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RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics. | LitMetric

RapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics.

Microbiome Res Rep

School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa K1H8M5, Ontario, Canada.

Published: April 2024

AI Article Synopsis

Article Abstract

Our gut microbiome has its own functionalities which can be modulated by various xenobiotic and biotic components. The development and application of a high-throughput functional screening approach of individual gut microbiomes accelerates drug discovery and our understanding of microbiome-drug interactions. We previously developed the rapid assay of individual microbiome (RapidAIM), which combined an optimized culturing model with metaproteomics to study gut microbiome responses to xenobiotics. In this study, we aim to incorporate automation and multiplexing techniques into RapidAIM to develop a high-throughput protocol. To develop a 2.0 version of RapidAIM, we automated the protein analysis protocol, and introduced a tandem mass tag (TMT) multiplexing technique. To demonstrate the typical outcome of the protocol, we used RapidAIM 2.0 to evaluate the effect of prebiotic kestose on individual human gut microbiomes biobanked with five different workflows. We describe the protocol of RapidAIM 2.0 with extensive details on stool sample collection, biobanking, culturing and stimulation, sample processing, metaproteomics measurement, and data analysis. The analysis depth of 5,014 ± 142 protein groups per multiplexed sample was achieved. A test on five biobanking methods using RapidAIM 2.0 showed the minimal effect of sample processing on live microbiota functional responses to kestose. Depth and reproducibility of RapidAIM 2.0 are comparable to previous manual label-free metaproteomic analyses. In the meantime, the protocol realizes culturing and sample preparation of 320 samples in six days, opening the door to extensively understanding the effects of xenobiotic and biotic factors on our internal ecology.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149095PMC
http://dx.doi.org/10.20517/mrr.2023.57DOI Listing

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