Metabolites

24 pages, 377 KiB

Open AccessReview

An Overview of Pre-Analytical Factors Impacting Metabolomics Analyses of Blood Samples

by Amy Thachil, Li Wang, Rupasri Mandal, David Wishart and Tom Blydt-Hansen

Metabolites 2024, 14(9), 474; https://doi.org/10.3390/metabo14090474 (registering DOI) - 28 Aug 2024

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Discrepant sample processing remains a significant challenge within blood metabolomics research, introducing non-biological variation into the measured metabolome and biasing downstream results. Inconsistency during the pre-analytical phase can influence experimental processes, producing metabolome measurements that are non-representative of in vivo composition. To minimize [...] Read more.

Discrepant sample processing remains a significant challenge within blood metabolomics research, introducing non-biological variation into the measured metabolome and biasing downstream results. Inconsistency during the pre-analytical phase can influence experimental processes, producing metabolome measurements that are non-representative of in vivo composition. To minimize variation, there is a need to create and adhere to standardized pre-analytical protocols for blood samples intended for use in metabolomics analyses. This will allow for reliable and reproducible findings within blood metabolomics research. In this review article, we provide an overview of the existing literature pertaining to pre-analytical factors that influence blood metabolite measurements. Pre-analytical factors including blood tube selection, pre- and post-processing time and temperature conditions, centrifugation conditions, freeze–thaw cycles, and long-term storage conditions are specifically discussed, with recommendations provided for best practices at each stage. Full article

(This article belongs to the Special Issue Metabolomics and Machine Learning for Improved Diagnostics and as a Tool to Accelerate Drug Development)

15 pages, 732 KiB

Open AccessArticle

Iron Homeostasis-Related Parameters and Hepcidin/Ferritin Ratio: Emerging Sex-Specific Predictive Markers for Metabolic Syndrome

by Baraah T. Abu AlSel, Abdelrahman A. Mahmoud, Elham O. Hamed, Noor A. Hakim, Abdulmajeed A. A. Sindi, Najlaa M. M. Jawad, Amani M. T. Gusti, Manal S. Fawzy and Noha M. Abd El-Fadeal

Metabolites 2024, 14(9), 473; https://doi.org/10.3390/metabo14090473 (registering DOI) - 28 Aug 2024

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Abstract

Metabolic syndrome (MetS) is a worldwide public health challenge. Accumulating evidence implicates elevated serum ferritin and disruptions in iron metabolism as potential elements linked to an increased risk of MetS. This study investigates the relationship between iron homeostasis—including hepcidin levels, serum iron concentration, [...] Read more.

Metabolic syndrome (MetS) is a worldwide public health challenge. Accumulating evidence implicates elevated serum ferritin and disruptions in iron metabolism as potential elements linked to an increased risk of MetS. This study investigates the relationship between iron homeostasis—including hepcidin levels, serum iron concentration, unsaturated iron-binding capacity (UIBC), and the hepcidin/ferritin (H/F) ratio—and MetS. In this descriptive cross-sectional study, 209 participants aged 24–70 were categorized into two groups: 103 with MetS and 106 without MetS. All participants underwent medical assessment, including anthropometric measures, indices of glycemic control, lipid profiles, and iron-related parameters. Participants were further stratified by the Homeostasis Model Assessment—Insulin Resistance index into three subgroups: insulin-sensitive (IS) (<1.9), early insulin resistance (EIR) (>1.9 to <2.9), and significant insulin resistance (SIR) (>2.9). Notable increments in serum ferritin and hepcidin were observed in the SIR group relative to the IS and EIR groups, with a significant association between metabolic parameters. The UIBC and serum ferritin emerged as significant predictors of MetS, particularly in men, with an area under the curve (AUC) of 0.753 and 0.792, respectively (p ≤ 0.001). In contrast, hepcidin was notably correlated with MetS in women, with an AUC of 0.655 (p = 0.007). The H/F ratio showed superior predictive capability for MetS across both sexes (at cutoff level = 0.67). Among women, this ratio had an AUC of 0.639 (p = 0.015), and for men, it had an AUC of 0.792 (p < 0.001). Hypertension proved an independent risk factor for MetS, affirming its role in metabolic dysregulation. The findings highlight a significant interconnection between iron homeostasis parameters and MetS, with sex-specific variations underscoring the importance of personalized diagnostic criteria. The crucial role of the H/F ratio and the UIBC as emerging predictive markers for MetS indicates their potential utility in identifying at-risk individuals. Further longitudinal research is essential to establish causality and explore the interplay between these biomarkers and MetS. Full article

