PubMed

Metabolites. 2024 Nov 8;14(11):606. doi: 10.3390/metabo14110606.ABSTRACTThis review presents the latest research on chromatography-based metabolomics for bioorganic research of honey, considering targeted, suspect, and untargeted metabolomics involving metabolite profiling and metabolite fingerprinting. These approaches give an insight into the metabolic diversity of different honey varieties and reveal different classes of organic compounds in the metabolic profiles, among which, key metabolites such as biomarkers and bioactive compounds can be highlighted. Chromatography-based metabolomics strategies have significantly impacted different aspects of bioorganic research, including primary areas such as botanical origins, honey origin traceability, entomological origins, and honey maturity. Through the use of different tools for complex data analysis, these strategies contribute to the detection, assessment, and/or correlation of different honey parameters and attributes. Bioorganic research is mainly focused on phytochemicals and their transformation, but the chemical changes that can occur during the different stages of honey formation remain a challenge. Furthermore, the latest user- and environmentally friendly sample preparation methods and technologies as well as future perspectives and the role of chromatography-based metabolomic strategies in honey characterization are discussed. The objective of this review is to summarize the latest metabolomics strategies contributing to bioorganic research onf honey, with emphasis on the (i) metabolite analysis by gas and liquid chromatography techniques; (ii) key metabolites in the obtained metabolic profiles; (iii) formation and accumulation of biogenic volatile and non-volatile markers; (iv) sample preparation procedures; (v) data analysis, including software and databases; and (vi) conclusions and future perspectives. For the present review, the literature search strategy was based on the PRISMA guidelines and focused on studies published between 2019 and 2024. This review outlines the importance of metabolomics strategies for potential innovations in characterizing honey and unlocking its full bioorganic potential.PMID:39590842 | DOI:10.3390/metabo14110606

Metabolites. 2024 Nov 8;14(11):603. doi: 10.3390/metabo14110603.ABSTRACTThe circular RNA circH19 has been implicated in the regulation of gene expression and various biological processes, including obesity. Objectives: This study aimed to elucidate the metabolic changes in plasma after circH19 knockdown in a diet-induced obese (DIO) mouse model. Methods: Plasma samples were collected following the intervention and subjected to non-targeted metabolomics analysis using liquid chromatography-mass spectrometry (LC-MS). Metabolic profiling was performed to identify and quantify metabolites, followed by multivariate statistical analysis to discern differential metabolic signatures. Results: A total of 1250 features were quantified, resulting in the upregulation of 564 metabolites and the downregulation of 686 metabolites in the circH19 knockdown group compared to the control mice. Metabolic pathway analysis revealed disruptions in lipid metabolism, amino acid turnover, and energy production pathways. Notably, the intervention led to a substantial decrease in circulating lipids and alterations in the plasma amino acid profile, indicative of an impact on protein catabolism and anabolic processes. The observed shifts in lipid and amino acid metabolism suggest potential therapeutic avenues for obesity and related metabolic disorders. Conclusions: The circH19 knockdown in DIO mice led to significant alterations in plasma metabolites, highlighting its potential role in the regulation of obesity and metabolic disorders.PMID:39590839 | DOI:10.3390/metabo14110603

Metabolites. 2024 Nov 7;14(11):602. doi: 10.3390/metabo14110602.ABSTRACTBackground: Untargeted lipidomics using collision-induced dissociation-based tandem mass spectrometry (CID-MS/MS) is essential for biological and clinical applications. However, annotation confidence still relies on manual curation by analytical chemists, despite the development of various software tools for automatic spectral processing based on rule-based fragment annotations. Methods: In this study, we present a novel machine learning model, MS2Lipid, for the prediction of known lipid subclasses from MS/MS queries, providing an orthogonal approach to existing lipidomics software programs in determining the lipid subclass of ion features. We designed a new descriptor, MCH (mode of carbon and hydrogen), to increase the specificity of lipid subclass prediction in nominal mass resolution MS data. Results: The model, trained with 6760 and 6862 manually curated MS/MS spectra for the positive and negative ion modes, respectively, classified queries into one or several of 97 lipid subclasses, achieving an accuracy of 97.4% in the test set. The program was further validated using various datasets from different instruments and curators, with the average accuracy exceeding 87.2%. Using an integrated approach with molecular spectral networking, we demonstrated the utility of MS2Lipid by annotating microbiota-derived esterified bile acids, whose abundance was significantly increased in fecal samples of obese patients in a human cohort study. This suggests that the machine learning model provides an independent criterion for lipid subclass classification, enhancing the annotation of lipid metabolites within known lipid classes. Conclusions: MS2Lipid is a highly accurate machine learning model that enhances lipid subclass annotation from MS/MS data and provides an independent criterion.PMID:39590838 | DOI:10.3390/metabo14110602

