Ribière Céline, Beugnot Réjane, Parisot Nicolas, Gasc Cyrielle, Defois Clémence, Denonfoux Jérémie, Boucher Delphine, Peyretaillade Eric, Peyret Pierre
EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France.
Genoscreen, Campus de l'Institut Pasteur de Lille, 59000, Lille, France.
Methods Mol Biol. 2016;1399:167-82. doi: 10.1007/978-1-4939-3369-3_10.
Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.
微生物群落广泛存在于地球表面且极其多样，在生态系统功能中发挥着关键作用。因此，尽管新一代测序（NGS）技术极大地增进了我们对微生物多样性的认识，但仍有必要降低生物复杂性，以便更好地理解微生物的功能。为实现这一目标，我们描述了一种基于溶液杂交选择（SHS）方法的有前景的途径，用于从宏基因组和宏转录组样本中选择性富集目标特异性生物标志物。该方法的成功很大程度上取决于确定灵敏、特异且具有探索性的探针，以评估完整的目标基因库。实际上，在这种方法中，RNA探针被用于捕获携带感兴趣生物标志物的大DNA或RNA片段，这可能有助于将感兴趣群落的结构与功能联系起来。
