Santos Andres, van Aerle Ronny, Barrientos Leticia, Martinez-Urtaza Jaime
Applied and Molecular Biology Laboratory, Centre of Excellence in Translational Medicine, Universidad de La Frontera, Avenida Alemania 0458, 4810296 Temuco, Chile.
Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Avenida Francisco Salazar 01145, 481123 Temuco, Chile.
Comput Struct Biotechnol J. 2020 Jan 31;18:296-305. doi: 10.1016/j.csbj.2020.01.005. eCollection 2020.
Assessment of bacterial diversity through sequencing of 16S ribosomal RNA (16S rRNA) genes has been an approach widely used in environmental microbiology, particularly since the advent of high-throughput sequencing technologies. An additional innovation introduced by these technologies was the need of developing new strategies to manage and investigate the massive amount of sequencing data generated. This situation stimulated the rapid expansion of the field of bioinformatics with the release of new tools to be applied to the downstream analysis and interpretation of sequencing data mainly generated using Illumina technology. In recent years, a third generation of sequencing technologies has been developed and have been applied in parallel and complementarily to the former sequencing strategies. In particular, Oxford Nanopore Technologies (ONT) introduced nanopore sequencing which has become very popular among molecular ecologists. Nanopore technology offers a low price, portability and fast sequencing throughput. This powerful technology has been recently tested for 16S rRNA analyses showing promising results. However, compared with previous technologies, there is a scarcity of bioinformatic tools and protocols designed specifically for the analysis of Nanopore 16S sequences. Due its notable characteristics, researchers have recently started performing assessments regarding the suitability MinION on 16S rRNA sequencing studies, and have obtained remarkable results. Here we present a review of the state-of-the-art of MinION technology applied to microbiome studies, the current possible application and main challenges for its use on 16S rRNA metabarcoding.
通过对16S核糖体RNA（16S rRNA）基因进行测序来评估细菌多样性，这是环境微生物学中广泛使用的一种方法，特别是自从高通量测序技术出现以来。这些技术带来的另一项创新是需要开发新的策略来管理和研究产生的大量测序数据。这种情况促使生物信息学领域迅速扩展，发布了新工具，主要应用于对主要使用Illumina技术产生的测序数据进行下游分析和解读。近年来，第三代测序技术已经得到发展，并与之前的测序策略并行且互补地应用。特别是，牛津纳米孔技术公司（ONT）推出了纳米孔测序，它在分子生态学家中非常受欢迎。纳米孔技术价格低廉、便于携带且测序通量高。这项强大的技术最近已用于16S rRNA分析，并显示出有前景的结果。然而，与之前的技术相比，专门为分析纳米孔16S序列设计的生物信息学工具和协议较为匮乏。由于其显著特点，研究人员最近开始对MinION在16S rRNA测序研究中的适用性进行评估，并取得了显著成果。在此，我们对应用于微生物组研究的MinION技术的最新进展、其当前可能的应用以及在16S rRNA宏条形码分析中使用的主要挑战进行综述。
