Metabolomic Analysis of Germinated Brown Rice at Different Germination Stages

Investigating potential freshness indicators for packaged oysters through multivariate statistical analysis

Pacific oysters (Crassostrea gigas) are globally renowned shellfish. In South Korea, oysters are commonly packaged with filling water in polyethylene bags. Previous studies have proposed various freshness and quality parameters for oysters, including pH, volatile basic nitrogen content, glycogen content, and viable cell count. We aimed to identify the objective indicators of oyster freshness during storage and distribution using metabolomic analysis and multivariate statistical techniques. Packaged oyster samples were analyzed for metabolites using gas chromatography-mass-spectrometry during 9-days storage at 5 °C or 15 °C. Additionally, the pH, turbidity, and soluble protein content of the filling water were measured. Multivariate statistical analyses, including principal component analysis, partial least squares discriminant analysis, and orthogonal projections to latent structure-discriminant analysis revealed statistically significant results, demonstrating metabolite clustering based on storage duration. In conclusion, this study introduced crucial freshness indicators for stored or distributed oysters by utilizing metabolomic analysis and multivariate statistical techniques.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-024-01693-y.

Integrative LC-MS and GC-MS metabolic profiling unveils dynamic changes during barley malting

Malting involves complex biochemical transformations affecting sensory and quality attributes. Despite extensive research on storage carbohydrates and proteins in malting, the lack of a detailed metabolic understanding of this process limits our ability to assess and enhance malt quality. This study employed untargeted GC-MS and LC-MS metabolite profiling across six malting timepoints to identify 4980 known metabolites, 82 % of which exhibited significant changes during the malting process. Here we identified stage-dependent metabolic shifts and dynamic chemical classes and pathways between each studied stage. These results can guide the fine-tuning of malting conditions to improve malt quality for beer production and other malt-based applications. Additionally, metabolites with antimicrobial properties were identified, underscoring the interplay between barley and microbial metabolic processes during malting. Further research into these microbial metabolites and cognate microbes may lead to novel malting assessment traits for high-quality and safe malted barley.

Impact of germination on the techno-functional properties, nutritional composition, and health-promoting compounds of brown rice and its products: A review

Rice is a popular grain and forms part of the daily diet of people throughout the world. However, the consumption of rice and its products is sometimes limited by its high glycemic index due to its high starch content, low protein content and quality, and low bioavailability of minerals due to the presence of anti-nutritional factors. This has partly stimulated research interest in recent times toward the use of bioprocessing techniques such as germination as cheap and natural means to improve the nutritional quality, digestibility, and health properties of cereals, including rice, to partially achieve nutrition and food security in the developing regions of the world. This review highlights the impact of germination on the nutritional quality, health-promoting properties, and techno-functional characteristics of germinated brown rice grains and their products. The review demonstrated that germinated rice grains and their products have improved nutritional quality and digestibility, modified functional properties, and showed antioxidant, anti-inflammatory, anti-diabetic, anti-obesity, anti-cancer, and anti-cardiovascular activities. Germination appears to be a suitable bioprocessing method to improve the nutritional quality and bioactive constituents and modify the techno-functional properties of rice grains for diverse food applications and improved global nutrition and food safety.

Differences in the metabolites of brown and milled rice grains of semiwaxy and conventional japonica varieties

In this study, we analyzed the differences in metabolites between semiwaxy japonica rice (Yangnongxiang 28 [YNX28]) and conventional japonica rice (Hongyang 5 [HY5]) before and after brown rice milling. The metabolites of brown and milled rice grains from the two rice varieties were analyzed by LC-MS-based nontargeted metabolomics. A total of 266 differentially abundant metabolites (DMs) were tentatively identified in brown rice grains of YNX28 (YNX28B) compared with milled rice grains of YNX28 (YNX28H), and these included 248 upregulated and 12 downregulated DMs. A total of 273 (234 upregulated and 39 downregulated) DMs were tentatively identified in brown rice grains of HY5 (HY5B) compared with milled rice grains of this variety (HY5H). Kyoto Encyclopedia of Genes and Genomes pathway involved and enrichment analyses revealed that 53 and 7 metabolite pathways were enriched and significantly enriched (p < 0.05), respectively, in the DMs identified in YNX28B compared with YNX28H, and the main enriched pathways were related to starch and sucrose metabolism, glycerol phospholipid metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism. Forty-six metabolite pathways were enriched in DMs identified in HY5B compared with HY5H, and these included 16 pathways that were significantly enriched (p < 0.05); in addition, the main enriched pathways were related to starch and sucrose metabolism, glycerol phospholipid metabolism, arginine and proline metabolism, and glycine, serine and threonine metabolism. This study provides a theoretical reference for further on the changes in metabolites during rice processing and provides a basis for improving the nutritional quality in rice. PRACTICAL APPLICATION: Original data were obtained regarding the changes of different metabolites in semiwaxy japonica rice and conventional japonica rice before and after processing. The purpose of this study was to investigate the difference of metabolite loss in two rice varieties before and after processing. This paper reports on the differences of metabolites between the two types of japonica rice before and after processing, as well as the changes of key metabolites before and after processing, it also provides important theoretical basis for developing new rice varieties with good nutritional quality.

