Microbiota and Metabolite Changes in 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: 31 August 2025 | Viewed by 6419

Special Issue Editor


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Guest Editor
Laboratory of Marketing and Technology of Aquatic Products and Foods, Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, University of Thessaly, 38446 Volos, Greece
Interests: food microbiology; molecular microbiology; fermentation; food biotechnology; food spoilage
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Special Issue Information

Dear Colleagues,

Fermented products are among the most popular foodstuffs, being a vital part of many diets and dietary trends, worldwide. Their unique sensory characteristics, as well as the health benefits they confer to consumers, have caused the consumption of such products to exponentially increasing year after year. Fermentation process is the result of the metabolic and/or enzymatic activity of a specific fraction of microorganisms that prevail against the other indigenous microbiota and produce a variety of metabolic compounds that shape the sensorial attributes of the final products. Throughout fermentation, many changes take place regarding the microbial consortia and metabolic profile. The formation of a specific metabolic profile is strongly affected by several factors (e.g., raw materials, fermentation conditions, indigenous microbiota, potential use of starter cultures, etc.), which require deep investigation to be fully understood. Thus, studying the microbial community changes that occur and respective metabolites that are formed throughout the fermentation process (raw material, initial and middle stages, and final product) is of great interest. These studies allow us to obtain useful information about (i) the microbial fraction that prevails and leads the whole process, (ii) the metabolites that are produced during processing and how they change until the end of fermentation, (iii) how specific microorganisms are correlated with specific metabolites, and (iv) the impact on the final product.

Therefore, the present Special Issue aims to collect original research and review articles assessing important aspects related to the microbiota and metabolites changes during fermentation (initial stage, middle stages, and final product) of several food and beverages (e.g., meat, seafood, dairies, alcoholic drinks, vegetables, etc.). On a general scale, studies dealing with (i) the relationship between the microbial communities and metabolites of fermented foods and beverages, (ii) the microbial and metabolic succession at different fermentation stages, and (iii) the relationship between microbiota and/or the metabolic profile with the formation of the sensorial attributes of the final product are very welcome.

Dr. Dimitrios A. Anagnostopoulos
Guest Editor

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 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 products
  • fermentation stages
  • microbiota
  • metabolites
  • sensorial attributes

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Published Papers (4 papers)

