) to exclude the influence of confounding covariates

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

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

• Simply use DESeq2/EdgeR for differential analysis

• Species abundance sorting stacked column chart and analysis of species differences between treatments

• ggplot2 version clustering tree + species abundance stacked plot

• R language: quickly generate many distinct colors

• 50 ggplot2 visualization cases

• R Language Conference: Summary of metagenomic data analysis and visualization routines

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

• R language learning notes heat map drawing

• Get the clustered and standardized results of the pheatmap heatmap

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

• R does linear regression

• Plot correlation coefficient matrix corrplot

• Correlation matrix visualization ggcorrplot

• Draw interactive graphics recharts

• Interactive visualization CanvasXpress

• Cluster analysis factoextra

• LDA analysis, plotting and adding confidence-ggord

• Resolving scatterplot sample label overlap with ggrepel

• Add P-value or significance mark ggpubr

• R language can complete difference statistics and visualization in batches with one click

• Alpha diversity dilution curve rarefraction curve

• How to draw lines connecting each component of a stacked bar chart: highlighting changes between groups

• Shock chart shows time series changes between groups ggalluvial

• Sankey plot riverplot

• Sequential arrangement of classified stacked column charts and adding appropriate bar labels

• A brief analysis of multi-group comparisons of non-parametric tests in R language and the graphic art of faceting and grouping

• Analysis of microbial environmental factors ggvegan

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

• Colorful evolutionary trees and heat maps are more suitable for ggtree

• Multiple regression tree analysis mvpart

• Random Forest randomForest Classification Regression

• Weighted gene co-expression network analysis WGCNA

• SPIEC-EASI microbial network construction example

• circlize package draws circos-plot

• R language to build a cool online blog system

• Draw personalized heatmaps using the ComplexHeatmap package

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

• Science combination chart interpretation: related corrplot+environmental factors connection

• gganimate draws animated graphs to observe continuous changing data

• Pathview package: Integrating expression profile data to visualize KEGG pathways

• ggcor: Correlation coefficient matrix Science-level combination chart

• ggridges package: time dynamic choppy graph

• gg.gap: Excellent and perfect solution for ggplot-order truncated coordinate axes gg.gap draws truncated plots

• Landscape World China Province

• Reproduce Science’s main image Maptree step by step

• Implementation of mixed linear model based on R

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

• Draw stacked column chart with clustering tree in R language

• R language perfectly reproduces the STAMP result graph

• Abundance distribution map drawing of microbial communities based on KEGG prediction function

• Frequency distribution plot and scatter plot SOP

• path analysis diagram

Microbiome R package

• Microbiome Statistics and Visualization—Getting Started with Phyloseq

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

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

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

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

network

• Development of network methods and introduction of the latest iDIRECT method

• R language visual reproduction of the network diagram layout in the Nature sub-journal of the Zhou concentrated team

• Science: Combination Chart Drawing

• MetagenoNets: Online metagenomic network analysis practical tutorial Interpretation of NAR articles

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

• Implementation of network graph in R-igraph

• Gephi easily draws beautiful network diagrams

• Microbial network construction: MENA, LSA, SparCC and CoNet  

• SparCC microbial network construction example

• Cytoscape: MCODE package implements network modular analysis GIANT package analyzes Z and P-score of the network Create a network with bar and pie nodes Figure

• Yiwen learns static and dynamic network drawing based on R

• Overview of Network Analysis - Introduction to Network Basics

Experimental design and technology

• An article explaining how to conduct research on plant endophytes

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

• Cell Reports: Removing 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 “weird” animal models for microbiome research

• Sample biological replicate data selection 1 Necessity  2 How many replicates are needed? Sample size determined

• Sample naming Notes Examples

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

• NBT: Minimum Information Standard 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 obtain Rhizosphere/Rhizoplane

• Microbiome: Comparison of methods for storing samples at room temperature

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

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

• Microbiome: A new method for amplicon detection of single-celled eukaryotes and parasites in environmental samples

• Rob Knight: PCR doesn’t need to be done in three parallels and then mixed!

• Effect of DNA extraction methods on plankton community research results

basic knowledge

• Audio Column-Metagenomic Vocabulary—001 Metagenome

• Nature review: Microbiota, metagenome, microbiome can’t be distinguished clearly

• Microbiome: Microbiome noun definition

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

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

• If amplicon analysis also 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

• Principle of overall difference assessment between groups using Adonis and ANOSIM methods

• PCoA distance algorithm encyclopedia

• Understand PCA and PCoA

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

• Basic knowledge of metagenomics

• Overview of functional gene diversity research

• Amplicon SCI routine1 Differences in community structure 2 Differences between groups 3 Summary

• Environmental factor correlation analysis—CCA or RDA

• The things behind the P value

• Easily understand the top ten commonly used algorithms in machine learning

• One article to understand the application of random forests in microecology

• The ROC curve you want to know

• Related analysis: Spearman, Kendall and Pearson

• Learn whole-genome sequencing data analysis 1Sequencing technology 2fasta&fastq

• Understand the development and application of Nanopore sequencing technology in one article

• Wheat's life vector collection stickers - from seed germination to maturity

Literature interpretation

*Author's interpretation (the author of the paper personally tells the results of the article and the story behind it).

The light of national journals

• mLife | Guo Xue of Tsinghua University and others Climate warming reshapes the seasonal dynamic changes of grassland soil microbial communities

• Fundamental Research: The mechanism by which root exudates affect carbon turnover by regulating soil microorganisms

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

• SBIO | The negative interaction between the Xinong Weige macrogroup and soybean soil bacterial phyla affects the dynamic changes and functions of the community

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

• JIPB: Baiyang group reviews root microbiome community construction and its contribution to plant adaptability

Nature

• Nature｜Study on human-to-human transmission of intestinal and oral microbiomes

• Nature | Biosynthetic potential of the global marine microbiome

• Nature | Zhu Xuan/Chen Fuhe/Yuan Guoyong et al. 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 modulates brain autoimmunity

• Nature | Jiangxi Nongda Huang Lusheng/Chen Congying et al. reveal the mechanism of pig blood type genes regulating intestinal flora

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

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

• Nature: Cheng Lei/Li Meng et al. discovered a new carbon metabolism pathway in methanogenic archaea

