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Fulltext LC-MS data for metabolomics analysis of Garcinia mangostana L. seed germination

Mazlan O, Aizat WM, Aziz Zuddin NS, Baharum SN, Noor NM

Data Brief, 2018 Dec;21:2221-2223.
PMID: 30555858 DOI: 10.1016/j.dib.2018.11.072

Metabolic regulation is important during seed germination for the establishment of seedling. The germination strategy of mangosteen (Garcinia mangostana L.) seed is thought to be unique due to its recalcitrant characteristic (sensitive to coldness and drying). To investigate the metabolic changes during seed germination, we performed metabolomics analysis on germinating mangosteen seed sown after zero, one, three, five, seven and nine days. Sampled mangosteen seeds were subjected to methanol extraction prior analysis using Liquid Chromatography-Time of Flight-Mass Spectrometry (LC-TOF-MS). MS data were further analyzed using ProfileAnalysis (version 2.1). This is one of the earliest reports in metabolite identification and profiling of mangosteen seed at different germination stages. This data article refers to the article entitled "Metabolite profiling of mangosteen seed germination highlights metabolic changes related to carbon utilization and seed protection" (Mazlan et al., 2019) [1].

Matched MeSH terms: Metabolomics
Fulltext Mass spectrometry dataset for LC-MS metabolomics analysis of Garcinia mangostana L. seed development

Mazlan O, Aizat WM, Baharum SN, Azizan KA, Noor NM

Data Brief, 2018 Dec;21:548-551.
PMID: 30370325 DOI: 10.1016/j.dib.2018.10.025

Garcinia mangostana L. (mangosteen) seed is recalcitrant, prone to low temperature and drying which limit its long-term storage. Therefore, it is imperative to understand the metabolic changes throughout its development, to shed some light into the recalcitrant nature of this seed. We performed metabolomics analysis on mangosteen seed at different stages of development; six, eight, ten, twelve and fourteen weeks after anthesis. Seed samples were subjected to methanol extraction prior analysis using liquid chromatography - mass spectrometry (LC-MS). The MS data acquired were analyzed using ProfileAnalysis (version 2.1). This data article refers to the article entitled "Metabolomics analysis of developing Garcinia mangostana seed reveals modulated levels of sugars, organic acids and phenylpropanoid compounds" (Mazlan et al., 2018) [1].

Matched MeSH terms: Metabolomics
Recent Development in Omics Studies

Aizat WM, Ismail I, Noor NM

Adv Exp Med Biol, 2018 11 2;1102:1-9.
PMID: 30382565 DOI: 10.1007/978-3-319-98758-3_1

The central dogma of molecular biology (DNA, RNA, protein and metabolite) has engraved our understanding of genetics in all living organisms. While the concept has been embraced for many decades, the development of high-throughput technologies particularly omics (genomics, transcriptomics, proteomics and metabolomics) has revolutionised the field to incorporate big data analysis including bioinformatics and systems biology as well as synthetic biology area. These omics approaches as well as systems and synthetic biology areas are now increasingly popular as seen by the growing numbers of publication throughout the years. Several journals which have published most of these related fields are also listed in this chapter to overview their impact and target journals.

Matched MeSH terms: Metabolomics/trends*
Fulltext Physical fitness in community-dwelling older adults is linked to dietary intake, gut microbiota, and metabolomic signatures

Castro-Mejía JL, Khakimov B, Krych Ł, Bülow J, Bechshøft RL, Højfeldt G, et al.

Aging Cell, 2020 03;19(3):e13105.
PMID: 31967716 DOI: 10.1111/acel.13105

When humans age, changes in body composition arise along with lifestyle-associated disorders influencing fitness and physical decline. Here we provide a comprehensive view of dietary intake, physical activity, gut microbiota (GM), and host metabolome in relation to physical fitness of 207 community-dwelling subjects aged +65 years. Stratification on anthropometric/body composition/physical performance measurements (ABPm) variables identified two phenotypes (high/low-fitness) clearly linked to dietary intake, physical activity, GM, and host metabolome patterns. Strikingly, despite a higher energy intake high-fitness subjects were characterized by leaner bodies and lower fasting proinsulin-C-peptide/blood glucose levels in a mechanism likely driven by higher dietary fiber intake, physical activity and increased abundance of Bifidobacteriales and Clostridiales species in GM and associated metabolites (i.e., enterolactone). These factors explained 50.1% of the individual variation in physical fitness. We propose that targeting dietary strategies for modulation of GM and host metabolome interactions may allow establishing therapeutic approaches to delay and possibly revert comorbidities of aging.