Metabolites. 2024 Nov 7;14(11):600. doi: 10.3390/metabo14110600.ABSTRACTBackground: Ovarian cancer (OC) remains one of the most lethal cancers among women due to most cases going undiagnosed until later stages. The early detection and treatment of this malignancy provides the best prognosis, but the lack of an accurate and sensitive screening tool combined with ambiguous symptoms hinders these diagnoses. In contrast, screening for cervical cancer via Papanicolaou (Pap) tests is a widespread practice that greatly reduces the cancer's mortality rates. Interestingly, previous studies show evidence of OC cells in Pap tests, suggesting that proteins, and potentially lipids, shed from ovarian tumors end up in the cervix. The goal of this study is to evaluate the practicality of using Pap tests as biospecimens for OC-screening-related metabolomics. Methods: To evaluate the effectiveness of using residual Pap test samples as biospecimens for potential metabolomics work, 29 Pap test samples, collected from women over the age of 50 with normal cytology and no visible blood contamination, were first obtained from the University of Minnesota, with IRB approval. These samples were centrifuged to recover the cell pellets from the supernatants. The cell pellets underwent a biphasic extraction, followed by an RP-LC-MS analysis, while the supernatants underwent two separate extractions and analyses, including RP-LC-MS and HILIC-LC-MS. Non-targeted features were detected in the range of 220-1000 m/z to determine the sensitivity and scope of the various extraction and analytical workflows, as well as evaluating residual Pap test samples as viable metabolomics biospecimens. Results: The biphasic extraction and subsequent RP-LC-MS analysis of the isolated cell pellets from all 29 samples yielded informative, exploratory data, highlighting the potential of using residual Pap test samples as biospecimens for metabolomics, specifically lipidomics, studies. Each sample was analyzed in both the positive and negative ion mode, yielding the detection of 7318 in the positive ion mode and 3733 in the negative ion mode. Using multiple reference libraries, 22.85% and 36.19% of these features were annotated in the positive and negative ion mode, respectively. Among these detected features, 453 unique lipids, representative of 20 different lipid subclasses, were annotated in all 29 samples. Of the various lipid subclasses represented from the detected lipids, ceramides, triacylglycerols, hexosylceramides, and phosphatidylcholines contributed to over half (53.3%) of the detected lipids at 16.2%, 13.0%, 12.8%, and 11.3%, respectively. Conclusions: The detection of these 453 common lipids across all patients establishes a relative lipidome baseline for women over the age of 50 with normal cervical cytology. This exploratory study is the first investigation to utilize residual Pap test samples as biospecimens in a metabolomics/lipidomics workflow.PMID:39590836 | DOI:10.3390/metabo14110600

Metabolites. 2024 Nov 7;14(11):598. doi: 10.3390/metabo14110598.ABSTRACTBackground: Long COVID-19 has been characterized by the presence of symptoms lasting longer than 4 weeks after the acute infection. The pathophysiology of clinical manifestations still lacks knowledge. Objective: The objective of this paper was to evaluate metabolite abundance in the saliva of long COVID patients 60 days after hospital discharge. Methods: A convenience sample was composed of 30 post-discharge patients with long COVID and seven non-COVID-19 controls. All COVID-19 patients were evaluated by demographic characteristics, spirometry, 6 min walk test (6mWT), Saint George Respiratory Questionnaire (SGRQ), and body composition. Metabolomics was performed on saliva. Results: The long COVID-19 patients were 60.4 ± 14.3 years-old, and 66% male. Their lean body mass was 30.7 ± 7.3 kg and fat mass, 34.4 ± 13.7 kg. Spirometry evaluation showed forced vital capacity (FVC) of 3.84 ± 0.97 L with 96.0 ± 14.0% of the predicted value, and forced expiratory volume in the first second (FEV1) of 3.11 ± 0.83 L with 98.0 ± 16.0 of the predicted value. The long COVID-19 patients had reduced maximal inspiratory (90.1 ± 31.6 cmH2O) and maximal expiratory (97.3 ± 31.0 cmH2O) pressures. SGRQ showed domain symptoms of 32.3 ± 15.2, domain activities of 41.9 ± 25.6, and domain impact 13.7 ± 11.4, with a mean of 24.3 ± 14.9%. Physical capacity measured by distance covered in the 6mWT was 418.2 ± 130 m with a 73.3% (22.3-98.1) predictive value. The control group consisted of 44.1 ± 10.7-year-old men with a body mass index of 26.5 ± 1.66 Kg/m2. Metabolomics revealed 19 differentially expressed metabolites; expression was lower in 16 metabolites, and 2 metabolites were absent in the COVID-19 patients compared to controls. Calenduloside G methyl ester (p = 0.03), Gly Pro Lys (p = 0.0001), and creatine (p = 0.0001) expressions were lower in patients than controls. Conclusions: Long COVID-19 patients present less abundance of calenduloside G methyl ester, Gly Pro Lys, and creatine in saliva than healthy controls. Lower creatine abundance may be related to reduced physical capacity and fatigue.PMID:39590834 | DOI:10.3390/metabo14110598