• Nature | Biogeographic study of prokaryotic genes

• Nature: An archaea located at the "junction" of prokaryotes and eukaryotes has been isolated

• Nature: Study on the spatial distribution of complex bacterial communities

• Nature: Jeff Dangl’s team reveals that the genus Vitis phagocytogenum maintains root growth in the microbiome

• Nature: Rob Knight's team finds blood and tissue microbiome can diagnose cancer

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

• Nature: Li Hai and others reveal that intestinal flora is involved in shaping the B lymphocyte antigen receptor repertoire

• Nature: Human placenta should really be sterile

• Nature: Advanced Institute of Chinese Academy of Sciences discovered an evolutionary stability strategy for spatially expanded habitat colonization

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

• Nature: iHMP's "Microbiome and Inflammatory Bowel Disease"

• Nature: iHMP's "Microbiome and Prediabetes"

• Nature: 25 milestones in human microbiota research

• Nature: The first systematic study of the influence of intestinal microorganisms on drug metabolism

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

• Nature: Announcements from bacteria—quorum sensing effect

• Nature: Skin microbiota-host interactions

• Nature: The fungus invades the pancreas from the intestine and enriches Malassezia bacteria

• Nature: How gut bacteria affect the brain and help eliminate fear-related behaviors

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

• Nature Special Topic: The Present and Future of Gut Microbiota Research

• Nature: Acquired bacterial defense genes discovered in human gut microbiota

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

• Nature review: Research progress on intestinal flora and colorectal cancer

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

Scinece

• Science | Infant gut microbiome changes strongly across lifestyles

• Science | Natural products in reconstructed microbial genomes from ancient DNA samples from the Middle and Upper Paleolithic

• Science | Landmark study using microbes to identify cancer accused of 'significant error'

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

• Science｜Changing microbial communities could enhance trees’ tolerance to climate change

• Science | Giant bacteria discovered in mangroves challenge conventional notion of nuclear membrane-less

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

• Science: Fang Gang's group at Mount Sinai School of Medicine in New York quantitatively analyzed the impact of bacterial contamination on eukaryotic DNA 6mA

• Science perspective: There is little cooperation between different bacterial species - rational use of the ubiquitous competitive relationship between bacteria to replace antibiotics

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

• Science: Archaeal ammonia oxidation in an oxygen-free world

• Science: How do leguminous plants build "nitrogen-fixing factories"? Murray's group has made important progress in the mechanism of root-nodule symbiosis.

• Science: The Xiang Hua/Li Ming group of the Institute of Microbiology, Chinese Academy of Sciences reveals a new toxin-antitoxin RNA system that protects CRISPR-Cas

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

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

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

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

• Science: The main role of nitrite-oxidizing bacteria in the dark ocean

• Science: Another star flora can regulate intestinal immunity?

• Science: The nitrogen fix

• Science: Comparative genome reveals phenotypic evolution mechanism of silverside fish in response to fishing behavior

• Science Comment | Just add one kind of bacteria, tomatoes not only resist salt stress but also increase yield by 65%!

• Science: Microbiome “gold rush”, discovering new antibacterial agents from the human body

• Science: Pathogens activate the disease-suppressing function of plant endophytes

• Science: Review of how gut microbiota affects social behavior

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

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

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

• Science: The 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 in plants and microbes: Interactions with symbiotic and pathogenic microbes drive plant evolution!

• Science: Big data reveals the diversity and functional landscape of intestinal flora of wild animals

• Science: Global dryland grazing and ecosystem services

Cell

• Cell | High-precision analysis of correlations between drugs, microbiome, and mortality in cancer patients

• Cell | Ultra-deep metagenome! Restore lost gut microbes

• Cell | Stanford University enables the design, construction and in vivo enhancement of complex gut microbiomes

• Cell | Stanford University Reveals Effects of Strain Removal on Metabolic Output and Interactions of the Gut Microbiome

• Cell | Dietary sugar-induced microbial dysbiosis undermines immune-mediated protection against metabolic syndrome

• Cell: Tsinghua University's Cheng Gong group reveals that an odor volatile from skin flora promotes flavivirus-infected hosts to attract mosquitoes

• Cell review: single-cell approaches in human microbiome research

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

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

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

• Cell: Tick genomic and metagenomic data

• Cell: A reverse ecology approach using gene flow to define microbial populations Introduction to PopCOGenT

• Cell: Zhejiang University Zhang Xing/Zhu Yong group reveals bacterial flagellar motor structure, assembly and torque transmission mechanism

• 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 signaling

• Cell: Earthly Heritage

• Cell: How plant roots allow beneficial microorganisms to colonize

• Cell Review: Human Gut Microbiota - From Association to Regulation

• Cell: Cross-kingdom interactions of root microorganisms promote the 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: Transformation of absolutely heterotrophic organisms into completely autotrophic organisms

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

Naturereview

• Nat. Rev. Microbiol. | Zuo Tao’s group from Sun Yat-sen University explains intestinal phages and host immunity

• Nat. Rev. Microbiol. | Academician Zhu Yongguan and others reviewed the soil plastic environment

• Nat. Rev. Bioeng. | Zuo Tao's group from Sun Yat-sen University details the engineering transformation of intestinal microecology

• Nature review | The potential of intestinal flora in the prevention and treatment of cardiometabolic diseases

• Nature Food | Zhejiang University builds 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 Microbial Community Formation

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

• Nature Review: An article reveals how the life and death process of soil microorganisms affects biogeochemistry

• Nature Review: From Soil to Clinic - Impact of Microbial Secondary Metabolites on Antibiotic Tolerance and Drug Resistance

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

• Shu Wensheng and Huang LinanNature review microbial diversity in extreme environments

• NRM: Human Microbial Culture and Cultureomics

• NRM: The formation mechanism and prevention trends of cyanobacteria blooms

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

• NRM: Tracing the “roots”: Microbial ecology of plant rhizosphere

• The driving role of NRM key species in microbial community structure and function

• NRM: The microbiome of permafrost

• NRM: Intraspecific diversity: explaining strains in the microbiome

• Nature review: A guide to microbiome analysis for doctorsPart 1 Part

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

• NRM: Improving crop yields? Crop microbiome is key

• NRM: emerging culture technology for uncultured microorganisms

• NRM: Aging and lifespan of microorganisms

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

• Nature review: Microorganisms and climate change

• Nature Review: A Century of Research on Bacteriophages

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

• NRG: Applications and Challenges of Clinical Metagenomics

• NRM: Microbes evolve and transform along the parasitism-symbiosis continuum!

