Perspectives on Microbiota of Fermented Foods

A special issue of Fermentation (ISSN 2311-5637). This special issue belongs to the section "Fermentation for Food and Beverages".

Deadline for manuscript submissions: closed (10 November 2023) | Viewed by 14465

Special Issue Editors


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Guest Editor
Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Gottingen, Germany
Interests: fungi; Asepergillus; secondary metabolites; food fermentation
Special Issues, Collections and Topics in MDPI journals
School of Food Science and Technology, Shihezi University, Shihezi, China
Interests: microbiology; transcriptome; genome; metabolome; proteome
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Microbial fermentation is an important technique used for food preservation and processing that converts substrates, such as carbohydrates, proteins, and lipids, in raw materials into beneficial metabolites (organic acids, alcohols, amino acids, peptides, fatty acids, etc.) by inoculation of microorganisms for better nutritional composition, sensory, and functional properties. Fermented foods are usually initiated by natural inoculation, fermentation starter (Qu), artificially auxiliary strains, or in a pit rich in related microorganisms. In the brewing process, lots of microorganisms, including bacteria or fungi, may be cooperatively involved. In other words, the microbiota of fermented foods is the main driving force for the fermentation process. Therefore, this Special Issue aims to present recent advances in the microbiota of fermented foods. We encourage the submission of manuscripts that include, but are not limited to:

  • Application and development prospects of microbiota in fermented foods.
  • Differences in microbiota structure in fermented foods produced by traditional and industrial fermentation processes.
  • Reveal the relationship between microbiota and metabolic activities of fermented products.
  • Succession of microbiota biodiversity in fermented foods.
  • Screening and characteristics of functional microorganisms in fermented foods.
  • Effects of microorganisms on organoleptic, nutritional, and functional attributes during food fermentation.
  • Correlation of microorganisms with environment and gut health.
  • Application of core microbes in enhancing quality of fermented foods.

Dr. Wanping Chen
Dr. Bin Wang
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Fermentation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • fermented food
  • microbial diversity
  • fermentation optimization
  • metabolic engineering
  • high throughput screening
  • food microbiology
  • microbiota
  • flavors
  • microorganism application

Published Papers (7 papers)

