从复杂微生物组或环境中鉴定并比较微生物

NGS提供一种无需培养的方法来鉴定使用其他方法可能无法发现的细菌或真菌

16S和ITS rRNA测序

16S和ITS rRNA测序(内部转录间隔区核糖体RNA测序)是常用的扩增子测序方法,可用于鉴定和比较给定样本中的细菌或真菌。基于NGS的ITS和16S rRNA基因测序可比较来自复合微生物组或环境中难以研究甚至不可能研究的样本的系统发育和分类,它们都是该应用领域的成熟方法。

原核生物的16S rRNA基因长约1500 bp,包含9个散布在保守区域之间的可变区。16S rRNA的可变区经常用于不同微生物群落的属或种系统进化分类。1 rRNA顺反子的ITS1区域是鉴定宏基因组样本中真菌物种的常用DNA标记。2

Bacteria

16S and Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) sequencing are common amplicon sequencing methods used to identify and compare bacteria or fungi present within a given sample. NGS-based ITS and 16S rRNA gene sequencing are well-established methods for comparing sample phylogeny and taxonomy from complex microbiomes or environments that are difficult or impossible to study.

The prokaryotic 16S rRNA gene is approximately 1500 bp long, with nine variable regions interspersed between conserved regions. Variable regions of the 16S rRNA gene are frequently used for phylogenetic classification of genus or species in diverse microbial populations.1 The ITS1 region of the rRNA cistron is a commonly used DNA marker for identifying fungal species in metagenomic samples.2

16S rRNA Sequencing with the iSeq 100 System

Using the 16S metagenomics workflow with the iSeq 100 System, you can achieve genus-level sensitivity for surveys of bacterial populations.

Read Application Note

16S和ITS核糖体RNA NGS方法的一个主要优点是它们提供了一种经济高效的技术,可以鉴定传统方法可能无法发现的菌株。与毛细管测序或基于PCR的方法不同,新一代测序无需培养即可分析样本中的整个微生物群落。

微生物学家通过16S rRNA NGS可以将菌群宏基因组学研究的灵敏度提升至属水平。使用NGS进行ITS分析可以快速鉴定真菌,有助于我们深入了解真菌微生物组。此外,NGS还能在单次测序运行中分析多个样本。

