Lipidomics in Microbiology

Lipids are a class of metabolites with diverse chemical structures. Lipids are not only components of cell membranes and energy storage substances, but also perform a variety of important biological functions in life activities. As a branch of metabolomics, lipidomics is a discipline that systematically studies lipids and their interacting molecules in organisms, tissues or cells. Microbial lipidomics can help with phenotypic studies, infectiousness studies, drug resistance mechanism studies, and studies of lipids and their interacting molecules in microorganisms.

Applications of lipidomics in microbiology

• Biomarker discovery

A variety of stress responses in microorganisms are accompanied by disordered lipid metabolism, so the search for lipid biomarkers is of great importance for microbial studies. For example, microbial fermentation produces ethanol, which is a renewable energy source that can be used to cope with the energy crisis we are currently facing. However, the process is inhibited by furans, phenols and acetic acid produced by Saccharomyces cerevisiae during the fermentation process. Comparative lipidomic studies of parental (SC) and furan-resistant (SCF), phenol-resistant (SCP), and acetic acid-resistant (SCA) bacteria revealed that phosphatidylcholine, phosphatidylinositol, and phosphatidic acid distinguish SC from SCF, SCP, and SCA, respectively, and are biomarkers of these three resistant bacteria.

• Search for drug targets and new drug development

The study of lipid metabolites and related enzymes as a target to find new drug targets plays an important role in new drug development. For example, the formation of the periplasm of Candida parapsilosis is accompanied by the upregulation of FAs2 gene when the environmental oxygen content is low. In response to this phenomenon, some scholars observed the growth of FAs2 knockout bacteria with exogenous addition of different long-chain FAs, and the results showed that the virulence of the mutant bacteria was significantly reduced, and they could not produce unsaturated FAs, form normal biofilm, and be killed by macrophages. This suggests that FAs may be potential therapeutic targets. Lipidomics can provide information on the changes of microbial lipids and related enzymes, which can help to elucidate microbial-related mechanisms of action and play an important role in microbiology research.

• Optimization of fermentation conditions

Ethanol production during fermentation is important for the efficient production of fuel alcohol, wine, and other alcoholic beverages. However, increasing ethanol concentration can slow down the conversion of sugars to ethanol. A study was conducted to evaluate the relationship between lipids and fermentation kinetic parameters by performing lipidomic studies on 22 industrial brewer's yeasts with different ethanol tolerance. The results showed that lipid composition was related to ethanol concentration as an indicator of ethanol tolerance of the strains and that the maximum cell concentration affecting ethanol tolerance was also related to lipids. Among them, strains with low ethanol production were associated with higher levels of phosphatidylinositol in the early stages of fermentation, while strains with higher cell concentration and ethanol production were associated with phosphatidylcholine.

Schematic overview of the lipidomic data process and analysis workflow (Ding et al., 2021).

Lipidomics research methods in microbiology

Improvements in mass spectrometry have greatly contributed to the development of lipidomics, especially soft ionization techniques such as matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). MALDI is a widely used ionization method for protein research and has been successfully applied to lipid analysis.

The advantages of MALDI are: (1) the higher the solubility of lipids and matrices in organic solvents, the better the signal-to-noise ratio and reproducibility; and (2) compared with ESI, MALDI is more tolerant to salt and is suitable for the analysis of polar lipids, such as phospholipids.

Triple quadrupole (3Q) generates a large amount of molecular structure information and has become a common mass analyzer in lipidomics. It has four scanning modes: product-ion scan, precursor-ion scan, neutral-loss scan and selected reaction monitoring, but the quality accuracy and resolution are not very high. Other mass analyzers, such as time-of-flight mass spectrometry (TOF) and ion-trap mass spectrometry (Ion-Trap) have high accuracy and resolution and can be used to determine the elemental composition of lipid molecules.

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Reference:

1. Ding, S., Bale, N. J., et al. (2021). Lipidomics of environmental microbial communities. II: Characterization using molecular networking and information theory. Frontiers in microbiology, 12, 1920.