(This article belongs to the Special Issue Obesity and Metabolic Dysfunction: Disease Development and Breaking the Cycle)

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24 pages, 3447 KiB

Open AccessArticle

The Legacy Effect of Mountain Pine Beetle Outbreaks on the Chemical and Anatomical Defences of Surviving Lodgepole Pine Trees

by Gigi Baker, Shiyang Zhao, Jennifer G. Klutsch, Guncha Ishangulyyeva and Nadir Erbilgin

Metabolites 2024, 14(9), 472; https://doi.org/10.3390/metabo14090472 - 27 Aug 2024

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Abstract

The recent mountain pine beetle outbreaks have caused widespread mortality among lodgepole pine trees in western North America, resulting in a reduced population of surviving trees. While previous studies have focused on the cascading impacts of these outbreaks on the physiology and growth [...] Read more.

The recent mountain pine beetle outbreaks have caused widespread mortality among lodgepole pine trees in western North America, resulting in a reduced population of surviving trees. While previous studies have focused on the cascading impacts of these outbreaks on the physiology and growth of the surviving trees, there remains a need for a comprehensive study into the interactions among various physiological traits and the growth in post-outbreak stands. Specifically, the relationship between chemical (primarily terpenes) and anatomical (mainly resin ducts) defences, as well as the allocation of non-structural carbohydrates (NSCs) to support these defence modalities, is poorly understood. To address these gaps, we conducted a field survey of surviving lodgepole pine trees in post-mountain pine beetle outbreak stands in western Canada. Our retrospective analysis aimed at determining correlations between the post-outbreak concentrations of monoterpenes, diterpenes, and NSCs in the phloem and the historical resin duct characteristics and growth traits before and after the outbreak. We detected strong correlations between the post-outbreak concentrations of monoterpenes and historical resin duct characteristics, suggesting a possible link between these two defence modalities. Additionally, we found a positive relationship between the NSCs and the total concentrations of monoterpenes and diterpenes, suggesting that NSCs likely influence the production of these terpenes in lodgepole pine. Furthermore, historical tree growth patterns showed strong positive correlations with many individual monoterpenes and diterpenes. Interestingly, while surviving trees had enhanced anatomical defences after the outbreak, their growth patterns did not vary before and after the outbreak conditions. The complexity of these relationships emphasizes the dynamics of post-outbreak stand dynamics and resource allocations in lodgepole pine forests, highlighting the need for further research. These findings contribute to a broader understanding of conifer defences and their coordinated responses to forest insect outbreaks, with implications for forest management and conservation strategies. Full article

(This article belongs to the Section Plant Metabolism)

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17 pages, 1998 KiB

Open AccessArticle

Disposition of Oral Nalbuphine and Its Metabolites in Healthy Subjects and Subjects with Hepatic Impairment: Preliminary Modeling Results Using a Continuous Intestinal Absorption Model with Enterohepatic Recirculation

by Swati Nagar, Amale Hawi, Thomas Sciascia and Ken Korzekwa

Metabolites 2024, 14(9), 471; https://doi.org/10.3390/metabo14090471 - 27 Aug 2024

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Abstract

Nalbuphine (NAL) is a mixed κ-agonist/μ-antagonist opioid with extensive first-pass metabolism. A phase 1 open-label study was conducted to characterize the pharmacokinetics (PKs) of NAL and select metabolites following single oral doses of NAL extended-release tablets in subjects with mild, moderate, and severe [...] Read more.