Matched MeSH terms: Metabolomics/methods
Fulltext Metabolomics data of Mitragyna speciosa leaf using LC-ESI-TOF-MS

Veeramohan R, Azizan KA, Aizat WM, Goh HH, Mansor SM, Yusof NSM, et al.

Data Brief, 2018 Jun;18:1212-1216.
PMID: 29900296 DOI: 10.1016/j.dib.2018.04.001

Mitragyna speciosa is a psychoactive plant known as "ketum" in Malaysia and "kratom" in Thailand. This plant is distinctly known to produce two important alkaloids, namely mitragynine (MG) and 7-hydroxymitragynine (7-OH-MG) that can bind to opioid receptors [1]. MG was reported to exhibit antidepressant properties in animal studies [2]. These compounds were also proposed to have the potential to replace opioid analgesics with much lower risks of side effects [3]. To date, there are only over 40 metabolites identified in M. speciosa [4,5]. To obtain a more complete profile of secondary metabolites in ketum, we performed metabolomics study using mature leaves of the green M. speciosa variety. The leaf samples were extracted using methanol prior to liquid chromatography-electrospray ionization-time of flight-mass spectrometry (LC-ESI-TOF-MS) analysis. This data can be useful to for the identification of unknown metabolites that are associated with alkaloid biosynthesis pathway in M. speciosa.

Matched MeSH terms: Metabolomics
Fulltext Comparative metabolomics analysis reveals alkaloid repertoires in young and mature Mitragyna speciosa (Korth.) Havil. Leaves

Veeramohan R, Zamani AI, Azizan KA, Goh HH, Aizat WM, Razak MFA, et al.

PLoS One, 2023;18(3):e0283147.
PMID: 36943850 DOI: 10.1371/journal.pone.0283147

The fresh leaves of Mitragyna speciosa (Korth.) Havil. have been traditionally consumed for centuries in Southeast Asia for its healing properties. Although the alkaloids of M. speciosa have been studied since the 1920s, comparative and systematic studies of metabolite composition based on different leaf maturity levels are still lacking. This study assessed the secondary metabolite composition in two different leaf stages (young and mature) of M. speciosa, using an untargeted liquid chromatography-electrospray ionisation-time-of-flight-mass spectrometry (LC-ESI-TOF-MS) metabolite profiling. The results revealed 86 putatively annotated metabolite features (RT:m/z value) comprising 63 alkaloids, 10 flavonoids, 6 terpenoids, 3 phenylpropanoids, and 1 of each carboxylic acid, glucoside, phenol, and phenolic aldehyde. The alkaloid features were further categorised into 14 subclasses, i.e., the most abundant class of secondary metabolites identified. As per previous reports, indole alkaloids are the most abundant alkaloid subclass in M. speciosa. The result of multivariate analysis (MVA) using principal component analysis (PCA) showed a clear separation of 92.8% between the young and mature leaf samples, indicating a high variance in metabolite levels between them. Akuammidine, alstonine, tryptamine, and yohimbine were tentatively identified among the many new alkaloids reported in this study, depicting the diverse biological activities of M. speciosa. Besides delving into the knowledge of metabolite distribution in different leaf stages, these findings have extended the current alkaloid repository of M. speciosa for a better understanding of its pharmaceutical potential.

