The metagenomics approach has revolutionised the fields of bacterial diversity, ecology and evolution, as well as derived applications like bioremediation and obtaining bioproducts. A further associated conceptual change has also occurred since in the metagenomics methodology the species is no longer the unit of study, but rather partial genome arrangements or even isolated genes. In spite of this, concepts coming from ecological and evolutionary fields traditionally centred on the species, like the concept of niche, are still being applied without further revision. A reformulation of the niche concept is necessary to deal with the new operative and epistemological challenges posed by the metagenomics approach. To contribute to this end, I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept in metagenomic studies. In particular, I raise the necessity of including the microbial genetic background as another variable into the niche space.

中文翻译：

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宏基因组学和利基概念。

宏基因组学方法彻底改变了细菌多样性、生态学和进化领域，以及生物修复和获得生物产品等衍生应用领域。还发生了进一步相关的概念变化，因为在宏基因组学方法中，物种不再是研究单位，而是部分基因组排列甚至孤立的基因。尽管如此，传统上以物种为中心的生态和进化领域的概念，如生态位的概念，仍然没有进一步修订而被应用。为了应对宏基因组学方法带来的新的操作和认识论挑战，需要重新制定生态位概念。为此，我回顾了生态位概念在生态学和微生物研究中的过去和现在的使用，表明需要在宏基因组学的背景下使用一个新的、更新的定义。最后，我对在宏基因组研究中利用生态位概念的更充分的概念背景提出了一些见解。特别是，我提出了将微生物遗传背景作为另一个变量纳入生态位空间的必要性。