More and more, scientific advancements in energy production, plant nutrition, and bioremediation rely on characterizing microbial communities beyond their genomes and messenger RNA molecules into how they function in their environment. But current techniques for characterizing microbes from their environment universally fail to provide a way to sort based solely on function, rather they rely entirely on genome inference.

Researchers at Pacific Northwest National Laboratory have developed function-based microbial probes that identify, sort, and quantify microbes, enzymes, toxins, and the like in biological environments such as soil, water, air, and host-associated organisms. The technique couples the measurement of biochemical activity with the identification of species, such as microbes and enzymes, involved in that activity. For example, by inserting a probe into the microbiome, researchers can identify which members of the community are involved in the degradation of various resources, such as cellulose, chitin, proteins, and lignin. PNNL can provide the probes for use or a method and kit for building probes or for performing function-based sorting of communities.

The technique has been used to study an enzyme related to drug metabolism and important for microbial carbon acquisition. The probe successfully revealed the composition of the microbiome and proved that simply numbering species, a common approach today, isn’t enough to quantify function. 

APPLICABILITY

Microbial probes could be used to identify microbes, enzymes, toxins, and the like involved in microbiomes that could support

• biofuel or bioenergy production
• nutrient cycling through soils, plants, animals, or the human body
• bioremediation
• toxin detection
• single-cell genome sequencing.