Metabolites. 2024 Nov 5;14(11):594. doi: 10.3390/metabo14110594.ABSTRACTBACKGROUND/OBJECTIVES: The biostimulant SuperFifty, produced from the brown algae Ascophyllum nodosum, can improve crop quality and yield and mitigate stress tolerance in model and crop plants such as Arabidopsis thaliana, pepper, and tomato. However, the effect of SuperFifty on raspberries and strawberries has not been well studied, especially in terms of nutritional properties and yield. The aim of this study was to investigate the effect of SuperFifty on the quality and quantity of raspberry and strawberry fruits, with a focus on metabolic composition and essential elements, which together determine the nutritional properties and total yield of these two crops.METHODS: Metabolome analysis was performed by liquid chromatography-mass spectrometry analysis (LC-MS), and essential elements analysis was performed by inductively coupled plasma-mass spectrometry (ICP-MS).RESULTS: Here, we demonstrate that SuperFifty increases the fruit size of both raspberries and strawberries and enhances the yield in these two berry crops by 42.1% (raspberry) and 33.9% (strawberry) while preserving the nutritional properties of the fruits. Metabolome analysis of 100 metabolites revealed that antioxidants, essential amino acids, organic acids, sugars, and vitamins, such as glutathione, alanine, asparagine, histidine, threonine, serine, tryptophan, sucrose, citric acid, pantothenic acid (vitamin B5), as well as other primary metabolites, remain the same in the SuperFifty-primed fruits. Secondary metabolites, such as caffeic acid, p-coumaric acid, kaempferol, and quercetin, also maintained their levels in the SuperFifty-primed fruits. Analysis of essential elements demonstrated that elements important for human health, such as Zn, Mn, Fe, B, Cu, K, and Ca, maintain the same levels in the raspberry and strawberry fruits obtained from the biostimulant-primed plants. Magnesium, an important element known as a co-factor in many enzymatic reactions related to both plant physiology and human health, increased in both raspberry and strawberry fruits primed with SuperFifty. Finally, we discuss the potential financial and health benefits of the SuperFifty-induced priming for both growers and consumers.CONCLUSIONS: We demonstrate that SuperFifty significantly enhances the yield of both raspberries and strawberries, improves the marketable grade of the fruits (larger and heavier fruits), and enhances the nutritional properties by elevating Mg content in the fruits. Altogether, this biostimulant-induced molecular priming offers an environmentally friendly, efficient, and sustainable way to enhance the yield and quality of berry crops, with clear benefits to both berry producers and customers.PMID:39590830 | DOI:10.3390/metabo14110594

Metabolites. 2024 Nov 4;14(11):593. doi: 10.3390/metabo14110593.ABSTRACTBackground: The incidence of many diseases increases with age and leads to multimorbidity, characterized by the presence of multiple diseases in old age. This phenomenon is closely related to systemic metabolic changes; the most suitable way to study it is through metabolomics. The use of accumulated metabolomic data to characterize this phenomenon at the system level may provide additional insight into the nature and strength of aging-disease relationships. Methods: For this purpose, metabolic changes associated with human aging and metabolic alterations under different pathological conditions were compared. To do this, the published results of metabolomic studies on human aging were compared with data on metabolite alterations collected in the human metabolome database through metabolite set enrichment analysis (MSEA) and combinatorial analysis. Results: It was found that human aging and pathological conditions involve the set of the same metabolic pathways with a probability of 99.96%. These data show the high identity of the aging process and the development of diseases at the metabolic level and allow to identify the set of metabolic pathways reflecting age-related changes closely associated with health. Based on these pathways, a metapathway was compiled, changes in which are simultaneously associated with health and age. Conclusions: The knowledge about the strength of the convergence of aging and pathological conditions has been supplemented by the rigor evidence at the metabolome level, which also made it possible to outline the age and health-relevant place in the human metabolism.PMID:39590829 | DOI:10.3390/metabo14110593

