New Microfluidic Device Enables Characterization of Environmental Microbes

The Science

Microbes play critical roles in global scale environmental processes such as carbon cycling and the movement and degradation of environmental contaminants at waste sites. Understanding and predicting the roles of particular types of microbes in these processes remains extremely challenging, since over 90% of environmental microbes cannot be grown in the lab and existing approaches do not allow identification of specific cell types or quantification of their abundance. Researchers at Lawrence Berkeley National Laboratory and Sandia National Laboratories have now developed a new microfluidic device called µFlowFISH that enables the high-throughput identification of the types and abundance of microbes from environmental samples. Microbial cells are moved through the chip-mounted device using electrical currents, fluorescently labeled using diagnostic probes, and counted in a flow cytometry chamber. After initial testing with microbes that could be cultured, µFlowFISH was used to analyze microbes in groundwater samples from the DOE Hanford 100H cleanup site, targeting organisms known to be involved in uranium immobilization. Results from the device were in good agreement with more cumbersome and time-intensive techniques, requiring 100-fold less sample and far less time. Coupled to “omics” methods for comprehensive microbial community analysis, µFlowFISH presents a powerful new tool for dissecting microbial community structure and function in a variety of environments.


The μFlowFISH seamlessly integrates two components: a hybridization chamber formed between two photopolymerized membranes, where cells and probes are electrophoretically loaded, incubated and washed, and a downstream cross structure for electrokinetically focusing cells into a single-file flow for flow cytometry analysis. The device is capable of analyzing a wide variety of bacteria including aerobic, facultative and anaerobic bacteria and was initially tested and validated using cultured microbes, including Escherichia coli. Combined labeling and detection efficiencies of 74–97% were observed in experiments with simple mixtures of cultured cells, confirming specific labeling.

BER Program Manager

Dawn Adin

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Peng, L., R. J. Meagher, Y. K. Light, S. Yilmaz, R. Chakraborty, A. P. Arkin, T. C. Hazen, and A. K. Singh. 2011. “Microfluidic Fluorescence In Situ Hybridization and Flow Cytometry (µFlowFISH),” Lab on a Chip 16, 2673–79. DOI:10.1039/c1lc20151d.