Xu Lab

Adaptive graph learning of microbial phylogeny enables accurate and interpretable microbiome-based host phenotype prediction

Wed, 01 Jul 2026 00:00:00 +0000

Conserved 3′ stem-loop structures enable comprehensive analysis of bacterial transcription termination in metagenomes

Wed, 01 Jul 2026 00:00:00 +0000

Natural carrier-free self-assembled binary polyphenol nanoparticles remodel the gut microenvironment for inflammatory bowel disease prevention

Mon, 01 Jun 2026 00:00:00 +0000

Scikit-bio: a fundamental Python library for biological omic data analysis

Sun, 01 Feb 2026 00:00:00 +0000

Dietary Nisin Exacerbates Diabetic Vascular Complications through Gut Microbiota Modulation and NF-κB Signaling

Thu, 01 Jan 2026 00:00:00 +0000

High-Resolution Microbiome Analysis of Host-Rich Samples Using 2bRAD-M without Host Depletion

Sat, 01 Nov 2025 00:00:00 +0000

Decoding Oral Leukoplakia: Microbiome Dysbiosis and Inflammatory Dynamics Unveiled in a Rat Model

Wed, 01 Oct 2025 00:00:00 +0000

Survival and Safety Evaluation of Bifidobacterium Longum Subsp. Longum ZS-8 in Healthy Adults, Determined Using PMAxx-qPCR and Amplicon Sequencing

Mon, 01 Sep 2025 00:00:00 +0000

RNA–ligand interaction scoring via data perturbation and augmentation modeling

Fri, 01 Aug 2025 00:00:00 +0000

Metatranscriptomics Uncovers Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects

Tue, 01 Jul 2025 00:00:00 +0000

Systematic Analyses Uncover Robust Salivary Microbial Signatures and Host-Microbiome Perturbations in Oral Squamous Cell Carcinoma

Wed, 01 Jan 2025 00:00:00 +0000

Impacts of food additives on gut microbiota and host health

Fri, 01 Nov 2024 00:00:00 +0000

Epimedium polysaccharides mitigates textitPorphyromonas gingivalis-exacerbated intestinal inflammation by suppressing the Th17 pathway and modulating the gut microbiota

Tue, 01 Oct 2024 00:00:00 +0000

Screening of Lactic Acid Bacteria from Freshwater Fish Intestines and Their Effects on Growth, Immunity, and Disease Resistance in Zebrafish

Mon, 01 Apr 2024 00:00:00 +0000

A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Fri, 01 Mar 2024 00:00:00 +0000

Partial order relation–based gene ontology embedding improves protein function prediction

Fri, 01 Mar 2024 00:00:00 +0000

Lab NAS: Access and Usage Guide

Sun, 07 Jan 2024 00:00:00 +0000

Nas的功能概览

目前NAS主机校内访问地址

219.220.17.76（已经弃用）

10.160.16.1

下载实验室的文件

1. 校内访问，采用FTP协议连接，具体操作如下：

Windows系统需要打开文件管理器（随便打开一个文件夹）, 在地址栏目中输入 \\10.160.16.1
Mac系统服务器地址栏：smb://10.160.16.1
实验室账号用户：登录，填入账号名和密码，可以下载和上传，删除文件
实验室的相关文件路径：web/lab-禁止外传

windows访问流程

Mac访问流程

2. 校外访问，请访问以下链接：

网址链接：https://gofile.me/7zLiM/Cz2Sqe3IN
访问密码：xulab

下载速度比较慢：200k/s左右，仅提供下载权限

如果要上传文件或者下载自己的文件，请点击右上角登录，进入管理界面

校外连接校内服务器

IP地址：ad322hs0577.vicp.fun 端口：24467（流量1G/月，仅用于ssh，切勿传文件）

（通过贝锐花生壳平台做的内网穿透，可以通过外网访问内网的nas）

再通过命令：ssh -p 8088 chenjiongjin@222.204.6.66 ，访问服务器

网络通路的逻辑图：

本地主机->贝锐服务器（ad322hs0577.vicp.fun:24467）->nas主机（219.220.17.76:22）->前湖服务器(222.204.6.66:8088)

