Untargeted metabolomics using liquid chromatography–mass spectrometry (LC–MS) is currently the gold-standard technique to determine the full chemical diversity in biological samples. However, this ...approach still has many limitations; notably, the difficulty of accurately estimating the number of unique metabolites profiled among the thousands of MS ion signals arising from chromatograms. Here, we describe a new workflow, MS-CleanR, based on the MS-DIAL/MS-FINDER suite, which tackles feature degeneracy and improves annotation rates. We show that implementation of MS-CleanR reduces the number of signals by nearly 80% while retaining 95% of unique metabolite features. Moreover, the annotation results from MS-FINDER can be ranked according to the database chosen by the user, which enhance identification accuracy. Application of MS-CleanR to the analysis of Arabidopsis thaliana grown in three different conditions fostered class separation resulting from multivariate data analysis and led to annotation of 75% of the final features. The full workflow was applied to metabolomic profiles from three strains of the leguminous plant Medicago truncatula that have different susceptibilities to the oomycete pathogen Aphanomyces euteiches. A group of glycosylated triterpenoids overrepresented in resistant lines were identified as candidate compounds conferring pathogen resistance. MS-CleanR is implemented through a Shiny interface for intuitive use by end-users (available at https://github.com/eMetaboHUB/MS-CleanR).
•Tuna are important traded and valued fish products requiring effective traceability.•The metabolic profile of 194 tuna from three co-occurring wild species was assessed.•Four discriminant metabolite ...groups were identified in tuna white and red muscles.•1H NMR allowed to discriminate wild tuna species, size categories and provenance.
Tunas are among the most traded and valued fish species, and good traceability of tuna products in the world market is needed to protect both consumers and tuna stocks. To that purpose, high-resolution proton nuclear magnetic resonance (1H NMR) spectroscopy combined with multivariate data analysis was used to investigate the molecular components of the aqueous extract of white and red muscles in three species of wild tropical tuna species, namely yellowfin tuna (Thunnus albacares), skipjack tuna (Katsuwonus pelamis) and bigeye tuna (T. obesus). Principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA) applied to the processed 1H NMR spectra showed significant separation according to the species and size category (i.e., small tunas < 80 cm fork length vs large tunas > 80 cm fork length), the storage conditions on-board the purse-seine vessels (i.e., brine- vs deep-freezing), and the geographical origin (i.e., where the tuna was caught: Mozambique Channel vs western-central Indian Ocean). The major groups of metabolites responsible for differentiation in PLS-DA score plots were the dipeptides (anserine, carnosine) and organic acids (lactate, creatine/phosphocreatine) in the white muscle, and the free amino acids, essential nutrients (choline and its derivatives, phosphatidylethanolamine), dipeptides and organic acids in the red muscle. Our results showed that NMR-based metabolomics is a powerful tool to efficiently discriminate specific profiles among wild tuna species, raw muscle tissues, fish storage conditions and tuna geographical origin.
Phytochemical extracts are highly complex chemical mixtures. In the context of an increasing demand for phytopharmaceuticals, assessment of the phytochemical equivalence of extraction procedures is ...of utmost importance. Compared to routine analytical methods, comprehensive metabolite profiling has pushed forward the concept of phytochemical equivalence. In this study, an untargeted metabolomic approach was used to cross-compare four marketed extracts from
obtained with three different extraction processes: ethanolic, hexanic and sCO
(supercritical carbon dioxide). Our approach involved a biphasic extraction of native compounds followed by liquid chromatography coupled to a high-resolution mass spectrometry based metabolomic workflow. Our results showed significant differences in the contents of major and minor compounds according to the extraction solvent used. The analyses showed that ethanolic extracts were supplemented in phosphoglycerides and polyphenols, hexanic extracts had higher amounts of free fatty acids and minor compounds, and sCO
samples contained more glycerides. The discriminant model in this study could predict the extraction solvent used in commercial samples and highlighted the specific biomarkers of each process. This metabolomic survey allowed the authors to assess the phytochemical content of extracts and finished products of
and unequivocally established that sCO
, hexanic and ethanolic extracts are not chemically equivalent and are therefore unlikely to be pharmacologically equivalent.