• NRM: Methods and resources for studying drug resistance genes using metagenomic sequencing

• NRM: Unique and common features of mycorrhizal symbiosis

• NRM: How to get your ideal microbiome

• NRM: General principles and best practices for engineering microbiomes

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

• NRG: Methods and resources for studying drug resistance genes using metagenomic sequencing

• NRM: Plant-microbiome interactions: from community assembly to plant healthupper lower

Nature sub-journal

• Nature Food | Nanjing Institute of Soil Liang Yuting's group reveals microbial strategies to promote crop growth under aluminum acid stress

• Nature Food | Machine learning and metagenomics reveal common antimicrobial resistance signatures across multiple chicken farms and slaughterhouses in China

• Nature Food | Nannong Jiang Jiandong's group reveals the global distribution pattern and future changes of plant beneficial bacteria (full version)

• Nautre method | CheckM2 quickly, scalable and accurate assessment of microbial genome quality based on machine learning

• Nature Methods | Comparison of single- and multi-sample metagenomic binning reveals widespread hidden contamination

• Nature Methods | Caltech develops microbial enrichment method for high-host metagenomic samples

• Nature Computational Science | Jia Gengjie's group at the Institute of Genomics, Chinese Academy of Agricultural Sciences uses electronic medical records to build a human disease space

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

• Nature Biotechnology | Automation and machine learning for high-throughput microbial culturomics to isolate the microbiome

• Nature Microbiol | Nannong Zhang Ruifu's group reveals the interaction model in rhizosphere colonization of plant probiotics

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

• Nature Microbiology | Reconstructing host information in human intestinal metagenomes

• Nature sub-journal | Chu Haiyan Formation-Soil biodiversity and urban green space ecosystem functions (Comments by Zhu Yongguan/Wei Gehong)

• Nature sub-journal | New breakthrough from Neinong Da Zhang and Heping’s team—Human intestinal microbiome at high resolution Full text interpretation

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

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

• 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 to participate in nitrogen utilization*

• Nature Microbiology | Chen Yun/Bai Yang/Yu Yunlong et al. identify highly effective strains resistant to wheat scab and their mechanism of action

• Nature Microbiology | Wang Zhang/Chen Rongchang/Zhou Hongwei-Respiratory flora-host interaction mechanism in COPD

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

• Nature Protocols: Bacterial culture panel method-high-throughput isolation, culture and identification of root bacteria

• Nature protocols｜Jin Jianshi's group at the Institute of Zoology, Chinese Academy of Sciences released the high-throughput identification and absolute quantification method flow of single bacteria in flora

• Nature Microbiology | The green secret of goat poop

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

• Nature sub-journal | The carbon sequestration rate in groundwater is similar to the carbon sequestration rate in oligotrophic marine systems

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

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

• Nature sub-journal | Drawing an interaction map of plant phyllosphere flora to establish genotype-phenotype relationships

• Nature sub-journal | Zhou Ji’s team reveals that long-term climate warming leads to a decrease in grassland soil microbial diversity

• Nature Methods | Evaluation of CAMI2 Metagenomic Analysis Method

• NBT: Wang Jun and others use AI to “dig” antimicrobial peptides in the intestines super efficiently

• Nature sub-journal: Metagenomic assembly of genome to achieve lineage analysis

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

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

• NBT: Wang Yunhao, Ou Jianhui and others review nanopore sequencing technology

• Nature sub-journal | Analysis of dynamic changes in intestinal fungal flora and clinical outcomes in hematopoietic stem cell transplantation by Zhai Bing and others (recruiting postdocs and research assistants)

• NBT cover: Nanopore genome sequencing for rapid clinical diagnosis of bacterial lower respiratory tract infections

• NBT: MaPS-seq sequencing method reveals the spatial distribution of intestinal microorganisms

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

• NBT: Predicting gut microbiome diversity using the blood metabolome

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

• NBT: Exploiting cellular triglyceride storage to improve polyketide potency in Streptomyces

• NBT: a new approach to improve binning and assembly of metagenomes

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

• Nature Geoscience: Who is behind the restriction of asymbiotic nitrogen fixation*

• Nature Medicine: iHMP’s “Microbiome and Preterm Birth”

• Nature Medicine: Dynamics of the intestinal virome and bacteriome in early infant 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 the host under low-temperature TEM

• Nature Microbiology: Fang Gang's group reveals bacterial epigenetic regulation of Clostridium difficile sporulation*

• Nature Microbiology: Video interpretation! Siderophores: the “secret weapon” in the battle to defend scarce resources in the crop rhizosphere

• Nature Microbiology: Methods for phylogenetic analysis of microbiome data

• Nature Microbiology: Bacterial communities in global sewage treatment plants revealed!

• Nature Microbiology: Wang Sibao's group reveals the molecular mechanism of antimalarial resistance of intestinal symbiotic bacteria in Anopheles mosquitoes

• Review of Nature Microbiology: Diversity, ecological functions and evolutionary history of Archaea

• [Nature Microbiology: Standardized species classification method for archaeal genomes

• Nature Climate Change: Zhou’s team revealed 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 agroecosystems

• Nature Plants: University of British Columbia reveals new mechanism by which plants shape the rhizosphere microbiome

• Nature sub-journal: Sundaresan group-continuously disrupts the microbiome composition of rice after long-term drought (commented by Song Yi)

• Nature Plants: Root microorganisms can remotely improve plants' ability to cope with 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: Kenichi Tsuda's group at Huazhong Agricultural University uses in situ bacterial transcription and proteomics in plants to identify pathogenic bacterial proteins that are attacked by host immunity.