连接NAS设备

校内访问

访问链接：10.160.16.1:5004

输入账号密码登录

校外访问

访问链接：http://QuickConnect.cn/labxu666

输入账号密码登录

用NAS上传公共数据库

DeepPhylo: Phylogeny-Aware Microbial Embeddings Enhanced Predictive Accuracy in Human Microbiome Data Analysis

Mon, 01 Jan 2024 00:00:00 +0000

Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression

Fri, 01 Dec 2023 00:00:00 +0000

Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression

Tue, 01 Aug 2023 00:00:00 +0000

Effects of Vaginal Microbiota Transfer on the Neurodevelopment and Microbiome of Cesarean-Born Infants: A Blinded Randomized Controlled Trial

Sat, 01 Jul 2023 00:00:00 +0000

Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria

Wed, 01 Mar 2023 00:00:00 +0000

Activity

Mon, 24 Oct 2022 00:00:00 +0000

Contact

Mon, 24 Oct 2022 00:00:00 +0000

People

Mon, 24 Oct 2022 00:00:00 +0000

Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge

Sat, 01 Oct 2022 00:00:00 +0000

Systematic evaluation of antimicrobial food preservatives on glucose metabolism and gut microbiota in healthy mice

Thu, 01 Sep 2022 00:00:00 +0000

Cancer type classification using plasma cell-free RNAs derived from human and microbes

Fri, 01 Jul 2022 00:00:00 +0000

Diurnal and eating-associated microbial patterns revealed via high-frequency saliva sampling

Wed, 01 Jun 2022 00:00:00 +0000

Microbial and Nonvolatile Chemical Diversities of Chinese Dark Teas Are Differed by Latitude and Pile Fermentation

Sun, 01 May 2022 00:00:00 +0000

Gut Microbiome-Targeted Modulations Regulate Metabolic Profiles and Alleviate Altitude-Related Cardiac Hypertrophy in Rats

Tue, 01 Feb 2022 00:00:00 +0000

StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data

Sat, 01 Jan 2022 00:00:00 +0000

Gut Microbiota from Green Tea Polyphenol-Dosed Mice Improves Intestinal Epithelial Homeostasis and Ameliorates Experimental Colitis

Wed, 01 Sep 2021 00:00:00 +0000

Zebrafish model for human gut microbiome-related studies: advantages and limitations

Tue, 01 Jun 2021 00:00:00 +0000

Toxicant substitutes in immunological assays for mycotoxins detection: A mini review

Sat, 01 May 2021 00:00:00 +0000

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition

Fri, 01 Jan 2021 00:00:00 +0000

Alteration in gut microbiota is associated with dysregulation of cytokines and glucocorticoid therapy in systemic lupus erythematosus

Sun, 01 Nov 2020 00:00:00 +0000

Vitamin D metabolites and the gut microbiome in older men

Sun, 01 Nov 2020 00:00:00 +0000

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search

Wed, 01 Apr 2020 00:00:00 +0000

Human Skin, Oral, and Gut Microbiomes Predict Chronological Age

Sat, 01 Feb 2020 00:00:00 +0000

Bioinformatics Guide for Beginners

Sat, 07 Dec 2019 00:00:00 +0000

以下为开启生物信息学习的简易入门教程及小贴士，仅供参考。

LINUX

PYTHON

QIIME 2

详细内容请自行浏览 QIIME 2 官网。
以下经验基于 2018.11 版，如用其他版本请注意对应教程页左侧的版本号。

安装小贴士

Windows 用户请先装虚拟机 → Linux 系统 → 再装 QIIME 2（注意是 qiime2，不是 qiime）。
全程记录版本号与命令行，方便复现。

必跑教程

重点掌握 “Moving Pictures” 教程：
搞清每一步在做什么、输出文件含义、如何查 help。

Artifact API

可在 Jupyter Notebook 内直接调用
qiime2.Artifact.load() / .view() 等接口，方便交互分析。

Moving Pictures 精要

1. Metadata / Mapping 文件

- metadata记录原始数据，样本信息等，metadata需为tsv格式。
- metadata第一列名应为sampleid，注意sampleid列中的样本名不可以含有下划线（deblur DOESN'T support sample IDs with underscores, including the sample IDs in your metadata and sequence files, or your manifest file)
- metadata的要求请参照[Metadata in QIIME 2](https://docs.qiime2.org/2019.10/tutorials/metadata/)

