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Fermentation
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Perspectives on Microbiota of Fermented Foods, 2nd Edition
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Perspectives on Microbiota of Fermented Foods, 2nd Edition

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

Deadline for manuscript submissions: 20 October 2026 | Viewed by 5902

Special Issue Editors

Dr. Junnan Xu

E-Mail Website
Guest Editor
School of Food Science and Engineering, Ningxia University, Yinchuan, China
Interests: food biotechnology; microbial fermentation; food microbial safety control
Prof. Dr. Haitian Fang

E-Mail Website
Guest Editor
School of Food Science and Engineering, Ningxia University, Yinchuan 750021, China
Interests: food biomanufacturing; microbiology and metabolic engineering; probiotics and prebiotics; fermentation; microbial resources
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 typically initiated by natural inoculation, a fermentation starter (Qu), artificially added auxiliary strains, or in a pit rich in related microorganisms. In the brewing process, numerous microorganisms, including bacteria and fungi, may be involved cooperatively. 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 the environment and gut health.
  • Application of core microbes in enhancing the quality of fermented foods.

Dr. Junnan Xu
Prof. Dr. Haitian Fang
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 250 words) can be sent to the Editorial Office for assessment.

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 2100 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

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Related Special Issue

Published Papers (5 papers)

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Research

23 pages, 3677 KB  
Article
Metagenomic and Metabolomic Insights into Microbial Community Dynamics and Flavor Metabolite Formation in Novel Versus Traditional Strong-Flavor Daqu
by Guanhua Jiao, Haoyu Tian, Junqing Wang, Nan Li, Kaiquan Liu, Piwu Li, Fengyong Lu, Qi Wang, Ruiming Wang and Peng Du
Fermentation 2026, 12(5), 235; https://doi.org/10.3390/fermentation12050235 - 11 May 2026
Viewed by 238
Abstract
Daqu is the core saccharifying and fermenting agent in Baijiu production and a pivotal factor in flavor formation. Challenges that often hinder traditional strong-flavor Daqu brewing include low enzymatic activity and insufficient aroma. Therefore, we have developed a novel Daqu brewing system. Furthermore, [...] Read more.
Daqu is the core saccharifying and fermenting agent in Baijiu production and a pivotal factor in flavor formation. Challenges that often hinder traditional strong-flavor Daqu brewing include low enzymatic activity and insufficient aroma. Therefore, we have developed a novel Daqu brewing system. Furthermore, we investigated the differences in flavor profiles between traditional and novel Daqu by performing headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). We comparatively analyzed the microbial communities, metabolic functions, and flavor compositions in the two Daqu types via absolute quantitative metagenomics. Functional microorganisms were significantly enriched in the novel Daqu, which exhibited enhanced carbohydrate metabolism and a highly robust acidic environment owing to the fostering of core functional genera such as Aspergillus, Saccharomyces, and Pediococcus. This significantly increased the aldehyde and organic acid levels, which resulted in pronounced aldehydic and acidic sensory characteristics. Carbohydrate-Active EnZyme (CAZy) profiling confirmed the significantly elevated abundance of glycoside hydrolases (GHs) and glycosyltransferases (GTs) in novel Daqu, which improved starch bioconversion and synthesis of flavor precursors. Thus, this study shows that novel Daqu promotes ethanol accumulation and the synthesis of flavor compounds like acetals by strengthening the core microbiota and metabolic networks. These findings provide a theoretical foundation for enriching the aromatic complexity of Baijiu. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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18 pages, 2566 KB  
Article
Heterologous Expression of gadA and speA from Alicyclobacillus acidoterrestris Enhances the Acid Resistance and Fermentative Activity of Lactiplantibacillus plantarum
by Xiya Cao, Linan Duan, Yurou Ren, Hao Liang, Kexin Li, Xinyao Guo, Jiali Wang, Junmei Ma and Junnan Xu
Fermentation 2026, 12(3), 143; https://doi.org/10.3390/fermentation12030143 - 8 Mar 2026
Viewed by 760
Abstract
