Bacterial Metabolomics: Sample Preparation Methods

Abstract

Metabolomics is a comprehensive analysis of metabolites existing in biological systems. As one of the important “omics” tools, the approach has been widely employed in various fields in helping to better understand the complex cellular metabolic states and changes. Bacterial metabolomics has gained a significant interest as bacteria serve to provide a better subject or model at systems level. The approach in metabolomics is categorized into untargeted and targeted which serves different paradigms of interest. Nevertheless, the bottleneck in metabolomics has been the sample or metabolite preparation method. A custom-made method and design for a particular species or strain of bacteria might be necessary as most studies generally refer to other bacteria or even yeast and fungi that may lead to unreliable analysis. The paramount aspect of metabolomics design comprises sample harvesting, quenching, and metabolite extraction procedures. Depending on the type of samples and research objective, each step must be at optimal conditions which are significantly important in determining the final output. To date, there are no standardized nor single designated protocols that have been established for a specific bacteria strain for untargeted and targeted approaches. In this paper, the existing and current developments of sample preparation methods of bacterial metabolomics used in both approaches are reviewed. The review also highlights previous literature of optimized conditions used to propose the most ideal methods for metabolite preparation, particularly for bacterial cells. Advantages and limitations of methods are discussed for future improvement of bacterial metabolomics.

The media composition as a crucial element in high-throughput metabolic network reconstruction

“…Similarly, targeted gap filling has improved the prediction of known auxotrophies by reconciling experimental data with computational prediction in the gut microbiome [ 43 ]. A complementary and culture independent approach is to screen the exo-metabolome and profile accessible metabolites [ 44 ]. The most common techniques involve gas chromatography–mass spectroscopy, liquid chromatography–mass spectroscopy or nuclear magnetic resonance for targeted (i.e.…”

“…The most common techniques involve gas chromatography–mass spectroscopy, liquid chromatography–mass spectroscopy or nuclear magnetic resonance for targeted (i.e. profiling for specific metabolites) or untargeted (obtaining a whole metabolite footprint) metabolomics [ 44 – 46 ]. This approach has been used successfully to determine the available metabolites for nutrient uptake in flux balance simulations [ 47 , 48 ] and can be used to further constrain the available nutrient and biomass precursors in the media composition for automated gap filling.…”

Influence of bacterial and alveolar cell co-culture on microbial VOC production using HS-GC/MS

“…Exhaled breath metabolomics with its ease of collection and sputum independence represents a technique that could overcome these limitations ( Filipiak et al, 2015 ; Hilton et al, 2016 ; Kos et al, 2021 ; Ahmed et al, 2022 ). In addition, the characterisation and detection of changes in metabolic activity, that may precede disease symptoms, could provide invaluable information regarding bacterial presence, viability and activity ( Tounta et al, 2021 ; Mohd Kamal et al, 2022 ). However, as with all omics data, the challenge lies in clinically integration ( van Karnebeek et al, 2018 ).…”

Proteomics and metabolomics analyses of Streptococcus agalactiae isolates from human and animal sources

“…It has also provided important information for elucidating the disease pathophysiology and identifying novel biomarkers 10 . The availability of databases on bacterial gene regulation and metabolic pathways allows for the investigation of prevalent bacterial systems, such as strain identification and differentiation, drug mechanisms of action, and metabolic changes in response to antimicrobial treatment 11 .…”