Matched MeSH terms: Metabolomics
Fulltext A comparative UHPLC-Q/TOF-MS-based eco-metabolomics approach reveals temperature adaptation of four Nepenthes species

Wong C, Ling YS, Wee JLS, Mujahid A, Müller M

Sci Rep, 2020 12 14;10(1):21861.
PMID: 33318532 DOI: 10.1038/s41598-020-78873-3

Nepenthes, as the largest family of carnivorous plants, is found with an extensive geographical distribution throughout the Malay Archipelago, specifically in Borneo, Philippines, and Sumatra. Highland species are able to tolerate cold stress and lowland species heat stress. Our current understanding on the adaptation or survival mechanisms acquired by the different Nepenthes species to their climatic conditions at the phytochemical level is, however, limited. In this study, we applied an eco-metabolomics approach to identify temperature stressed individual metabolic fingerprints of four Nepenthes species: the lowlanders N. ampullaria, N. rafflesiana and N. northiana, and the highlander N. minima. We hypothesized that distinct metabolite regulation patterns exist between the Nepenthes species due to their adaptation towards different geographical and altitudinal distribution. Our results revealed not only distinct temperature stress induced metabolite fingerprints for each Nepenthes species, but also shared metabolic response and adaptation strategies. The interspecific responses and adaptation of N. rafflesiana and N. northiana likely reflected their natural habitat niches. Moreover, our study also indicates the potential of lowlanders, especially N. ampullaria and N. rafflesiana, to produce metabolites needed to deal with increased temperatures, offering hope for the plant genus and future adaption in times of changing climate.

Matched MeSH terms: Metabolomics*
Fulltext Application of the Metabolomics Approach in Food Authentication

Selamat J, Rozani NAA, Murugesu S

Molecules, 2021 Dec 14;26(24).
PMID: 34946647 DOI: 10.3390/molecules26247565

The authentication of food products is essential for food quality and safety. Authenticity assessments are important to ensure that the ingredients or contents of food products are legitimate and safe to consume. The metabolomics approach is an essential technique that can be utilized for authentication purposes. This study aimed to summarize food authentication through the metabolomics approach, to study the existing analytical methods, instruments, and statistical methods applied in food authentication, and to review some selected food commodities authenticated using metabolomics-based methods. Various databases, including Google Scholar, PubMed, Scopus, etc., were used to obtain previous research works relevant to the objectives. The review highlights the role of the metabolomics approach in food authenticity. The approach is technically implemented to ensure consumer protection through the strict inspection and enforcement of food labeling. Studies have shown that the study of metabolomics can ultimately detect adulterant(s) or ingredients that are added deliberately, thus compromising the authenticity or quality of food products. Overall, this review will provide information on the usefulness of metabolomics and the techniques associated with it in successful food authentication processes, which is currently a gap in research that can be further explored and improved.

Matched MeSH terms: Metabolomics*
Fulltext Metabolic profiling of Lactococcus lactis under different culture conditions

Azizan KA, Baharum SN, Mohd Noor N

Molecules, 2012 Jul 03;17(7):8022-36.
PMID: 22759915 DOI: 10.3390/molecules17078022

Gas chromatography mass spectrometry (GC-MS) and headspace gas chromatography mass spectrometry (HS/GC-MS) were used to study metabolites produced by Lactococcus lactis subsp. cremoris MG1363 grown at a temperature of 30 °C with and without agitation at 150 rpm, and at 37 °C without agitation. It was observed that L. lactis produced more organic acids under agitation. Primary alcohols, aldehydes, ketones and polyols were identified as the corresponding trimethylsilyl (TMS) derivatives, whereas amino acids and organic acids, including fatty acids, were detected through methyl chloroformate derivatization. HS analysis indicated that branched-chain methyl aldehydes, including 2-methylbutanal, 3-methylbutanal, and 2-methylpropanal are degdradation products of isoleucine, leucine or valine. Multivariate analysis (MVA) using partial least squares discriminant analysis (PLS-DA) revealed the major differences between treatments were due to changes of amino acids and fermentation products.

Matched MeSH terms: Metabolomics/methods*
Fulltext Brain Cortical and Hippocampal Dopamine: A New Mechanistic Approach for Eurycoma longifolia Well-Known Aphrodisiac Activity and Its Chemical Characterization

Ezzat SM, Ezzat MI, Okba MM, Hassan SM, Alkorashy AI, Karar MM, et al.