sequence files
- 序列文件通常为fastq/fna格式，less可查看，gz文件用zless查看。
- 序列文件是已经去掉了barcode/primer/adaptor的clean data。
- demux后的序列文件通过提供manifest来导入，注意不同日期批次的qiime2在menifast格式上可能存在区别，所以一定要确认你正在使用的qiime2的版本。
- 注意:所有的序列都应该测的是同一段区域（起点相同），序列之间才具有可比性，否则序列比对是没有意义的。
barcode files
- barcode用来区别该序列来自于哪个样本，类似于商品的条形码。来自同一个样本的序列用相同barcode标记，所以根据barcode可以知道哪条序列属于哪个样本。
demultiplex
- 根据barcode信息，判断sequence是来自哪个样本，从而得到每个样本含有哪些序列，有多少序列。
- 如为反向互补序列，demux 时选择参数 --p-rev-comp-mapping-barcodes。
quality control
- 推荐deblur:deblur较传统的OTU聚类的方法，可以得到更精确的亚OTUs的信息。该方法是分别对单个样本进行分析，当样本来自不同批次或不同数据集时，该方法同样适用。
- 如果input是paired end sequence data，在deblur时实际上只会用到正向序列，而不会用到反向序列。如有需要用到反向序列，可join reads。
- qiime deblur denoise-16S 需要注意的参数： (a) --p-no-hashed-feature-ids 即保留原始序列（ATGC格式）。 (b) --p-min-reads (c) 查看deblur.qzv：理论上deblur之后剩下的序列数为(1-error rate)**trim length（其中error rate=0.005）；以100个碱基长度为例，deblur之后剩下的序列>(1-0.005)**100才比较合理
generate a tree
- moving picture中介绍了rooted tree
- 其他建树的方法有fragment insertion sepp
diversity analysis
- 参数--p-sample-depth的选择，可参考rarefaction curve，选择曲线上升到平台期为宜。
- diversity的分析前，不要忘记对table做rarefy！rarefaction的意义在于，当抽样深度不同时，rarefaction使不同测序深度间变得有可比性。
- alpha diversity: how many kinds of microbes are there单个样本内含有多少微生物。可从以下几个方面比较：（1）richness 种类（例如2个样本，1号含100种微生物，2号含150种微生物，这里只考虑种类，不考虑数量）；（2）evenness 均匀度（例如2个样本，1号含A3B3C3,2号A1B1C7，字母代表不同的OTU，数字代表个数，那么这个例子中1号OTU分布显然比2号更均匀）。常用计算alpha div的方法有：（1）observed otus (richness) 只计算每个样本中otu的种类；（2）evenness (evenness) 解释见上；（3）shannon (richness + evenness) 既考虑种类又考虑均匀度；（4）simpson (richness + evenness) 同上；（5）faith’s phylogenetic distance 除了还考虑种类和均匀度，还考虑进化距离……
- beta diversity: similarity and dissimilarity between two different samples两个样本间的相似性或不同
- 在coursera课程Gut Check: Exploring Your Microbiome中，有关于diversity有生动的说明，请自行移步。另外可参考Studying Microbial Diversity。
taxonomy assignment
- 根据实际情况，可选择用pre-trained Naive Bayes classifier ;如不适用，可根据自己的primer来train classfier。
- qiime feature-classifier classify-sklearn --p-read-orientation [reverse-complement|same]默认是自动检测前100个bases，然后判断是reverse还是same，一般默认参数就行。
ANCOM：得到差异表达的OTU
- ancom默认进行比较的两组样本是相互独立的，且仅有少量的（少于25%）的OTUs在两组间发生了改变。如果有大量序列改变，则不适用。
- 其他differential abundance计算方法还有q2-aldex2, q2-songbird, q2-conrcob等。

