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Fermentation
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Development and Application of Starter Cultures, 2nd Edition
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Development and Application of Starter Cultures, 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: 15 February 2026 | Viewed by 13015

Special Issue Editors

Dr. Roberta Comunian

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Guest Editor
Agris Sardegna, Agenzia Regionale per la Ricerca in Agricoltura, Associated Member of the JRU MIRRI-IT, Loc. Bonassai, SS291 km 18.600, 07100 Sassari, Italy
Interests: food microbiology; fermented food; microbial biodiversity; microbial culture collections; lactic acid bacteria; starter cultures; fingerprint; antibiotic resistance
Special Issues, Collections and Topics in MDPI journals
Dr. Luigi Chessa

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Guest Editor
Agris Sardegna, Agenzia Regionale per la Ricerca in Agricoltura, Associated Member of the JRU MIRRI-IT, Loc. Bonassai, SS291 km 18.600, 07100 Sassari, Italy
Interests: food microbiology; fermented food; microbial biodiversity; microbial culture collections; lactic acid bacteria; starter cultures; fingerprint; antibiotic resistance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent decades, starter cultures have been developed to aid raw material processing with the aim of obtaining different types of fermented food products. In fact, properly developed selected starters represent a convenient solution to easily and safely carry out the fermentation when the concentration of the microbiota colonizing the production environment and the raw material itself turns out to be inadequate, or natural starter cultures are difficult to obtain and manage.  

Different purposes can be pursued when developing a starter culture: (a) selecting a low, defined number of species/strains, on the basis of their strong aptitude to fulfil the biochemical processes required by each production technology and for their suitability to be grown in the laboratory; or (b) trying to reproduce autochthonous biodiverse natural cultures where an indefinite number of species and strains, starter and nonstarter (but crucial during the whole fermentation and ripening of food), coexist in equilibrium. Both choices have pros and cons. On one hand, selected cultures, because of and despite their high technological efficiency, easily become the dominant microbiota of the product, causing a dramatic decrease in microbial biodiversity and the loss of peculiar sensory characteristics of fermented food. In fact, this kind of culture is widely applied, at high concentration, to industrial level productions that do not possess geographic niches and typicity.

On the contrary, natural microbial communities have a strain composition which is not reproducible in any place other than that of their origin, contributing to preserve microbial biodiversity and enriching products with peculiar sensory features that bind them to the territory. Indeed, autochthonous natural starter cultures usually characterize the most typical and high-quality agri-food products. However, their technological performance is not standardized and their use is not risk-free since, together with useful autochthonous microorganisms, even pathogen or spoilage ones could potentially be inoculated and allowed to contaminate the product.

The goal of this Special Issue is to host innovative or review papers facing the challenge of developing starter cultures or, at least, laying the foundation for them, which could be applicable on an artisanal, pilot or industrial scale, able to guarantee safety, quality constancy, and technological performance reproducibility, and preserve biodiversity and peculiar sensory characteristics usually linked to traditional products, while overcoming the problems associated with the daily propagation of natural cultures. Furthermore, papers dealing with whether and how fermented product consumption could affect human gastro-intestinal tract microbiota, and eventually the health of the consumers, would be welcome.

Dr. Roberta Comunian
Dr. Luigi Chessa
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

  • starter cultures
  • fermented food
  • microbial biodiversity
  • metagenomics
  • traditional foods
  • food safety
  • antibiotic resistance
  • microbial culture collections
  • gut microbiota
  • probiotics

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Related Special Issue

Published Papers (7 papers)