Metabolites. 2024 Nov 1;14(11):591. doi: 10.3390/metabo14110591.ABSTRACTBackground: Plants of Nitraria, belonging to the Zygophyllaceae family, are not only widely distributed at an altitude of about 1000 m but also at an altitude of about 3000 m, which is a rare phenomenon. However, little is known about the effect of altitude on the accumulation of metabolites in plants of Nitraria. Furthermore, the mechanism of the high-altitude adaptation of Nitraria has yet to be fully elucidated. Methods: In this study, metabolomics and transcriptomics were used to investigate the differential accumulation of metabolites of Nitraria berries and the regulatory mechanisms in different altitudes. Results: As a result, the biosynthesis of flavonoids is the most significant metabolic pathway in the process of adaptation to high altitude, and 5 Cyanidins, 1 Pelargonidin, 3 Petunidins, 1 Peonidin, and 4 Delphinidins are highly accumulated in high-altitude Nitraria. The results of transcriptomics showed that the structural genes C4H (2), F3H, 4CL (2), DFR (2), UFGT (2), and FLS (2) were highly expressed in high-altitude Nitraria. A network metabolism map of flavonoids was constructed, and the accumulation of differential metabolites and the expression of structural genes were analyzed for correlation. Conclusions: In summary, this study preliminarily offers a new understanding of metabolic differences and regulation mechanisms in plants of Nitraria from different altitudes.PMID:39590827 | DOI:10.3390/metabo14110591

Metabolites. 2024 Oct 30;14(11):587. doi: 10.3390/metabo14110587.ABSTRACTBackground/Objectives: Profiling of metabolites and lipids in biological samples can provide invaluable insights into life-sustaining chemical processes. The ability to detect both metabolites and lipids in the same sample can enhance these understandings and connect cellular dynamics. However, simultaneous detection of metabolites and lipids is generally hampered by chromatographic systems tailored to one molecular type. This void can be filled by direct infusion mass spectrometry (MS), where all ionizable molecules can be detected simultaneously. However, in direct infusion MS, the high chemical complexity of biological samples can introduce limitations in detectability due to matrix effects causing ionization suppression. Methods: Decreased sample complexity and increased detectability and molecular coverage was provided by combining our direct infusion probe (DIP) with liquid-liquid extraction (LLE) and directly sampling the different phases for direct infusion. Three commonly used LLE methods for separating lipids and metabolites were evaluated. Results: The butanol-methanol (BUME) method was found to be preferred since it provides high molecular coverage and have low solvent toxicity. The established BUME DIP-MS method was used as a fast and sensitive analysis tool to study chemical changes in insulin-secreting cells upon glucose stimulation. By analyzing the metabolome at distinct time points, down to 1-min apart, we found high dynamics of the intracellular metabolome. Conclusions: The rapid workflow with LLE DIP-MS enables higher sensitivity of phase separated metabolites and lipids. The application of BUME DIP-MS provides novel information on the dynamics of the intracellular metabolome of INS-1 during the two phases of insulin release for both metabolite and lipid classes.PMID:39590823 | DOI:10.3390/metabo14110587