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Research

14 pages, 4248 KiB  
Article
The Heat Treatment of a Lactobacilli Probiotic to Derive a Postbiotic Has Minor Effects on the Metabolomic Profile
by Samuel C. G. Jansseune, Aart Lammers, Wouter H. Hendriks, Jürgen van Baal and Peter A. Wierenga
Fermentation 2025, 11(2), 87; https://doi.org/10.3390/fermentation11020087 - 10 Feb 2025
Viewed by 1283
Abstract
Lactobacillus rhamnosus CNCM I-3698 (LR98) and L. formosensis CNCM I-3699 (LF99) are two probiotic bacterial strains used in industry in a co-fermentation process to produce a probiotic (Pro) and the associated postbiotic (Post). The latter is produced through inactivation of the viable cells [...] Read more.
Lactobacillus rhamnosus CNCM I-3698 (LR98) and L. formosensis CNCM I-3699 (LF99) are two probiotic bacterial strains used in industry in a co-fermentation process to produce a probiotic (Pro) and the associated postbiotic (Post). The latter is produced through inactivation of the viable cells in the Pro by a high-temperature short-time (HTST) treatment. The impact of the inactivation process on the metabolomic profile of the Post was investigated. A growth substrate (Control) was fermented using a co-culture of LR98 and LF99 to produce the Pro and then HTST treated (~105 °C; 5 bar; 7 s) to derive the Post. Analysis of the semi-polar metabolome yielded 1412 unique features, from which 105 compounds were identified. The HTST process decreased the peak area in the Post of most features by <10%. Due to fermentation, an increase (fold change > 2; adjusted-p < 0.05) in the peak area was observed for 29 identified compounds, including 15 with known immunomodulatory, anti-oxidative or antibacterial property. The HTST treatment decreased the peak area of 4 of these compounds by >10% and 25 compounds by <10%. The HTST treatment to yield the Post induced minimal changes in the metabolomic profile, while the fermentation to produce the Pro yielded metabolites with known biological activity. Full article
(This article belongs to the Special Issue Microbiota and Metabolite Changes in Fermented Foods)
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17 pages, 4018 KiB  
Article
Isolation and Identification of Novel Non-Dairy Starter Culture Candidates from Plant Matrix Using Backslopping Propagation
by Maret Andreson, Jekaterina Kazantseva, Aili Kallastu, Taaniel Jakobson, Inga Sarand and Mary-Liis Kütt
Fermentation 2024, 10(12), 663; https://doi.org/10.3390/fermentation10120663 - 23 Dec 2024
Viewed by 1252
Abstract
The majority of non-dairy starter cultures on the market are originally isolated from milk and therefore do not provide the most optimal fermentation for plant matrices. Developing plant-derived starter cultures is essential for creating high-quality, tasty dairy alternatives. This study aims to isolate [...] Read more.
The majority of non-dairy starter cultures on the market are originally isolated from milk and therefore do not provide the most optimal fermentation for plant matrices. Developing plant-derived starter cultures is essential for creating high-quality, tasty dairy alternatives. This study aims to isolate and characterize bacterial strains with the potential to be used as non-dairy starters from plant sources via backslopping evolution. A natural consortium of macerated plants was inoculated into two oat and two pea commercial drinks and backslopped for seventeen cycles to evolve the bacterial consortium at 25 °C, 34 °C, and 42 °C. The results showed that the initial natural consortium contained less than 1% lactic acid bacteria, and after the seventeenth cycle, lactic acid bacteria dominated in all investigated consortia. Oat Od1-25 and Od2-42 and pea Pd1-34 and Pd1-42 samples were selected for strain isolation based on amplicon-based metagenetic analysis of 16S rRNA gene sequencing and sensory properties. The strain isolation was performed using an out-plating technique, and colonies were identified by MALDI-TOF mass spectrometry. Altogether, eleven lactic acid bacteria species of plant origin were obtained. The strains belonged to the Leuconostoc, Enterococcus, Lactobacillus, and Lactococcus genera. Full article
(This article belongs to the Special Issue Microbiota and Metabolite Changes in Fermented Foods)
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10 pages, 3394 KiB  
Article
The Metagenomic Properties of Uşak Tarhana Dough
by Naciye Afranur Mitaf, Dudu Simsek Kirca and Omer Simsek
Fermentation 2024, 10(12), 620; https://doi.org/10.3390/fermentation10120620 - 4 Dec 2024
Cited by 2 | Viewed by 1069
Abstract
This study investigated the bacterial diversity of geographically indicated Uşak tarhana using metagenomics. Tarhana dough samples were collected from local producers in different regions of the Uşak province. The samples were analyzed for their chemical and microbiological properties. The microbiota was examined through [...] Read more.
This study investigated the bacterial diversity of geographically indicated Uşak tarhana using metagenomics. Tarhana dough samples were collected from local producers in different regions of the Uşak province. The samples were analyzed for their chemical and microbiological properties. The microbiota was examined through metagenomic analysis using high-throughput sequencing, followed by bioinformatic processing with QIIME2 and DADA2 tools. Taxonomic analyses revealed that Lactiplantibacillus plantarum and Fructilactobacillus sanfranciscensis were the dominant species in most samples. In Silico analysis confirmed the presence of Fructilactobacillus sanfranciscensis in the tarhana fermentation microbiota. Diversity analyses, including Shannon and Chao1 indices, indicated significant variation in microbial diversity and homogeneity among the samples. Differences in microbiota diversity were observed between tarhana produced in the northern and southern regions of Uşak. The bacterial diversity of the tarhana samples showed partial differences at the micro-local level, and these results suggested that the slight variation in bacterial diversity between the northern and southern regions might be related to mild climatic transition. Full article
(This article belongs to the Special Issue Microbiota and Metabolite Changes in Fermented Foods)
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14 pages, 2273 KiB  
Article
Dynamic Changes in Microbial Communities and Chemical Compounds during the Semi-Dry Fermentation Processing of Coffea arabica
by Xiaojing Shen, Wenjuan Yuan, Qi Wang, Bintao Peng, Yi Guo, Kunyi Liu and Weiwei Jiang
Fermentation 2024, 10(8), 435; https://doi.org/10.3390/fermentation10080435 - 19 Aug 2024
Cited by 4 | Viewed by 1283
Abstract
The semi-dry fermentation processing (SFP) of Coffea arabica is a traditional primary processing method in the coffee industry, which crucially impacts the coffee’s flavor. To further obtain useful information on microbial communities and chemical compounds during the SFP of C. arabica from Yunnan, [...] Read more.
The semi-dry fermentation processing (SFP) of Coffea arabica is a traditional primary processing method in the coffee industry, which crucially impacts the coffee’s flavor. To further obtain useful information on microbial communities and chemical compounds during the SFP of C. arabica from Yunnan, China, the microbial community structures and the differentially changed non-volatile compounds (DCnVCs) were comprehensively analyzed. The results showed that Tatumella, Staphylococcus, Klebsiella, Brevundimonas, and Gluconobacter were the most prevalent bacteria genera, and Candida, Hannaella, Hanseniaspora, Pichia, and Lachancea were the most abundant fungal genera. Furthermore, 117 DCnVCs were found in the fermentation-finished samples compared to the raw materials. Therefore, this study can provide useful information for understanding the SFP of coffee beans, and its impact on coffee’s quality parameters. Full article
(This article belongs to the Special Issue Microbiota and Metabolite Changes in Fermented Foods)
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