• Nature Plants: Sino-German cooperation discovers key biological mechanisms of mutualism between corn roots and rhizosphere beneficial microorganisms

• Nature Plants: Wang Mengcen's group at Zhejiang University reveals new disease-resistant functions of rice seed endophytes

• Nature Plants: Wang Xuelu’s team at Henan University reveals the evolution and molecular mechanism of compatibility between soybeans and rhizobia

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

• Nature Food Review: He Jizheng's group at the University of Melbourne reviews the potential of indigenous crop 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 | Ohio State's Yu Zhongtang group systematically reveals viral dark matter in the rumen ecosystem

• NC | CUHK and Yunnan Institute of Endemic Diseases - Bat virus co-infection, cross-species transmission and potential zoonotic virus spillover risks

• NC | Dai Lei's group at the Advanced Academy of Chinese Academy of Sciences develops SEER-FISH imaging technology to analyze the spatial structure of the microbiome

• Nat. Commun | Zhang Weipeng's group at Ocean University of China reveals the main sulfur-oxidizing bacterial groups in marine biofilm communities and their mechanism of action

• NC | Ma Yingfei's group at the Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences reveals the diversity of human intestinal archaeal viruses

• NC | Cai Lei's group at the Chinese Academy of Sciences reveals that cross-kingdom synthetic bacteria enhance tomato resistance to Fusarium wilt disease

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

• NC | Yang Gaowen's group at the College of Grassland Science, China Agricultural University revealed that multi-factor interference can reduce the positive effect of soil microbial diversity.

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

• NC | Tao Liang's group of West Lake University-TMPRSS2 "assists" viral infection and mediates host invasion of Clostridium sordellii hemorrhagic toxin

• NC | Gut Cells and Lactobacilli Work Together to Prevent Candida Infection

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

• NC: HKU Zhang Tong team-Omics-based drug resistance gene risk assessment framework

• Nat Commun | Gao Cheng and others from the Institute of Microbiology, Chinese Academy of Sciences have made progress in studying the functional pattern of microorganisms

• NC: Hao Haiping and Zheng Xiao of China Pharmaceutical University found that diet-microbe interaction alleviates intestinal damage

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

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

• NC: Wang Guanhong of the Institute of Zoology, Chinese Academy of Sciences and others review genetic technology to prevent and control mosquito-borne diseases

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

• NC: Zhongnong Xu Ling/UC Berkeley Coleman-Derr-Interaction mechanism between plants and rhizosphere microorganisms under drought (postdoctoral fellow)

• NC: Ecological study of inorganic sulfur-assisted metabolism genes in bacteriophages

• NC: Hainan University Zhang Xiaohua’s team discovered a new mechanism for Mariana Trench microorganisms to resist high pressure

• NC: Microbiota construction—randomness v. determinism, drought stress, host screening, unified dynamics (reviewed by Guo Liangdong and Yang Jun)*

• NC: Nannong Shen Qirong and Zhang Ruifu’s team reveals that diversity-induced deterministic bacterial assembly processes limit community functions

• 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 bee gut microbes

• NC: In response to drought, bacteria collapsed but fungi remained stable (pure network analysis published in Nature sub-journal)

• NC: Jia Zhongjun Group of Nantu Institute of Technology - Microbial mechanism of methane oxidation in rice 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 to all members of the anti-CRISPR protein family

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

• NC: Scientists from the Institute of Microbiology build a mouse intestinal microbial resource library

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

• NC: Impact of global change factors on soil microbial diversity and function

• NC: Cable bacteria reduce methane emissions in rice-growing soil

• NC: iGDA, a computational framework for reconstructing strain-level metagenomic sequences from third-generation sequencing

• NC: Liu Wei/Pan Yufeng et al. found that intestinal microorganisms can affect the aggressive behavior of fruit flies

npj journal

• NPJBM | Li Wenjun’s group at Sun Yat-sen University uses culture group-based metagenomics strategies to reveal microbial dark matter resources in special desert habitats

• npj | Zhang Demin’s team at Ningbo University reveals the regulatory mechanism of bacterial communities in shrimp biofloc culture systems

• npj | Wang Dehua/Zhang Xueying et al. reveal the mechanism by which desert rodents tolerate high salt through the "bacteria-gut-kidney" axis

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

• npj Microbiomes | Global emergent properties of bacterial communities induce drought resistance in Arabidopsis thaliana

Science and Advance series

• Science Advances | Wang Gaofeng's group at the Plastic Surgery Department of Nanfang Hospital reveals that skin symbiotic microorganisms promote hair follicle regeneration

• SA: Yang Yuanhe's group at the Institute of Botany reveals the key regulatory role of mineral protection and microbial attributes on frozen soil carbon dynamics

• SA | Tianhao Accu16S bacterial absolute quantitative technology helps discover the mechanism of "gut-bone axis" regulating bone necrosis

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

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

• SA: Pair-like analysis reveals impaired detoxification function of intestinal flora in patients with autism

• Adv. Intell. Syst. | Qingdao University publishes research on microbiome multi-label disease detection based on deep learning and host information embedding

• AS: Xihu Zheng Jusheng/Ju Feng-The accumulation of specific drug-resistant genes in the human intestine may lead to an increased risk of diabetes

• AS | CUHK Ding Tao/Tian Guobao et al. reveal that the differential input of oral flora shapes two lung types related to health conditions

• Adv Sci | Chen Zhenxia’s group at Huazhong Agricultural University reveals the potential reasons for gender differences in colorectal cancer

• AS | Zhejiang University’s Ma Bin group uses global-scale metagenomics to track ARG-carrying pathogens in soil

• Science Advances｜Wang Fengping’s team at Shanghai Jiao Tong University reveals the co-evolution history of deep archaea and the early Earth

Why are there so few Science sub-journals? Because the number of magazines and articles is the smallest, one order of magnitude less than the Nature sub-journal.