Importing Data

tsv, csv, txt文件可转化成The Biological Observation Matrix (BIOM) format再导入。

Emperor Animation

emperor可实现动画：在qiime2 view中打开emperor.qzv文件，右侧栏选择animation列，选择gradient（时间轴上的分组）和trajectory（样本的分组）category（它们的value必须是分类值，不能是数值）。

Tips

查看tutorial时需注意当前版本，应与安装的版本相对应（tutorial页面最左有版本信息），否则有些代码时可能会出现报错。
命名不要有空格和中文，不要取模棱两可的名字，时间久了可能自己都不记得这个文件是什么。名字长一点都没关系。
原则上不产生重复文件，可创建hard/symbolic link。
不要轻易覆盖raw data。
碰到解决不了的问题可在qiime2 forum上找是否有同样的问题，通常可以找到。或可以自己在上面提问。
所有command lines都要做好记录，要知道每一个文件是如何生成的，出现问题的时候能够追根溯源。同时，要记录好qiime2及其他工具的版本信息。
重要的文本文件用git做version control。
图片保存格式为pdf或者svg（矢量图）。
做项目时，一个项目创建一个文件夹，与该项目相关的文件都保存在该目录下。

课程推荐

Data Analysis

经过学习以上部分，有了基础概念之后，跟着这个网址进行数据分析课程的学习
参考用书“Python for Data Analysis”，涉及pandas，numpy，matplotlib，seaborn…

Microbiome

Gut Check: Exploring Your Microbiome

阅读推荐

期刊

推荐期刊：Nature、Science、Cell、PNAS、Nature Communications、Nature Microbiology、Microbiome、Cell Host & Microbes、ISME Journal、Gut、Gastroenterology、Genome Research、mBio、mSystems

Tips

看文献时，Abstract → Figures → Discussion
看文献时也要了解作者，通过作者去了解别人实验室的研究方向，可以学习别人实验上的思路/实验设计/延续性等。
带着批判性思维阅读What？Why？How？ 为什么要做这个实验，数据是否支持结论，统计方法是否正确，你接下来会怎么做等。
在自己研究方向上进行阅读，形成知识架构。什么是已知的，什么的未知的，提出问题，多思考如何解决问题。
文献汇报选择与自己研究直接相关的文章，有助于自己文献阅读的连续性。
实验汇报用1套PPT，每次在之前的基础上积累完善。包括背景介绍，提出问题，如何解决，用什么方法解决，结果，下阶段的计划安排。

书籍

I Contain Multitudes by Ed Yong
Missing Microbes by Martin J. Blaser
A Primer for Computational Biology（免费电子书）

其他工具

calour

熟悉tutorial
得到otuTable后，通常会用calour工具进行一些探索性的分析，用calour工具可以非常方便地对data进行filtering。

matplotlib/seaborn

最常用的画图工具，推荐教程： matplotlib-tutorial
mutipage pdf 可同时保存多张图片

jupyter notebook/jupyterlab & ipython

Don’t forget we can look at what any function does by using %psource
Don’t hardcode。同一套代码写成function后调用。写function注意逻辑性。

git commands

Github hello world tutorial git and github
Git commands command-line fundamentals（视频介绍）
重要的文件用git做version control，尤其是自己写的文本文件。了解简单的git add/commit/pull/push等命令的使用。

coursera-dl

coursera课程可通过coursera-dl命令进行下载，详见coursera-dl github。

Phylogenomics of 10,575 Genomes Reveals Evolutionary Proximity between Domains Bacteria and Archaea

Sun, 01 Dec 2019 00:00:00 +0000

Chlorogenic Acid Attenuates Cadmium-Induced Intestinal Injury in Sprague--Dawley Rats