Evid Based Complement Alternat Med, 2019;2019:7543460.
PMID: 31275418 DOI: 10.1155/2019/7543460

Eurycoma longifolia Jack (Fam.: Simaroubaceae), known as Tongkat Ali (TA), has been known as a symbol of virility and sexual power for men. Metabolic profiling of the aqueous extract of E. longifolia (AEEL) using UPLC-MS/MS in both positive and negative modes allowed the identification of seventeen metabolites. The identified compounds were classified into four groups: quassinoids, alkaloids, triterpenes, and biphenylneolignans. AEEL is considered safe with oral LD50 cut-off >5000 mg/kg. Oral administration of 50, 100, 200, 400, or 800 mg/kg of AEEL for 10 consecutive days to Sprague-Dawley male rats caused significant reductions in mounting, intromission, and ejaculation latencies and increased penile erection index. AEEL increased total body weight and relative weights of seminal vesicles and prostate. Total and free serum testosterone and brain cortical and hippocampal dopamine content was significantly elevated in treated groups with no significant effects on serotonin or noradrenaline content.

Matched MeSH terms: Metabolomics
Fulltext Metabolite profiling of Andrographis paniculata (Burm. f.) Nees. young and mature leaves at different harvest ages using 1H NMR-based metabolomics approach

Tajidin NE, Shaari K, Maulidiani M, Salleh NS, Ketaren BR, Mohamad M

Sci Rep, 2019 11 14;9(1):16766.
PMID: 31727911 DOI: 10.1038/s41598-019-52905-z

Andrographis paniculata (Burm. F.) Nees. is considered as the herb of the future due to its precious chemical compounds, andrographolide (ANDRO), neoandrographolide (NAG) and 14-deoxyandrographolide (DAG). This study aims to profile the metabolites in young and mature leaf at six different harvest ages using 1HNMR-based metabolomics combined with multivariate data analysis. Principal component analysis (PCA) indicated noticeable and clear discrimination between young and mature leaves. A comparison of the leaves stage indicated that young leaves were separated from mature leaves due to its larger quantity of ANDRO, NAG, DAG, glucose and sucrose. These similar metabolites are also responsible for the PCA separation into five clusters representing the harvest age at 14, 16, 18, 20, 22 weeks of leaves extract. Loading plots revealed that most of the ANDRO and NAG signals were present when the plant reached at the pre-flowering stage or 18 weeks after sowing (WAS). As a conclusion, A. paniculata young leaves at pre-flowering harvest age were found to be richer in ANDRO, NAG and DAG compared to mature leaves while glucose and choline increased with harvest age. Therefore, young leaves of A. paniculata should be harvested at 18 WAS in order to produce superior quality plant extracts for further applications by the herbal, nutraceutical and pharmaceutical industries.

Matched MeSH terms: Metabolomics/methods*
Metabolomics in tea products; a compile of applications for enhancing agricultural traits and quality control analysis of Camellia sinensis

Farag MA, Elmetwally F, Elghanam R, Kamal N, Hellal K, Hamezah HS, et al.

Food Chem, 2023 Mar 15;404(Pt B):134628.
PMID: 36283313 DOI: 10.1016/j.foodchem.2022.134628

Tea is one of the world's most popular beverages, with several health benefits. Polyphenols are the predominant constituents to account for its health benefits. Despite the well-known benefits of tea on health, the uniqueness of its aroma, taste, and features is an added value that contribute to the increased popularity of this beverage worldwide, and they are associated with the alterations in the metabolites during tea processing and cultivation. The manufacturing of tea consists of several stages with various processes as withering, fixing, rolling, fermentation and drying. The classification into tea types is according to such processing. The high-quality production of the various tea classes also depends on agricultural conditions, such as shading, plucking, climate, and soil composition. Metabolomics is well recognized as an effective tool for evaluating the quality of tea products. Applications in controlling the quality of tea products and adulterant detection are discussed in this review.

Matched MeSH terms: Metabolomics
Fulltext Global serum metabolomics profiling of colorectal cancer

Hashim NAA, Ab-Rahim S, Suddin LS, Saman MSA, Mazlan M

Molecular and clinical oncology, 2019 Jul;11(1):3-14.
PMID: 31289671 DOI: 10.3892/mco.2019.1853