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Research

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16 pages, 2154 KB  
Article
Low-Cost Production Process of Saccharomyces cerevisiae Yeast for Craft Beer Fermentation
by Jessica Rodríguez, Domenica Villavicencio, Alys Raza, Fernanda Hernández-Alomía, Carlos Bastidas-Caldes and María Alejandra Cruz
Fermentation 2025, 11(12), 688; https://doi.org/10.3390/fermentation11120688 - 12 Dec 2025
Viewed by 895
Abstract
The production of craft beer depends on the quality and availability of yeast. However, many small breweries in developing countries face high costs due to their reliance on imported yeast strains. Developing efficient and low-cost propagation methods is therefore essential for sustainable production. [...] Read more.
The production of craft beer depends on the quality and availability of yeast. However, many small breweries in developing countries face high costs due to their reliance on imported yeast strains. Developing efficient and low-cost propagation methods is therefore essential for sustainable production. A lager-type Saccharomyces cerevisiae strain (SC-Lager2) was propagated using both synthetic and low-cost alternative media. The latter was formulated with malt extract as a carbon source and yeast extract obtained from brewery by-products as a nitrogen source. A Plackett–Burman design identified significant factors influencing growth (p < 0.05), and a full factorial design (24) optimized conditions. Growth kinetics and biomass yield were validated at laboratory (2 L) and pilot (83 L) scales. Maltose, yeast extract, zinc sulfate, and agitation significantly affected cell density and viability (p < 0.05). Under optimized conditions, 100% viability, a maximum cell density of 1.4 × 1010 cells/mL, and a biomass yield of 10 g/L were achieved values that were statistically higher (p < 0.05) than those obtained with the synthetic medium. The maximum specific growth rate (μmax) increased by 52%, while doubling time decreased by 39%. Overall, the use of agro-industrial by-products reduced medium costs by approximately 65% compared to conventional synthetic formulations. The proposed low-cost medium provides a scalable, economical, and sustainable solution for yeast propagation, reducing production costs while maintaining high cell viability and performance. This approach supports the autonomy and competitiveness of the craft beer sector in developing regions. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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18 pages, 1612 KB  
Article
Effects of Autochthonous Starter Cultures on the Quality Characteristics of Traditionally Produced Sucuk
by Mükerrem Kaya, Bilge Sayın, Kübra Çinar Topçu and Güzin Kaban
Fermentation 2025, 11(12), 672; https://doi.org/10.3390/fermentation11120672 - 28 Nov 2025
Viewed by 622
Abstract
This study aimed to evaluate the impact of autochthonous strains (Pediococcus pentosaceus 128b, Latilactobacillus sakei S15, Lactiplantibacillus plantarum S91, L. plantarum S24 and Staphylococcus carnosus G109) used as mono and mixed starter cultures on the quality attributes of traditionally produced sucuk, a [...] Read more.
This study aimed to evaluate the impact of autochthonous strains (Pediococcus pentosaceus 128b, Latilactobacillus sakei S15, Lactiplantibacillus plantarum S91, L. plantarum S24 and Staphylococcus carnosus G109) used as mono and mixed starter cultures on the quality attributes of traditionally produced sucuk, a Turkish dry fermented sausage, in a local small-scale facility. At the end of ripening, samples underwent comprehensive microbiological and physicochemical analyses. The use of autochthonous starter cultures (ASC) showed no statistically significant influence on thiobarbituric acid-reactive substances and water activity value. Lower pH values were observed in groups with autochthonous lactic acid bacteria strains (ALABS) compared to the control group. However, ALABS inhibited Micrococcus/Staphylococcus growth by rapidly lowering the pH, except in the groups with S. carnosus G109. The use of ASC led to an increase in the L* values of sucuk samples, except monoculture L. plantarum S91. The correlation heat map illustrating the relationships between the starter cultures and volatile compounds revealed that all groups containing L. plantarum S91 exhibit a volatile compound profile different from other single or mixed cultures. According to the results of the principal component analysis performed to determine the relationship between the chemical groups of the starter cultures and volatile compounds, the groups containing L. plantarum S91 differed from the other groups and showed positive correlations with phenols, furans, acids, terpenes, aromatic hydrocarbons, ketones, nitrogenous compounds, esters, and aliphatic hydrocarbons. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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25 pages, 1971 KB  
Article
From Raw Milk Microbiome to Cheese: The Challenge of Indigenous Natural Starter Culture Exploitation
by Luigi Chessa, Antonio Paba, Ilaria Dupré, Margherita Addis, Carlo Piga, Massimo Pes and Roberta Comunian
Fermentation 2025, 11(12), 660; https://doi.org/10.3390/fermentation11120660 - 25 Nov 2025
Viewed by 792
Abstract
A freeze-dried natural starter culture (NSC) was developed and assessed for its suitability in producing a semi-cooked, 60-day-ripened cheese resembling the protected designation of origin (PDO) Pecorino Sardo. The culture, derived from raw ewe’s milk from a dairy farm involved in the study, [...] Read more.
A freeze-dried natural starter culture (NSC) was developed and assessed for its suitability in producing a semi-cooked, 60-day-ripened cheese resembling the protected designation of origin (PDO) Pecorino Sardo. The culture, derived from raw ewe’s milk from a dairy farm involved in the study, without thermal decontamination to preserve indigenous microbiota, was enriched with two strain-level-characterised, biodiverse mixtures of Streptococcus thermophilus (Str-mix) and Lactobacillus delbrueckii (Lb-mix). This study evaluated the technological robustness and adaptability of NSC enriched with biodiverse Str-mix and Lb-mix across three different artisanal dairy-processing environments with varying milk compositions and equipment levels at plants located in different geographic areas. During cheesemaking, technological, physico-chemical, and compositional parameters were monitored, along with microbial characterisation of milks and 1-day cheeses. After 60 days of ripening, cheeses were characterised from the microbiological, physico-chemical, and compositional perspectives. Furthermore, nutritional labelling was established, and consumer acceptance was determined. Results showed that the starter (NSC + Str-mix + Lb-mix) demonstrated strong and reproducible technological performance in all dairies, regardless of the milk’s chemical and microbial composition variability. Sensory quality was preserved in cheeses ripened for up to 180 days. These preliminary findings seem to support the use of freeze-dried, raw-milk-derived natural cultures in artisanal cheesemaking as a way to preserve microbial diversity and to reconnect with traditional practices that enhance both the tangible and intangible assets of modern society. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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19 pages, 5168 KB  