Fri, 01 Nov 2019 00:00:00 +0000

Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads

Tue, 01 Oct 2019 00:00:00 +0000

Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2

Thu, 01 Aug 2019 00:00:00 +0000

Trace Evidence Potential in Postmortem Skin Microbiomes: From Death Scene to Morgue

Wed, 01 May 2019 00:00:00 +0000

Intermittent Hypoxia and Hypercapnia Reproducibly Change the Gut Microbiome and Metabolome across Rodent Model Systems

Mon, 01 Apr 2019 00:00:00 +0000

A Gut Microbiome Signature for Cirrhosis Due to Nonalcoholic Fatty Liver Disease

Fri, 01 Mar 2019 00:00:00 +0000

Calour: an Interactive, Microbe-Centric Analysis Tool

Fri, 01 Feb 2019 00:00:00 +0000

An examination of data from the American Gut Project reveals that the dominance of the genus Bifidobacterium is associated with the diversity and robustness of the gut microbiota

Tue, 01 Jan 2019 00:00:00 +0000

Identification of New High Affinity Targets for Roquin Based on Structural Conservation

Sat, 01 Dec 2018 00:00:00 +0000

Striped UniFrac: Enabling Microbiome Analysis at Unprecedented Scale

Thu, 01 Nov 2018 00:00:00 +0000

Antibiotic-Induced Microbiome Depletion Alters Metabolic Homeostasis by Affecting Gut Signaling and Colonic Metabolism

Sun, 01 Jul 2018 00:00:00 +0000

Best Practices for Analysing Microbiomes

Sun, 01 Jul 2018 00:00:00 +0000

American Gut: an Open Platform for Citizen Science Microbiome Research

Fri, 01 Jun 2018 00:00:00 +0000

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information

Fri, 01 Jun 2018 00:00:00 +0000

Taxon-Specific Aerosolization of Bacteria and Viruses in an Experimental Ocean-Atmosphere Mesocosm

Tue, 01 May 2018 00:00:00 +0000

Exposure to toxic metals triggers unique responses from the rat gut microbiota

Sun, 01 Apr 2018 00:00:00 +0000

Gut Microbiota Offers Universal Biomarkers across Ethnicity in Inflammatory Bowel Disease Diagnosis and Infliximab Response Prediction

Thu, 01 Feb 2018 00:00:00 +0000

Microbiome Data Accurately Predicts the Postmortem Interval Using Random Forest Regression Models

Thu, 01 Feb 2018 00:00:00 +0000

Guiding longitudinal sampling in IBD cohorts

Mon, 01 Jan 2018 00:00:00 +0000

Microbial effects of livestock manure fertilization on freshwater aquaculture ponds rearing tilapia (Oreochromis shiranus) and North African catfish (Clarias gariepinus)

Mon, 01 Jan 2018 00:00:00 +0000

A Communal Catalogue Reveals Earth's Multiscale Microbial Diversity

Wed, 01 Nov 2017 00:00:00 +0000

Microbiome Tools for Forensic Science

Fri, 01 Sep 2017 00:00:00 +0000

Evidence for Fungal and Chemodenitrification Based N₂O Flux from Nitrogen Impacted Coastal Sediments

Thu, 01 Jun 2017 00:00:00 +0000

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

Sat, 01 Apr 2017 00:00:00 +0000

Normalization and Microbial Differential Abundance Strategies Depend upon Data Characteristics

Sun, 01 Jan 2017 00:00:00 +0000

Lifestyle chemistries from phones for individual profiling

Tue, 01 Nov 2016 00:00:00 +0000

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

Fri, 01 Jul 2016 00:00:00 +0000

Microbiome-wide association studies link dynamic microbial consortia to disease

Fri, 01 Jul 2016 00:00:00 +0000

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies

Wed, 01 Jun 2016 00:00:00 +0000

Open-Source Sequence Clustering Methods Improve the State Of the Art

Mon, 01 Feb 2016 00:00:00 +0000

Experiment-Assisted Secondary Structure Prediction with RNAstructure