Metagenomics and marker gene approaches, coupled with high-throughput sequencing technologies, have revolutionized the field of microbial ecology. Metagenomics is a culture-independent method that allows the identification and characterization of organisms from all kinds of samples. Whole-genome shotgun sequencing analyses the total DNA of a chosen sample to determine the presence of micro-organisms from all domains of life and their genomic content. Importantly, the whole-genome shotgun sequencing approach reveals the genomic diversity present, but can also give insights into the functional potential of the micro-organisms identified. The marker gene approach is based on the sequencing of a specific gene region. It allows one to describe the microbial composition based on the taxonomic groups present in the sample. It is frequently used to analyse the biodiversity of microbial ecosystems. Despite its importance, the analysis of metagenomic sequencing and marker gene data is quite a challenge. Here we review the primary workflows and software used for both approaches and discuss the current challenges in the field.

中文翻译：

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微生物生态学中的宏基因组方法：全基因组和标记基因测序分析的更新。

宏基因组学和标记基因方法，加上高通量测序技术，彻底改变了微生物生态学领域。宏基因组学是一种独立于培养物的方法，可以从各种样品中识别和表征生物体。全基因组鸟枪法测序分析所选样本的总 DNA，以确定生命各个领域是否存在微生物及其基因组内容。重要的是，全基因组鸟枪法测序方法揭示了存在的基因组多样性，但也可以深入了解所识别微生物的功能潜力。标记基因方法基于特定基因区域的测序。它允许人们根据样品中存在的分类群来描述微生物组成。它经常用于分析微生物生态系统的生物多样性。尽管宏基因组测序和标记基因数据的分析很重要，但它是一个相当大的挑战。在这里，我们回顾了这两种方法所使用的主要工作流程和软件，并讨论了该领域当前的挑战。