Enhancing the acid tolerance of Lactiplantibacillus plantarum is essential for improving its fermentation performance and metabolic activity under acidic conditions, thereby strengthening its probiotic functionality. In this study, the glutamate decarboxylase gene (gadA) and the arginine decarboxylase gene (speA) [...] Read more.
Enhancing the acid tolerance of Lactiplantibacillus plantarum is essential for improving its fermentation performance and metabolic activity under acidic conditions, thereby strengthening its probiotic functionality. In this study, the glutamate decarboxylase gene (gadA) and the arginine decarboxylase gene (speA) from Alicyclobacillus acidoterrestris DSM 3922T were heterologously expressed in L. plantarum WCFS1 to enhance its acid resistance. Recombinant expression vectors pMG36e-gadA and pMG36e-speA were constructed and introduced into L. plantarum WCFS1 via electroporation. The acid tolerance, cell membrane integrity, intracellular pH, ATP content, gene expression profiles, and enzyme activities of the recombinant L. plantarum WCFS1-gadA and WCFS1-speA were systematically evaluated. The results demonstrate that both recombinant strains exhibited significantly higher acid tolerance than the control strains. Under acid stress, the expression of gadA and speA was up-regulated, accompanied by enhanced activities of glutamate and arginine decarboxylases. In addition, the recombinant strains maintained higher intracellular pH and ATP levels compared with the control strain. Furthermore, the fermentative activity results support their potential applicability in fruit juice fermentation. Collectively, the heterologous expression of gadA and speA effectively improved the acid tolerance of L. plantarum, providing both mechanistic insights into acid stress adaptation and a theoretical basis for developing industrially robust, acid-resistant probiotic strains. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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19 pages, 629 KB  
Article
From Probiotic Screening to Postbiotic Potential: An Integrated In Vitro Assessment of Endogenous Non-Saccharomyces Yeast Isolates
by Furkan Aydın, Halil İbrahim Kahve and Fatma Şahmurat
Fermentation 2026, 12(2), 90; https://doi.org/10.3390/fermentation12020090 - 4 Feb 2026
Cited by 2 | Viewed by 1330
Abstract
Yeasts isolated from fermented foods have attracted increasing attention for their probiotic potential; however, studies on yeast-derived postbiotics remain limited. In this study, endogenous yeast strains belonging to Kluyveromyces marxianus (n = 3), Yarrowia lipolytica (n = 3), Pichia fermentans ( [...] Read more.
Yeasts isolated from fermented foods have attracted increasing attention for their probiotic potential; however, studies on yeast-derived postbiotics remain limited. In this study, endogenous yeast strains belonging to Kluyveromyces marxianus (n = 3), Yarrowia lipolytica (n = 3), Pichia fermentans (n = 3), and Debaryomyces hansenii (n = 3) were evaluated for their in vitro probiotic properties. A multi-criteria decision-making analysis using the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) identified K. marxianus ETP12, P. fermentans SJ2023, and Y. lipolytica ARTP9.2 as the most promising strains for postbiotic production. Among them, K. marxianus ETP12 exhibited the highest functional potential and was subjected to comprehensive postbiotic characterization. The postbiotic of K. marxianus ETP12 was further characterized for total phenolic content, antioxidant capacity (DPPH and ABTS scavenging activities), phenolic compound profile, biofilm inhibition capacity, free amino acid composition, and fatty acid profile. The results revealed a diverse phenolic composition, primarily consisting of fumaric acid, quercetin, gallic acid, and quinic acid. A total of 29 essential, non-essential, and bioactive amino acids were identified, with lysine, leucine, and glycine as the predominant components. Fatty acid profiling indicated the predominance of palmitic and stearic acids, accompanied by medium-chain fatty acids. Notably, it exhibited strong biofilm-inhibition activity against S. aureus ATCC 25923 and C. sakazakii ATCC 29544. Overall, these findings demonstrate that K. marxianus ETP12 represents a valuable source of multifunctional postbiotics with potential applications in the development of functional foods and nutraceuticals. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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16 pages, 2437 KB  
Article
Antifungal Effect of Lactiplantibacillus plantarum Y48 Postbiotics Combined with Potassium Sorbate in Bread
by Yasemin Kaya, Sevda Dere, Fatih Bozkurt, Dilara Devecioglu, Funda Karbancioglu-Guler, Mustafa Sengul and Enes Dertli
