An Integrated Multi-Omics Analysis Defines Key Pathway Alterations in a Diet-Induced Obesity Mouse Model.

Obesity is a multifactorial disease with many complications and related diseases and has become a global epidemic. To thoroughly understand the impact of obesity on whole organism homeostasis, it is helpful to utilize a systems biological approach combining gene expression and metabolomics across tissues and biofluids together with metagenomics of gut microbial diversity. Here, we present a multi-omics study on liver, muscle, adipose tissue, urine, plasma, and feces on mice fed a high-fat diet (HFD). Gene expression analyses showed alterations in genes related to lipid and energy metabolism and inflammation in liver and adipose tissue. The integration of metabolomics data across tissues and biofluids identified major differences in liver TCA cycle, where malate, succinate and oxaloacetate were found to be increased in HFD mice. This finding was supported by gene expression analysis of TCA-related enzymes in liver, where expression of malate dehydrogenase was found to be decreased. Investigations of the microbiome showed enrichment of Lachnospiraceae, Ruminococcaceae, Streptococcaceae and Lactobacillaceae in the HFD group. Our findings help elucidate how the whole organism metabolome and transcriptome are integrated and regulated during obesity.

Metabolic footprinting for investigation of antifungal properties of Lactobacillus paracasei.

Lactic acid bacteria with antifungal properties are applied for biopreservation of food. In order to further our understanding of their antifungal mechanism, there is an ongoing search for bioactive molecules. With a focus on the metabolites formed, bioassay-guided fractionation and comprehensive screening have identified compounds as antifungal. Although these are active, the compounds have been found in concentrations that are too low to account for the observed antifungal effect. It has been hypothesized that the formation of metabolites and consumption of nutrients during bacterial fermentations form the basis for the antifungal effect, i.e., the composition of the exometabolome. To build a more comprehensive view of the chemical changes induced by bacterial fermentation and the effects on mold growth, a strategy for correlating the exometabolomic profiles with mold growth was applied. The antifungal properties were assessed by measuring mold growth of two Penicillium strains on cell-free ferments of three strains of Lactobacillus paracasei pre-fermented in a chemically defined medium. Exometabolomic profiling was performed by reversed-phase liquid chromatography in combination with mass spectrometry in electrospray positive and negative modes. By multivariate data analysis, the three strains of Lb. paracasei were readily distinguished by the relative difference of their exometabolomes. The relative differences correlated with the relative growth of the two Penicillium strains. Metabolic footprinting proved to be a supplement to bioassay-guided fractionation for investigation of antifungal properties of bacterial ferments. Additionally, three previously identified and three novel antifungal metabolites from Lb. paracasei and their potential precursors were detected and assigned using the strategy.

Liquid chromatography-mass spectrometry for metabolic footprinting of co-cultures of lactic and propionic acid bacteria.

Co-cultures of specific lactic and propionic acid bacteria have been shown to have an antagonistic effect against yeast and moulds in dairy systems. In studies of these co-cultures by bioassay-guided fractionation and analysis, numerous compounds have been reported to inhibit yeast and moulds. Although active, the compounds do not account for the full effect observed. Instead, the inhibitory action in the co-culture is believed to be a result of synergy between known exo-metabolites, depletion of nutrients, and/or compounds not yet identified. Untargeted metabolomics or metabolic footprinting could be a potent approach to elucidation of the mechanism. The purpose of this review is to discuss the two pre-requisites for such a study--the compound classes expected in the co-cultures, and on the basis of these, the most suitable analytical technique(s). Ultrahigh-performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (MS) via electrospray ionisation (ESI) operated in both positive and negative modes is regarded as the optimum instrumental technique. The applicability of a range of liquid chromatographic techniques ranging from ion-pair (IPC) and hydrophilic interaction (HILIC) to reversed-phase chromatography (RPC) is discussed in terms of the expected metabolome. Use of both HILIC and RPC is suggested, on account of the complementarity of these modes. The most promising strategy uses a combination of the two electrospray polarities and two modes of LC. The strategy recommended in this study does not include all compound classes, and suggestions for supplementary methods are listed.