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

Wright, Aaron; Hudson, LaRae A.; Garcia, Whitney L.

doi:10.1002/ijch.202200099

Cited by 4 publications

(3 citation statements)

References 86 publications

(163 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Work to pair this approach with proteomics or metabolomics for an encompassing view of the activity of environmental microbes is in progress and will expand modeling efforts to further describe the phenotype interaction network of microbes in a complex sample. Due to the breadth of existing ABPP work, numerous ABPs have been reported for a wide variety of functions [ 42 ]. Combining this library of ABPs with our microbial phenotype selection pipeline will enable examination of several phenotypes across environments.…”

Section: Discussionmentioning

confidence: 99%

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

Reichart,

Steiger,

Van Fossen

et al. 2023

ISME Communications

View full text Add to dashboard Cite

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 function or rely on annotated databases. Functional assays are necessary for understanding in situ microbial activity to better describe and improve microbiome biology. Targeting enzyme activity through activity-based protein profiling enhances the accuracy of functional studies. Here, we introduce a pipeline of coupling activity-based probing with fluorescence-activated cell sorting, culturing, and downstream activity assays to isolate and examine viable populations of cells expressing a function of interest. We applied our approach to a soil microbiome using two activity-based probes to enrich for communities with elevated activity for lignocellulose-degradation phenotypes as determined by four fluorogenic kinetic assays. Our approach efficiently separated and identified microbial members with heightened activity for glycosyl hydrolases, and by expanding this workflow to various probes for other function, this process can be applied to unique phenotype targets of interest.

show abstract

Section: Discussionmentioning

confidence: 99%

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

Reichart,

Steiger,

Van Fossen

et al. 2023

ISME Communications

View full text Add to dashboard Cite

show abstract

“…Omics-based screening can identify these microbial-derived compounds and reveal their mechanisms of action, enabling the development of new antimicrobials or probiotics for infectious diseases, inflammatory disorders, and metabolic syndromes (Garia et al, 2024 ). Plant-microbe interaction omics can also help personalize medicine by revealing inter-individual microbial community variability and dietary component interactions (Wright et al, 2023 ; Speckmann et al, 2024 ).…”

Section: Omics Advancement and Applicationsmentioning

confidence: 99%

Omics approaches in understanding the benefits of plant-microbe interactions

Jain,

Sarsaiya,

Singh

et al. 2024

Front. Microbiol.

View full text Add to dashboard Cite

Plant-microbe interactions are pivotal for ecosystem dynamics and sustainable agriculture, and are influenced by various factors, such as host characteristics, environmental conditions, and human activities. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized our understanding of these interactions. Genomics elucidates key genes, transcriptomics reveals gene expression dynamics, proteomics identifies essential proteins, and metabolomics profiles small molecules, thereby offering a holistic perspective. This review synthesizes diverse microbial-plant interactions, showcasing the application of omics in understanding mechanisms, such as nitrogen fixation, systemic resistance induction, mycorrhizal association, and pathogen-host interactions. Despite the challenges of data integration and ethical considerations, omics approaches promise advancements in precision intervention and resilient agricultural practices. Future research should address data integration challenges, enhance omics technology resolution, explore epigenomics, and understand plant-microbe dynamics under diverse conditions. In conclusion, omics technologies hold immense promise for optimizing agricultural strategies and fortifying resilient plant-microbe alliances, paving the way for sustainable agriculture and environmental stewardship.

show abstract

“…18–20 This review focusses on studies employing chemical probes to elucidate biological processes involved in the interplay of animal hosts with pathogenic bacteria/mycobacteria and how this communication can contribute to virulence. Host interactions with the microbiome, 21–25 viruses, 26–28 or protozoans, 29,30 have been reviewed elsewhere. Moreover, recent reviews have covered related topics such as chemical proteomics to elucidate bacterial biology, 31 host biology during infection, 32 or cell–cell communication.…”

Section: Introductionmentioning

confidence: 99%

Monitoring host–pathogen interactions using chemical proteomics

Weigert Muñoz,

Zhao,

Sieber

2024

RSC Chem. Biol.

View full text Add to dashboard Cite

show abstract

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

Abstract: Dedicated to Professor Benjamin Cravatt on the occasion of him being awarded the 2022 Wolf Prize in Chemistry.

Cited by 4 publications

References 86 publications

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

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

Omics approaches in understanding the benefits of plant-microbe interactions

Monitoring host–pathogen interactions using chemical proteomics

Contact Info

Product

Resources

About