16S和ITS测序研究案例

Sequencing a Mouthful of Microbes
对口腔微生物进行测序

Saca la Lengua项目使用了16S和18S rRNA测序来鉴定生活在人类口腔中的细菌和真菌。

阅读访谈录
eDNA Sequencing Offers Powerful Look at Biodiversity
eDNA测序可提供生物多样性的强大视图

Michael Bunce博士使用新一代测序和宏条形码方法来研究环境DNA(eDNA)。

阅读访谈录
NGS is Revealing the Mysterious World of Microbes
神秘的微生物世界

Phil Hugenholtz博士解释了16S rRNA和鸟枪法宏基因组测序之间的区别,并讲述了NGS对他的研究产生了怎样的影响。

阅读访谈录
使用iSeq 100系统进行16S宏基因组学分析

通过iSeq 100系统开展16S宏基因组学工作流程,可使菌群研究的灵敏度达到种属水平。

阅读应用说明
真菌测序与分类

利用ITS宏基因组学工作流程可对不同类型的样本中的真菌进行种属水平的检测。

阅读应用说明
微生物学方法指南

该指南提供了您所需的全部信息,从文库制备到最后的数据分析。为您实验室的各种微生物学应用选择最佳工具。

获取指南
Microbiology Methods Guide
16S rRNA测序方案
16S rRNA测序方案

查看16S rRNA扩增子测序的演示方案和常见问题,以及来自利用该方案制备的文库和在MiSeq系统上运行产生的示例数据集。

查看实验方案
ITS rRNA测序方案
ITS rRNA测序方案

查看演示实验方案,了解如何分析真菌或宏基因组样本、引物序列以及BaseSpace Sequence Hub的分析工作流程。

查看实验方案
微生物与宏基因组学研究综述

宏基因组学是发展最快的科学学科之一。这篇文档重点介绍了近期发表的在宏基因组学研究中应用Illumina测序技术的文献。

查看PDF
微生物与宏基因组学研究综述

Illumina提供支持16S和ITS rRNA测序的产品,从文库制备到数据分析和解读。我们演示的工作流程可以帮助您消除实验中的相关猜测。

点击下方的查看工作流程各步骤所使用的产品。

Nextera XT v2 Index Kit

多重样本可以提高样本通量。

iSeq 100系统

具有经济实惠,快速且触手可及的测序能力,可在任何实验室进行靶向或小型基因组测序。

MiSeq系统

快速、准确、简便,适用于微生物学的深层次应用。

使用BaseSpace Apps进行分类学分类

16S Metagenomics

利用Illumina审核的GreenGenes分类数据库对16S rRNA靶向扩增子read进行分类学分类。

DRAGEN Metagenomics Pipeline

进行read物种分类,并提供单个样本和汇总报告。

MetaPhlAn

宏基因组系统发育分析(MetaPhlAn)工具可利用鸟枪法宏基因组测序数据分析微生物群落组成。

One Codex

在BaseSpace Sequence Hub使用快速、全面、准确的数据平台快速评估样本,进行宏基因组学分析。

Frequently Purchased Together

鸟枪法宏基因组测序
Bacteria

这种测序方法能够对给定的复杂样本中存在的所有生物体的所有基因进行全面的检测。微生物学家可以利用该方法评估细菌多样性,并检测各种环境中微生物的丰度。

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环境DNA测序
Environmental DNA

eDNA测序是一种研究生物多样性和监测生态系统变化的新兴方法。对于某些样本类型,结合16S或ITS测序与其他方法有助于揭示生态样本中完整的多样性信息。

了解更多

16s rRNA is a subunit of a ribosome found in all bacteria and archaea. It is 1500 nucleotides long and contains nine variable regions interspersed between conserved regions.

16s rRNA sequencing is a culture-free method to identify and compare bacterial diversity from complex microbiomes or environments that are difficult to study. It is commonly used to identify bacteria present within a given sample down to the genus and/or species level. Specifically, it is an amplicon-based sequencing method that targets the 16s rRNA bacteria-specific genetic marker using a single amplicon focused on a single gene.

Because the 16s rRNA sequence is ubiquitous in bacteria and archaea, it can be used to identify a wide diversity of microbes within a single sample and single workflow. Through 16s rRNA sequencing, one can identify taxa present in a sample. This leads to a greater understanding of our microbial communities and their interactions with us.

Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). In this case, 16s means it takes 16 Svedberg units of time for the ribosome to sediment in a solution.

All bacteria and archaea have a 16s rRNA sequence.

In amplicon sequencing of 16S rRNA, the primers used bind within regions that are not 100% conserved across bacteria. This leads to some regions of certain bacteria not being included in sequencing. Additionally, chloroplasts have some homology to 16s rRNA genes and may amplify. Because microbiome samples can come from a wide variety of sources with variable compositions, it’s recommended to use control samples when investigating new sample types.

16S DNA refers to the gene in the bacterial genome that codes for the 16S rRNA. 16S rRNA is the rRNA that is transcribed from the 16S DNA gene. The Illumina 16S Metagenomic Sequencing Library Preparation protocol uses DNA as input, and the PCR primers target the variable regions V3 and V4 of the 16S DNA gene for the amplicon PCR.

The 16S Demonstrated Protocol provides an option for creating Illumina compatible libraries from the target of your choice. Fungi and other organisms do not have 16s rRNA genes, however, they have other conserved regions such as 18S and ITS regions. Any amplicon can be used to do similar diversity analysis studies.

The internal transcribed spacer 1 (ITS1) region of the rRNA cistron is a commonly used DNA marker for identification of fungal species in metagenomic sample. ⁵

iSeq 100系统
iSeq 100系统

iSeq 100系统让新一代测序比以往更简单,也更经济。

了解更多
MiSeq系统
MiSeq系统

MiSeq台式测序仪支持靶向测序和微生物基因组应用,测序质量高、数据分析简单和具有云端存储功能。

了解更多
Nextera XT和Nextera DNA Flex
Nextera XT和Nextera DNA Flex

为小型基因组、扩增子、质粒和其他应用制备测序文库。

查看产品
MiSeq、16S rRNA测序和美国肠道计划
16S rRNA测序和"公众科学利"计划

新一代测序技术使人类微生物组研究成为可能,例如美国肠道计划。

观看视频
16S rRNA测序在线讲座
16S rRNA测序在线讲座

详细了解我们的16S rRNA测序演示方案,包括数据可视化和成功案例。

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参考文献
  1. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol. 1991;173(2):697–703
  2. Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci. 2012;109(16):6241-6
  3. The Human Microbiome Project Consortium (2012) Structure, function and diversity of the healthy human microbiome. Nature 486:207–14.
  4. McCafferty J, Mühlbauer M, Gharaibeh RZ, Arthur JC, Perez-Chanona E., et al. (2013) Stochastic changes over time and not founder effects drive cage effects in microbial community assembly in a mouse model. ISME Journal doi: 10.1038/ismej.2013.106.