Nalbuphine (NAL) is a mixed κ-agonist/μ-antagonist opioid with extensive first-pass metabolism. A phase 1 open-label study was conducted to characterize the pharmacokinetics (PKs) of NAL and select metabolites following single oral doses of NAL extended-release tablets in subjects with mild, moderate, and severe hepatic impairment (Child–Pugh A, B, and C, respectively) compared to healthy matched subjects. NAL exposures were similar for subjects with mild hepatic impairment as compared to healthy subjects and nearly three-fold and eight-fold higher in subjects with moderate and severe hepatic impairment, respectively. Datasets obtained for healthy, moderate, and severe hepatic impaired groups were modeled with a mechanistic model that incorporated NAL hepatic metabolism and enterohepatic recycling of NAL and its glucuronidated metabolites. The mechanistic model includes a continuous intestinal absorption model linked to semi-physiological liver–gallbladder–compartmental PK models based on partial differential equations (termed the PDE-EHR model). In vitro studies indicated that cytochromes P450 CYP2C9 and CYP2C19 are the major CYPs involved in NAL oxidation, with glucuronidation mainly catalyzed by UGT1A8 and UGT2B7 isozymes. Complex formation and elimination kinetics of NAL and four main metabolites was well predicted by PDE-EHR. The model is expected to improve predictions of drug interactions and complex drug disposition. Full article

(This article belongs to the Special Issue The Role of Metabolites in Translational and Clinical Pharmacology)

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13 pages, 4863 KiB

Open AccessArticle

Application of ATR-FTIR Spectroscopy for Analysis of Salt Stress in Brussels Sprouts

by Su-Min Yun, Cheol-Soo Kim, Jeung-Joo Lee and Jung-Sung Chung

Metabolites 2024, 14(9), 470; https://doi.org/10.3390/metabo14090470 - 26 Aug 2024

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Abstract

Salt stress is one of the environmental stresses that significantly reduces crop productivity and quality worldwide. Methods to overcome salt stress include developing salt-resistant crops by inserting various resistance genes or to diagnosing and responding to the effects of salt stress at an [...] Read more.

Salt stress is one of the environmental stresses that significantly reduces crop productivity and quality worldwide. Methods to overcome salt stress include developing salt-resistant crops by inserting various resistance genes or to diagnosing and responding to the effects of salt stress at an early stage. In this study, we investigate the effects of salinity stress on growth, photosynthetic efficiency, and metabolic changes in Brussels sprouts (Brassica oleracea var. gemmifera). Fresh weight and leaf area decreased significantly with increasing NaCl concentration, indicating that salinity stress has a detrimental effect on plant growth. However, chlorophyll fluorescence parameters did not show significant changes, suggesting that photosynthetic efficiency was not significantly affected over 10 days. Fourier transform infrared (FTIR) spectroscopy revealed notable metabolic adjustments, especially in lipids, plastids, proteins, and carbohydrates, indicating biosynthesis of protective compounds such as anthocyanins and proline in response to salinity stress. Pearson correlation analysis confirmed a strong relationship between NaCl concentration and the observed physiological and metabolic changes. The findings highlight the potential of FTIR spectroscopy as a non-destructive tool for early detection of salinity stress and timely intervention to improve crop resilience and yield. This study highlights the widespread application of FTIR spectroscopy in agricultural research to manage abiotic stresses in crops. Full article

(This article belongs to the Topic Application of Analytical Technology in Metabolomics)