Cell sub-journal

• Cell Host & Microbe | Zuo Tao's group from Sun Yat-sen University explains the role of intestinal microecology in the efficacy of hematopoietic stem cell transplantation after drug use

• Cell Host & Microbe | Wang Zhang reveals the molecular mechanism by which respiratory flora disturbance promotes the decline of lung function in chronic obstructive pulmonary disease

• Cell Sub-Journal | Ma Yingfei/Dai Lei-Bacteriophage culture group analyzes intestinal dark matter (comments by Tong Yigang/Cui Jie/Guo Chunjun)

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

• Cell sub-journal: Liang Guanxiang's group at Tsinghua University reviews the process of human virome from origin to maturity and the corresponding regulatory mechanisms

• Cell Sub-Journal: 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

• Cell Sub-Journal: Stick to You - Bacterial auxin-mediated bacterial colonization of plant roots

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

• CHM: Study on host-targeted microbial-derived bacteriocins against diarrhea in early weaned piglets

• CHM Review: Site Characteristics of the Oral Microbiota: Micron-Scale Habitats and Niches

• CHM Review - Establishing Causal Relationships: Opportunities for Synthetic Microbiota in Plant Microbiota Research

• CHM: Modular characteristics of rhizobial microbial communities and their evolutionary relationship with symbiotic rhizobia

• CHM: Virome diversity in adult identical twins correlates with gut microbiome diversity

• CHM: Li Jianfeng’s group at Sun Yat-sen University reveals that plants use bacteria to acquire fungal resistance

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

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

• Cell Metab | Liu Xingyin’s group reveals new anti-tumor immunity mechanisms of intestinal microorganisms and their metabolite indole-3-lactic acid

• Breakthroughs and bottlenecks in TiMM microbiome research

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

• Cell Reports: Wei Fuwen's group at the Institute of Zoology, Chinese Academy of Sciences analyzed the function of seasonal changes in the intestinal flora of giant pandas

• Cell Reports | The assembly mechanism of microbial communities with metabolic division of labor in the Wu Xiaolei/Nie Yong group of Peking University

Gut

• Gut | Chen Weihua/Zhao Xingming team reveals that the use of proton pump inhibitors significantly promotes the spread of bacteria from the mouth to the intestines and its risk of disease

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

• Gut | Zhou Wei and other teams from China Pharmaceutical University 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 development trajectory of intestinal flora in children with autism (commented by Zhao Fangqing)

• Gut: Fecal virome transplantation reduces symptoms of type 2 diabetes and obesity in mice

• Gut: The original microbial origin of the human body and reproductive health* Pregnancy health is crucial to the child

• Gut: Stability and dynamic changes of human oral flora* Popular science: Oral microorganisms "Your energy is beyond my imagination"

• Gut-2018-Identification of intestinal biomarkers for early liver cancer

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

• Gut Microbes | Chengdu Traditional Chinese Medicine Fan Gang et al. Changes in the enterovirome are associated with type II diabetes and diabetic nephropathy

PNAS

• PNAS | China Agricultural University Zhou Xin’s team discovered that bees maintain host-specific intestinal bacteria by calling the immune system

• PNAS | About Bo Barker Jørgensen

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

• PNAS | Academician Zhu Yongguan’s team uses single-cell Raman combined with targeted metagenomics to reveal soil active antibiotic resistance group

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

• PNAS: Uniqueness of the human skin microbiome and mammalian phylogenetic symbioses

• PNAS: Asking about the stochastic and deterministic processes of microbial community succession - who is in charge?

Microbiome

• Microbiome | The Qu Mingren/Li Yanjiao group of Jiangxi Agricultural University reveals the dynamic changes in the interaction between rumen microorganisms and the body of newly introduced cattle during the stress transition period

• Microbiome | Zhang Demin/Guo Haipeng group of Ningbo University reveals the microecological mechanism of Litopenaeus vannamei resistance to vibriosis

• Microbiome | New progress in research on the environmental adaptive evolution of methanotrophic symbionts in the deep-sea Acropod clam, where the ocean is located

• Microbiome | Northwest Agricultural University reveals the long-term effects of key rumen bacteria and microbial metabolome on the lactation performance of adult dairy goats

• Microbiome | Liu Qingyou/Chen Weihua constructed goat intestinal microbial genome catalog

• Microbiome | Zhao Xingming’s group at Fudan University reveals the “intestinal-type” structure of four human fungi

• Microbiome | Li Meng's team at Shenzhen University Institute of Advanced Studies uses second- and third-generation metagenomic sequencing technology to analyze the metabolic potential of mangrove microorganisms

• Microbiome | Sun Yanni’s group at City University of Hong Kong publishes a high-resolution bacterial strain identification tool

• Microbiome | Shandong University and Max Planck Institute reveal epiphytic bacterial groups shared by different macroalgae

• Microbiome | Xinong reveals the mechanism by which high-fat diet disrupts peripheral tryptophan-kynurenine metabolism homeostasis

• Microbiome | CUHK's Ding Tao group reveals the characteristics of oropharyngeal flora shaped by common respiratory virus infections in the human body

• Microbiome | Peking University Wu Xiaolei/Nie Yong group: Artificial neural network predicts activated sludge microbial community composition

• Microbiome | Xinong Wei Gehong reveals the response and detoxification of rhizosphere bacteria to the allelopathic effects of licorice

• Microbiome | Institute of Microbiology Chen Yihua/Shenzhen Bay Tang Xiaoyu-Human-related bacteria adopt unusual pathways to synthesize 3-acetylated tetramers to adapt to the environment

• Microbiome | Xinong Weigehong's team reveals that plant domestication shapes wheat rhizosphere microbiome assembly and metabolic functions

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

• Microbiome | Jilin University Fu Yunhe's group reveals the new mechanism of "rumen/intestinal mastitis"

• Microbiome | Wang Jiaqi/Zhao Shengguo, Chinese Academy of Agricultural Sciences: Constructing a microsphere in-situ culture method to isolate important urea-decomposing bacteria from the bovine rumen

• Microbiome | Jiang Jingzhe’s team from the Nanhai Institute of Water Resources reveals the huge diversity of viruses in filter-feeding oysters

• Microbiome | Professor Hu Shengwei’s team at Shihezi University reveals the composition and function of the horse intestinal microbiome

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

• Microbiome | Jilin University Fu Yunhe's group reveals new mechanism of "enterogenic mastitis"

• Microbiome | Agricultural microbial resources team reveals vertical transmission mechanism of endogenous core microbiome in rice seeds

• Microbiome | Zhou Zhichao and others develop functional analysis software METABOLIC based on microbial genomes (video)

• Mirobiome | Sun Weimin’s team from the Institute of Soil, 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 rhizosphere microbial community in the pathogenesis of soil-borne Fusarium wilt

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

• Microbiome | Academician Yin Yulong’s team Yin Jia’s group has achieved important results in the field of pig probiotics research

