Abstract
Microbiologists traditionally study population rather than individual cells, as it is generally assumed that the status of individual cells will be similar to that observed in the population. However, the recent studies have shown that the individual behavior of each single cell could be quite different from that of the whole population, suggesting the importance of extending traditional microbiology studies to single-cell level. With recent technological advances, such as flow cytometry, next-generation sequencing (NGS), and microspectroscopy, single-cell microbiology has greatly enhanced the understanding of individuality and heterogeneity of microbes in many biological systems. Notably, the application of multiple ‘omics’ in single-cell analysis has shed light on how individual cells perceive, respond, and adapt to the environment, how heterogeneity arises under external stress and finally determines the fate of the whole population, and how microbes survive under natural conditions. As single-cell analysis involves no axenic cultivation of target microorganism, it has also been demonstrated as a valuable tool for dissecting the microbial ‘dark matter.’ In this review, current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level were critically summarized, including single-cell isolation methods and experimental strategies of single-cell analysis with NGS. In addition, perspectives on the future trends of technology development in the field of single-cell analysis was also presented.
Highlights
Microbiologists usually study microorganisms by deciphering their physiology, internal interactions, and even genetic information
The recent studies have shown that cell-to-cell heterogeneity at both cellular and molecular levels in isogenic population could be an order of magnitude greater than previously thought (Lidstrom and Meldrum, 2003), suggesting the importance of extending traditional microbiology studies to the single-cell level
We summarize current state-of-the-art tools and methods for genomic and transcriptomic analysis of microbes at single-cell level, including single-cell isolation methods and experimental strategies of single-cell analysis with next-generation sequencing (NGS), and provide some perspectives on the future trends of technology development in single-cell analysis field
Summary
Microbiologists usually study microorganisms by deciphering their physiology, internal interactions, and even genetic information. Previous reports found that by using microfluidic devices, microbial single-cell analysis could obtain a better performance comparing with the traditional tube-based approach (de Bourcy et al, 2014). Two groups independently reported high-throughput microbial single-cell analysis protocols based on self-designed microfluidic devices (Hosokawa et al, 2017; Lan et al, 2017) These two protocols shared some similarities in single microbe encapsulation and lysis protocols. This method provides another possible method for single-cell RNA-seq in prokaryotic microbes, especially with the rRNA depletion methods mentioned above
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