Microbiota、microbiome、metagenome的區(qū)別
中國微生物菌種查詢網(wǎng) / 2018-07-13 10:40:12
摘 要：
在閱讀文獻的時候經(jīng)常會碰到microbiota、metagenome、microbiome三個關鍵詞。Microbiota（微生物群，也稱微生物組）指研究動植物體上共生或病理的微生物生態(tài)群體，包括細菌、古菌、原生動物、真菌和病毒。Microbiome通常認為與Microbiota同義，但這兩個詞還是有一定區(qū)別。Microbiome既包括微生物，又包括其基因組。Metagenomics（宏基因組）指直接研究環(huán)境樣品的遺傳學材料。
我們每天在閱讀的文獻，總會碰到microbiota、metagenome、microbiome這三個關鍵字，那它們的具體意思是指什么呢。
一、Microbiota——微生物群（也稱微生物組）
微生物群是指研究動植物體上共生或病理的微生物生態(tài)群體。微生物群包括細菌、古菌、原生動物、真菌和病毒。研究表明其在宿主的免疫、代謝和激素等方面非常重要。近義詞Microbiome微生物組既包括微生物，又包括其基因組。
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——宏基因組
宏基因是指直接研究環(huán)境樣品作為遺傳學材料。廣義來説其包括環(huán)境基因組、生態(tài)基因組學和群體基因組學。傳統(tǒng)的微生物學和微生物基因測序依賴于單克隆的培養(yǎng)，早期環(huán)境基因測序克隆16s rRNA基因等特定基因來確定自然樣品中的生物多樣性。此方法將會漏掉大量末被培養(yǎng)的微生物多樣性。最近研究采用鳥槍法或PCR直接測序方法來獲得樣品群體中所有成員無偏好的基因。因為這類方法可以展現(xiàn)從前無法發(fā)現(xiàn)的微生物多樣性，因此宏基因組方法提供了革命性的工具去理解我們整個生活的世界。隨著測序價格的下降，宏基因組允許微生物生態(tài)研究比之前更大的尺度和更多細節(jié)。
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——微生物組
通常認為Microbiome與Microbiota同義，但這兩個詞還是有一定區(qū)別的。下面這篇Nature的Review，用圖形的方法對這三個詞進行了定義和描述，讓我們來學習一下：
Microbiota、microbiome、metagenome的區(qū)別
圖1. 微生物群、宏基因組和微生物組的定義。
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.