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Research

12 pages, 2856 KiB  
Article
The Differences in the Composition of Maillard Components between Three Kinds of Sauce-Flavor Daqu
by Qi Zhu, Liangqiang Chen, Xiuxin Pu, Guocheng Du, Fan Yang, Jianjun Lu, Zheng Peng, Juan Zhang and Huabin Tu
Fermentation 2023, 9(9), 860; https://doi.org/10.3390/fermentation9090860 - 21 Sep 2023
Cited by 2 | Viewed by 1154
Abstract
Sauce-flavor Daqu is a saccharifying and fermenting agent for sauce-flavor baijiu. Three kinds of Daqu (White Daqu (WQ), Yellow Daqu (YQ), and Black Daqu (BQ)) with different qualities are formed owing to the stacking fermentation. Maillard reaction is an important factor that causes [...] Read more.
Sauce-flavor Daqu is a saccharifying and fermenting agent for sauce-flavor baijiu. Three kinds of Daqu (White Daqu (WQ), Yellow Daqu (YQ), and Black Daqu (BQ)) with different qualities are formed owing to the stacking fermentation. Maillard reaction is an important factor that causes significant differences among the three kinds of high-temperature Daqu, which is also an important source of flavor substances. However, there is a lack of research on the composition differences of Maillard reaction products in the three types of Daqu. In our study, HS-SPME-GC/MS, Py-GC/MS, and high-throughput sequencing were used to investigate the small molecule volatile Maillard substances, melanoidin (macromolecular Maillard substance) composition, and microbial community of three kinds of Daqu. The results showed that there were significant differences in the composition of Maillard products (furans, pyrazines, and melanoidin structure) between the three kinds of Daqu. The melanoidin was mainly composed of furans, pyrrolopyrazines, phenols, and indoles, the proportions of which were different in the three types of Daqu. BQ contained more Maillard products, making the melanoidin more complex. Kroppenstedtia, Monascus, and Thermoascus were the biomarkers of BQ, which contribute to the Maillard reaction. This study is of great significance to further deepen the understanding of the formation mechanism of BQ. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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14 pages, 1536 KiB  
Article
Dynamics of Microbial Communities in Nitrite-Free and Nutritionally Improved Dry Fermented Sausages
by Núria Ferrer-Bustins, Belén Martín, Mar Llauger, Ricard Bou, Sara Bover-Cid and Anna Jofré
Fermentation 2023, 9(4), 403; https://doi.org/10.3390/fermentation9040403 - 21 Apr 2023
Cited by 3 | Viewed by 1489
Abstract
Dry fermented sausage innovation trends are linked to consumer preferences for clean label and sodium-reduced foods. This study aims to evaluate the effect of the formulation and production process temperature on the dynamics of bacterial communities in fuet-type dry fermented sausages using metataxonomics. [...] Read more.
Dry fermented sausage innovation trends are linked to consumer preferences for clean label and sodium-reduced foods. This study aims to evaluate the effect of the formulation and production process temperature on the dynamics of bacterial communities in fuet-type dry fermented sausages using metataxonomics. Six fuet batches were manufactured, including formulations without and with the addition of nitrifying salts (replaced or not by pork liver auto-hydrolysate as a colouring agent), processed at 3 to 12 °C, and a partial replacement of NaCl by KCl, processed at 12 °C. Fermentation was performed spontaneously or by a starter culture. Physicochemical characterisation and culture-dependent and independent bacterial analyses were performed at day 0, 4 and 12, at the end of ripening (aw < 0.90) and after storage. Temperature was the most important factor determining the change in pH, aw and lactic acid bacteria levels while the presence of a starter culture promoted a pH decrease. Metataxonomic analysis showed that low temperature processes and the absence of nitrifying salts allowed the growth of spoilage-related species, while sausages submitted to a mild temperature containing a starter culture and nitrifying salts showed less bacterial diversity. Liver auto-hydrolysate added putative probiotic species to the product. This study provides valuable information to manufacturers who want to innovate safely. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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20 pages, 29690 KiB  
Article
Microbial Diversity Using a Metataxonomic Approach, Associated with Coffee Fermentation Processes in the Department of Quindío, Colombia
by Aida Esther Peñuela-Martínez, Anyela Vanessa Velasquez-Emiliani and Carlos A. Angel
Fermentation 2023, 9(4), 343; https://doi.org/10.3390/fermentation9040343 - 29 Mar 2023
Cited by 6 | Viewed by 2270
Abstract
Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the [...] Read more.
