Metagenomics and untargeted metabolomics analyses to unravel the formation mechanism of characteristic metabolites in Cantonese soy sauce during different fermentation stages

Cantonese soy sauce (CSS) is an important Chinese condiment due to its distinctive flavor. Microorganisms play a significant role in the flavor formation of CSS during fermentation. However, the correlation between microbes and flavor compounds as well as the potential fermentation mechanism remained poorly uncovered. Here we revealed the dynamic changes of microbial structure and characteristics metabolites as well as their correlation of CSS during the fermentation process. Metagenomics sequencing analysis showed that Tetragenococcus halophilus, Weissella confusa, Weissella paramesenteroides, Aspergillus oryzae, Lactiplantibacillus plantarum, Weissella cibaria were top six dominant species from day 0 to day 120. Sixty compounds were either positively or tentatively identified through untargeted metabolomics profile and they were 27 peptides, amino acids and derivatives, 8 carbohydrates and conjugates, 14 organic acids and derivatives, 5 amide compounds, 3 flavonoids and 3 nucleosides. Spearman correlation coefficient indicated that Tetragenococcus halophilus, Zygosaccharomyces rouxii, Pediococcus pentosaceus and Aspergillus oryzae were significantly related with the formation of taste amino acids and derivatives, peptides and functional substances. Additionally, the metabolisms of flavor amino acids including 13 main free amino acids were also profiled. These results provided valuable information for the production practice in the soy sauce industry.

Expanded clinical phenotype and untargeted metabolomics analysis in RARS2-related mitochondrial disorder: a case report

BACKGROUND

RARS2-related mitochondrial disorder is an autosomal recessive mitochondrial encephalopathy caused by biallelic pathogenic variants in the gene encoding the mitochondrial arginyl-transfer RNA synthetase 2 (RARS2, MIM *611524, NM_020320.5). RARS2 catalyzes the transfer of L-arginine to its cognate tRNA during the translation of mitochondrially-encoded proteins. The classical presentation of RARS2-related mitochondrial disorder includes pontocerebellar hypoplasia (PCH), progressive microcephaly, profound developmental delay, feeding difficulties, and hypotonia. Most patients also develop severe epilepsy by three months of age, which consists of focal or generalized seizures that frequently become pharmacoresistant and lead to developmental and epileptic encephalopathy (DEE).

CASE PRESENTATION

Here, we describe a six-year-old boy with developmental delay, hypotonia, and failure to thrive who developed an early-onset DEE consistent with Lennox-Gastaut Syndrome (LGS), which has not previously been observed in this disorder. He had dysmorphic features including bilateral macrotia, overriding second toes, a depressed nasal bridge, retrognathia, and downslanting palpebral fissures, and he did not demonstrate progressive microcephaly. Whole genome sequencing identified two variants in RARS2, c.36 + 1G > T, a previously unpublished variant that is predicted to affect splicing and is, therefore, likely pathogenic and c.419 T > G (p.Phe140Cys), a known pathogenic variant. He exhibited significant, progressive generalized brain atrophy and ex vacuo dilation of the supratentorial ventricular system on brain MRI and did not demonstrate PCH. Treatment with a ketogenic diet (KD) reduced seizure frequency and enabled him to make developmental progress. Plasma untargeted metabolomics analysis showed increased levels of lysophospholipid and sphingomyelin-related metabolites.

CONCLUSIONS

Our work expands the clinical spectrum of RARS2-related mitochondrial disorder, demonstrating that patients can present with dysmorphic features and an absence of progressive microcephaly, which can help guide the diagnosis of this condition. Our case highlights the importance of appropriate seizure phenotyping in this condition and indicates that patients can develop LGS, for which a KD may be a viable therapeutic option. Our work further suggests that analytes of phospholipid metabolism may serve as biomarkers of mitochondrial dysfunction.

Physicochemical, microbiological and metabolomics changes in yogurt supplemented with lactosucrose

Lactosucrose (LS) is a known prebiotic that has gained recognition for its low caloric content and various health benefits. However, its potential in food applications remains largely unexplored. In this study the effects of adding LS to milk at concentrations (0 %, 2 %, 5 % and 8 % w/v) for yogurt production, and the relevant changes in yogurt texture, microbial composition and metabolomics were investigated. Our findings revealed that LS played a role in promoting the formation of a structured gel during fermentation, resulting in increased elasticity and viscosity while reducing fluidity. Additionally incorporating high doses of LS into yogurt led to reduced post-acidification, enhanced survival of starter bacteria, improved water retention capacity and overall texture throughout a refrigerated storage period of 21 days. Notably higher concentrations of LS (8 % w/v) exhibited effects on enhancing yogurt quality. Furthermore, untargeted metabolomics analysis using UPLC Q TOF MS/MS revealed 45 differentially expressed metabolites, including up-regulated L-arginine, L-proline and L-glutamic acid along with the down-regulated glutathione, L-tyrosine, L-phenylalanyl and L-proline. These differential metabolites were primarily associated with amino acid metabolism such as thiamine metabolism, nicotinic acid salt and nicotinamide metabolism, and pyrimidine metabolism. As a result, the inclusion of LS in yogurt had an impact on the production of various beneficial metabolites in yogurt, highlighting the importance of combining prebiotic LS with probiotics to obtain desired physiological benefits of yogurt.