Metabolomics and machine learning technique revealed that germination enhances the multi-nutritional properties of pigmented rice

Enhancing the dietary properties of rice is crucial to contribute to alleviating hidden hunger and non-communicable diseases in rice-consuming countries. Germination is a bioprocessing approach to increase the bioavailability of nutrients in rice. However, there is a scarce information on how germination impacts the overall nutritional profile of pigmented rice sprouts (PRS). Herein, we demonstrated that germination resulted to increase levels of certain dietary compounds, such as free phenolics and micronutrients (Ca, Na, Fe, Zn, riboflavin, and biotin). Metabolomic analysis revealed the preferential accumulation of dipeptides, GABA, and flavonoids in the germination process. Genome-wide association studies of the PRS suggested the activation of specific genes such as CHS1 and UGT genes responsible for increasing certain flavonoid compounds. Haplotype analyses showed a significant difference (P < 0.05) between alleles associated with these genes. Genetic markers associated with these flavonoids were incorporated into the random forest model, improving the accuracy of prediction of multi-nutritional properties from 89.7% to 97.7%. Deploying this knowledge to breed rice with multi-nutritional properties will be timely to address double burden nutritional challenges.

Combined transcriptome and metabolome analyses reveal the mechanisms of ultrasonication improvement of brown rice germination

This study investigated the effects of ultrasonication treatment on the germination rate of brown rice. Brown rice grains were subjected to ultrasound (40 kHz/30 min) and then incubated for 36 h at 37 °C to germinate the seeds. Ultrasonic treatment increased the germination rate of brown rice by up to ∼28 % at 30 h. Transcriptomic and metabolomic analyses were performed to explore the mechanisms underlying the effect of ultrasonic treatment on the brown rice germination rate. Comparing the treated and control check samples, 867 differentially expressed genes (DEGs) were identified, including 638 upregulated and 229 downregulated), as well as 498 differentially accumulated metabolites (DAMs), including 422 up accumulated and 76 down accumulated. Multi-omics analysis revealed that the germination rate of brown rice was promoted by increased concentrations of low-molecular metabolites (carbohydrates and carbohydrate conjugates, fatty acids, amino acids, peptides, and analogues), and transcription factors (ARR-B, NAC, bHLH and AP2/EREBP families) as well as increased carbon metabolism. These findings provide new insights into the mechanisms of action of ultrasound in improving the brown rice germination rate and candidate DEGs and DAMs responsible for germination have been identified.

Changes in the chemical, physical, and sensory properties of rice according to its germination rate

This study aimed to decipher the association among the physicochemical properties, sensory quality, and germination rate of rice samples stored at different storage conditions and for different durations (stored at 10, 20, and 30 °C for 8 months). The germination rate of the samples varied from 0.3 to 98.7%. A reduced germination rate increased the lipid oxidation, hardness, and most pasting properties of rice, whereas seed viability, moisture content, and adhesiveness were reduced. Amylose and protein contents were not influenced by the changes in germination rate. However, with a decrease in germination rate, the surface endosperm cells were aggregated, whereas the sizes of inner endosperm cells in cooked rice were reduced. Several metabolites involved in rice sensory quality were also altered, and a related pathway was proposed. Collectively, these results suggest that germination rate could serve as a potential indicator to track the changes in rice quality.

Quantitatively unravelling the effect of altitude of cultivation on the volatiles fingerprint of wheat by a chemometric approach

The cultivation of crops at high elevations in response to climate changes leads to modifications in the volatile organic compounds (VOCs) profile. The VOCs profile of common and durum wheat grown in different fields sited at three different elevations over two years was analysed. Partial least square analysis (PLS2) evidenced the effect of altitude on VOCs variance that was hidden among others (cultivation year, species, farm) not correlated with it. PLS1 analysis was further carried out using VOCs as explanatory variables and altitude as dependent variable to find the linear combination of VOCs able to continuously predict the altitude of samples. Selected VOCs, related to biotic, abiotic and oxidative stress conditions, could describe the changes in VOCs profile of wheat induced by altitude increase. Furthermore, common and durum wheat showed different responses to stress at high altitude. These results could be considerably useful for wheat product classification and authentication.

Metabolite profile and antioxidant potential of wheat (Triticum aestivum L.) during malting

In addition to barley, wheat malt is considered an important beer material because of the recent popularity of wheat beer in the global market. The changes in metabolite profiles and antioxidant potential of wheat samples collected every 24 h during malting were investigated. Dynamic metabolite changes through ¹H NMR-based metabolomics approaches, quantitative individual phenolic acids by high-performance liquid chromatography and antioxidant potential by colorimetric methods were assessed. Orthogonal projection to latent structure with discriminant analysis showed that metabolites were responsible for discrimination of each malting stage for wheat. Phenolic acids, whose main component was ferulic acid, increased with time during wheat malting. Much higher phenolic acid contents were found in rootlets/acrospires than in the bodies of dried wheat malt. The overall results of this study provide novel information on changes in dynamic metabolites during wheat malting.

