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Microbiology and Genomic Analysis of Fermented Foods
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Microbiology and Genomic Analysis of Fermented Foods

A special issue of Foods (ISSN 2304-8158). This special issue belongs to the section "Food Microbiology".

Deadline for manuscript submissions: closed (15 June 2023) | Viewed by 8754

Special Issue Editors

Dr. Hasan Tanguler

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Guest Editor
Food Engineering Department, Nigde Omer Halisdemir University, Niğde, Turkey
Interests: fermented products; microflora; volatile compounds; shelf life
Prof. Dr. Bulent Kabak

E-Mail Website
Guest Editor
1. Department of Food Engineering, Faculty of Engineering, Hitit University, Corum, Turkey
2. Biotechnology Laboratory, Machinery and Manufacturing Technology Application and Research Center, Hitit University, Corum, Turkey
Interests: mycotoxin; pesticides; food safety; food analysis; food contaminants; risk assessment
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, humanity has focused on the nutritional and sensory properties, as well as the positive effects on health, of fermented products as well as the microorganisms that are effective in the production of these products. Traditionally, in the manufacturing of fermented products, symbiotic bacteria mixes (lactic acid bacteria and acetic acid bacteria), LAB–yeast mixtures, and only yeasts or LAB could be effective. In addition, some of them are probiotic microorganisms. Their growth during the fermentation and isolation, identification, and genomic analyses of microorganisms found in the fermentation medium has recently been determined with new methods, and new information can be obtained in this way. On the other hand, numerous biochemical changes occur in fermentation: flavor components are formed, and the textures of vegetables change. The flavor components of fermented products are caused by the metabolism or enzymatic activity of microorganisms that are effective in fermentation. Factors that affect flavor production during fermentation are raw material type, food ingredients, biological factors (presence of desired microorganisms and the use of a starter culture), pH, temperature, nutrients (nitrogen and carbon sources), water activity, aeration, and contamination sources. In conclusion, there is still insufficient information about important industrial fermented products belonging to certain geographical regions, their microbiology, and genomic analyses.

Dr. Hasan Tanguler
Prof. Dr. Bulent Kabak
Guest Editors

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Keywords

  • fermented foods
  • fermented beverages
  • identification
  • microbial growth
  • volatiles
  • shelf life

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Published Papers (4 papers)

