Evaluation of Sample Preparation Methods for Inter-Laboratory Metabolomics Investigation of Streptomyces lividans TK24.

Howbeer Muhamadali,Kenneth Simoens,Bart Nicolai,Yun Xu,Kristel Bernaerts,Royston Goodacre

doi:10.3390/metabo10090379

Howbeer Muhamadali, Kenneth Simoens + Show 4 more

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https://doi.org/10.3390/metabo10090379

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Abstract

In the past two decades, metabolomics has proved to be a valuable tool with many potential applications in different areas of science. However, there are still some challenges that need to be addressed, particularly for multicenter studies. These challenges are mainly attributed to various sources of fluctuation and unwanted variations that can be introduced at pre-analytical, analytical, and/or post-analytical steps of any metabolomics experiment. Thus, this study aimed at using Streptomyces lividans TK24 as the model organism in a cross-laboratory experiment in Manchester and Leuven to evaluate the reproducibility of a standard sample preparation method, and determine the optimal sample format (cell extract or quenched biomass) required to preserve the metabolic profile of the cells during cross-lab sample transportation and storage. Principal component analysis (PCA) scores plot of the gas chromatography-mass spectrometry (GC-MS) data from both laboratories displayed clear growth-dependent clustering patterns which was in agreement with the Procrustes analysis findings. In addition, the data generated in Manchester displayed tight clustering of cell pellets (quenched biomass) and metabolite extracts, confirming the stability of both sample formats during the transportation and storage period.

Highlights

Streptomyces spp. are unique amongst the bacteria as they form filamentous mycelia and secrete a large number of natural products (NPs) including hydrolytic enzymes and secondary metabolites with key pharmaceutical and industrial applications [1], such as antibacterial molecules [2], anticancer agents [3], immunosuppressants [4], and insecticides [5]
Since the term metabolome was first proposed by Oliver et al in 1998 [12], the application of mass spectrometry-based metabolomics approaches in the field of microbiology has received increasing interest, which is evident from the exponential rise in the number of publications in this area
In order to investigate the effects of transport and storage of bacterial samples for metabolomics, we designed a study where a set of identical samples of S. lividans were generated in Leuven

Summary

Introduction

Streptomyces spp. are unique amongst the bacteria as they form filamentous mycelia and secrete a large number of natural products (NPs) including hydrolytic enzymes and secondary metabolites with key pharmaceutical and industrial applications [1], such as antibacterial molecules [2], anticancer agents [3], immunosuppressants [4], and insecticides [5]. It is such ability of these bacteria that has made them an ideal host for the production of various recombinant proteins. The application of a top-down approach, starting with metabolomics assessment of a bioprocess and subsequently moving to genomics methods [10], utilizing a priori knowledge of the whole metabolic network and regulatory systems, may allow for the detection of target pathways and rate-limiting metabolites at key fermentation times, and support future metabolic-engineering strategies which are needed within a synthetic biology framework [11].

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