Digestomics: an emerging strategy for comprehensive analysis of protein catabolism

Potential Benefits of Egg White Proteins and Their Derived Peptides in the Regulation of the Intestinal Barrier and Gut Microbiota: A Comprehensive Review

Impaired intestinal barrier function can impede the digestion and absorption of nutrients and cause a range of metabolic disorders, which are the main causes of intestinal disease. Evidence suggests that proper dietary protein intake can prevent and alleviate intestinal diseases. Egg white protein (EWP) has received considerable attention, because of its high protein digestibility and rich amino acid composition. Furthermore, bioactive peptides may have an increased repair effect due to their high degradation efficiency in the gut. In this study, we aimed to review the effects of EWP and its bioactive peptides on intestinal structural repair. The potential modulation mechanisms by which EWP and their peptides regulate the gut microbiota and intestinal barrier can be summarized as follows: (1) restoring the structure of the intestinal barrier to its intact form, (2) enhancing the intestinal immune system and alleviating the inflammatory response and oxidative damage, and (3) increasing the relative abundance of beneficial bacteria and metabolites. Further in-depth analysis of the coregulation of multiple signaling pathways by EWP is required, and the combined effects of these multiple mechanisms requires further evaluation in experimental models. Human trials can be considered to understand new directions for development.

A multi-centre peptidomics investigation of food digesta: current state of the art in mass spectrometry analysis and data visualisation

Mass spectrometry has become the technique of choice for the assessment of a high variety of molecules in complex food matrices. It is best suited for monitoring the evolution of digestive processes in vivo and in vitro. However, considering the variety of equipment available in different laboratories and the diversity of sample preparation methods, instrumental settings for data acquisition, statistical evaluations, and interpretations of results, it is difficult to predict a priori the ideal parameters for optimal results. The present work addressed this uncertainty by executing an inter-laboratory study with samples collected during in vitro digestion and presenting an overview of the state-of-the-art mass spectrometry applications and analytical capabilities available for studying food digestion. Three representative high-protein foods - skim milk powder (SMP), cooked chicken breast and tofu - were digested according to the static INFOGEST protocol with sample collection at five different time points during gastric and intestinal digestion. Ten laboratories analysed all digesta with their in-house equipment and applying theirconventional workflow. The compiled results demonstrate in general, that soy proteins had a slower gastric digestion and the presence of longer peptide sequences in the intestinal phase compared to SMP or chicken proteins, suggesting a higher resistance to the digestion of soy proteins. Differences in results among the various laboratories were attributed more to the peptide selection criteria than to the individual analytical platforms. Overall, the combination of mass spectrometry techniques with suitable methodological and statistical approaches is adequate for contributing to the characterisation of the recently defined digestome.

Assessment of In Vitro Digestive Behavior of Lactic-Acid-Bacteria Fermented Soy Proteins: A Study Comparing Colloidal Solutions and Curds

This study investigated the effect of lactic-acid-bacteria fermentation on the microstructure and gastrointestinal digestibility of soy proteins using a digestomics approach. Fermented soy protein isolates (FSPIs) under varied fermentation-terminal pH demonstrated a colloidal solution (FSPI-7.0/6.0) or yogurt-like curd (FSPI-5.0/4.0) state. Cryo-electron microscopy figures demonstrated the loosely stacked layer of FSPI-7.0/6.0 samples, whereas a denser gel network was observed for FSPI-5.0/4.0 samples. Molecular interactions shifted from dominant ionic bonds to hydrophobic forces and disulfide bonds. The gastric/intestinal digestion demonstrated that the curd samples afforded a significantly low particle size and high-soluble protein and peptide contents in the medium and late digestive phases. A peptidomics study showed that the FSPI-6.0 digestate at early intestinal digestion had a high peptidome abundance, whereas FSPI curd digestates (FSPI-5.0/4.0) elicited a postponed but more extensive promotion during medium and late digestion. Glycinin G2/G4 and β-conglycinin α/α' subunits were the major subunits promoted by FSPI-curds. The spatial structures of glycinin G2 and β-conglycinin α subunits demonstrated variations located in seven regions. Glycinin G2 region 6 (A349-K356) and β-conglycinin α subunit region 7 (E556-E575), which were located at the interior of the 3D structure, were the key regions contributing to discrepancies at the late stage.