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16 pages, 3813 KiB

Open AccessArticle

Combining the Vaginal Microbiome and Serum Metabolome to Screen for Potential Biomarkers of Early Pregnancy in Cows

by Yan Luo, Zhen Wang, Xin Zhao, Jiankang Xing, Zhiliang Chen, Wenxue Zhao, Xiaoqing Long, Yanbing Zhang and Yongbin Shao

Metabolites 2024, 14(9), 469; https://doi.org/10.3390/metabo14090469 - 26 Aug 2024

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Abstract

Early pregnancy diagnostic techniques are of significant importance in livestock farming, particularly in dairy farming. This study aimed to screen artificially inseminated cows for potential biomarkers at day 21 of pregnancy using microbiota–metabolomics analysis. The microbiome analysis revealed significant changes (p < [...] Read more.

Early pregnancy diagnostic techniques are of significant importance in livestock farming, particularly in dairy farming. This study aimed to screen artificially inseminated cows for potential biomarkers at day 21 of pregnancy using microbiota–metabolomics analysis. The microbiome analysis revealed significant changes (p < 0.05) in the composition and abundance of the vaginal microbiota in cows after pregnancy. Notably, there was an increase in the abundance of [Eubacterium]_hallii_group (p < 0.05) associated with the production of short-chain fatty acids in the pregnant group compared with the non-pregnant group. Furthermore, significant alterations were observed in the serum metabolome, with notable changes in the concentrations of prolyl-hydroxyproline (Pro-Hyp) (p < 0.01) and bonactin (p < 0.01). The majority of differential metabolites clustered within the pathways of amino acid metabolism and lipid metabolism, with lipid metabolism exhibiting a higher proportion and playing a pivotal role in early pregnancy. An enzyme-linked immunosorbent assay was employed to quantify three key metabolites of the arachidonic acid pathway. The results demonstrated significant decreases in serum concentrations of leukotriene B4 (LTB4) (p < 0.05) and prostaglandin F2α (PGF2α) (p < 0.01) and no significant changes in arachidonic acid (AA) (NS) concentrations after 21 days of gestation in cows. Spearman’s correlation analysis was utilized to investigate the interrelationship between the vaginal microbiota and serum metabolites. In conclusion, the present study demonstrated that biomaterials such as bonactin, Pro-hyp, LTB4, PGF2α in serum metabolites and [Eubacterium]_hallii_group in the vaginal flora of cows could be utilized as potential biomarkers for 21 days of gestation in cows. Full article

(This article belongs to the Section Animal Metabolism)

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14 pages, 444 KiB

Open AccessArticle

Association of Initial Muscle Fitness with Weight Loss and Metabolically Healthy Status in Children and Adolescents with Obesity: A Retrospective Study

by Wenya Shang, Jiaqi Kong, Mengxue Zhang, Tao Chen, Linlin Zhao, Kun Wang and Qin Yang

Metabolites 2024, 14(9), 468; https://doi.org/10.3390/metabo14090468 - 24 Aug 2024

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Abstract

This retrospective study aimed to investigate the association of initial muscular fitness (MF) with weight loss and metabolic health status in 282 children and adolescents with obesity during 3 to 4 weeks of diet- and exercise-based interventions. Metabolically healthy obesity (MHO) definitions established [...] Read more.

This retrospective study aimed to investigate the association of initial muscular fitness (MF) with weight loss and metabolic health status in 282 children and adolescents with obesity during 3 to 4 weeks of diet- and exercise-based interventions. Metabolically healthy obesity (MHO) definitions established in 2023 and MF standards based on the 2021 Chinese children’s grip strength grading were applied. The proportion of metabolically unhealthy obesity (MUO) was higher in the high MF group than in their low MF counterparts at baseline. After the intervention, neither group transitioned from MUO to MHO due to the high frequency of low HDL-C. High MF females showed a higher percentage of high systolic blood pressure (SBP) than low MF females before and after intervention. High MF males exhibited greater improvements in waist circumference, hip circumference, waist-hip ratio, triglycerides, total cholesterol, and LDL-C than low MF males. The benefits of weight loss and blood lipids obtained by males are more evident than those obtained by females under the same MF level. Thus, attention should be paid to females during weight loss regardless of MF levels. Precision therapy should prioritize the management of blood pressure and avoid excessive reduction in HDL-C levels to sustain metabolic health. Full article