• Microbiome | Northeast Agricultural University Shi Baoming/Meng Qingwei et al. reveal that host-microbe interaction mediates immunity in pig enteritis

• Microbiome | Wang Jiaqi + Zhao Shengguo, Chinese Academy of Agricultural Sciences: Opportunities and challenges in metagenomic-guided isolation and cultivation of uncultured microorganisms

• Microbiome: Microeukaryotic intestinal parasites in wastewater treatment plants: diversity, activity and removal

• Microbiome: Li Xiangdong Group of Hong Kong Polytechnic - Hospital-derived inhalable 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: Xinong Wei Gehong's team simplifies the synthesis of bacterial flora to prevent and treat astragalus root rot by activating ISR

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

• Microbiome: Hainan University Zhang Jiachao, Rob Knight and others reveal the adaptive evolution rules of probiotics in the host intestines

• Microbiome: Yang Jun Group of the Institute of Urban Environmental Protection-Small salinity changes change the construction process and network stability of micro-eukaryotic plankton communities in urban reservoirs

• Microbiome: Zhejiang University Ma Zhonghua team-new mechanism of biocontrol bacteria inhibiting pathogenic fungi

• Microbiome: Liu Shuangjiang’s group at the Institute of Microbiology established the human intestinal microbiome resource bank (hGMB)

• Microbiome | Zhang Huiming’s team at the Chinese Academy of Sciences reveals that RNA-mediated DNA methylation affects plant root microbial communities

• Microbiome: Coexistence model of methanogenic bacteria in rice field soil from the Liang Yuting Formation of Nantu Institute of Technology

• Microbiome: The composition and functional genes of rural environmental microorganisms may be protective against respiratory and allergic diseases

• Microbiome: the relationship between host genetics, intestinal flora and complex diseases in the Chinese population

• Microbiome: What proportion of Earth's prokaryotes have had their genomes sequenced?

• Microbiome: The definition of the microbiome revisited: old concepts and new challenges

• Microbiome: Kraken2 performs 16S species annotation quickly and accurately, beating QIIME2 in seconds

• Microbiome: a new group of predatory bacteria - unique habitat adaptability of Bradymonadales bacteria

• Microbiome: Succession patterns of microbial communities during the transition from active to inactive states in deep-sea hydrothermal sulfide chimneys

• Microbiome: Xie Kabin's group at Huazhong Agricultural University uses the CRISPR system to reduce host contamination in 16S rRNA gene sequencing*

• Microbiome: Nantusuo Sunbo Group reveals the mechanism by which intercropping reshapes the rhizosphere microbiome and promotes growth

• Microbiome: The Nanjing Agricultural University team has made important progress in the ecological function of myxobacterial predation

• Microbiome: Sino-foreign collaboration reveals enzymes used by microbial communities to degrade complex microbial polymers (Video Introduction)

• Microbiome: Environmental filtering drives unique spatial distribution of soil archaea in farmland ecosystems*

• Microbiome: Soil microbes drive nutrient cycling in the soil profile of a conversion of farmland to forest system*

• Microbiome: Nitrogen-fixing bacteria and nitrogen fixation are inhibited after 40 years of fertilization Press release: Chu Haiyan's group at the Nanjing Institute of Soil and Technology reveals the mechanism of long-term fertilization inhibiting nitrogen fixation by rhizosphere microorganisms*< /span>

• Microbiome: Root exudates drive soil memory to defend against plant pathogens*

• Microbiome: New progress in the relationship between potato scab and soil microbiome*

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

• Microbiome: Chicken intestinal microbiome metagene set (reviewed by Zhang Heping, Wei Hong, and Qin Nan)*

• Microbiome: Applying multi-dimensional meta-omics methods to collaboratively reveal the inter-bacterial correlations of target substrate metabolism in complex bacterial communities*

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

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

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

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

• Microbiome: skin and gut microbial responses to nuclear contamination in wild mammals

• Microbiome: The journey of microorganisms through plant generations

• Microbiome: Nannong Zhang Ruifu’s team reveals that changes in the grassland microbiome caused by grazing drive the transformation of soil organic carbon and the improvement of productivity

• Microbiome: Institute of Genetics and Development, 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 implements the process of rapid and reproducible analysis of metagenomes NG-meta-profiler

• Microbiome: The first "social relationship" network of Earth's microorganisms was drawn at Zhejiang University!

• Microbiome: Re-discussing the effect of amplicon function prediction analysis (Picrust)

• Microbiome: Species-level classification using 16S rRNA gene data sets

• Microbime: setting standards in microbiomics

• Microbiome: Domestication of rice seeds ecologically and 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 differentiation of ecological roles of the maize microbiome

• Microbiome: Metagenomes reveal signatures of resistance in tundra, temperate grasslands and tropical soils

NAME

• ISME | Zhu Zuobin/Wang Liang et al. discovered that genetic variation of intestinal microorganisms is involved in the regulation of host lifespan, sleep, movement and other functions

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

• ISME | Professor Hu Feng’s team from Nanjing Agricultural University reveals the mechanism of benzo[a]pyrene stress affecting the ecological adaptation strategies of earthworm enterovirome

• ISME | West Lake Jufeng Formation-Active predatory characteristics and diversity of myxobacteria in sewage treatment plants and their global distribution patterns

• ISME | Xinong Wei Gehong's team has made important progress in the study of environmental adaptation strategies of microbial communities in the desert "fat island"

• Deciphering the survival-pathogenesis trade-off mechanism of rhizosphere beneficial bacteria VOCs in reducing soil biological barriers of Ralstonia solanacearum

• ISME Comm | Applications of machine learning and deep learning in microbiome research

• ISME | Jiang Yu from Xinong/Huang Huoqing from the Animal Husbandry Medical Institute and others released a genome set of intestinal protozoa, subverting a century of knowledge

• ISME: Surface cyanobacteria sink to 1,000 meters deep to fix nitrogen

• ISME | Zhejiang University Huang Jianhua/Chen Xuexin et al. reveal a new mechanism by which parasitoids regulate host nutritional metabolism

• ISME | Arabidopsis secondary metabolites regulate microbiome-mediated nematode invasion

• ISME | Shen Qirong's team and Wei Zhong's group-Rhizosphere microbiome diagnosis of soil biological disorders

• ISME | Hydrothermal microbial communities reveal vent zone biogeography and evolutionary history of thermophilia

• ISME | Shen Qirong’s team has made progress in organic fertilizer-driven interaction between protists and Bacillus to prevent and control soil-borne diseases

• ISME: Yuan Zhilin et al. of the Academy of Forestry - Convergent evolution of gene families and balanced selection mechanism for symbiotic development of dominant fungi in fir

• ISME: Hu Feng/Zhu Yongguan et al. reveal the mechanism of soil phage-host bacteria cooperative response to organochlorine pesticide stress

• ISME: Nannong Zhang Ruifu's group revealed that Bacillus stimulates resident rhizosphere microorganisms to promote plant growth through metabolic interactions!