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Research

18 pages, 3141 KiB  
Article
Effect of Three Different Preservatives on the Microbiota of Shalgam, a Traditional Lactic Acid Fermented Beverage
by Gamze Nur Mujdeci, Hasan Tanguler, Hasan Macit and Bulent Kabak
Foods 2023, 12(22), 4075; https://doi.org/10.3390/foods12224075 - 9 Nov 2023
Cited by 2 | Viewed by 1655
Abstract
Shalgam is a traditional Turkish beverage derived from the natural fermentation of purple carrots (Daucus carota) that boasts valuable antioxidant and prebiotic properties. These features of shalgam increase efforts to enhance its shelf life and ensure safe consumption. In this study, [...] Read more.
Shalgam is a traditional Turkish beverage derived from the natural fermentation of purple carrots (Daucus carota) that boasts valuable antioxidant and prebiotic properties. These features of shalgam increase efforts to enhance its shelf life and ensure safe consumption. In this study, the effects of three different preservatives (sodium benzoate, potassium sorbate, or natamycin) on the physicochemical and microbiological properties of shalgam produced at laboratory scale and stored at room temperature for six months were investigated. Each preservative was used in four different concentrations (25, 100, 400, and 800 mg/L) to assess their impacts on the population of lactic acid bacteria (LAB) and yeast. After determining the total acidity and pH of the samples, colorimetric measurements were performed. The isolated LAB were defined using the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF/TOF MS) method. The addition of preservatives did not significantly affect the pH of the shalgam samples (3.44–3.52) compared to the control sample (3.43). However, a slight increase was observed in the total acidity of preservative-treated samples, with the highest level (5.61 g/L lactic acid) recorded in samples containing 100 mg/L sodium benzoate. Lacticaseibacillus paracasei subsp. paracasei, which has the potential to impart probiotic properties to shalgam, was the predominant LAB species in both non-treated and preservative-treated samples. The use of preservatives significantly reduced the total number of yeasts, which may cause spoilage in shalgam. The results indicate that using sodium benzoate at a concentration of 100 mg/L is the optimum method for shalgam production, resulting in the highest total acidity value obtained. Overall, the findings provide a significant contribution to prolonging the shelf life of shalgam, a beverage with immense production and consumption potential worldwide. Full article
(This article belongs to the Special Issue Microbiology and Genomic Analysis of Fermented Foods)
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16 pages, 5589 KiB  
Article
Metagenomic Insights into the Microbiome and Resistance Genes of Traditional Fermented Foods in Arabia
by Muhammad Yasir, Areej A. Alkhaldy, Samah Abdullah Soliman, Safaa A. Turkistani and Esam I. Azhar
Foods 2023, 12(18), 3342; https://doi.org/10.3390/foods12183342 - 6 Sep 2023
Cited by 1 | Viewed by 2347
Abstract
This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods—mish, jibneh, zabadi, and pickles—were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were [...] Read more.
This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods—mish, jibneh, zabadi, and pickles—were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were sequenced using 16S amplicons and shotgun metagenomics. Alpha and beta diversity indicated inter- and intra-variation in the studied fermented foods’ bacterial communities. In the case of mish, the replicates were clustered. Twenty-one genera were found to be significantly different (FDR < 0.05) in abundance in pairwise comparison of fermented foods. Five high-quality, metagenome-assembled genomes (MAGs) of Lactococcus lactis, Lactobacillus helveticus, Pseudoalteromonas nigrifaciens, Streptococcus thermophiles, and Lactobacillus acetotolerans were retrieved from the shotgun sequencing representing the dominant taxa in the studied fermented foods. Additionally, 33 genes that cause antimicrobial resistance (ARGs) against ten different antibiotic classes were detected. Metabolic pathways were abundant in the studied metagenomes, such as amino acid metabolism, carbohydrate metabolism, cofactors, and vitamin biosynthesis. Metagenomic evaluation of Arabian fermented foods, including the identification of probiotics, pathogenic bacteria, and ARGs, illustrates the importance of microbiological analysis in evaluating their health effects. Full article
(This article belongs to the Special Issue Microbiology and Genomic Analysis of Fermented Foods)
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18 pages, 3322 KiB  
Article
Microbial Community Succession and Its Correlation with Quality Characteristics during Gray Sufu Fermentation
by Lei Zhao, Yang Liu, Qiong Xu, Yi Yu, Guojian Zheng, Yue Wang, Qingping Zhang, Xiaoqian Xu, Nana Zhang, Jiayue Chu, Yuzhu Zhang, Yingyi Sun, Qin Zhao, Yinan Zhang, Qinfeng Qu and Jiang Zhong
Foods 2023, 12(14), 2767; https://doi.org/10.3390/foods12142767 - 20 Jul 2023
Cited by 7 | Viewed by 1645
Abstract
Gray sufu, a traditional fermented food derived from soybeans, undergoes a complex fermentation process. This study aimed to investigate the dynamics of the microbial community during sufu fermentation and its relationship with key quality characteristics. Through systematic sampling of sufu at different phases [...] Read more.
Gray sufu, a traditional fermented food derived from soybeans, undergoes a complex fermentation process. This study aimed to investigate the dynamics of the microbial community during sufu fermentation and its relationship with key quality characteristics. Through systematic sampling of sufu at different phases of fermentation, 143 bacterial genera and 84 fungal genera involved in the process were identified. Among these, Chishuiella, Enterococcus, Lactococcus, and Weissella emerged as the predominant bacterial communities. After seven days of ripening fermentation, Trichosporon supplanted Diutina as the predominant fungus, accounting for more than 84% of all fungi. Using redundancy analysis, significant correlations between microbiota and physicochemical properties were uncovered. Chishuiella and Empedobacter displayed positive relationships with pH, soluble protein, and amino nitrogen content. In addition, five biogenic amines were detected, and it was determined that tyramine accounted for more than 75% of the total biogenic amines in the final gray sufu products. Spearman correlation analysis revealed significant positive relationships between Lactococcus, Enterococcus, Tetragenococcus, Halanaerobium, and Trichosporon and the five biogenic amines examined. These findings shed light on the complex interactions between microorganisms and biogenic amines during the fermentation of gray sufu, thereby facilitating the development of microbial regulation strategies for better quality control. Full article
(This article belongs to the Special Issue Microbiology and Genomic Analysis of Fermented Foods)
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14 pages, 5814 KiB  
Article
Mechanism of Enhancing Pyrazines in Daqu via Inoculating Bacillus licheniformis with Strains Specificity
by Qiuxiang Tang, Xiaoru Chen, Jun Huang, Suyi Zhang, Hui Qin, Yi Dong, Chao Wang, Xiaojun Wang, Chongde Wu, Yao Jin and Rongqing Zhou
Foods 2023, 12(2), 304; https://doi.org/10.3390/foods12020304 - 9 Jan 2023
Cited by 15 | Viewed by 2284
Abstract
Despite the importance of pyrazines in Baijiu flavor, inoculating functional strains to increase the contents of pyrazine in Daqu and how those interact with endogenic communities is not well characterized. The effects of inoculating Bacillus licheniformis with similar metabolic capacity on pyrazine and [...] Read more.
Despite the importance of pyrazines in Baijiu flavor, inoculating functional strains to increase the contents of pyrazine in Daqu and how those interact with endogenic communities is not well characterized. The effects of inoculating Bacillus licheniformis with similar metabolic capacity on pyrazine and community structure were assessed in the Daqu complex system and compared with traditional Daqu. The fortification strategy increased the volatile metabolite content of Daqu by 52.40% and the pyrazine content by 655.99%. Meanwhile, results revealed that the pyrazine content in Daqu inoculated isolate J-49 was 2.35–7.41 times higher than isolate J-41. Both isolates have the almost same capability of 2,3-butanediol, a key precursor of pyrazine, in pure cultured systems. Since the membrane fatty acids of isolate J-49 contain unsaturated fatty acids, it enhances the response-ability to withstand complex environmental pressure, resulting in higher pyrazine content. PICRUSt2 suggested that the increase in pyrazine was related to the enzyme expression of nitrogen metabolism significantly increasing, which led to the enrichment of NH4+ and 2,3-butanediol (which increased by 615.89%). These results based on multi-dimensional approaches revealed the effect of functional bacteria enhancement on the attribution of Daqu, laid a methodological foundation regulating the microbial community structure and enhanced the target products by functional strains. Full article
(This article belongs to the Special Issue Microbiology and Genomic Analysis of Fermented Foods)
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