Integrating metabolomics and metatranscriptomics to explore the formation pathway of aroma-active volatile phenolics and metabolic profile during industrial radish paocai fermentation

Environmental community transcriptomics: strategies and struggles

Transcriptomics is the study of RNA transcripts, the portion of the genome that is transcribed, in a specific cell, tissue, or organism. Transcriptomics provides insight into gene expression patterns, regulation, and the underlying mechanisms of cellular processes. Community transcriptomics takes this a step further by studying the RNA transcripts from environmental assemblies of organisms, with the intention of better understanding the interactions between members of the community. Community transcriptomics requires successful extraction of RNA from a diverse set of organisms and subsequent analysis via mapping those reads to a reference genome or de novo assembly of the reads. Both, extraction protocols and the analysis steps can pose hurdles for community transcriptomics. This review covers advances in transcriptomic techniques and assesses the viability of applying them to community transcriptomics.

Insight into the autochthonous lactic acid bacteria as starter culture for improving the quality of Sichuan radish paocai: Changes in microbial diversity and metabolic profiles

Paocai is a traditional Chinese fermented vegetable product popular in Asian countries. Recently, functional starters were used to control the fermentation process and improve the quality of paocai. In this study, three autochthonous lactic acid bacteria including Lactiplantibacillus plantarum LB6, Lactiplantibacillus pentosus LB3, and Weissella cibaria W51 were selected as starters and the effect of the starters on the fermentation of paocai was investigated. The results suggested that the inoculated fermentation led to a lower nitrite peak and more pronounced changes in pH and total titratable acid in the early stage of fermentation, compared with natural fermentation. Analysis of the flavor compounds indicated that the total content of volatile organic compounds of paocai through natural fermentation was significantly lower than that in inoculated fermentation. As for free amino acids, in the early stage of fermentation, the types and contents of free amino acids in the inoculated fermentation paocai were higher than those in the blank group. In the later stage of fermentation, the contents of amino acids representing umami and sweet tastes were also higher than those in the blank group. The bacterial community analysis showed that Lactobacillus and Lactococcus were the dominant bacteria in both inoculated fermentation and natural fermentation. Then, the correlations among physicochemical properties, microbial community and flavor compounds were revealed, and it was found that the dominant bacteria such as Lactococcus, Leuconostoc, Lactobacillus and Weissella displayed a considerable impact on the physical and chemical properties and flavor of paocai. In addition, the metabolic pathways involved in flavor formation and the abundance of related enzymes were elucidated. The abundance of enzymes involved in generating prephenic acid, 2-methylbutanoic acid, L-lactic acid, D-lactic acid, butanoic acid, etc., and in the pathway of producing flavor substances (His, Met, ethyl hexanoate, etc.) was up-regulated in the inoculated fermentation. Results presented in this study may provide a reference for the development of paocai starters and further guidance for the flavor improvement of Sichuan paocai.

Innovative omics strategies in fermented fruits and vegetables: Unveiling nutritional profiles, microbial diversity, and future prospects

Fermented fruits and vegetables (FFVs) are not only rich in essential nutrients but also contain distinctive flavors, prebiotics, and metabolites. Although omics techniques have gained widespread recognition as an analytical strategy for FFVs, its application still encounters several challenges due to the intricacies of biological systems. This review systematically summarizes the advances, obstacles and prospects of genomics, transcriptomics, proteomics, metabolomics, and multi-omics strategies in FFVs. It is evident that beyond traditional applications, such as the exploration of microbial diversity, protein expression, and metabolic pathways, omics techniques exhibit innovative potential in deciphering stress response mechanisms and uncovering spoilage microorganisms. The adoption of multi-omics strategies is paramount to acquire a multidimensional network fusion, thereby mitigating the limitations of single omics strategies. Although substantial progress has been made, this review underscores the necessity for a comprehensive repository of omics data and the establishment of universal databases to ensure precision in predictions. Furthermore, multidisciplinary integration with other physical or biochemical approaches is imperative, as it enriches our comprehension of this intricate process.

Exploring community succession and metabolic changes in corn gluten meal-bran mixed wastes during fermentation

Addressing the challenge of sustainable agricultural processing waste management is crucial. Protein sources are essential for livestock farming, and one viable solution is the microbial fermentation of agricultural by-products. In this study, the microorganisms utilized for fermentation were Pichia fermentans PFZS and Limmosilactobacillus fermentum LFZS. The results demonstrated that the fermented corn gluten meal-bran mixture (FCBM) effectively degraded high molecular weight proteins, resulting in increases of approximately 23.3%, 367.6%, and 159.3% in crude protein (CP), trichloroacetic acid-soluble protein (TCA-SP), and free amino acid (FAA), respectively. Additionally, there was a significant enhancement in the content of beneficial metabolites, including total phenols, carotenoids, and microorganisms. FCBM also effectively reduced anti-nutritional factors while boosting antioxidant and anti-inflammatory substances, such as dipeptides and tripeptides. The fermentation process was marked by an increase in beneficial endophytes, which was closely correlated with the enhancement of beneficial metabolites. Overall, FCBM provides a theoretical basis for substituting traditional protein resources in animal husbandry.

