A Probe-Enabled Approach for the Selective Isolation and Characterization of Functionally Active Subpopulations in the Gut Microbiome

Journal Article · Sat Nov 24 04:00:00 EST 2018 · Journal of the American Chemical Society

DOI:https://doi.org/10.1021/jacs.8b09668· OSTI ID:1496809

Whidbey, Christopher ^[1]; Sadler, Natalie C. ^[1]; Nair, Reji N. ^[1]; Volk, Regan F. ^[1]; DeLeon, Adrian J. ^[1]; Bramer, Lisa M. ^[1]; Fansler, Sarah J. ^[1]; Hansen, Joshua R. ^[1]; Shukla, Anil K. ^[1]; Jansson, Janet K. ^[1]; Thrall, Brian D. ^[1]; Wright, Aaron T. ^[2]

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1. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
2. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States; The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman, Washington 99163, United States

Increasing evidence has shown that microorganisms present in the mammalian gut have a major impact on the metabolism of xenobiotics – chemicals foreign to the body including drugs and environmental contaminants – either by modulating host metabolism or by transforming xenobiotics or their metabolites directly. Being able to predict these interactions will be critical to develop precision medicine strategies utilizing the gut microbiota. However, current knowledge of which microbes are responsible for a given activity is severely limited and is further complicated by the sheer diversity of gut microbes between individuals. Current approaches including metagenomic and metatranscriptomic analyses can only identify enzymes and organisms that have the potential to catalyze a specific reaction, but cannot determine if an enzyme is truly active within the gut. To identify the microorganisms that are directly responsible for an activity in the gut of an individual, new functional approaches are needed. Here, we present an activity-based probe (ABP) approach to define the microbial populations responsible for a specific xenobiotic metabolizing activity. We developed an ABP for β-glucuronidases, enzymes capable of reversing a major pathway in phase II metabolism that is responsible for xenobiotic elimination. Using this ABP, we covalently labelled active β-glucuronidases both in vitro and in bacterial cells in the mouse gut microbiota. Cells possessing β-glucuronidase activity were then fluorescently labeled, isolated using fluorescence-activated cell sorting (FACS), and identified by sequencing. We found that glucuronidase active bacteria in the murine gut are taxonomically diverse, and even within phyla the taxa displaying function are highly disparate. Perturbation of the gut microbiota with vancomycin decreased but did not eliminate β-glucuronidase activity, which corresponded to a shift in the β-glucuronidase active population. These data demonstrate that the metabolic activity of the gut microbiota can be plastic and that during perturbation, functional capacity may be maintained by phylogenetically disparate populations. This work highlights the utility of ABPs to identify currently unknown functional microbial subpopulations responsible for a specific activity of interest within the gut of an individual.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1496809
• Report Number(s): PNNL-SA-127532
• Journal Information: Journal of the American Chemical Society, Journal Name: Journal of the American Chemical Society Journal Issue: 1 Vol. 141; ISSN 0002-7863
• Publisher: American Chemical Society (ACS)
• Country of Publication: United States
• Language: English