Sample Preparation in Microbial Metabolomics: Advances and Challenges

Heiter V M Boness; Hanna C de Sá; Emile K P Dos Santos; Gisele A B Canuto

doi:10.1007/978-3-031-41741-2_7

Sample Preparation in Microbial Metabolomics: Advances and Challenges

Adv Exp Med Biol. 2023:1439:149-183. doi: 10.1007/978-3-031-41741-2_7.

Authors

Heiter V M Boness¹, Hanna C de Sá¹, Emile K P Dos Santos¹, Gisele A B Canuto²

Affiliations

¹ Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil.
² Department of Analytical Chemistry, Institute of Chemistry, Federal University of Bahia, Salvador, BA, Brazil. gisele.canuto@ufba.br.

PMID: 37843809
DOI: 10.1007/978-3-031-41741-2_7

Abstract

Microbial metabolomics has gained significant interest as it reflects the physiological state of microorganisms. Due to the great variability of biological organisms, in terms of physicochemical characteristics and variable range of concentration of metabolites, the choice of sample preparation methods is a crucial step in the metabolomics workflow and will reflect on the quality and reliability of the results generated. The procedures applied to the preparation of microbial samples will vary according to the type of microorganism studied, the metabolomics approach (untargeted or targeted), and the analytical platform of choice. This chapter aims to provide an overview of the sample preparation workflow for microbial metabolomics, highlighting the pre-analytical factors associated with cultivation, harvesting, metabolic quenching, and extraction. Discussions focus on obtaining intracellular and extracellular metabolites. Finally, we introduced advanced sample preparation methods based on automated systems.

Keywords: Cellular cultivation; Extracellular metabolome; Intracellular metabolome; Metabolic quenching; Metabolite extraction; Microbial metabolomics; Sample preparation.

MeSH terms

Metabolome*
Metabolomics* / methods
Reproducibility of Results
Specimen Handling