(This article belongs to the Special Issue Obesity and Metabolic Syndrome in Children: Insights, Interventions and Emerging Perspectives)

16 pages, 1898 KiB

Open AccessArticle

A Deep Mining Strategy for Peptide Rapid Identification in Lactobacillus reuteri Based on LC–MS/MS Integrated with FBMN and De Novo Sequencing

by Yilang Zuo, Shilin Gong, Li Zhang, Jie Zhou, Jian-Lin Wu and Na Li

Metabolites 2024, 14(9), 467; https://doi.org/10.3390/metabo14090467 - 23 Aug 2024

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Abstract

Lactobacillus reuteri (L. reuteri) is widely recognized as a probiotic that produces prebiotics. However, studies on bioactive peptides or amino acid (AA) derivatives produced by L. reuteri are still lacking, whereas many bioactive peptides and AA derivatives have been found in [...] Read more.

Lactobacillus reuteri (L. reuteri) is widely recognized as a probiotic that produces prebiotics. However, studies on bioactive peptides or amino acid (AA) derivatives produced by L. reuteri are still lacking, whereas many bioactive peptides and AA derivatives have been found in other Lactobacillus species. In addition, rapid identification of peptides is challenged by the large amount of data and is limited by the coverage of protein databases. In this study, we performed a rapid and thorough profile of peptides in L. reuteri incorporating Global Natural Products Social Molecular Networking (GNPS) platform database searching, de novo sequencing, and deep mining, based on feature-based molecular networking (FBMN). According to FBMN, it was found that peptides containing identical or similar AA compositions were grouped into the same clusters, especially cyclic dipeptides (CDPs). Therefore, the grouping characteristics of clusters, differences in precursor ions, and characteristic fragment ions were utilized for the mining of deeply unknown compounds. Through this strategy, a total of 192 compounds, including 184 peptides, were rapidly identified. Among them, 53 CDPs, including four novel ones, were found for the first time in L. reuteri. Then, one of the novel CDPs, cyclo(5-OMe-Glu-4-OH-Pro), was isolated and characterized, which was consistent with the identification results. Moreover, some of the identified peptides exhibited considerable interactions with seven anti-inflammatory-related target proteins through molecular docking. According to the binding energies of peptides with different AA consistencies, it was considered that the existence of unnatural AAs in CDPs might contribute to their anti-inflammatory activity. These results provide a valuable strategy for the rapid identification of peptides, including CDPs. This study also reveals the substance basis for the potential anti-inflammatory effects exerted by L. reuteri. Full article

(This article belongs to the Section Bioinformatics and Data Analysis)

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14 pages, 2082 KiB

Open AccessArticle

Untargeted Blood Lipidomics Analysis in Critically Ill Pediatric Patients with Ventilator-Associated Pneumonia: A Pilot Study

by Christina Virgiliou, Olga Begou, Argyro Ftergioti, Maria Simitsopoulou, Maria Sdougka, Emmanuel Roilides, Georgios Theodoridis, Helen Gika and Elias Iosifidis

Metabolites 2024, 14(9), 466; https://doi.org/10.3390/metabo14090466 - 23 Aug 2024

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Abstract

This study aims to explore the diagnostic potential of blood lipid profiles in suspected ventilator-associated pneumonia (VAP). Early detection of VAP remains challenging for clinicians due to subjective clinical criteria and the limited effectiveness of current diagnostic tests. Blood samples from 20 patients, [...] Read more.