Pythium oligandrum
is a soil-borne oomycete associated with rhizosphere and root tissues. Its ability to enhance plant growth, stimulate plant immunity and parasitize fungal and oomycete preys has ...led to the development of agricultural biocontrol products. Meanwhile, the effect of
P. oligandrum
on mutualistic interactions and more generally on root microbial communities has not been investigated. Here, we developed a biological system comprising
P. oligandrum
interacting with two legume plants,
Medicago truncatula
and
Pisum sativum. P. oligandrum
activity was investigated at the transcriptomics level through an RNAseq approach, metabolomics and finally metagenomics to investigate the impact of
P. oligandrum
on root microbiota. We found that
P. oligandrum
promotes plant growth in these two species and protects them against infection by the oomycete
Aphanomyces euteiches
, a devastating legume root pathogen. In addition,
P. oligandrum
up-regulated more than 1000 genes in
M. truncatula
roots including genes involved in plant defense and notably in the biosynthesis of antimicrobial compounds and validated the enhanced production of
M. truncatula
phytoalexins, medicarpin and formononetin. Despite this activation of plant immunity, we found that root colonization by
P. oligandrum
did not impaired symbiotic interactions, promoting the formation of large and multilobed symbiotic nodules with
Ensifer meliloti
and did not negatively affect the formation of arbuscular mycorrhizal symbiosis. Finally, metagenomic analyses showed the oomycete modifies the composition of fungal and bacterial communities. Together, our results provide novel insights regarding the involvement of
P. oligandrum
in the functioning of plant root microbiota.
This study examined the fatty acid composition of three sympatric tropical tuna species (bigeye Thunnus obesus, yellowfin T. albacares and skipjack tuna Kastuwonus pelamis) sampled in the Western ...Indian Ocean in 2013. The fatty acid compositions of neutral and polar lipids, respectively involved in energy storage and cell membrane structure, were explored and compared in four tissues (red and white muscles, liver and gonads), according to biological (size, sex and maturity) and environmental (season and area) factors. The liver and the red muscle were the fattest tissues (i.e., higher levels of storage lipids) in all species and polar lipids were the lowest in the white muscle. Species and tissue types explained most differences in fatty acid compositions, while environmental factors had limited effects, except in the hepatic cell membrane where fatty acid composition varied with monsoons. Docosahexaenoic acid (22:6n-3) was the major fatty acid in both polar and neutral lipid fractions, especially in muscles. Eicosapentaenoic acid (20:5n-3) and oleic acid (18:1n-9) were in higher proportion in neutral than in polar lipids. Arachidonic acid (20:4n-6) and 22:6n-3, together with docosapentaenoic acid (22:5n-6) and stearic acid (18:0), showed preferential accumulation in polar lipids. 20:4n-6 was particularly involved in cell membranes of ovary and white muscle. Overall, an important inter-individual variability in fatty acid compositions of structural lipids was found within tissue types despite considering biological factors that are most likely to influence this type of lipids. It suggests that fatty acid profiles are influenced by individual-specific behaviors.
•Sympatric tropical tuna (bigeye, yellowfin and skipjack tuna) were sampled in the Indian Ocean.•Trophic niche partitioning was quantitatively assessed using time-integrated tracers.•Intra- and ...inter-species competition in three tropical tuna species were detected.•Diet shifts at ∼100cm FL were detected in the larger tuna species (bigeye and yellowfin).•New insights into the mechanisms involved in tropical tuna coexistence were provided.
This study examined the trophic ecology of three sympatric tropical tuna species (bigeye BET, skipjack SKJ, and yellowfin YFT) sampled in the Western Indian Ocean throughout 2013. Specifically we explored inter-specific resource partitioning and ontogenetic variability using neutral fatty acids and stable isotope analysis of liver and muscle from small (⩽100cm fork length, FL) and large (>100cm FL) tuna collected in mixed schools at the surface by purse-seine. Both biochemical tracers were used to calculate trophic niche indices that collectively revealed high potential for resource overlap, especially among small tuna. Resource overlap appeared strongest between BET and YFT, with SKJ tissues having high carbon isotope (δ13C) values (−17±0.3‰), lower nitrogen isotope (δ15N) values (11.4±0.6‰), and higher relative proportion of poly-unsaturated fatty acids (PUFA) than the two other species, indicating a different diet. Size was found to be a strong predictor for most biochemical tracers in the three species with δ13C, δ15N and total lipid content in the liver. In the larger species (YFT and BET), proportions of mono-unsaturated fatty acids typically increased with size, while quantities of PUFA decreased. In addition to ontogenetic variability, trophic markers were shown to vary between sampling area and season: higher lipid reserves and δ15N values, and lower δ13C values occurred during monsoon periods around Seychelles than in the Mozambique Channel (parted from about 1500km). Our multi-tracer approach reveals the magnitude of potential competitive interactions in mixed tropical tuna schools at both small and large sizes and demonstrates that ontogenetic niche differentiation acts as a major factor of coexistence in tropical tuna.