Heterogenetic mechanism in high-temperature Daqu fermentation by traditional craft and mechanical craft: From microbial assembly patterns to metabolism phenotypes

The mechanical process has a widely usage in large-scale high-temperature Daqu (HTD) enterprises, however, the quality of the mechanical HTD is gapped with the HTD by traditional process. Currently, the understanding of the mechanism behind this phenomenon is still over-constrained. To this end, the discrepancies in fermentation parameters, enzymatic characteristics, microbial assembly and succession patterns, metabolic phenotypes were compared between traditional HTD and mechanical HTD in this paper. The results showed that mechanical process altered the temperature ramping procedure, resulting in a delayed appearance of the peak temperature. This alteration shifted the assembly pattern of the initial bacterial community from determinism to stochasticity, while having no impact on the stochastic assembly pattern of the fungal community. Concurrently, mechanical pressing impeded the accumulation of arginase, tetramethylpyrazine, trimethylpyrazine, 2-methoxy-4-vinylphenol, and butyric acid, as the target dissimilarities in metabolism between traditional HTD and mechanical HTD. Pearson correlation analysis combined with the functional prediction further demonstrated that Bacillus, Virgibacillus, Oceanobacillus, Kroppenstedtia, Lactobacillus, and Monascus were mainly contributors to metabolic variances. The Redundancy analysis (RDA) of fermented environmental factors on functional ASVs indicated that high temperature, high acid and low moisture were key positive drivers on the microbial metabolism for the characteristic flavor in HTD. Based on these results, heterogeneous mechanisms between traditional HTD and mechanical HTD were explored, and controllable metabolism targets were as possible strategies to improve the quality of mechanical HTD.

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

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

Metabolomics and metatranscriptomics reveal the influence mechanism of endogenous microbe (Staphylococcus succinus) inoculation on the flavor of fermented chili pepper

This study integrated metabolomic and metatranscriptomic techniques to examine how the endogenous microbe, Staphylococcus succinus, influenced the essential flavor of fermented chili peppers. The mechanisms governing spontaneous fermentation and S. succinus-inoculated fermentation were also elucidated. Esters (e.g., ethyl undecanoate, isoamyl acetate, and methyl salicylate), terpenes (e.g., terpinen-4-ol), and alcohols (e.g., α-terpineol, linalool, and 4-methyl-3-heptanol) were found to be the key aroma-active compounds, aspartic acid (Asp) and glutamic acid (Glu) were identified as primary flavoring free amino acids. Notably, during the early stages of S. succinus-inoculated fermentation, the production of these essential metabolites was abundant, while their gradual increase over time was observed in the case of spontaneous fermentation. Metatranscriptomic analysis revealed that S. succinus inoculation could up-regulate genes related to glycolysis, amino acid metabolism, and aroma compound synthesis. These changes sequentially boosted the production of sweet and umami free amino acids, enhanced organic acid levels, increased unique aroma compound generation, and further improved the flavor and quality of the fermented chili peppers. Therefore, S. succinus inoculation can augment the sensory quality of fermented chili peppers, making this strain a promising candidate for Sichuan pickle fermentation starters.

Effect of inoculating Pichia spp. starters on flavor formation of fermented chili pepper: Metabolomics and genomics approaches

The influence of Pichia spp. on flavor formation and metabolic pathways during chili pepper fermentation was investigated in this study. Multiple omics approaches were employed, including metabolomics analysis to identify volatile and non-volatile flavor compounds, and genomic analysis to gain insights into the underlying molecular mechanism driving flavor formation of chili peppers inoculated with Pichia spp. The results showed that inoculation with Pichia spp. accelerated fermentation process of chili peppers compared to spontaneous fermentation. Metabolomics analysis showed P. fermentans promoted characteristic terpenes [e.g., (Z)-β-ocimene and linalool], L-glutamate, gamma-aminobutyric acid, and succinate production, while P. manshurica produced more alcohols (e.g., isoamyl alcohol and phenylethyl alcohol) and phenols (e.g., 4-ethylguaiacol and 2-methoxy-4-methylphenol). Genomics analysis revealed that a substantial portion of the genes in Pichia spp. were associated with amino acid and carbohydrate metabolism. Specifically, the pathways involved in amino acid metabolism and the release of glycoside-bound aromatic compounds were identified as the primary drivers behind the unique flavor of fermented chili peppers, facilitated by Pichia spp.

Cold Plasma Controls Nitrite Hazards by Modulating Microbial Communities in Pickled Radish

The hazard of nitrite caused by microorganisms is the main food safety problem in the pickle production. To seek a method to control the nitrite hazards of pickles by regulating microbial community without additional substances, we focused on cold plasma because Gram-negative and Gram-positive bacteria have different degrees of sensitivity to the sterilization of cold plasma. Using radish pickles as the experimental object, based on colony counting, dynamic monitoring of pH and nitrite, qPCR and high-throughput sequencing, it was found that when the raw material was treated with dielectric barrier discharge (DBD) cold plasma at 40 kV for 60 s, Gram-negative bacteria with the potential to produce nitrite were preferentially sterilized. Meanwhile, Gram-positive bacteria dominated by the lactic acid bacteria were retained to accelerate the acid production rate, initiate the self-degradation of nitrite in advance and significantly reduce the peak value and accumulation of nitrite during the fermentation process of pickled radish. This study preliminarily verified that DBD cold plasma can inhibit the nitrite generation and accelerate the self-degradation of nitrite by regulating the structure and abundance of microbial community in radish pickles, which provides an important reference for the control of nitrite hazards in the fermentation process of pickles without additives.