Chemical Reporters for Exploring Microbiology and Microbiota Mechanisms

Abstract

The advances made in bioorthogonal chemistry and the development of chemical reporters have afforded new strategies to explore the targets and functions of specific metabolites in biology. These metabolite chemical reporters have been applied to diverse classes of bacteria including Gram‐negative, Gram‐positive, mycobacteria, and more complex microbiota communities. Herein we summarize the development and application of metabolite chemical reporters to study fundamental pathways in bacteria as well as microbiota mechanisms in health and disease.

Contributions of Human-Associated Archaeal Metabolites to Tumor Microenvironment and Carcinogenesis

“…In the present study, we utilized more than 44,000 metagenome-assembled contiguous sequences (contigs) with length of >1,000 bp from publicly available databases to investigate the diversity of archaea, especially the cancer-related metabolites in different body sites. Microbial metabolites are believed to be the essential bridge connecting microbiota, tumor microenvironment, and cancer development ( 28 , 30 ). Our study provides a framework for better investigating the correlation of archaeal metabolites with cancer.…”

Engineering bacterial surface interactions using DNA as a programmable material

“…Such a highly heterogeneous interface not only allows bacteria to deal with various molecular recognitions and cellular communications, but also provides chemists numerous handles for further surface functionalizations, allowing artificial control of diverse bacterial properties. 45,46 Fig. 3 presents an overview of three major types of bacterial interactions occurring on the interface, including bacteria-bacteria, bacteria-abiotic surface, and bacteria-host cell interactions.…”

Exploration of Chemical Biology Approaches to Facilitate the Discovery and Development of Novel Antibiotics

“…Chemical probes can be introduced to whole cells or lysates to specifically label the biomolecules they interact with via either affinity binding alone (chemical reporters; one-step labeling strategy; Figure 3C, 1) or affinity binding combined with bioorthogonal (or "click") reactions (activity-based probes; two-step labeling strategy; Figure 3C, 2). ABP profiling (ABPP) facilitates the investigation of microbiota-metabolite interactions, microbiome composition, and microbiome dynamics (22). Advances in chemoproteomic techniques have greatly facilitated the detection of covalent probe-tagged proteins following ABPP routine in the last few years (23).…”

“…A number of chemical reporters and ABPs have been developed and applied to study various classes of microbes, including Gram-negative, Gram-positive, mycobacteria, and even more complex microbiota communities (Figure 4). Among bacterial molecules tagged by chemical reporters are surface glycans, peptidoglycans (PG), lipopolysaccharides (LPS), capsular polysaccharides (CPS), glycoproteins, amino acids, lipids, and secondary bile acids (produced by the microbial transformation of host bile acids) (22).…”