Activity-Based Protein Profiling-Enabling Multimodal Functional Studies of Microbial Communities

Abstract

Microorganisms living in community are critical to life on Earth, playing numerous and profound roles in the environment and human and animal health. Though their essentiality to life is clear, the mechanistic underpinnings of community structure, interactions, and functions are largely unexplored and in need of function-dependent technologies to unravel the mysteries. Activity-based protein profiling offers unprecedented molecular-level characterization of functions within microbial communities and provides an avenue to determine how external exposures result in functional alterations to microbiomes. Herein, we illuminate the current state and prospective contributions of ABPP as it relates to microbial communities. We provide details on the design, development, and validation of probes, challenges associated with probing in complex microbial communities, provide some specific examples of the biological applications of ABPP in microbes and microbial communities, and highlight potential areas for development. The future of ABPP holds real promise for understanding and considerable impact in microbiome studies associated with personalized medicine, precision agriculture, veterinary health, environmental studies, and beyond.

Keywords: Activity-based probes; Activity-based protein profiling; Microbial communities; Microbiomes.

Fig. 1

Multimodal analyses of microbial communities by ABPP. Probes can be used for enrichment and proteomics identification and quantification of target proteins in complex microbiomes or via attachment of a fluorophore spatial resolution of functional cells and proteins can be determined and/or cells can be isolated by cell sorting and sequenced. The future may also see function-dependent live cell sorting for subsequent cultivation and enhanced characterization of active cells from microbiomes

Fig. 2

Potential applications and challenges for ABPs in microbial communities. Once designed, probes can be used coupled to an enrichable moiety or surface. The probes can then be used for ABPP to identify and quantify active enzymes (top left) or used to functionally annotate proteins of unknown function (top right). Alternatively, the probe can be coupled to a fluorophore and then applied to the sample. This allows the use of FACS to isolate microbes possessing that function for cultivation or sequencing (bottom left) as well as imaging to study the spatial distribution of activity (bottom right)