Accurate diagnosis of colorectal cancer (CRC) relies on the use of invasive tools such as colonoscopy and sigmoidoscopy. Non-invasive tools are less sensitive in detecting the disease, particularly in the early stage. A number of researchers have used metabolomics analyses on serum/plasma samples of patients with CRC compared with normal healthy individuals in an effort to identify biomarkers for CRC. The aim of the present review is to compare reported serum metabolomics profiles of CRC and to identify common metabolites affected among these studies. A literature search was performed to include any experimental studies on global metabolomics profile of CRC using serum/plasma samples published up to March 2018. The Quality Assessment of Diagnostic Accuracy Studies (QUADAS) tool was used to assess the quality of the studies reviewed. In total, nine studies were included. The studies used various analytical platforms and were performed on different populations. A pathway enrichment analysis was performed using the data from all the studies under review. The most affected pathways identified were protein biosynthesis, urea cycle, ammonia recycling, alanine metabolism, glutathione metabolism and citric acid cycle. The metabolomics analysis revealed levels of metabolites of glycolysis, tricarboxylic acid cycle, anaerobic respiration, protein, lipid and glutathione metabolism were significantly different between cancer and control samples. Although the majority of differentiating metabolites identified were different in the different studies, there were several metabolites that were common. These metabolites include pyruvic acid, glucose, lactic acid, malic acid, fumaric acid, 3-hydroxybutyric acid, tryptophan, phenylalanine, tyrosine, creatinine and ornithine. The consistent dysregulation of these metabolites among the different studies suggest the possibility of common diagnostic biomarkers for CRC.

Matched MeSH terms: Metabolomics
Fulltext Global metabolomics profiling of colorectal cancer in Malaysian patients

Amir Hashim NA, Ab-Rahim S, Wan Ngah WZ, Nathan S, Ab Mutalib NS, Sagap I, et al.

Bioimpacts, 2021;11(1):33-43.
PMID: 33469506 DOI: 10.34172/bi.2021.05

Introduction:
The serum metabolomics approach has been used to identify metabolite biomarkers that can diagnose colorectal cancer (CRC) accurately and specifically. However, the biomarkers identified differ between studies suggesting that more studies need to be performed to understand the influence of genetic and environmental factors. Therefore, this study aimed to identify biomarkers and affected metabolic pathways in Malaysian CRC patients.
Methods:
Serum from 50 healthy controls and 50 CRC patients were collected at UKM Medical Centre. The samples were deproteinized with acetonitrile and untargeted metabolomics profile determined using liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOFMS, Agilent USA). The data were analysed using Mass Profiler Professional (Agilent, USA) software. The panel of biomarkers determined were then used to identify CRC from a new set of 20 matched samples.
Results:
Eleven differential metabolites were identified whose levels were significantly different between CRC patients compared to normal controls. Based on the analysis of the area under the curve, 7 of these metabolites showed high sensitivity and specificity as biomarkers. The use of the 11 metabolites on a new set of samples was able to differentiate CRC from normal samples with 80% accuracy. These metabolites were hypoxanthine, acetylcarnitine, xanthine, uric acid, tyrosine, methionine, lysoPC, lysoPE, citric acid, 5-oxoproline, and pipercolic acid. The data also showed that the most perturbed pathways in CRC were purine, catecholamine, and amino acid metabolisms.
Conclusion:
Serum metabolomics profiling can be used to identify distinguishing biomarkers for CRC as well as to further our knowledge of its pathophysiological mechanisms.

Matched MeSH terms: Metabolomics
Fulltext Metabolomics Profiling on Different Stages of Colorectal Cancer: A Systematic Review

Yusof HM, Ab-Rahim S, Suddin LS, Saman MSA, Mazlan M

Malays J Med Sci, 2018 Sep;25(5):16-34.
PMID: 30914860 MyJurnal DOI: 10.21315/mjms2018.25.5.3

Colorectal cancer (CRC) is one of the leading causes of cancer-related deaths worldwide. Early diagnosis and accurate staging of the disease is vital to improve the prognosis. Metabolomics has been used to identify changes in metabolite profiles in the different stages of cancer in order to introduce new non-invasive molecular tools for staging. In this systematic review, we aim to identify the common metabolite changes in human biological samples and the dominant metabolic pathways associated with CRC progression. A broad systematic search was carried out from selected databases. Four reviewers screened and reviewed the titles, abstracts, and full-text articles according to the inclusion and exclusion criteria. Quality assessment was conducted on the eight articles which met the criteria. Data showed that the metabolites involved with redox status, energy metabolism and intermediates of amino acids, choline and nucleotides metabolism were the most affected during CRC progression. However, there were differences in the levels of individual metabolites detected between the studies, and this might be due to the study population, sample preparation, analytical platforms used and statistical tools. In conclusion, this systematic review highlights the changes in metabolites from early to late stages of CRC. Moreover, biomarkers for prognosis are important to reduce CRC-related mortality.

