Combinatorial Click Chemistry Labeling to Study Live Human Gut-Derived Microbiota Communities

Area of Science:

• Microbiology
• Molecular Biology
• Biotechnology

Background:

• Gut bacteria significantly impact host health and disease.
• Mechanistic studies of gut microbial communities are hindered by a lack of real-time analysis technologies for live bacteria.
• Current methods limit the dynamic tracing of heterogeneous bacterial populations at the strain level.

Purpose of the Study:

• To develop a novel technology for real-time, strain-level dynamic tracing of live gut bacterial communities.
• To enable detailed mechanistic studies of complex microbial ecosystems.
• To overcome limitations in current methodologies for analyzing live bacterial interactions.

Main Methods:

• Developed COMBInatorial cliCK-chemistry (COMBICK) labeling for both aerobic and anaerobic human gut-derived bacteria.
• Applied COMBICK labeling to clinical isolates, including the Enterobacteriaceae family.
• Demonstrated applicability of COMBICK on anaerobic strains directly isolated from human stool samples.

Main Results:

• Successfully enabled dynamic tracing of live, heterogeneous bacterial communities at the strain level.
• Showcased the ability to differentiate an exponentially increasing number of labeled bacteria based on available fluorophores and machine capabilities.
• Validated the method's effectiveness on diverse bacterial strains, including clinically relevant ones.

Conclusions:

• COMBICK labeling provides a powerful tool for real-time studies of bacterial communities across various ecosystems.
• This technology significantly advances mechanistic research in the microbiome field by enabling unprecedented insights into live bacterial dynamics.
• The method supports the analysis of complex and heterogeneous microbial populations, including those from clinical settings.