This study aims to explore the diagnostic potential of blood lipid profiles in suspected ventilator-associated pneumonia (VAP). Early detection of VAP remains challenging for clinicians due to subjective clinical criteria and the limited effectiveness of current diagnostic tests. Blood samples from 20 patients, with ages between 6 months and 15 years, were collected at days 1, 3, 6, and 12, and an untargeted lipidomics analysis was performed using a Ultra high Pressure Liquid Chromatography hyphenated with High Resolution Mass Spectrometry UPLC-HRMS (TIMS-TOF/MS) platform. Patients were stratified based on modified pediatric clinical pulmonary index score (mCPIS) into high (mCPIS ≥ 6, n = 12) and low (mCPIS < 6, n = 8) VAP suspicion groups. With the untargeted lipid profiling, we were able to identify 144 lipid species from different lipid groups such as glycerophospholipids, glycerolipids, and sphingolipids, in the blood of children with VAP. Multivariate and univariate statistical analyses revealed a distinct distribution of blood lipid profiles between the studied groups, indicating the potential utility of lipid biomarkers in discriminating VAP presence. Additionally, specific lipids were associated with pharyngeal culture results, notably the presence of Klebsiella pneumoniae and Staphylococcus aureus, underscoring the importance of lipid profiling in identifying the microbial etiology of VAP. Full article

(This article belongs to the Special Issue Metabolomics: An Emerging Potential Approach to Study Critical Illnesses, 2nd Edition)

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18 pages, 2528 KiB

Open AccessArticle

The Effects of Maternal Nutrient Restriction during Mid to Late Gestation with Realimentation on Fetal Metabolic Profiles in the Liver, Skeletal Muscle, and Blood in Sheep

by Brandon I. Smith, Manuel A. Vásquez-Hidalgo, Xiaomeng Li, Kimberly A. Vonnahme, Anna T. Grazul-Bilska, Kendall C. Swanson, Timothy E. Moore, Sarah A. Reed and Kristen E. Govoni

Metabolites 2024, 14(9), 465; https://doi.org/10.3390/metabo14090465 - 23 Aug 2024

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Abstract

Poor maternal nutrition during gestation negatively affects offspring growth and metabolism. To evaluate the impact of maternal nutrient restriction and realimentation on metabolism in the fetal liver, skeletal muscle, and circulation, on day 50 of gestation, ewes (n = 48) pregnant with [...] Read more.

Poor maternal nutrition during gestation negatively affects offspring growth and metabolism. To evaluate the impact of maternal nutrient restriction and realimentation on metabolism in the fetal liver, skeletal muscle, and circulation, on day 50 of gestation, ewes (n = 48) pregnant with singletons were fed 100% (CON) or 60% (RES) of requirements until day 90 of gestation, when a subset of ewes (n = 7/treatment) were euthanized, and fetal samples were collected. The remaining ewes were maintained on a current diet (CON-CON, n = 6; RES-RES, n = 7) or switched to an alternative diet (CON-RES, RES-CON; n = 7/treatment). On day 130 of gestation, the remaining ewes were euthanized, and fetal samples were collected. Fetal liver, longissimus dorsi (LD), and blood metabolites were analyzed using LC-MS/MS, and pathway enrichment analysis was conducted using MetaboAnalyst. Then, 600, 518, and 524 metabolites were identified in the liver, LD, and blood, respectively, including 345 metabolites that were present in all three. Nutrient restriction was associated with changes in amino acid, carbohydrate, lipid, and transulfuration/methionine metabolic pathways, some of which were alleviated by realimentation. Fetal age also affected metabolite abundance. The differential abundance of metabolites involved in amino acid, methionine, betaine, and bile acid metabolism could impact fetal epigenetic regulation, protein synthesis, lipid metabolism, and signaling associated with glucose and lipid metabolism. Full article

(This article belongs to the Special Issue Unlocking the Mysteries of Muscle Metabolism in the Animal Sciences)

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Metabolites, Volume 14, Issue 9 (September 2024) – 10 articles

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