Matched MeSH terms: Metabolomics
Sequential Hybrid Three-Dimensional Gas Chromatography with Accurate Mass Spectrometry: A Novel Tool for High-Resolution Characterization of Multicomponent Samples

Yan D, Wong YF, Whittock SP, Koutoulis A, Shellie RA, Marriott PJ

Anal Chem, 2018 04 17;90(8):5264-5271.
PMID: 29575899 DOI: 10.1021/acs.analchem.8b00142

A novel sequential three-dimensional gas chromatography-high-resolution time-of-flight mass spectrometry (3D GC-accTOFMS) approach for profiling secondary metabolites in complex plant extracts is described. This integrated system incorporates a nonpolar first-dimension (1Dnp) separation step, prior to a microfluidic heart-cut (H/C) of a targeted region(s) to a cryogenic trapping device, directly followed by the rapid reinjection of a trapped solute into a polar second-dimension (2DPEG) column for multidimensional separation (GCnp-GCPEG). For additional separation, the effluent from 2DPEG can then be modulated according to a comprehensive 2D GC process (GC×GC), using an ionic liquid phase as a third-dimension (3DIL) column, to produce a sequential GCnp-GCPEG×GCIL separation. Thus, the unresolved or poorly resolved components, or regions that require further separation, can be precisely selected and rapidly transferred for additional separation on 2D or 3D columns, based on the greater separation realized by these steps. The described integrated system can be used in a number of modes, but one useful approach is to target specific classes of compounds for improved resolution. This is demonstrated through the separation and detection of the oxygenated sesquiterpenes in hop ( Humulus lupulus L.) essential oil and agarwood ( Aquilaria malaccensis) oleoresin. Improved resolution and peak capacity were illustrated through the progressive comparison of the tentatively identified components for GCnp-GCPEG and GCnp-GCPEG×GCIL methods. Relative standard deviations of intraday retentions (1 tR, 2 tR,, and 3 tR) and peak areas of ≤0.01, 0.07, 0.71, and 7.5% were achieved. This analytical approach comprising three GC column selectivities, hyphenated with high-resolution TOFMS detection, should be a valuable adjunct for the improved characterization of complex plant samples, particularly in the area of plant metabolomics.

Matched MeSH terms: Metabolomics
Fulltext Immunity and cell metabolism

Marina Mohd Bakri

Malaysian Journal of Medicine and Health Sciences, 2019;15(108):12-12.
MyJurnal

Over the past decade, research involving immunometabolism, has been gaining much interest. The immune cell re-sponses of an individual may be influenced by metabolites released by the host or derived from the microbiota. How-ever, the immune response of an individual may vary depending on the health condition of an individual. During infection, the metabolic processes derived from the infectious diseases can effect the function of immune cells and thus determine the response or survival of the host during infection. Immunometabolism also has a role in tumor development although the mechanism of how tumor cells influence immune cell function is not well understood. Among the major meatbolic pathways that have been studied in immune cells include glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, fatty acid oxidation, fatty acid synthesis and amino acid metabolism. Understanding the tight connection between metabolomics and immunity in health and disease will be crucial as this could lead to therapeutic interventions or in developing metabolomic biomarkers in immunology.

Matched MeSH terms: Metabolomics
Microbial dynamics, metabolomic profiles, and the correlation between them during fermentation of serofluid dish

Wei J, Ren W, Wang L, Liu M, Tian X, Ding G, et al.