Metabolites. 2024 Oct 28;14(11):586. doi: 10.3390/metabo14110586.ABSTRACTBACKGROUND/OBJECTIVES: This study provides the first insights to the fecal metabolome of the giraffe (Giraffa camelopardalis). By using untargeted metabolomics via gas chromatography time-of-flight mass spectrometry (GCxGC/TOF-MS), this study primarily aims to provide results of the impact that external stimuli, such as supplemental feeding (SF) practices, seasonal variation and sex, might have on the fecal metabolome composition of healthy, free-roaming giraffes.METHODS: Untargeted GCxGC/TOF-MS analysis was applied to the feces collected from thirteen giraffes (six males and seven females) from six different locations within the central Free State Province of South Africa over a period of two years. Statistical analysis of the generated data was used to identify the metabolites that were significantly different between the giraffes located in environments that provided SF and others where the giraffes only fed on the natural available vegetation. The same metabolomics analysis was used to investigate metabolite concentrations that were significantly different between the wet and dry seasons for a single giraffe male provided with SF over the two-year period, as well as for age and sex differences.RESULTS: A total of 2042 features were detected from 26 giraffe fecal samples. Clear variations between fecal metabolome profiles were confirmed, with higher levels of amino acid-related and carbohydrate-related metabolites for giraffes receiving SF. In addition, a separation between the obtained profiles of samples collected from a single adult male giraffe during the wet and dry seasons was identified. Differences, such as higher levels of carbohydrate-related metabolites and organic compounds during the wet season were noted. Distinct variations in profiles were also identified for the metabolites from fecal samples collected from the six males and seven females, with higher concentrations in carbohydrate-related metabolites and alkanes for female giraffes comparatively.CONCLUSIONS: This is the first study to investigate the composition of the fecal metabolome of free-roaming giraffes, as well as the effects that external factors, such as environmental exposures, feeding practices, seasonal variations, age and sex, have on it. This novel use of fecal metabolomics assists in developing non-invasive techniques to determine giraffe populations' health that do not require additional stressors such as capture, restraint and blood collection. Ultimately, such non-invasive advances are beneficial towards the conservation of wildlife species on a larger scale.PMID:39590822 | DOI:10.3390/metabo14110586

Metabolites. 2024 Oct 25;14(11):576. doi: 10.3390/metabo14110576.ABSTRACTThis Special Issue was published to celebrate 10+ years of research and services at the UC Davis West Coast Metabolomics Center (WCMC) [...].PMID:39590812 | DOI:10.3390/metabo14110576

Metabolites. 2024 Oct 25;14(11):574. doi: 10.3390/metabo14110574.ABSTRACTBackground/objective: Approximately one-third of pregnant individuals in the U.S. are affected by obesity, which can adversely impact the in utero environment and offspring. This study aimed to investigate the differences in urine metabolomics between children exposed and unexposed to maternal obesity. Methods: In a study nested within a larger pregnancy cohort of women-offspring pairs, we measured untargeted metabolomics using liquid chromatography-mass spectrometry in urine samples from 68 children at 4-8 years of age. We compared metabolite levels between offspring exposed to maternal obesity (body mass index [BMI] ≥ 30.0 kg/m2) vs. unexposed (maternal BMI 18.5-24.9 kg/m2) and matched them on covariates, using two-sample t-tests, with additional sensitivity analyses based on children's BMI. This study reports statistically significant results (p ≤ 0.05) and potentially noteworthy findings (fold change > 1 or 0.05 < p < 0.15), considering compounds' involvement in common pathways or similar biochemical families. Results: The mean (SD) maternal age at study enrollment was 28.0 (6.3) years, the mean child age was 6.6 (0.8) years, 56% of children were male, and 38% of children had a BMI in the overweight/obese range (BMI ≥ 85th percentile). Children exposed to maternal obesity had lower levels of 5-hydroxyindole sulfate and 7-hydroxyindole sulfate and higher levels of secondary bile acids. Phenylacetic acid derivatives were lower in offspring exposed to obesity and in offspring who had a current BMI in the overweight/obese range. Exposure to maternal obesity was associated with lower levels of androgenic steroid dehydroepiandrosterone sulfate (DHEA-S). Conclusions: In this preliminary study, children exposed to maternal obesity in utero had differences in microbiome-related metabolites in urine suggestive of altered microbial catabolism of tryptophan and acetylated peptides. Some of these differences were partially attributable to the offspring's current BMI status. This study highlights the potential of urine metabolomics to identify biomarkers and pathways impacted by in utero exposure to maternal obesity.PMID:39590810 | DOI:10.3390/metabo14110574