• ISME: New strategy for reducing soil biological barriers of Ralstonia solanacearum in Nannongweizhong

• ISME: Challenges in constructing and analyzing microbial networks

• ISME: Determinants of short-term and long-term sulfur utilization by soil microorganisms-based on 13C, 15N, 14C and 35S multi-isotope labeling results

• ISME: Xinong Shen Xihui + Wei Gehong + Wang Yao reveal new mechanism of bacterial iron acquisition and outer membrane vesicle recruitment

• ISME: Root recruitment of specific bacterial flora enhances plant resistance to salt stress

• ISME: Yuan Zhilin's group at the Yalin Institute of the Chinese Academy of Forestry reveals the positive selection mechanism of the gene island of dark-septate endophytic fungi in roots in saline-alkali soil

• ISME: Nanjing Institute of Soil and Technology Liang Yuting Group-Effects of microbial metabolism and residue-mediated fertilization on soil organic carbon under different climate conditions

• ISME: Li Wenjun’s group at CUHK has made progress on the ecological function and evolution of dark matter in actinomycete life

• ISME: Guo Jianhua Group of the University of Queensland-Artificial sweeteners can promote the spread of bacterial resistance

• ISME: Multi-omics reveals mercury methylating bacteria in hypoxic environment

• ISME: The Institute of Microbiology, Chinese Academy of Sciences reveals a new mechanism for bacteria to utilize light energy!

• ISME: Chu Haiyan's group at the Nanjing Institute of Soil, Chinese Academy of Sciences reveals that the biodiversity of key bacterial groups determines crop yields

• ISME: Wu Xiaolei's group at Peking University discovered that vesicles provide a new way for bacteria to utilize environmental heme

• ISME: Nannong Shen Qirong’s team accurately predicts the occurrence of soil blight based on big data Pure Health Information ISME

• ISME: Spatiotemporal dynamics of archaeal communities in offshore sediments: community construction mechanisms and co-occurrence relationships

• ISME: The nutritional energy strategy of marine ammonia-oxidizing archaea determines its biogeographic distribution pattern (Qin Wei's group is recruiting PhDs/postdocs)

• ISME: Zhang Zhibin's group at the Institute of Zoology, Chinese Academy of Sciences revealed that intestinal microorganisms mediate the upward effect of rainfall changes on the population of Bruce's vole*

• ISME: Balance of community building processes mediates species coexistence in farmland soil microbial communities*

• ISME: The resistance group of sewage treatment plants is driven by bacterial composition and gene exchange and the resistance expression in the effluent is active*

• ISME: Yang Jun's group from the Institute of Urban Environmental Protection reveals that reservoir cyanobacteria affect the community succession and species coexistence of eukaryotic plankton*

• ISME: Host gender can determine gut microbial response to parasitic infection*

• ISME: Integrated analysis reveals global diversity of the plasticosphere microbiome

• ISME: Subgingival microbiota associated with periodontitis in patients with type 2 diabetes

• ISME: Li Xia's group at Huazhong Agricultural University discovered the relationship between changes in the soybean rhizosphere microbiome and the efficiency of rhizobia symbiosis

• ISME: Pathogens mediate the assembly of beneficial microbial communities in plant rhizosphere

• ISME: Fructose in mycorrhizal fungal hyphal secretions serves as a signal to trigger phosphate-solubilizing bacteria to activate phytic acid

• ISME: Challenges in Microbial Ecology: Building Predictive Understandings of Community Function and Dynamics

• ISME: Experts open up the debate - what is the meaning of "1% of microorganisms can be cultivated"?

• ISME: Applications and misuses of correlation analysis in microbial ecology

• ISME: Shen Nongluan Junbo's group reveals the function of horizontally transferred genes

• ISME: Effects of carbon dioxide and nitrogen levels on plant root surface microbiota and function

• ISME: Comparative genomics reveals cyanobacterial evolution and habitat adaptation characteristics

• ISME Commun: Huazhong Agricultural University has made new progress in the convergence mechanism of bacterial flora

• ISME Comm | Disturbance and recovery of river plankton communities during and after the COVID-19 pandemic

Genome Biology/Research

• GB: City University of Hong Kong’s Sun Yanni group publishes VirStrain, a highly accurate virus strain identification tool

• GB: Zhao Fangqing’s group reveals the evolution patterns and determinants of intestinal flora in early life

• GB: MITER uses microbiome time series data to infer features associated with changes in host status

• GB: Xu Jian/Wang Shi/Huang Shi cooperate to develop a new microbiome sequencing method 2bRAD-M

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

• GR | Southern University of Science and Technology Xia Yu Group-Nanopore selective sequencing enriches 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 the water fly genome map and intestinal microbiome degradation rules

Protein & Cell

• Protein & Cell | Liu Yongxin’s group at the 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 system identifies off-target effects of multiple CRISPR tools

• Protein & Cell: Gut Microbiota in Cardiovascular Disease and Potential Therapeutic Applications

• PC: The role of intestinal flora and their metabolites in metabolic diseases

• PC: Chen Feng and others discuss how oral flora affects the whole body*

• PC: A comprehensive summary of the effects of microbiota on drug efficacy and toxicity*

Molecular Plant/New Phyto/Plant Comm

• Molecular Plant | Academician Shen Qirong’s team achieved new breakthroughs in the research and development of rhizosphere synbiotic biologically targeted regulation products

• MP | Dongnong Wu Fengzhi/Nannong Weizhong-Plant interspecific interactions mediated by root exudates shape the disease-suppressing ability of the rhizosphere microbiome

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

• MP Review: Systems Biology of Plant-Microbe Interactions

• MP: Microbial cross-kingdom balance maintains plant health

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

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

• New Phytologist | The Sun Bo/Liang Yuting group of the Southern Institute of Soil and Geosciences of the Chinese Academy of Sciences reveals microbial strategies to promote crop growth in low-fertility soils

• New Phytologist: The Sun Bo/Liang Yuting group of the Nanjing Institute of Soilology, Chinese Academy of Sciences reveals the coupling relationship between the spatial turnover rate of underground microorganisms and aboveground plants

• New Phyto | Shen Qirong’s team, Li Rong, and others analyze the mechanism by which bioorganic fertilizer cultivates rhizosphere flora in disease-suppressive soil to resist the invasion of pathogenic bacteria.

