Phenotyping of gut microbiota: Focus on capillary electrophoresis

Abstract

The analysis of the microbial metabolome is crucial to fully understand the symbiotic relation between humans and microbes. That is why an explosion of metabolomics took place in the area. So far, at least several hundreds of microbial metabolites have been shown to be statistically altered when humans undergo a plethora of commonly faced perturbations. NMR and MS, usually coupled with GC, LC and CE have revealed their identities. CE is a robust analytical platform for the analysis of polar and ionic metabolites that are essential in order to assess the cells' activity. Due to its novelty, only 5% of the metabolomics studies investigate gut microbiota using CE, even though the metabolites found by CE as being significantly altered in human microbiota represent around 23% of the total number of metabolites identified by metabolomics tools. Herein, we discuss the advances of metabolomics in the frame of other OMICS techniques for human gut microbiota analysis. Afterwards, we focus on sample treatment, analytical methods and data processing in CE coupled to any detector that have been reported to date in order to enhance metabolite coverage in the art, and to identify metabolite markers that cannot be covered by other platforms but are of key importance for determining microbial activity and human health.

Metabolomics reveals synergy between Ag and g-C3N4 in Ag/g-C3N4 composite photocatalysts: a unique feature among Ag-doped biocidal materials

“…Cell metabolomes were extracted using a multi-solvent extraction with methanol and water to guarantee the widest diversity of extracted metabolites (Ferrer et al 2017). Samples (1000 μL) containing irradiated cells were centrifuged for 1 min at 16,000 × g and 4 °C, and after removing the supernatant, the cell (or cell debris) pellets were immediately mixed with 1.2 mL of cold (− 80 °C) liquid chromatography (LC)-grade methanol (Sigma-Aldrich, MO, US).…”

“…Note that there are two main reasons to analyse both fractions (water and methanol) together. First, it is more comprehensive not to separate the fractions, which renders a more reliable result, as the mixture is closer to the composition of the metabolome of the original sample (Gosalbes et al 2015;Ferrer et al 2017;González-Riano et al 2020). Second, it avoids analytic variability between subsamples (water and methanol separately), which means less potential bias from a long sequence of analysis.…”

“…Samples were analysed in randomized runs, during which they were incubated in an autosampler at 4 °C. The analytical runs for both polarities were set up to start with the analysis of 10 quality controls (QCs), prepared by pooling and mixing equal volumes of each metabolite solution (Ferrer et al 2017), followed by the samples; a QC sample was injected between blocks of 9 unblinded samples until the end of the run. Ten biological replicates were analysed per sample type, with all samples randomized for analysis.…”

Metagenomic and metabolomic analysis of the short-term and long-term effects of antibiotic therapy on the intestinal microbiota in growing kittens and their relation to the overall health status of these kittens

“…Identification of these new molecules has led to the discovery of new disease biomarkers, has allowed understanding of impaired signalment pathways in diseases states, and contributed to the concept of personalized medicine. 54 Targeted metabolomics is the type of analysis in which predefined metabolites are investigated based on a reference database. Untargeted metabolomics is used for identification of every small microbial molecule present in a sample.…”