Article
Green Tea Modulates Temporal Dynamics and Environmental Adaptation of Microbial Communities in Daqu Fermentation
by Liang Zhao, Fangfang Li, Hao Xiao, Tengfei Zhao, Yanxia Zhong, Zhihui Hu, Lu Jiang, Xiangyong Wang and Xinye Wang
Fermentation 2025, 11(9), 511; https://doi.org/10.3390/fermentation11090511 - 31 Aug 2025
Viewed by 882
Abstract
This study investigated the impact of green tea addition on microbial community dynamics during Daqu fermentation, a critical process in traditional baijiu production. Four Daqu variants (0%, 10%, 20%, 30% tea) were analyzed across six fermentation periods using 16S rRNA/ITS sequencing, coupled with [...] Read more.
This study investigated the impact of green tea addition on microbial community dynamics during Daqu fermentation, a critical process in traditional baijiu production. Four Daqu variants (0%, 10%, 20%, 30% tea) were analyzed across six fermentation periods using 16S rRNA/ITS sequencing, coupled with STR, TDR, Sloan neutral model, and phylogenetic analyses. Results showed time-dependent increases in bacterial/fungal richness, with 30% tea maximizing species richness. Tea delayed bacterial shifts until day 15 but accelerated fungal reconstruction from day 6, expanding the temporal response window. While stochastic processes dominated initial assembly (77–94% bacteria, 88–99% fungi), deterministic processes intensified with tea concentration, particularly in fungi (1% → 12%). Tea increased bacterial dispersal limitation and reduced phylogenetic conservatism of endogenous factors. This work proposed a framework for rationally engineering fermentation ecosystems by decoding evolutionary-ecological rules of microbial assembly. It revealed how plant-derived additives can strategically adjust niche partitioning and ancestral constraints to reprogram microbiome functionality. These findings provided a theoretical foundation in practical strategies for optimizing industrial baijiu production through targeted ecological interventions. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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7 pages, 1119 KB  
Communication
Preparing Sponge Dough for Making Bread Using Wheat Flour Cultured in 5% Saline
by Naganori Ohisa, Kazuto Endo and Toshikazu Komoda
Fermentation 2025, 11(4), 206; https://doi.org/10.3390/fermentation11040206 - 10 Apr 2025
Viewed by 1591
Abstract
A 5% salt solution was used to make sponge dough from wheat flour. We devised a new starter (wheat flour saline culture) by adding 5% saline to wheat flour and incubating it for 24 h. The dough’s rise was enhanced by adding wheat [...] Read more.
A 5% salt solution was used to make sponge dough from wheat flour. We devised a new starter (wheat flour saline culture) by adding 5% saline to wheat flour and incubating it for 24 h. The dough’s rise was enhanced by adding wheat flour saline culture to the dough: after two hours, the dough volume increased by 20–30% compared to the control. Furthermore, the specific volume of the bread increased from 2.25 cm3/g in the control to 2.73–3.47 cm3/g when sugar or other auxiliary ingredients were not added to it. Wheat flour saline culture contained a large number of halotolerant bacteria. The addition of wheat flour saline culture increased the air bubble size and specific volume of the bread. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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23 pages, 3717 KB  
Article
Influence of Yeast Interactions on the Fermentation Process and Aroma Production in Synthetic Cocoa Pulp vs. Real Mucilage Media
by Lydie Besançon, Da Lorn, Christelle Kouamé, Joël Grabulos, Marc Lebrun, Angélique Fontana, Sabine Schorr-Galindo, Renaud Boulanger, Caroline Strub and Alexandre Colas de la Noue
Fermentation 2024, 10(12), 662; https://doi.org/10.3390/fermentation10120662 - 21 Dec 2024
Cited by 4 | Viewed by 3602
Abstract
Cocoa fermentation plays a key role in defining chocolate’s flavor, with yeasts being central to this process. This study aimed to explore intraspecific genetic diversity of major indigenous yeasts (i.e., Saccharomyces cerevisiae and Pichia kudriavzevii), and their potential interaction in the cocoa [...] Read more.
Cocoa fermentation plays a key role in defining chocolate’s flavor, with yeasts being central to this process. This study aimed to explore intraspecific genetic diversity of major indigenous yeasts (i.e., Saccharomyces cerevisiae and Pichia kudriavzevii), and their potential interaction in the cocoa pulp environment. Their metabolic intraspecific diversity was characterized in synthetic cocoa pulp medium. Then, Saccharomyces cerevisiae, Pichia kudriavzevii, and other strains were introduced to each other to evaluate their potential negative interaction. Interesting strain associations were selected to further explore their interaction in synthetic cocoa pulp medium as well as real fresh cocoa pulp. From a fermentation campaign in Ivory Coast, a set of Saccharomyces (S.) cerevisiae and Pichia (P.) kudriavzevii strains were isolated from batches classified according to their chocolate quality (i.e., standard, intermediate, or premium chocolate). Less abundant species (i.e., Torulaspora franciscae, Kluyveromyces marxianus) were also isolated and tested for their potential negative interactions with S. cerevisiae and P. kudriavzevii. A set of strains were selected and cultured in single and in co-culture in a minimal cocoa pulp synthetic medium and in fresh cocoa pulp to highlight potential positive and/or negative interactions regarding fermentative aroma profile (i.e., higher alcohols, acetate esters, medium-chain fatty acids, and ethyl esters). The results highlighted the dominance of S. cerevisiae in fermentation kinetics and medium- to long-chain ester production, contrasted with P. kudriavzevii’s efficiency in short-chain ester synthesis. Intraspecific aroma profile variations can be pointed out. The co-cultures of P. kudriavzevii and S. cerevisiae strains isolated from the premium chocolate batch had a positive impact on the fermented pulp aroma profile. Negative interactions were observed with Torulaspora franciscae, which eliminated P. kudriavzevii’s aroma expression. Finally, the comparison of the data obtained for the minimal cocoa pulp synthetic medium compared to the cocoa pulp allowed us to draw conclusions about the use of synthetic media for studying cocoa fermentation. These findings emphasize the complex microbial interactions in cocoa fermentation that could shape future cocoa bean aroma. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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Review