• New Phytologist | Zhongnong Feng Gu's group reveals that the mycelial core microbiome helps AM fungi mineralize organic phosphorus

• 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 microecology

• GPB: The mechanism of inulin in improving glucose and lipid metabolism disorders

• GPB: Identification and mechanism research on the key active ingredients of Gegen Qinlian Decoction to regulate intestinal flora and treat diabetes.

• GPB: MicroPhenoDB quantitatively correlates metagenomes with pathogenic microorganisms, core genes, and human disease phenotypes

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

• BiB | The Jiang Jingzhe/Yuan Lihong/Sun Yanni team collaborates to develop a bioinformatics tool that can be used for rapid virus classification

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

• BiB | Wang Yiwen's group at the Shenzhen Institute of Genomics, Academy of Agricultural Sciences, proposed a multivariate algorithm framework to remove batch effects in microbiome data

• Bioinformatics: Liu Fu's group of Jilin University-Deep learning to identify short viral sequences Virtifier from metagenomic sequences

• Bioinformatics | Shen Wei/Hu Peng/Ren Hong team develops metagenomic species composition analysis software KMCP that takes into account prokaryotes and viruses

• Bioinformatics & BIB｜A website used by Sun Yanni’s group in Hong Kong City to identify and analyze phage sequences in metagenomic data

environment

• EST | Wu Dong et al.-The community advantage of pathogenic bacteria in the air ensures the occurrence characteristics of drug-resistant genes

MDPI

• Agronomy | Xinonglin Yanbing Group’s biological inoculants combined with corn rotation reduce sunflower parasitism

Current Opinion Series

• COM: Application of recombinant bacterial community system in root microbiome research*

• COM: Application of next-generation microbiome technologies in crop production – limitations and the need for knowledge-based solutions

• COM: Beyond Pathogens - Interactions of the Microbiome with the Plant Immune System

• COM: root-soil-microbe interaction

• COB: Recycling of 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 microorganisms

Communications Biology

Nature Press’s new open source journal aims to accept outstanding articles rejected by Nature Communications. This year it received its first impact factor, and it is expected to stabilize at around 8 points in 2-3 years (the average level of Nature Communicates and Scientific Reports).

• CB: Zhejiang University of Technology’s Qian Haifeng group and others found that plankton algae blooms promote the spread and transfer of resistance genes

• CB: Liang Yuting Formation of Nanjing Institute of Soil and Technology-The high stability and metabolic ability of the bacterial community promotes the rapid reduction of easily decomposable carbon in the soil

• CB: Hu Yongfei’s group at China Agricultural University constructed reference genes and genome sets for integrated chicken intestinal microbiome

Chinese science

• SCLS: Rice microbiome time series analysis*

• SCLS: Arabidopsis thaliana diheterpenoids regulate the root microbiome*

• SCLS | Shen Qirong’s team and Yuan Jun’s group-Soil plant system affects the intestinal microbial composition and feeding preferences of herbivores

• SCLS | Academician Zhu Yongguan and others-Bacteriophage technology suppresses the risk of antibiotic resistance and hides the pandemic

• SCLS: The Institute of Microbiology Fang Rongxiang/Zhang Lili team developed specific 16S primers for plant endophytic bacteria

• SCLS | Xie Liwei's team discovered that butyrate-Mct1 is a key pathway for intestinal flora to regulate skeletal muscle stem cell homeostasis

• From "microbiome" to "microbiome": Behind the change in the translation of microbiome is a complete change in research ideas and methods

• Science in China: Plant immunity research and green prevention and control of pests and diseases: progress, opportunities and challenges

• Scientific Bulletin: Construction and Application of Synthetic Microbial Communities

• Science Bulletin: Cui Jie's group published comparative viromics analysis results of deep and shallow marine molluscs

• Science Bulletin | Latest progress in research on intestinal flora and coronary heart disease

food

• Cai Lei of the Institute of Microbiology and others successfully carried out soybean origin traceability and pathogenic fungi quarantine screening using microbiome technology

Overview

• JAFC cover | Academician Shen Qirong’s team reviews how to regulate the rhizosphere microbiome to protect plant health

• Trends in Plant Science | Plant Microbiota 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 reviews aseptic and bacteriostatic techniques in host-microbial interaction research

• TiM | Jia Baolei of Korea Chung-Ang University and others review the mechanism of intestinal microbiome-mediated reduction of cholesterol levels

• Annual Review丨Wang Ertao's group of the Chinese Academy of Sciences published a review on mycorrhizal symbiosis

• TiG: Wang Guanhong and Jackson Champer review symbiotic bacteria and gene drive technology to prevent and control mosquito-borne diseases

• TiP: Hu Da Feng Group reviews the new role of host mimics secreted by pathogens in the development of plant diseases!

• Liu Shuangjiang: Research on the impact of microorganisms on economic and social development

• Nearly 9 points of life news 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's group of Nanjing Institute of Soil and Geosciences reviewed the technologies and methods of microbiomics and their applications

• TM: Microbial rare biosphere community assembly processes

• TM: Do intraspecific changes in rDNA copy number affect microbial community analysis?

• TM: Microbial invasion: processes, patterns and mechanisms

• TiM: Tsinghua University Yang Yunfeng-Emerging models of microbial functional traits

• BA: Research progress on rhizosphere microbiome improving plant salt tolerance*

• FEMS review: How to sort out the “balls of yarn” in microbial networks

• TEE review: Plant-soil feedback (PSF): bridging the 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: Biotechnological Potential and Applications of Microbial Communities

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