A structural metagenomics pipeline for examining the gut microbiome

ME Walker, JB Simpson, MR Redinbo - Current opinion in structural biology, 2022 - Elsevier
Metagenomic sequencing data provide a rich resource from which to expand our
understanding of differential protein functions involved in human health. Here, we outline a …

Activity‐Based Protein Profiling–Enabling Phenotyping of Host‐Associated and Environmental Microbiomes

AT Wright, LRA Hudson… - Israel Journal of Chemistry, 2023 - Wiley Online Library
Host‐associated and environmental microbiomes play central roles in human health,
biogeochemical cycling, response to ecosystem change, and agriculture. Scientific …

Chemoproteomic profiling reveals the mechanism of bile acid tolerance in bacteria

B Liu, S Zhuang, R Tian, Y Liu, Y Wang… - ACS Chemical …, 2022 - ACS Publications
Bile acids (BAs) are a class of endogenous metabolites with important functions. As
amphipathic molecules, BAs have strong antibacterial effects, preventing overgrowth of the …

Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended …

S Park, I Kim, G Chhetri, Y So… - … of Systematic and …, 2023 - microbiologyresearch.org
Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-
negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T …

Chemical proteomic analysis of bile acid-protein targets in Enterococcus faecium

X Yang, X Zhao, V Chen, HC Hang - RSC Chemical Biology, 2022 - pubs.rsc.org
Bile acids are important gut microbiota metabolites that regulate both host and microbial
functions. To identify the direct protein targets of bile acids in Enterococcus, we synthesized …

Simvastatin induces human gut bacterial cell surface genes

V Escalante, RR Nayak, C Noecker… - Molecular …, 2023 - Wiley Online Library
Drugs intended to target mammalian cells can have broad off‐target effects on the human
gut microbiota with potential downstream consequences for drug efficacy and side effect …

Activity-based protein profiling in microbes and the gut microbiome

L Han, PV Chang - Current Opinion in Chemical Biology, 2023 - Elsevier
Activity-based protein profiling (ABPP) is a powerful chemical approach for probing protein
function and enzymatic activity in complex biological systems. This strategy typically utilizes …

Activity-based metaproteomics driven discovery and enzymological characterization of potential α-galactosidases in the mouse gut microbiome

J Jiang, D Czuchry, Y Ru, H Peng, J Shen… - Communications …, 2024 - nature.com
The gut microbiota offers an extensive resource of enzymes, but many remain
uncharacterized. To distinguish the activities of similar annotated proteins and mine the …

Selection and enrichment of microbial species with an increased lignocellulolytic phenotype from a native soil microbiome by activity-based probing

NJ Reichart, AK Steiger, EM Van Fossen… - ISME …, 2023 - academic.oup.com
Multi-omic analyses can provide information on the potential for activity within a microbial
community but often lack specificity to link functions to cell, primarily offer potential for …

Chemoproteomic approaches for unraveling prokaryotic biology

KP Malarney, PV Chang - Israel journal of chemistry, 2023 - Wiley Online Library
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and
human health. Many of the functions that bacteria perform are mediated by proteins and …