Hosokawa Masahito, Nishikawa Yohei
Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-Cho, Shinjuku-Ku, Tokyo, 162-8480 Japan.
Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, 3-4-1 Okubo, Shinjuku-Ku, Tokyo, 169-8555 Japan.
Biophys Rev. 2023 Sep 8;16(1):69-77. doi: 10.1007/s12551-023-01124-y. eCollection 2024 Feb.
The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial genomes. Among the various genome sequencing activities, metagenomic analysis, which entails the direct analysis of uncultured microbial DNA, has had a profound impact on microbiome research and has emerged as an indispensable technology in this field. Despite its valuable contributions, metagenomic analysis is a "bulk analysis" technique that analyzes samples containing a wide diversity of microbes, such as bacteria, yielding information that is averaged across the entire microbial population. In order to gain a deeper understanding of the heterogeneous nature of the microbial world, there is a growing need for single-cell analysis, similar to its use in human cell biology. With this paradigm shift in mind, comprehensive single-cell genomics technology has become a much-anticipated innovation that is now poised to revolutionize microbiome research. It has the potential to enable the discovery of differences at the strain level and to facilitate a more comprehensive examination of microbial ecosystems. In this review, we summarize the current state-of-the-art in microbial single-cell genomics, highlighting the potential impact of this technology on our understanding of the microbial world. The successful implementation of this technology is expected to have a profound impact in the field, leading to new discoveries and insights into the diversity and evolution of microbes.
新一代测序技术的出现，使得以相对较低的成本获取大量DNA序列数据成为可能，从而在微生物基因组解码方面取得了众多突破。在各种基因组测序活动中，宏基因组分析直接对未培养的微生物DNA进行分析，对微生物组研究产生了深远影响，并已成为该领域不可或缺的技术。尽管宏基因组分析做出了重要贡献，但它是一种“整体分析”技术，分析包含多种微生物（如细菌）的样本，得出的信息是整个微生物群体的平均值。为了更深入地了解微生物世界的异质性，类似于其在人类细胞生物学中的应用，单细胞分析的需求日益增长。考虑到这一范式转变，全面的单细胞基因组学技术已成为备受期待的创新，有望彻底改变微生物组研究。它有潜力发现菌株水平的差异，并有助于更全面地审视微生物生态系统。在这篇综述中，我们总结了微生物单细胞基因组学的当前技术水平，强调了该技术对我们理解微生物世界的潜在影响。预计这项技术的成功应用将在该领域产生深远影响，带来关于微生物多样性和进化的新发现和新见解。
