Microbiota、microbiome、metagenome的区别

摘 要:

在阅读文献的时候经常会碰到microbiota、metagenome、microbiome三个关键词。Microbiota(微生物群,也称微生物组)指研究动植物体上共生或病理的微生物生态群体,包括细菌、古菌、原生动物、真菌和病毒。Microbiome通常认为与Microbiota同义,但这两个词还是有一定区别。Microbiome既包括微生物,又包括其基因组。Metagenomics(宏基因组)指直接研究环境样品的遗传学材料。

关键词: , ,

我们每天在阅读的文献,总会碰到microbiota、metagenome、microbiome这三个关键字,那它们的具体意思是指什么呢。

一、Microbiota——微生物群(也称微生物组

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微生物组既包括微生物,又包括其基因组

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.

二、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 persity in a natural sample. Such work revealed that the vast majority of microbial biopersity 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 persity 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.

三、Microbiome——微生物组

通常认为Microbiome与Microbiota同义,但这两个词还是有一定区别的。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:

Microbiota、microbiome、metagenome的区别

图1. 微生物群、宏基因组和微生物组的定义。

Figure 1: Definition of the microbiota, metagenome and microbiome

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.

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