Association of Plasma Selenium and Its Untargeted Metabolomic Profiling with Cervical Cancer Prognosis

Selenium is an essential trace element that shows beneficial or adverse health effects depending on the dose. However, its role in the prognosis of cervical cancer (CC) has been less reported. We aimed to explore the association between selenium status and prognosis in CC patients with different prognoses and to elucidate the underlying mechanism of selenium in CC prognosis. This cross-sectional observational study had a case-control design at the Harbin Medical University Cancer Hospital and was conducted using 29 CC cases with poor prognosis and 29 CC cases with good prognosis. Plasma selenium levels were measured using an atomic fluorescence spectrometer. Untargeted metabolomics was used to identify metabolites. Plasma selenium levels of the poor prognosis group (49.90 ± 13.81 µg/L) were lower than that of the good prognosis group (59.38 ± 13.00 µg/L, t = 2.69, P = 0.009). In the logistic regression analysis, plasma selenium levels were associated with lower poor prognosis risk [odds ratio (OR) = 0.952, 95% CI: 0.909-0.998]. Receiver operating characteristic curve analysis revealed an optimal cut-off point of plasma selenium levels ≤ 47.68 µg/L for poor prognosis of CC. Based on the cut-off selenium levels, patients with different prognoses were divided into high and low selenium groups. Metabolomic analysis revealed six differential metabolites among different prognoses with low and high selenium levels, and the glycerophospholipid (GPL) metabolism was enriched. Plasma selenium levels were positively correlated with metabolite levels. Our findings provided evidence that low plasma selenium levels may associate with a poor prognosis of CC. Low plasma selenium levels might suppress GPL metabolism and influence the prognosis of CC. This finding requires confirmation in future prospective cohort studies.

rpeA, a global regulator involved in mupirocin biosynthesis in Pseudomonas fluorescens NCIMB 10586

Mupirocin, a polyketide antibiotic produced by Pseudomonas fluorescens, is used as a topical antimicrobial treatment to cure various skin infections. Quorum sensing system plays an important role in regulation of mupirocin biosynthesis in P. fluorescens NCIMB 10586. In Pseudomonas, the RpeA/RpeB two-component signal transduction (TCST) system regulates quorum sensing system. However, the influences of the RpeA/RpeB TCST system on mupirocin production or other cell activities have not been studied. In this work, the homologous genes of rpeA and rpeB in P. fluorescens NCIMB 10586 were identified and inactivated in the chromosome, respectively. The deletion of rpeA reduced the mupirocin production from 160 in the wild-type to 21.3 mg/L along with slightly decreased cell growth, while no significant effected on mupirocin production in the rpeB mutant. Next, it was found that the RpeA/RpeB TCST system regulated the biosynthesis of mupirocin by modulating the quorum sensing system. Furthermore, untargeted metabolomics analysis was employed to detect the influences of RpeA on other cell activities modulated by quorum sensing system. Combined with quantitative real-time PCR, the results demonstrated that RpeA also regulated other cell activities including central carbon, amino acids, fatty acids, and purine metabolism. Overall, this study expands the current understanding of the RpeA/RpeB TCST system and provides several targets for increasing yields of mupirocin. KEY POINTS: • In P. fluorescens, the RpeA/RpeB TCST system regulates the biosynthesis of mupirocin. • RpeA modulates the cell activities through effecting the central carbon metabolism.

Serum untargeted metabolomics delineates the metabolic status in different subtypes of non-alcoholic fatty liver disease

AIMS

The aim of this study was to identify novel serum metabolites associated with non-alcoholic fatty liver disease (NAFLD), and to explore the metabolic discrepancies between Lean-NAFLD and Obese-NAFLD.

METHODS

Serum samples from patients with NAFLD (n = 161) and healthy participants (n = 149) were collected, and metabolites were analyzed with UPLC-Q-TOF MS/MS. Subgroup analyses were performed to explore the metabolic differences among Lean-NAFLD, Obese-NAFLD and healthy controls RESULTS: A total of 24 differentially present metabolites were found between patients with NAFLD and healthy controls. Marked metabolic pathway differences were observed among the NAFLD subtypes, including in fatty acid and amino acid metabolism. Ultimately, five metabolites (prasterone, indoxylsulfuric acid, sebacic acid, arachidonic acid and pregnenolone sulfate) were used to establish a diagnostic model to distinguish patients with NAFLD regardless of Lean- or Obese-NAFLD type.

CONCLUSIONS

This study suggested that significant metabolic differences existed among subtypes of NAFLD, and our model might be useful to distinguish patients with NAFLD. These findings may lay a foundation for the detection and treatment of NAFLD subtypes.

Alteration of plasma metabolites associated with chemoradiosensitivity in esophageal squamous cell carcinoma via untargeted metabolomics approach

BACKGROUND

To investigate the differences in plasma metabolomic characteristics between pathological complete response (pCR) and non-pCR patients and identify biomarker candidates for predicting the response to neoadjuvant chemoradiotherapy (nCRT) in esophageal squamous cell carcinoma (ESCC).

METHODS

A total of 46 ESCC patients were included in this study. Gas chromatography time-of- flight mass spectrometry (GC-TOF/MS) technology was applied to detect the plasma samples collected before nCRT via untargeted metabolomics analysis.

RESULTS

Five differentially expressed metabolites (out of 109) was found in plasma between pCR and non-pCR groups. Compared with non-pCR group, isocitric acid (p = 0.0129), linoleic acid (p = 0.0137), citric acid (p = 0.0473) were upregulated, while L-histidine (p = 0.0155), 3'4 dihydroxyhydrocinnamic acid (p = 0.0339) were downregulated in the pCR plasma samples. Pathway analyses unveiled that citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolic pathway were associated with ESCC chemoradiosensitivity.

CONCLUSION

The present study provided supporting evidence that GC-TOF/MS based metabolomics approach allowed identification of metabolite differences between pCR and non-pCR patients in plasma levels, and the systemic metabolic status of patients may reflect the response of ESCC patient to neoadjuvant chemoradiotherapy.