Metabolites. 2024 Oct 24;14(11):571. doi: 10.3390/metabo14110571.ABSTRACTBACKGROUND/OBJECTIVES: Menopause and related metabolites are associated with mortality. However, the relationship between earlier menopause, premature mortality, and the role of metabolomic signatures remains underexplored. This study investigated the association between earlier menopause and premature mortality, and the mediating effect of metabolomic signatures.METHODS: This prospective cohort study used data from the UK Biobank, including 33,687 post-menopausal women aged 40-69 years. Age at menopause was obtained from a baseline self-reported questionnaire and analyzed both as a continuous variable and in categories (<40, 40-49, and ≥50 years). Premature mortality was defined as deaths before 75 years. Cox regression was used to estimate hazard ratios (HRs), and elastic net regression identified metabolomic signatures related to menopause age. Mediation analysis was conducted to assess the proportion of the association explained by the metabolomic signature.RESULTS: During a median follow-up of 13.7 years, 1612 cases of premature mortality occurred. Compared to menopause at ≥50 years, earlier menopause (HR 1.17, 95% CI 1.04-1.30) and premature menopause (HR 1.60, 95% CI 1.28-2.00) were associated with higher risks of premature mortality. A metabolomic signature inversely associated with premature mortality (HR per SD increment, 0.79; 95% CI, 0.75-0.83) mediated 13.6% (95% CI, 1.9%-28.3%) of the association between earlier menopause and premature mortality.CONCLUSIONS: Earlier menopause is associated with an increased risk of premature mortality, partially mediated by a metabolomic signature related to age at menopause. These findings highlight the importance of metabolomic profiling in understanding menopause and mortality risks.PMID:39590807 | DOI:10.3390/metabo14110571

Mar Drugs. 2024 Nov 20;22(11):522. doi: 10.3390/md22110522.ABSTRACTThe CH2Cl2-MeOH extract of the Mediterranean sponge Crambe crambe was investigated via UHPLC-HRMS/MS employing manual dereplication and in silico mass spectrometry tools. A deconvolution approach was implemented for the extensive metabolic characterization of the sample, resulting in the annotation of 53 compounds. The analysis of data-dependent HRMS/MS scans was conducted to establish fragmentation patterns characteristic of each crambescin A, B, and C sub-families. Among the 39 compounds identified from these groups, 22 analogues were reported for the first time including 4 new homologous series that differed by the ratio of methylene units in the upper (n + 2) and lower (m + 2) alkyl side chains. More specifically, crambescins presenting m = 5 or 6 and n = 5 (compounds 7, 11, 22 and 24) as well as m = 5 or 6 and n = 4 (compounds 5, 6, 8, 9, 12 and 14) were characterized. Additionally, four new features, potentially corresponding to new crambescidin analogues (compounds 13, 15, 35, and 39), were also reported. The identity of the dereplicated features was further validated by studying crambescins' spectral similarities through a feature-based molecular networking approach. Overall, this study suggests UHPLC-HRMS/MS-through the integration of manual and computational dereplication approaches-as a valuable tool for the investigation and high-throughput characterization of the C. crambe metabolome.PMID:39590802 | DOI:10.3390/md22110522

Mar Drugs. 2024 Nov 15;22(11):518. doi: 10.3390/md22110518.ABSTRACTThe sustainable utilization of co-products derived from the salmon processing industry is crucial for enhancing the viability and decreasing the environmental footprint of both capture and aquaculture operations. Salmon (Salmo salar) is one of the most consumed fish worldwide and a major species produced in aquaculture. As such, significant quantities of salmon co-products are produced in pre-commercialization processing/steaking procedures. The present study characterized a specific co-product derived from the processing of salmon: minced salmon heads. More specifically, this work aimed to reveal the nutritional profile of this co-product, with a special focus on its lipid content, including thoroughly profiling fatty acids and fully appraising the composition in complex lipids (polar lipids and triglycerides) for the first time. The antioxidant potential of lipid extracts from this salmon co-product was also studied in order to bioprospect lipid functional properties and possibly unveil new pathways for added-value applications. Our analysis indicated that these minced salmon heads are exceptionally rich in lipids. Oleic acid is the most prevalent fatty acid in this co-product, followed by palmitic acid, stearic acid, and linoleic acid. Moreover, relevant lipid indexes inferred from the fatty acid composition of this co-product revealed good nutritional traits. Lipidome analysis revealed that triglycerides were clearly the predominant lipid class present in this co-product while phospholipids, as well as ceramides, were also present, although in minimal quantities. The bioprospecting of antioxidant activity in the lipid extracts of the minced salmon heads revealed limited results. Given the high concentration of triglycerides, minced salmon heads can constitute a valuable resource for industrial applications from the production of fish oil to biodiesel (as triglycerides can be easily converted into fatty acid methyl esters), as well as possible ingredients for cosmetics, capitalizing on their alluring emollient properties. Overall, the valorization of minced salmon heads, major co-products derived from the processing of one of the most intensively farmed fish in the world, not only offers economic benefits but also contributes to the sustainability of the salmon processing industry by reducing waste and promoting a more efficient use of marine bioresources.PMID:39590798 | DOI:10.3390/md22110518