J Sci Food Agric, 2020 Dec;100(15):5627-5636.
PMID: 32712996 DOI: 10.1002/jsfa.10690

BACKGROUND: Serofluid dish, a traditional Chinese fermented food, possesses unique flavors and health beneficial effects. These properties are likely due to the sophisticated metabolic networks during fermentation, which are mainly driven by microbiota. However, the exact roles of metabolic pathways and the microbial community during this process remain equivocal.
RESULTS: Here, we investigated the microbial dynamics by next-generation sequencing, and outlined a differential non-targeted metabolite profiling in the process of serofluid dish fermentation using the method of hydrophilic interaction liquid chromatography column with ultra-high-performance liquid chromatography-quadruple time-of-flight mass spectrometry. Lactobacillus was the leading genus of bacteria, while Pichia and Issatchenkia were the dominant fungi. They all accumulated during fermentation. In total, 218 differential metabolites were identified, of which organic acids, amino acids, sugar and sugar alcohols, fatty acids, and esters comprised the majority. The constructed metabolic network showed that tricarboxylic acid cycle, urea cycle, sugar metabolism, amino acids metabolism, choline metabolism, and flavonoid metabolism were regulated by the fermentation. Furthermore, correlation analysis revealed that the leading fungi, Pichia and Issatchenkia, were linked to organic acids, amino acid and sugar metabolism, flavonoids, and several other flavor and functional components. Antibacterial tests indicated the antibacterial effect of serofluid soup against Salmonella and Staphylococcus.
CONCLUSION: This work provides new insights into the complex microbial and metabolic networks during serofluid dish fermentation, and a theoretical basis for the optimization of its industrial production. © 2020 Society of Chemical Industry.

Matched MeSH terms: Metabolomics
Fulltext Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains

Wong EHJ, Ng CG, Goh KL, Vadivelu J, Ho B, Loke MF

Sci Rep, 2018 01 23;8(1):1409.
PMID: 29362474 DOI: 10.1038/s41598-018-19697-0

The biofilm-forming-capability of Helicobacter pylori has been suggested to be among factors influencing treatment outcome. However, H. pylori exhibit strain-to-strain differences in biofilm-forming-capability. Metabolomics enables the inference of spatial and temporal changes of metabolic activities during biofilm formation. Our study seeks to examine the differences in metabolome of low and high biofilm-formers using the metabolomic approach. Eight H. pylori clinical strains with different biofilm-forming-capability were chosen for metabolomic analysis. Bacterial metabolites were extracted using Bligh and Dyer method and analyzed by Liquid Chromatography/Quadrupole Time-of-Flight mass spectrometry. The data was processed and analyzed using the MassHunter Qualitative Analysis and the Mass Profiler Professional programs. Based on global metabolomic profiles, low and high biofilm-formers presented as two distinctly different groups. Interestingly, low-biofilm-formers produced more metabolites than high-biofilm-formers. Further analysis was performed to identify metabolites that differed significantly (p-value

Matched MeSH terms: Metabolomics/methods*
Windows Scanning Multiomics: Integrated Metabolomics and Proteomics

Shi J, Zhao J, Zhang Y, Wang Y, Tan CP, Xu YJ, et al.

Anal Chem, 2023 Dec 26;95(51):18793-18802.
PMID: 38095040 DOI: 10.1021/acs.analchem.3c03785

Metabolomics and proteomics offer significant advantages in understanding biological mechanisms at two hierarchical levels. However, conventional single omics analysis faces challenges due to the high demand for specimens and the complexity of intrinsic associations. To obtain comprehensive and accurate system biological information, we developed a multiomics analytical method called Windows Scanning Multiomics (WSM). In this method, we performed simultaneous extraction of metabolites and proteins from the same sample, resulting in a 10% increase in the coverage of the identified biomolecules. Both metabolomics and proteomics analyses were conducted by using ultrahigh-performance liquid chromatography mass spectrometry (UPLC-MS), eliminating the need for instrument conversions. Additionally, we designed an R-based program (WSM.R) to integrate mathematical and biological correlations between metabolites and proteins into a correlation network. The network created from simultaneously extracted biomolecules was more focused and comprehensive compared to those from separate extractions. Notably, we excluded six pairs of false-positive relationships between metabolites and proteins in the network established using simultaneously extracted biomolecules. In conclusion, this study introduces a novel approach for multiomics analysis and data processing that greatly aids in bioinformation mining from multiomics results. This method is poised to play an indispensable role in systems biology research.

Matched MeSH terms: Metabolomics/methods

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