The postprandial period represents one of the most challenging phenomena in whole-body metabolism, and it can be used as a unique window to evaluate the phenotypic flexibility of an individual in ...response to a given meal, which can be done by measuring the resilience of the metabolome. However, this exploration of the metabolism has never been applied to the arteriovenous (AV) exploration of organs metabolism. Here, we applied an AV metabolomics strategy to evaluate the postprandial flexibility across the liver and the intestine of mini-pigs subjected to a high fat-high sucrose (HFHS) diet for 2 months. We identified for the first time a postprandial signature associated to the insulin resistance and obesity outcomes, and we showed that the splanchnic postprandial metabolome was considerably affected by the meal and the obesity condition. Most of the changes induced by obesity were observed in the exchanges across the liver, where the metabolism was reorganized to maintain whole body glucose homeostasis by routing glucose formed de novo from a large variety of substrates into glycogen. Furthermore, metabolites related to lipid handling and energy metabolism showed a blunted postprandial response in the obese animals across organs. Finally, some of our results reflect a loss of flexibility in response to the HFHS meal challenge in unsuspected metabolic pathways that must be further explored as potential new events involved in early obesity and the onset of insulin resistance.
Blood circulation mainly aims at distributing the nutrients required for tissue metabolism and collecting safely the by-products of all tissues to be further metabolized or eliminated. The ...simultaneous study of arterial (A) and venous (V) specific metabolites therefore has appeared to be a more relevant approach to understand and study the metabolism of a given organ. We propose to implement this approach by applying a metabolomics (NMR) strategy on paired AV blood across the intestine and liver on high fat/high sugar (HFHS)-fed minipigs. Our objective was to unravel kinetically and sequentially the metabolic adaptations to early obesity/insulin resistance onset specifically on these two tissues. After two months of HFHS feeding our study of AV ratios of the metabolome highlighted three major features. First, the hepatic metabolism switched from carbohydrate to lipid utilization. Second, the energy demand of the intestine increased, resulting in an enhanced uptake of glutamine, glutamate, and the recruitment of novel energy substrates (choline and creatine). Third, the uptake of methionine and threonine was considered to be driven by an increased intestine turnover to cope with the new high-density diet. Finally, the unique combination of experimental data and modelling predictions suggested that HFHS feeding was associated with changes in tryptophan metabolism and fatty acid β-oxidation, which may play an important role in lipid hepatic accumulation and insulin sensitivity.
Abstract The rhizosphere, which serves as the primary interface between plant roots and the soil, constitutes an ecological niche for a huge diversity of microbial communities. Currently, there is ...little knowledge on the nature and the function of the different metabolites released by rhizospheric microbes to facilitate colonization of this highly competitive environment. Here, we demonstrate how the production of galbonolides, a group of polyene macrolides that inhibit plant and fungal inositol phosphorylceramide synthase (IPCS), empowers the rhizospheric Streptomyces strain AgN23, to thrive in the rhizosphere by triggering the plant’s defence mechanisms. Metabolomic analysis of AgN23-inoculated Arabidopsis roots revealed a strong induction in the production of an indole alkaloid, camalexin, which is a major phytoalexin in Arabidopsis. By using a plant mutant compromized in camalexin synthesis, we show that camalexin production is necessary for the successful colonization of the rhizosphere by AgN23. Conversely, hindering galbonolides biosynthesis in AgN23 knock-out mutant resulted in loss of inhibition of IPCS, a deficiency in plant defence activation, notably the production of camalexin, and a strongly reduced development of the mutant bacteria in the rhizosphere. Together, our results identified galbonolides as important metabolites mediating rhizosphere colonization by Streptomyces.
Hepatic metabolites provide valuable information on the physiological state of an organism, and thus, they are monitored in many clinical situations. Typically, monitoring requires several analyses ...for each class of targeted metabolite, which is time consuming. The present study aimed to evaluate a proton nuclear magnetic resonance (
H-NMR) method for obtaining quantitative measurements of aqueous and lipidic metabolites. We optimized the extraction protocol, the standard samples, and the organic solvents for the absolute quantification of lipid species. To validate the method, we analyzed metabolic profiles in livers of mice fed three different diets. We compared our results with values obtained with conventional methods and found strong correlations. The
H-NMR protocol enabled the absolute quantification of 29 aqueous metabolites and eight lipid classes. Results showed that mice fed a diet enriched in saturated fatty acids had higher levels of triglycerides, cholesterol ester, monounsaturated fatty acids, lactate, 3-hydroxy-butyrate, and alanine and lower levels of glucose, compared to mice fed a control diet. In conclusion, proton NMR provided a rapid overview of the main lipid classes (triglycerides, cholesterol, phospholipids, fatty acids) and the most abundant aqueous metabolites in liver.
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