Comparative Metabolomics Reveals Two Metabolic Modules Affecting Seed Germination in Rice (Oryza sativa)

The process of seed germination is crucial not only for the completion of the plant life cycle but also for agricultural production and food chemistry; however, the underlying metabolic regulation mechanism involved in this process is still far from being clearly revealed. In this study, one indica variety (Zhenshan 97, with rapid germination) and one japonica variety (Nipponbare, with slow germination) in rice were used for in-depth analysis of the metabolome at different germination stages (0, 3, 6, 9, 12, 24, 36, and 48 h after imbibition, HAI) and exploration of key metabolites/metabolic pathways. In total, 380 annotated metabolites were analyzed by using a high-performance liquid chromatography (HPLC)-based targeted method combined with a nontargeted metabolic profiling method. By using bioinformatics and statistical methods, the dynamic changes in metabolites during germination in the two varieties were compared. Through correlation analysis, coefficient of variation analysis and differential accumulation analysis, 74 candidate metabolites that may be closely related to seed germination were finally screened. Among these candidates, 29 members belong to the ornithine–asparagine–polyamine module and the shikimic acid–tyrosine–tryptamine–phenylalanine–flavonoid module. As the core member of the second module, shikimic acid’s function in the promotion of seed germination was confirmed by exogenous treatment. These results told that nitrogen flow and antioxidation/defense responses are potentially crucial for germinating seeds and seedlings. It deepens our understanding of the metabolic regulation mechanism of seed germination and points out the direction for our future research.

Comparative Metabolomics Analysis of Citrus Varieties

Many citrus varieties are hybridized to improve their quality and to overcome the effects of climate change. However, there is limited information on the effect of the chemical profiles of hybrid varieties on their quality. In this study, we analyzed 10 citrus varieties and evaluated the correlation with their general characteristics and antioxidant activities. Chemical profiles, including the contents of sugars, organic acid compounds, flavonoids, limonoids, and carotenoids, which are related to taste, color, and health benefits, were significantly different depending on the citrus varieties, leading to different antioxidant capacities and general quality parameters. Based on these data, the correlations were investigated, and 10 citrus varieties were clustered into four groups-Changshou kumquat and Jeramon (cluster I); Setoka (cluster II-1); Natsumi, Satsuma mandarin, and Navel orange (cluster II-2); Kanpei, Tamnaneunbong, Saybyeolbong, and Shiranui (cluster II-3). Moreover, a metabolomic pathway was proposed. Although citrus peels were not analyzed and the sensory and functional qualities of the citrus varieties were not investigated in this study, our results are useful to better understand the relationship between citrus quality and metabolite profiles, which can provide basic information for the development and improvement of new citrus varieties.

Integrated Analysis of Metabolome and Volatile Profiles of Germinated Brown Rice from the Japonica and Indica Subspecies

In the present study, germinated brown rice (GBR) from three Japonica and three Indica rice cultivars were subjected to metabolomics analysis and volatile profiling. The statistical assessment and pathway analysis of the metabolomics data demonstrated that in spite of significant metabolic changes in response to the germination treatment, the Japonica rice cultivars consistently expressed higher levels of several health-promoting compounds, such as essential amino acids and γ-aminobutyric acid (GABA), than the Indica cultivars. No clear discriminations of the volatile profiles were observed in light of the subspecies, and the concentrations of the volatile organic compounds (VOCs), including alkenes, aldehydes, furans, ketones, and alcohols, all exhibited significant reductions ranging from 26.8% to 64.1% after the germination. The results suggest that the Japonica cultivars might be desirable as the raw materials for generating and selecting GBR food products for health-conscious consumers.

Germinated Buckwheat: Effects of Dehulling on Phenolics Profile and Antioxidant Activity of Buckwheat Seeds

The aim was to investigate the effects of the cold dehulling of buckwheat seeds on their germination, total phenolic content (TPC), antioxidant activity (AA) and phenolics composition. Cold dehulling had no negative effects on germination rate and resulted in faster rootlet growth compared to hulled seeds. Although the dehulling of the seeds significantly decreased TPC and AA, the germination of dehulled seeds resulted in 1.8-fold and 1.9-fold higher TPC and AA compared to hulled seeds. Liquid chromatography coupled to mass spectrometry identified several phenolic compounds in free and bound forms. Rutin was the major compound in hulled seeds (98 µg/g dry weight), orientin and vitexin in 96-h germinated dehulled seeds (2205, 1869 µg/g dry weight, respectively). During germination, the increases in the major phenolic compounds were around two orders of magnitude, which were greater than the increases for TPC and AA. As well as orientin and vitexin, high levels of other phenolic compounds were detected for dehulled germinated seeds (e.g., isoorientin, rutin; 1402, 967 µg/g dry weight, respectively). These data show that dehulled germinated seeds of buckwheat have great potential for use in functional foods as a dietary source of phenolic compounds with health benefits.