J Fungi (Basel). 2024 Nov 15;10(11):794. doi: 10.3390/jof10110794.ABSTRACTEndophytic fungi are commonly used to control plant diseases, overcoming the drawbacks of chemical agents. The internal browning (IB) of postharvest pineapple fruit, a physiological disease, leads to quality losses and limits industrial development. This work investigated the relationship among the effects of Aspergillus niger (An) on IB controlling, flavonoid metabolism and the endophytic fungal community of pineapple through metabolomics, transcriptomics, microbiomics and microorganism mutagenesis technology. We obtained an endophyte An that can control the IB of pineapple and screened its mutant strain AnM, through chemical mutagenesis, that cannot control IB. The transcriptome of fungi showed that An and AnM were different in oxidative metabolism. Transcriptome and metabolome analyses of pineapple showed that An upregulated genes of flavonoid synthesis, including dihydroflavonol 4-reductase and flavonoid 3'-monooxygenase and increased the flavonoid content in pineapple fruit, i.e., Hispidulin, Hispidulin-7-O-Glucoside, and Diosmetin, while AnM could not. Microbiomics analysis identified an increase in the abundance of eight endophytic fungi in An-inoculated fruit, among which the abundance of six endophytic fungi (Filobasidium magnum, Naganishia albida, A. niger, Aureobasidium melanogenum, Kwoniella heveanensis and Lysurus cruciatus) was positively correlated with the content of three flavonoids mentioned above but not in AnM-inoculated fruit. Overall, this suggested, for the first time, that A. niger alleviated IB mainly by enhancing flavonoid synthesis and content and the abundance of endophytic fungi and by regulating the interaction between flavonoid content and endophytic fungi abundance in pineapple. This work adds to the understanding of the IB mechanism in postharvest pineapple and provides a new green approach for reducing postharvest losses and controlling physiological diseases.PMID:39590713 | DOI:10.3390/jof10110794

J Fungi (Basel). 2024 Nov 14;10(11):791. doi: 10.3390/jof10110791.ABSTRACTIn this study, a new species of Alanomyces was isolated as an endophyte from the bark of Azadirachta indica from Mulshi, Maharashtra. The identity of this isolate was confirmed based on the asexual morphological characteristics as well as multi-gene phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) nuclear ribosomal RNA (rRNA) regions. As this was the second species to be reported in this genus, we sequenced the genome of this species to increase our knowledge about the possible applicability of this genus to various industries. Its genome length was found to be 35.01 Mb, harboring 7870 protein-coding genes as per Augustus and 8101 genes using GeMoMa. Many genes were annotated using the Clusters of Orthologous Groups (COGs) database, the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Swiss-Prot, NCBI non-redundant nucleotide sequences (NTs), and NCBI non-redundant protein sequences (NRs). The number of repeating sequences was predicted using Proteinmask and RepeatMasker; tRNA were detected using tRNAscan and snRNA were predicted using rfam_scan. The genome was also annotated using the Pathogen-Host Interactions Database (PHI-base) and AntiSMASH. To confirm the evolutionary history, average nucleotide identity (ANIb), phylogeny based on orthologous proteins, and single nucleotide polymorphisms (SNPs) were carried out. Metabolic profiling of the methanolic extract of dried biomass and ethyl acetate extract of the filtrate revealed a variety of compounds of great importance in the pharmaceutical and cosmetic industry. The characterization and genomic analysis of the newly discovered species Alanomyces manoharacharyi highlights its potential applicability across multiple industries, particularly in pharmaceuticals and cosmetics due to its diverse secondary metabolites and unique genetic features it possesses.PMID:39590710 | DOI:10.3390/jof10110791