Coffee fermentation is a complex process, mainly involving bacteria and yeasts, whose interaction influences beverage quality. The way this process is conducted affects the interactions between these microorganisms. To identify microbial diversity in fermenting coffee, samples were collected from 20 farms in the Department of Quindío, Colombia. Metataxonomic analyses using high-throughput sequencing and volatile organic compound identification in green coffee beans were performed with HS-SPME and GC-MS. Potential relationships between some families and genera with different fermentation types and coffee quality were evaluated. In our results, samples presented with high richness and diversity were greater for bacteria than for yeast/fungi. The Enterobacteriaceae family dominated at the beginning of fermentation, while Leuconostoc, Lactobacillus, Gluconobacter, and Acetobacter genera dominated at the end, a finding related to pH reduction and final coffee quality. Overall, 167 fungal families were identified, but Saccharomyceaceae dominated from the beginning. Alcohols and esters were the main chemical classes identified in green coffee bean samples from these fermentations. These results will facilitate the identification process conditions that influence the presence and abundance of microorganisms related to quality as well as contributing to the design of strategies to conduct fermentations to improve the final quality of coffee. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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15 pages, 2641 KiB  
Article
Fermentation Dynamics of Naturally Fermented Palm Beverages of West Bengal and Jharkhand in India
by Souvik Das and Jyoti Prakash Tamang
Fermentation 2023, 9(3), 301; https://doi.org/10.3390/fermentation9030301 - 20 Mar 2023
Cited by 2 | Viewed by 3355
Abstract
The term ‘toddy’ represents a group of different varieties of mild-alcoholic palm beverages of coastal and inland India, produced from the fresh saps of various palm trees through uncontrolled natural fermentation. In this study, we analysed the successional changes of microbial [...] Read more.
The term ‘toddy’ represents a group of different varieties of mild-alcoholic palm beverages of coastal and inland India, produced from the fresh saps of various palm trees through uncontrolled natural fermentation. In this study, we analysed the successional changes of microbial abundances and various physico-chemical parameters during natural fermentation (0 h to 48 h) of taal toddy, prepared from Palmyra palm, and khejur toddy, prepared from date palm of West Bengal and Jharkhand in India. Microorganisms from different successional levels were isolated and grouped using repetitive element sequence-based PCR (rep-PCR) technique and identified by the sequencing of 16S rRNA gene and D1-D2 region of 26S rRNA gene for bacteria and yeasts, respectively. Enterococcus faecalis, Lactiplantibacillus plantarum, Lacticaseibacillus paracasei and yeast Saccharomyces cerevisiae were identified during natural fermentation of toddy. During the natural fermentation, the average pH and total sugar content in the samples of both taal and khejur toddy decreased, whereas a gradual rise was observed in the contents of acidity, total alcohol, total ester and total protein. Bio-active potential (presence of phenolics and flavonoids) of toddy was also analysed (0 h to 48 h), where contents of total phenolics, flavonoids and resulting anti-oxidant activity were found higher in the end-product than the fresh palm sap, indicating toddy as a functional low-alcoholic drink. Lastly, it can be concluded that the inter-variable dynamics and microbial interrelation, which in turn depend on a number of local factors, regulate the overall fermentation dynamics and determine the product quality. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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19 pages, 3418 KiB  
Article
Analysis of Bacterial Diversity in Fermented Grains of Baijiu Based on Culturomics and Amplicon Sequencing
by Jiaxuan Wang, Shuyue Hao and Qing Ren
Fermentation 2023, 9(3), 260; https://doi.org/10.3390/fermentation9030260 - 06 Mar 2023
Cited by 1 | Viewed by 1454
Abstract
Baijiu is a traditional distilled liquor in China. The unique flavor developed during the fermentation process of Baijiu is closely related to the microorganisms in the fermented grains of the Baijiu. Fermented grain is a solid material that has not been distilled after [...] Read more.
Baijiu is a traditional distilled liquor in China. The unique flavor developed during the fermentation process of Baijiu is closely related to the microorganisms in the fermented grains of the Baijiu. Fermented grain is a solid material that has not been distilled after the fermentation of Baijiu. It is of great significance to study the bacterial diversity in fermented grains and to isolate and culture them to reveal the formation mechanism of the flavor substances in Baijiu. In this study, the diversity of bacteria in fermented grains was studied by the combination of amplicon sequencing and culturomics, and a pure culture of culturable strains was obtained. The results of amplicon sequencing showed that the bacteria detected in the fermented grains were classified into 5 phyla, 8 classes, 24 orders, 34 families, and 45 genera, of which Lactobacillus (66.95%) and Acetobacter (32.36%) were the dominant genera. By using the method of culturomics, five pH gradients (pH = 3, 4, 5, 6, and 7) of enrichment culture medium and solid medium with different components were designed to enrich and isolate the culturable bacteria in the fermented grains. A total of 323 strains of bacteria were obtained, belonging to 53 genera and 118 species, and 14 suspected new species were obtained. Among the bacteria isolated by the culturomics, 14 genera were detected by amplicon sequencing, and 39 genera were not detected, indicating that the culturomics method can isolate and culture bacteria with low abundance in fermented grains. Compared with the traditional culture method, culturomics expanded the culturable bacteria in the fermented grains to 188%. The diversity of the bacteria in the fermented grains of Baijiu was analyzed by amplicon sequencing and culturomics, and the microbial community composition and relative abundance of fermented grains were comprehensively revealed. At the same time, the acquisition of more pure cultures of culturable bacteria provides more choices for the liquor-making microbial resource library. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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19 pages, 4169 KiB  
