Single-Bacteria Isolation and Selective Extraction Based on Microfluidic Emulsion and Sequential Micro-Sieves

A high proportion of the human microbiota remains unknown, largely due to the large bacterial diversity in microbiome. Key technical challenges include the single-bacteria isolation in order to extract individual bacterial strains from the microbial extracts. Here, a single-bacteria isolation and device is developed based on microfluidic emulsion for generating microdroplets to encapsulate single bacterium, followed by selectively extract the microdroplets for any downstream bacterial culture or analysis. The microfluidic device consists of T-junction and micro-sieve array was fabricated by soft lithography and replica molding. The droplet generated by T-junction could encapsulate bacteria in single bacteria level with high efficiency (~90%). The highest isolation rate for droplet capturing by sequential micro-sieve was over 95%. The medium with the mixture bacteria was injected into the device for the specific bacteria isolation. The target type of bacteria could be sorted with high accuracy (92%). These results indicate that the single-bacteria isolation and cultivation platform is proposed for human skin microbiome studies to evaluate which biological properties of the microbiome and host will yield important new insights in understanding human health and disease related to bacterial infections and general bacteriology.