Positive Interactions Between Lactic Acid Bacteria Could Be Mediated by Peptides Containing Branched-Chain Amino Acids

Lactic acid bacteria (LAB) are responsible for the sanitary, organoleptic, and health properties of most fermented products. Positive interactions between pairs of LAB strains, based on nitrogen dependencies, were previously demonstrated. In a chemically defined medium, using milk and lupin proteins as sole nitrogen source, two proteolytic strains were able to sustain the growth of non-proteolytic strains, but one did not. The objective of the present study was, thus, to determine which specific peptides were implicated in the positive interactions observed. Peptides produced and involved in the bacterial interactions were quantified using tandem mass spectrometry (LC-MS/MS). About 2,000 different oligopeptides ranging from 6 to more than 50 amino acids in length were identified during the time-course of the experiment. We performed a clustering approach to decipher the differences in peptide production during fermentation by the three proteolytic strains tested. We also performed sequence alignments on parental proteins and identified the cleavage site profiles of the three bacterial strains. Then, we characterized the peptides that were used by the non-proteolytic strains in monocultures. Hydrophobic and branched-chain amino acids within peptides were identified as essential in the interactions. Ultimately, better understanding how LAB can positively interact could be useful in multiple food-related fields, e.g., production of fermented food products with enhanced functional properties, or fermentation of new food matrices.

Insights Into the Complexity of Yeast Extract Peptides and Their Utilization by Streptococcus thermophilus

Streptococcus thermophilus, an extensively used lactic starter, is generally produced in yeast extract-based media containing a complex mixture of peptides whose exact composition remains elusive. In this work, we aimed at investigating the peptide content of a commercial yeast extract (YE) and identifying dynamics of peptide utilization during the growth of the industrial S. thermophilus N4L strain, cultivated in 1 l bioreactors under pH-regulation. To reach that goal, we set up a complete analytical workflow based on mass spectrometry (peptidomics). About 4,600 different oligopeptides ranging from 6 to more than 30 amino acids in length were identified during the time-course of the experiment. Due to the low spectral abundance of individual peptides, we performed a clustering approach to decipher the rules of peptide utilization during fermentation. The physicochemical characteristics of consumed peptides perfectly matched the known affinities of the oligopeptide transport system of S. thermophilus. Moreover, by analyzing such a large number of peptides, we were able to establish that peptide net charge is the major factor for oligopeptide transport in S. thermophilus N4L.

Plasma metabolomics reveals membrane lipids, aspartate/asparagine and nucleotide metabolism pathway differences associated with chloroquine resistance in Plasmodium vivax malaria

Background

Chloroquine (CQ) is the main anti-schizontocidal drug used in the treatment of uncomplicated malaria caused by Plasmodium vivax. Chloroquine resistant P. vivax (PvCR) malaria in the Western Pacific region, Asia and in the Americas indicates a need for biomarkers of resistance to improve therapy and enhance understanding of the mechanisms associated with PvCR. In this study, we compared plasma metabolic profiles of P. vivax malaria patients with PvCR and chloroquine sensitive parasites before treatment to identify potential molecular markers of chloroquine resistance.

Methods

An untargeted high-resolution metabolomics analysis was performed on plasma samples collected in a malaria clinic in Manaus, Brazil. Male and female patients with Plasmodium vivax were included (n = 46); samples were collected before CQ treatment and followed for 28 days to determine PvCR, defined as the recurrence of parasitemia with detectable plasma concentrations of CQ ≥100 ng/dL. Differentially expressed metabolic features between CQ-Resistant (CQ-R) and CQ-Sensitive (CQ-S) patients were identified using partial least squares discriminant analysis and linear regression after adjusting for covariates and multiple testing correction. Pathway enrichment analysis was performed using Mummichog.

Results

Linear regression and PLS-DA methods yielded 69 discriminatory features between CQ-R and CQ-S groups, with 10-fold cross-validation classification accuracy of 89.6% using a SVM classifier. Pathway enrichment analysis showed significant enrichment (p<0.05) of glycerophospholipid metabolism, glycosphingolipid metabolism, aspartate and asparagine metabolism, purine and pyrimidine metabolism, and xenobiotics metabolism. Glycerophosphocholines levels were significantly lower in the CQ-R group as compared to CQ-S patients and also to independent control samples.

Conclusions

The results show differences in lipid, amino acids, and nucleotide metabolism pathways in the plasma of CQ-R versus CQ-S patients prior to antimalarial treatment. Metabolomics phenotyping of P. vivax samples from patients with well-defined clinical CQ-resistance is promising for the development of new tools to understand the biological process and to identify potential biomarkers of PvCR.