Abstract

Single-cell genomics and transcriptomics can provide reliable context for assembled genome fragments and gene expression activity on the level of individual prokaryotic genomes. These methods are rapidly emerging as an essential complement to cultivation-based, metagenomics, metatranscriptomics, and microbial community-focused research approaches by allowing direct access to information from individual microorganisms, even from deep-branching phylogenetic groups that currently lack cultured representatives. Their integration and binning with environmental ‘omics data already provides unprecedented insights into microbial diversity and metabolic potential, enabling us to provide information on individual organisms and the structure and dynamics of natural microbial populations in complex environments. This review highlights the pitfalls and recent advances in the field of single-cell omics and its importance in microbiological and biotechnological studies.

Key points

• Single-cell omics expands the tree of life through the discovery of novel organisms, genes, and metabolic pathways.

• Disadvantages of metagenome-assembled genomes are overcome by single-cell omics.

• Functional analysis of single cells explores the heterogeneity of gene expression.

• Technical challenges still limit this field, thus prompting new method developments.

中文翻译：

---

微生物单细胞组学：问题的症结。

摘要

单细胞基因组学和转录组学可以为组装的基因组片段和单个原核基因组水平上的基因表达活性提供可靠的环境。通过允许直接访问单个微生物的信息，甚至是目前缺乏培养代表的深层系统发育群体的信息，这些方法正迅速兴起，成为对基于培养的宏基因组学，元转录组学和以微生物群落为重点的研究方法的必要补充。它们与环境组学数据的整合和分类已经为微生物多样性和代谢潜力提供了空前的见解，使我们能够提供有关单个生物以及复杂环境中天然微生物种群的结构和动态的信息。

关键点

•单细胞组学通过发现新的生物，基因和代谢途径来扩展生命之树。

•单细胞组学克服了元基因组组装基因组的缺点。

•单个细胞的功能分析探索了基因表达的异质性。

•技术挑战仍然限制了该领域，从而推动了新方法的发展。