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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.


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.




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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