Metagenomics Reveals the Microbial Community Responsible for Producing Biogenic Amines During Mustard [Brassica juncea (L.)] Fermentation

Yu, Yangyang; Li, Lü; Xu, Yujuan; Li, Hong; Yu, Yuanshan; Xu, Zhen-Lin

doi:10.3389/fmicb.2022.824644

Cited by 6 publications

(2 citation statements)

References 46 publications

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“…has previously been reported (Xu et al, 2018). Bacillus includes toxicogenic species and has been identified as the main producers of biogenic amines in fermented mustard (Yu et al, 2022), while some Bacillus species, e.g., B. marcorestinctum, are considered as beneficial for fermentation (Zhong et al, 2022). In contrast, no E. coli, Salmonella, and L. monocytogenes were detected.…”

Section: Other Microbial Groups and Potential Safety Concernsmentioning

confidence: 97%

Microbial communities of a variety of 75 homemade fermented vegetables

Thierry,

Madec,

Chuat

et al. 2023

Front. Microbiol.

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Fermentation is an ancient practice of food preservation. Fermented vegetables are popular in Eastern European and Asian countries. They have received a growing interest in Western countries, where they are mainly manufactured at domestic and artisanal scales and poorly characterized. Our aim was to investigate the microbial communities and the safety of French homemade fermented vegetables, in the frame of a citizen science project. Fermented vegetables and the data associated with their manufacture were collected from citizens and characterized for pH, NaCl concentration, and microbiology by culturomics and 16S DNA metabarcoding analysis. Lactic acid bacteria (LAB) and yeast isolates were identified by 16S rRNA gene sequencing and D1/D2 domains of the large subunit of the rRNA gene, respectively. The 75 collected samples contained 23 types of vegetables, mainly cabbage, followed by carrots and beets, and many mixtures of vegetables. They were 2 weeks to 4 years old, and their median pH was 3.56, except for two samples with a pH over 4.5. LAB represented the dominant viable bacteria. LAB concentrations ranged from non-detectable values to 8.7 log colony-forming units (CFU)/g and only depended on the age of the samples, with the highest most frequently observed in the youngest samples (<100 days). The 93 LAB isolates identified belonged to 23 species, the two mains being Lactiplantibacillus pentosus/plantarum and Levilactobacillus brevis. The other microbial groups enumerated (total aerobic bacteria, halotolerant bacteria, Gram-negative bacteria, and acetic acid bacteria) generally showed lower concentrations compared to LAB concentrations. No pathogenic bacteria were detected. Viable yeasts were observed in nearly half the samples, at concentrations reaching up to 8.0 log CFU/g. The 33 yeast clones identified belonged to 16 species. Bacterial metabarcoding showed two main orders, namely, Lactobacillales (i.e., LAB, 79% of abundance, 177 of the 398 total ASVs) and Enterobacterales (19% of abundance, 191 ASVs). Fifteen LAB genera were identified, with Lactiplantibacillus and Levilactobacillus as the most abundant, with 41 and 12% of total reads, respectively. Enterobacterales members were mainly represented by Enterobacteriaceae and Yersiniaceae. This study is the first wide description of the microbiota of a large variety of homemade fermented vegetables and documents their safety.

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Section: Other Microbial Groups and Potential Safety Concernsmentioning

confidence: 97%

Microbial communities of a variety of 75 homemade fermented vegetables

Thierry,

Madec,

Chuat

et al. 2023

Front. Microbiol.

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“…These findings have revealed the correlation between the types of ingredients used and the abundance of bacteria in fermented food. Aside from indicating the diversity of microbial communities, metagenomics has enabled the differentiation of the metabolic pathways of biogenic amines caused by various microbes during the fermentation of Brassica juncea [89]. The connection between the predominance of microbes and metabolism was also investigated in Yucha, which is a fermented food composed of fresh fish and cooked rice that is popular in China [90].…”

Section: Metagenomics In the Food Industrymentioning

confidence: 99%

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

Nam

Khoa

Trinh

et al. 2023

Foods

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Various fields have been identified in the “omics” era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.

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

Li,

He,

Liu

et al. 2024

Comp Rev Food Sci Food Safe

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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.

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Metagenomics Reveals the Microbial Community Responsible for Producing Biogenic Amines During Mustard [Brassica juncea (L.)] Fermentation

Cited by 6 publications

References 46 publications

Microbial communities of a variety of 75 homemade fermented vegetables

Microbial communities of a variety of 75 homemade fermented vegetables

Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions

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

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