Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption Ionization mass spectrometry

Authors: HANSEN, REBECCA - Iowa State University; DUENAS, MARIA EMILIA - Iowa State University; Looft, Torey; LEE, YOUNG-JIN - Iowa State University

Submitted to: Analytical and Bioanalytical Chemistry
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/17/2018
Publication Date: 10/30/2018
Citation: Hansen, R.L., Duenas, M.E., Looft, T., Lee, Y.J. 2018. Nanoparticle microarray for high-throughput microbiome metabolomics using matrix-assisted laser desorption ionization mass spectrometry. Analytical and Bioanalytical Chemistry. 411(1):147-156. https://doi.org/10.1007/s00216-018-1436-5.
DOI: https://doi.org/10.1007/s00216-018-1436-5

Interpretive Summary: The microbiome plays an important role influencing animal and human health. Bacteria of the intestinal microbiome exert their effects on their host in various ways through the production of molecules that may be absorbed by the digestive system. Metabolomics, which is the study of the metabolites in an ecosystem, allow researchers to identify important bacterial functions in the gut. Metabolomic methods however, are costly and time consuming. In this study, we developed a novel high-throughput metabolomics approach that uses sets of nanoparticles or matrices in a high-throughput (microarray) format. Chemicals in the intestinal microbiome selectivity bind nanoparticles of different composition and can be enriched for identification. Carefully chosen sets of nanoparticles can effectively enhance metabolite coverage and identification. This method does not detect as broad of a collection of chemicals as traditional mass spectrometry-based approaches, but can identify many compounds at a fraction of the cost. We validated this method using intestinal samples collected from turkeys fed or not fed antibiotics, as a proof of concept. Our high-throughput microarray technology, can be used to quickly acquire large data sets needed for the study of dynamic systems, to improve the identification of targets to improve animal health and production.

Technical Abstract: A high-throughput matrix-assisted laser desorption/ionization mass spectrometry (MALDI)-MS based metabolomics platform was developed using a pre-fabricated microarray of nanoparticles and organic matrices. Selected organic matrices, inorganic nanoparticle (NP) suspensions, and sputter coated metal NPs, as well as various additives, were tested for metabolomics analysis of the turkey gut microbiome. Four NPs and one organic matrix were selected as the optimal matrix set: a-cyano-4-hydroycinnamic acid, Fe3O4 and Au NPs in positive ion mode with 10 mM sodium acetate, and Cu and Ag NPs in negative ion mode with no additive. Using this set of five matrices, over two thousand unique metabolite features were reproducibly detected across intestinal samples from turkeys fed a diet amended with therapeutic or sub-therapeutic antibiotics (200 g/ton or 50 g/ton bacitracin methylene disalicylate (BMD), respectively), or non-amended feed. Among the thousands of unique features, 56 of them were chemically identified using MALDI-MS/MS, with the help of in-parallel liquid chromatography (LC)-MS/MS analysis. Lastly, as a proof of concept application, this protocol was applied to fifty two turkey cecal samples at three different time points from the antibiotic feed trial. Statistical analysis indicated variations in the metabolome of turkeys with different ages or treatments.