Microfluidics: A new tool for microbial single cell analyses in human microbiome studies

Abstract

Microbial cells behave differently in colonies and when singled out. The standard methods of microbiome studies present the average characteristics and behaviors of heterogeneous populations and lack the resolution to analyze microbes on a single cell level. Besides, the microbiome does not exist in pure colonies in human bodies, but naturally in complex communities. Therefore, it would be ideal to observe the microbes on a single cell level while maintaining their natural settings. Conventional dilution-to-extinction methods are capable of reducing the complexity of the communities to a minimal ecologically functional unit; however, new tools are needed to perform these studies. Recently, microfluidics as a new technology is gaining attention for various single cell applications because it offers the unique ability of handling nanoscale volume in microstructures, providing an attractive alternative to look at single microbial cells. Here, we compare different microfluidic technologies for microbial single cell studies and review the advancement of microfluidics for various microbial single cell analyses. Continuous microfluidics has been used in microbial single cell culture, whole genome sequencing, gene expression, and metabolic analyses; however, droplet microfluidics is becoming a new trend for its high-throughput single cell encapsulation ability. We envision that different microfluidic paradigms will be integrated in the future for their unique attributes and offer a versatile platform for systematic microbiome studies.