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Probe-enabled approaches for function-dependent cell sorting and characterization of microbiome subpopulations.

Andrea K Steiger¹, Sarah J Fansler¹, Christopher Whidbey²

¹Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States.

Methods in Enzymology

|May 18, 2020

Summary

Researchers can now isolate and study microbiome subpopulations by targeting enzyme activity using chemical probes and fluorescence-activated cell sorting, advancing microbiome research.

Keywords:

Activity-based protein profiling Cell sorting Chemical biology Chemical probes Function-dependent Gut microbiome Microbiome Soil microbiome

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Area of Science:

Microbiome Research
Enzymology
Chemical Biology

Background:

Microbiome complexity and heterogeneity pose challenges to understanding species roles and functions.
Genomics can identify microbiome species and proteins, but enzyme activity characterization remains limited.
Understanding functional roles is crucial for microbiome applications in gut and soil environments.

Purpose of the Study:

To describe the application of small molecule chemical probes for isolating and characterizing microbiome subpopulations based on enzymatic function.
To provide a resource for researchers studying the functional roles of microbiomes.

Main Methods:

Utilizing small molecule chemical probes to label microbes based on specific enzyme activity.
Implementing protocols for microbiome sample preparation suitable for functional analysis.
Employing fluorescence-activated cell sorting (FACS) for the isolation of functional subpopulations.

Main Results:

Demonstrated a strategy for isolating microbiome subpopulations based on enzymatic function.
Enabled characterization of microbial communities by targeting enzyme activity.
Provided a method to overcome limitations in assessing functional aspects of microbiomes.

Conclusions:

Small molecule chemical probes combined with FACS offer a powerful approach to functional microbiome analysis.
This strategy facilitates the isolation and characterization of specific functional microbial groups.
The described methods serve as a valuable resource for advancing microbiome research in diverse environments like the gut and soil.