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18 pages, 766 KB  
Review
Starter Cultures for the Production of Fermented Table Olives: Current Status and Future Perspectives
by Marilisa Giavalisco, Emanuela Lavanga, Annamaria Ricciardi and Teresa Zotta
Fermentation 2024, 10(7), 351; https://doi.org/10.3390/fermentation10070351 - 12 Jul 2024
Cited by 4 | Viewed by 3707
Abstract
Table olives are widely produced and consumed in the Mediterranean area. The production of table olives is mainly based on spontaneous fermentations, which may have several drawbacks (e.g., the development of undesirable microorganisms; organoleptic defects) compared to fermentative processes driven by starter cultures [...] Read more.
Table olives are widely produced and consumed in the Mediterranean area. The production of table olives is mainly based on spontaneous fermentations, which may have several drawbacks (e.g., the development of undesirable microorganisms; organoleptic defects) compared to fermentative processes driven by starter cultures (typically lactic acid bacteria, yeasts, or their combinations). Studies on the effect of starter cultures have been mainly focused on some technological traits (e.g., acidifying capability, the degradation of phenolic compounds, metabolite production) and, to a lesser extent, on the dynamics of olive microbiota during fermentation. Recently, the application of Amplicon Targeted—High-Throughput Sequencing (AT–HTS) has enabled improvement of the knowledge on the composition and evolution of microbial communities during fermentations, including the role of starter cultures. The AT–HTS approaches used so far, however, have several constraints (e.g., poor investigation of mycobiota and metabolically active microorganisms) that do not allow a full understanding of the complex microbial interactions occurring in fermented olives. The aim of this review is to provide insights into the role of starter cultures in fermented olives and highlight the need to apply, as for other fermented foods, integrated “omics” approaches to predict and exploit their metabolic potential to improve the final properties of products. Full article
(This article belongs to the Special Issue Development and Application of Starter Cultures, 2nd Edition)
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