Review：Microbiota, metagenome, microbiome傻傻分不清

原创 2017-08-02 刘永鑫 宏基因组

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进入微生物组领域也这么久了，每天阅读的文献，总会碰到microbiota, metagenome, microbiome这三个关键字，估计很多朋友不太清楚它们的具体意思什么。

首先从Wiki学习，这里还是非常专业的。

Microbiota 微生物群

微生物群是指研究动植物体上共生或病理的微生物生态群体。微生物群包括细菌、古菌、原生动物、真菌和病毒。研究表明其在宿主的免疫、代谢和激素等方面非常重要。近义词Microbiome微生物组即包括微生物，又包括其基因组。

附Wiki原文
A microbiota is an “ecological community of commensal, symbiotic and pathogenic microorganisms” found in and on all multicellular organisms studied to date from plants to animals. A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host. The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.
The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genomic characteristics, sometimes collectively referred to as a holobiont.

Metagenomics 宏基因组

宏基因是指直接研究环境样品作为遗传学材料。广义来説其包括环境基因组、生态基因组学和群体基因组学。传统的微生物学和微生物基因测序依赖于单克隆的培养，早期环境基因测序克隆16s rRNA基因等特定基因来确定自然样品中的生物多样性。此方法将会漏掉大量末被培养的微生物多样性。最近研究采用鸟枪法或PCR直接测序方法来获得样品群体中所有成员无偏好的基因。因为这类方法可以展现从前无法发现的微生物多样性，因此宏基因组方法提供了革命性的工具去理解我们整个生活的世界。随着测序价格的下降，宏基因组允许微生物生态研究比之前更大的尺度和更多细节。

Metagenomics is the study of genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. While traditional microbiology and microbial genome sequencing and genomics rely upon cultivated clonal cultures, early environmental gene sequencing cloned specific genes (often the 16S rRNA gene) to produce a profile of diversity in a natural sample. Such work revealed that the vast majority of microbial biodiversity had been missed by cultivation-based methods. Recent studies use either “shotgun” or PCR directed sequencing to get largely unbiased samples of all genes from all the members of the sampled communities. Because of its ability to reveal the previously hidden diversity of microscopic life, metagenomics offers a powerful lens for viewing the microbial world that has the potential to revolutionize understanding of the entire living world. As the price of DNA sequencing continues to fall, metagenomics now allows microbial ecology to be investigated at a much greater scale and detail than before.

Microbiome 微生物组

WiKi认为其与Microbiota同义，均为Microbiota词条。但其实这两个词区别还是很有的，看下图。

下面这篇Nature的Review，用图形的方法对这三个词进行了定义和描述，让我们来学习一下：

图1. 本综述中对微生物群、宏基因组和微生物组的定义。
每张图代表的是相同的群体，然而不同的方法可以定义此群体可提供的不同信息。

a. 微生物群：采用16S rRNA研究方法鉴定此环境中微生物的种类。
b. 宏基因组：微生物群的基因和基因组，包括质粒、强调群体的遗传学潜能。
c. 微生物组：微生物群的基因和基因组，以及微生物群的产物与宿主环境。

英文原始图注

Figure 1: Definition of the microbiota, metagenome and microbiome as used in this Review.

Each image represents the same population; however, different approaches to define the population provide different information.

a | Microbiota: 16S rRNA surveys are used to taxonomically identify the microorganisms in the environment.
b | Metagenome: the genes and genomes of the microbiota, including plasmids, highlighting the genetic potential of the population.
c | Microbiome: the genes and genomes of the microbiota, as well as the products of the microbiota and the host environment.
Abbreviation: rRNA, ribosomal RNA.

Reference

Figure 1: Definition of the microbiota, metagenome and microbiome as used in this Review. http://www.nature.com/nrurol/journal/v12/n2/fig_tab/nrurol.2014.361_F1.html
The microbiome of the urinary tract—a role beyond infection http://www.nature.com/nrurol/journal/v12/n2/full/nrurol.2014.361.html
【明概念】微生物组（microbiome）http://www.biotrainee.com/thread-156-1-1.html
http://www.microbe.net/2015/04/08/what-does-the-term-microbiome-mean-and-where-did-it-come-from-a-bit-of-a-surprise/
https://en.wikipedia.org/wiki/Microbiota
https://en.wikipedia.org/wiki/Metagenomics