J Fungi (Basel). 2024 Nov 1;10(11):759. doi: 10.3390/jof10110759.ABSTRACTThe intercropping of Morchella in pear orchards has important production value in improving the utilization rate and economic benefits of the orchard; however, there is little research on the intercropping model of pear-Morchella. In this study, metabolomics analysis found that compared with greenhouse cultivation, there were 104 and 142 metabolites significantly increased and decreased in the intercropping mode of M. sextelata, respectively. Among them, there was a significant accumulation of amino acids (phenylalanine, lysine, proline, citrulline, and ornithine), sugars (arabinitol and glucosamine), and organic acids (quinic acid, fumaric acid, and malic acid) related to the unique taste of Morchella in intercropping cultivation. In addition, research on the cultivation model using exogenous nutrient bags indicated that placing the density of six exogenous nutrient bags per square meter was most suitable for yield formation. Adding pear sawdust to the nutrient bags (PN) significantly increased the yield of morel per unit area. Moreover, soil microbial community analysis showed that fungal alpha diversity dramatically declined in PN-cultivated soil, which decreased the relative abundance of soil-borne fungal pathogens, including Fusarium and Aspergillus. Some beneficial soil bacteria abundance increased in the PN-used soil, such as Pedobacter, Pseudomonas, and Devosia. This study provides novel insights into the effects of intercropping on the internal quality of Morchella and enriches the theoretical knowledge on the consummation of the pear-Morchella model formation, further improving agricultural resource utilization efficiency and crop productivity.PMID:39590678 | DOI:10.3390/jof10110759

J Fungi (Basel). 2024 Oct 29;10(11):748. doi: 10.3390/jof10110748.ABSTRACTNatural products (NPs) are crucial for the development of novel antibiotics, anticancer agents, and immunosuppressants. To highlight the ability of fungi to produce structurally diverse NPs, this article focuses on the impact of genome mining and CRISPR-Cas9 technology in uncovering and manipulating the biosynthetic gene clusters (BGCs) responsible for NP synthesis. The CRISPR-Cas9 system, originally identified as a bacterial adaptive immune mechanism, has been adapted for precise genome editing in fungi, enabling targeted modifications, such as gene deletions, insertions, and transcription modulation, without altering the genomic sequence. This review elaborates on various CRISPR-Cas9 systems used in fungi, notably the Streptococcus pyogenes type II Cas9 system, and explores advancements in different Cas proteins for fungal genome editing. This review discusses the methodologies employed in CRISPR-Cas9 genome editing of fungi, including guide RNA design, delivery methods, and verification of edited strains. The application of CRISPR-Cas9 has led to enhanced production of secondary metabolites in filamentous fungi, showcasing the potential of this system in biotechnology, medical mycology, and plant pathology. Moreover, this article emphasizes the integration of multi-omics data (genomics, transcriptomics, proteomics, and metabolomics) to validate CRISPR-Cas9 editing effects in fungi. This comprehensive approach aids in understanding molecular changes, identifying off-target effects, and optimizing the editing protocols. Statistical and machine learning techniques are also crucial for analyzing multi-omics data, enabling the development of predictive models and identification of key molecular pathways affected by CRISPR-Cas9 editing. In conclusion, CRISPR-Cas9 technology is a powerful tool for exploring fungal NPs with the potential to accelerate the discovery of novel bioactive compounds. The integration of CRISPR-Cas9 with multi-omics approaches significantly enhances our ability to understand and manipulate fungal genomes for the production of valuable secondary metabolites and for promising new applications in medicine and industry.PMID:39590667 | DOI:10.3390/jof10110748

J Fungi (Basel). 2024 Oct 23;10(11):734. doi: 10.3390/jof10110734.ABSTRACTLyophyllum decastes is a commercially cultivated rare edible mushroom with high dietary and medicinal value. The mycelium physiological maturation was an important factor to the yield and quality of mushrooms obtained. However, it was impossible to obtain discriminative characteristics represented the maturity level of the mycelia from morphological features. In this article, we screened a candidate metabolite for evaluating the mycelium physiological maturation by metabolomic and transcriptomic analysis during mycelial vegetative growth stages of L. decastes. The results showed that mycelial vegetative growth 55 d had reached to physiological maturation according to the yield and quality of L. decastes, which the single bottle yield (307 g/bottle), the contents of flavonoids (2.94 mg/g dry weight), and 5 flavor amino acids (glutamate 177.90 μg/g, aspartate 95.74 μg/g, phenylalanine 31.68 μg/g, tyrosine 13.79 μg/g, and alanine 10.99 μg/g) were the highest. In addition, the metabolomic and transcriptomic analysis results showed that biosynthesis of secondary metabolites and amino acid had significant different during mycelial vegetative growth stages, and glutamine may be a candidate indicator to evaluate the mycelial physiological maturation. These findings contribute to improve our knowledge of mycelium physiological maturation and it will be used to increase mushroom yield and quality.PMID:39590654 | DOI:10.3390/jof10110734