Article
Analysis of the Microbial Community Structure and Volatile Metabolites of JIUYAO in Fangxian, China
by Wendi Zhang, Qing Ren, Zhongchao Wang, Huijie Liu, Mingquan Huang, Jihong Wu and Baoguo Sun
Fermentation 2022, 8(12), 754; https://doi.org/10.3390/fermentation8120754 - 18 Dec 2022
Cited by 2 | Viewed by 1658
Abstract
JIUYAO is an important saccharification starter in the production of huangjiu and is also an important source of flavor. In this study, the microbial community structure of JIUYAO from Fangxian was studied by high-throughput sequencing (HTS) technology for the first time. The volatile [...] Read more.
JIUYAO is an important saccharification starter in the production of huangjiu and is also an important source of flavor. In this study, the microbial community structure of JIUYAO from Fangxian was studied by high-throughput sequencing (HTS) technology for the first time. The volatile flavor compounds of the JIUYAO metabolites were also analyzed by headspace solid-phase microextraction combined with full two-dimensional gas chromatography-mass spectrometry (HS-SPME-GC×GC/MS) for the first time. The results showed that there were 15 dominant bacterial genera, including Weissella, Pediococcus, unclasssified_k_norank_d_Bacteria, Lactobacillus, Leuconostoc, etc. Thirteen species of dominant fungi included Wickerhamomyces, Saccharomycopsis, Rhizopus, etc. The different samples of JIUYAO were similar in their microbial species, but the number of species was significantly different. A total of 191 volatile flavor compounds (VFCs) were detected, among which esters, alcohols, acids, and alkenes were the main flavor compounds, and 21 terpenoids were also detected. In addition, the functional prediction of micro-organisms in JIUYAO revealed that global and overview maps, amino acid metabolism, and carbohydrate metabolism were the dominant categories. Through correlation analysis, 538 potential correlations between the dominant micro-organisms and the different flavor compounds were obtained. This study revealed the interactions between the micro-organisms and the volatile metabolites in JIUYAO, which provided reliable data for the analysis of the microbial community structure of Fangxian JIUYAO and provided theoretical support for the quality evaluation of JIUYAO. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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21 pages, 4634 KiB  
Article
Chemical and Sensory Characteristics of Different Red Grapes Grown in Xinjiang, China: Insights into Wines Composition
by Yuanyuan Miao, Huan Wang, Xiaoyu Xu, Piping Ye, Huimin Wu, Ruirui Zhao, Xuewei Shi and Fei Cai
Fermentation 2022, 8(12), 689; https://doi.org/10.3390/fermentation8120689 - 29 Nov 2022
Cited by 3 | Viewed by 2174
Abstract
Globally, the red wine market experienced a rapid growth in the last decade, due to the superior colour, taste, and nutritional quality. The red grapes used for vinification have individual characteristics varying within the regional environment. In this study, the quality of seven [...] Read more.
Globally, the red wine market experienced a rapid growth in the last decade, due to the superior colour, taste, and nutritional quality. The red grapes used for vinification have individual characteristics varying within the regional environment. In this study, the quality of seven grape cultivars, including Marselan, Yan 73, Muscat Hamburg, Kadarka, Merlot, Cabernet Sauvignon, and Crimpose, and their corresponding wines, were investigated based on high-performance liquid chromatography and headspace solid-phase microextraction coupled to gas chromatography–mass spectrometry. These techniques were performed to analyze the chemical compositions and volatile compounds of the tested samples, respectively. The results showed that tartaric acid (29.96% to 73.45%) and rutin (12.53% to 56.54%) were the dominant organic acid and phenolic compounds in grapes, respectively. Higher concentrations of organic acids and phenolic compounds, and the types of volatile compounds, were observed to be highest in the Cabernet Sauvignon grape. The antioxidant activity of wines ranged from 6.74 to 102.68 mmol TE/L, and Yan 73 wine had the highest antioxidant activity. A total of 69 volatile compounds consisting of 17 alcohols, 26 esters, 5 aldehydes, 9 acids, 7 ketones, and 5 other volatile compounds were identified in all tested wines, and 11 important aroma active substances (odor activity value > 1) were selected, consisting of β-ionone, phenethyl acetate, geranyl acetate, ethyl 9-decenoate, ethyl caprate, ethyl pelargonate, decanal, ethyl caprylate, 6-methyl-5-hepten-2-one, methyl 2-hexenoate, and ethyl hexanoate, which endow wines with a unique aroma. This work clearly describes the chemical and sensory characteristics of seven red grape cultivars in Xinjiang of China and provides diversity options for cultivars for winemaking. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods)
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