Fermentation 2025, 11(12), 675; https://doi.org/10.3390/fermentation11120675 - 1 Dec 2025
Cited by 1 | Viewed by 1550
Abstract
Mycotoxigenic molds pose a threat to human health and cause economic losses in bread production. To address this issue, postbiotics have emerged as promising natural bioprotective agents due to their antifungal properties. In this study, postbiotics were obtained from Lactiplantibacillus (Lp.) plantarum Y48, [...] Read more.
Mycotoxigenic molds pose a threat to human health and cause economic losses in bread production. To address this issue, postbiotics have emerged as promising natural bioprotective agents due to their antifungal properties. In this study, postbiotics were obtained from Lactiplantibacillus (Lp.) plantarum Y48, Liquorilactobacillus (Lq.) hordei SK-6, and Lp. plantarum VB-29 strains and subsequently lyophilized. The functional groups of the bioactive components in these postbiotics were identified using FTIR spectroscopy. Samples extracted with different solvents were analyzed for their volatile compound profiles by GC-MS, and the results were compared using principal component analysis (PCA). The antifungal activities of postbiotics were tested. Subsequently, the antifungal activity of Lp. plantarum Y48 postbiotic was evaluated on bread contaminated with Aspergillus niger and Penicillium expansum. The postbiotic was incorporated into the bread formulation both alone and in combination with potassium sorbate, and it was also applied to the bread surface as a spray. Notably, the formulation containing 3% postbiotic + 0.1% potassium sorbate completely inhibited the growth of A. niger and P. expansum. These results indicate that the combined use of Lp. plantarum Y48 postbiotic and potassium sorbate can effectively prevent mold growth in bread and holds potential as a natural bioprotective approach in food preservation applications. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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16 pages, 2268 KB  
Article
Correlations Between Flavor Profile and Microbial Community Succession in Probiotic-Fermented Burdock Root
by Chunzhi Xie, Heng Yuan, Shuxin Shi, Mengying Xu, Wenting Shi, Nannan Yu, Jinhui Hou and Yu Wang
Fermentation 2025, 11(11), 604; https://doi.org/10.3390/fermentation11110604 - 22 Oct 2025
Cited by 1 | Viewed by 1536
Abstract
Fresh burdock (Arctium lappa L.) roots were fermented with probiotic lactic acid bacteria, including Lactobacillus paracasei (L. paracasei), Lactobacillus plantarum (L. plantarum), and Lactobacillus casei (L.casei). The dynamic changes in volatile flavor compounds (VFCs) and microbial [...] Read more.
Fresh burdock (Arctium lappa L.) roots were fermented with probiotic lactic acid bacteria, including Lactobacillus paracasei (L. paracasei), Lactobacillus plantarum (L. plantarum), and Lactobacillus casei (L.casei). The dynamic changes in volatile flavor compounds (VFCs) and microbial community succession were compared during fermentation. Subsequently, correlations between bacteria and characteristic VFCs were analyzed, and potential functions were predicted. The results show that the types of VFCs increased from 25 to 54, and the total content increased from 7.852 ± 1.025 to 48.325 ± 0.624 mg/kg after fermentation for 7 days. Notably, esters and alcohols increased significantly. A total of 42 VFCs were identified as contributors to the overall flavor profile of the fermented burdock root. Among these, ethyl caproate, acetaldehyde, isoamyl acetate, hexaldehyde, phenylacetaldehyde, linalool, and 3-methylbutanol were regarded as the primary characteristic VFCs. Microbial composition analysis revealed three dominant phyla, two dominant genera, and three dominant species. Among them, L. paracasei and L. plantarum were the dominant species during fermentation. L. paracasei was positively correlated with multiple characteristic VFCs and was considered the core functional species in terms of flavor formation. Notably, L. paracasei exhibited a very strong correlation with acetaldehyde (ρ = 0.99). PICRUST2 function prediction further revealed that carbohydrate metabolism and amino acid metabolism were the core pathways of microbial metabolism and important sources of flavor precursors. This study demonstrates that lactic acid bacteria fermentation could markedly improve the flavor quality of burdock roots. Moreover, the formation of VFCs was closely correlated with complex microbial metabolism during fermentation. Full article
(This article belongs to the Special Issue Perspectives on Microbiota of Fermented Foods, 2nd Edition)
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