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Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations

A special issue of Applied Sciences (ISSN 2076-3417). This special issue belongs to the section "Food Science and Technology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 9110

Special Issue Editors

Prof. Dr. Nataša Hulak

E-Mail Website
Guest Editor
Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000 Zagreb, Croatia
Interests: molecular biology; epigenetics; microbiology; food and soil microbiology; gene resistance; pathogens (food and plant)
Prof. Dr. Gianluigi Mauriello

E-Mail Website
Guest Editor
Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici, Italy
Interests: fermented foods; food pathogens; food safety; probiotics; microencapsulation
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Katleen Raes

E-Mail Website
Guest Editor
Research Unit VEG-i-TEC, Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 8500 Kortrijk, Belgium
Interests: food fermentation; food by-product valorization; food technology and microbiology; antioxidants in food

Special Issue Information

Dear Colleagues,

In the ever-evolving landscape of biotechnology, the synergy between fermentation technology and microbial biotechnology continues to pave the way for groundbreaking advancements. This dynamic intersection of scientific disciplines has witnessed a surge in innovation, driven by the relentless pursuit of more sustainable and efficient processes in various industries. This Special Issue delves into the latest developments in fermentation technology and microbial biotechnology, shedding light on the transformative strides that researchers and experts have made in these fields. Modern fermentation processes have evolved with advanced monitoring and control systems. Real-time data analytics, artificial intelligence, and automation optimize conditions, enhancing yields, reducing production times, and improving product quality. These technological advancements play a crucial role in maximizing efficiency and minimizing environmental impact across industries. Moreover, microbial biotechnology utilizes microorganisms for various processes and has undergone significant advancements. Genetic engineering and synthetic biology enable the customization of microorganisms for specific industrial applications. This has led to improved productivity and resilience and the synthesis of desired compounds, impacting bioprocessing, healthcare, agriculture, and environmental management. Recent developments in fermentation technology and microbial biotechnology mark an exciting phase in biotechnological progress. The integration of cutting-edge technologies and interdisciplinary collaboration positions these fields at the forefront of scientific innovation, offering sustainable, efficient, and tailored solutions with profound implications for the future of technology and societal well-being.

Prof. Dr. Nataša Hulak
Prof. Dr. Gianluigi Mauriello
Prof. Dr. Katleen Raes
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. Applied Sciences is an international peer-reviewed open access semimonthly 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 2400 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

  • fermentation technology
  • microbial biotechnology
  • advances
  • innovation

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Published Papers (6 papers)

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Research

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18 pages, 1668 KiB  
Article
Use of Wickerhamomyces anomalus Strains from Biologically Aged Wines to Improve the Sensorial Profile of Young White Wines
by Juan Carbonero-Pacheco, Álvaro García-Jiménez, Juan Carlos García-García, Inés M. Santos-Dueñas, Teresa García-Martínez, Juan Moreno, Jaime Moreno-García and Juan Carlos Mauricio
Appl. Sci. 2025, 15(3), 1546; https://doi.org/10.3390/app15031546 - 3 Feb 2025
Viewed by 801
Abstract
Non-Saccharomyces yeasts play a significant role in winemaking, offering unique benefits and contributing to wine complexity and varied and desirable aromatic profiles. This work focuses on the sensory improvement of Pedro Ximénez white wines using selected strains of Wickerhamomyces anomalus isolated from [...] Read more.
Non-Saccharomyces yeasts play a significant role in winemaking, offering unique benefits and contributing to wine complexity and varied and desirable aromatic profiles. This work focuses on the sensory improvement of Pedro Ximénez white wines using selected strains of Wickerhamomyces anomalus isolated from biologically aged wines. Chemical and microbiological analyses confirmed the implantation of W. anomalus; these yeast strains appear to displace indigenous non-Saccharomyces species in the must and produce large amounts of ethyl acetate and lower ethanol content. Wines made with W. anomalus strains were judged negatively by the tasting panel due to a nail polish/varnish odor and a strong, bitter taste; however, when these wines were blended with wine normally produced by spontaneous fermentation, the judges rated them positively, highlighting fruity aromas not detected under other conditions. These results conclude that W. anomalus strains isolated from biologically aged wines could be useful for modulating the sensory profile of white wines. Moreover, their use in combination with other yeasts or in immobilized form could improve the results obtained and avoid the blending process. The high yield of ethyl acetate produced by these strains could be of interest as an alternative to current methods of producing this compound, including the use of these wines for the production of quality vinegar. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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20 pages, 2448 KiB  
Article
Evaluation of Probiotic Saccharomyces boulardii Yeast as a Distillery Strain
by Andrea Maria Patelski, Ksawery Pragłowski, Katarzyna Pielech-Przybylska, Maria Balcerek and Urszula Dziekońska-Kubczak
Appl. Sci. 2025, 15(3), 1392; https://doi.org/10.3390/app15031392 - 29 Jan 2025
Viewed by 838
Abstract
The probiotic properties of the yeast Saccharomyces boulardii are fairly well recognised, and research into the use of this strain in fermentation processes has been ongoing for several years. In this article, we have described the research results to evaluate the distillery potential [...] Read more.
The probiotic properties of the yeast Saccharomyces boulardii are fairly well recognised, and research into the use of this strain in fermentation processes has been ongoing for several years. In this article, we have described the research results to evaluate the distillery potential of S. boulardii yeast. Compared to Ethanol Red and Thermosacc Dry yeast, the probiotic strain formed slightly different amounts of volatile compounds and fermented the available sugars less vigorously. The final ethanol concentration formed by the probiotic yeast was close to that observed for the distillery strains. Rye distillates with an alcohol content of 40% (v/v) obtained with S. boulardii yeast, according to the sensory panel, were distinguished by their delicately composed flavour and were rated better than distillates after fermentation by distillery yeast. The results are promising for the possibility of production of niche distillates using probiotic yeast. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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20 pages, 1337 KiB  
Article
Effects of Various Inocula Combinations of Leuconostoc mesenteroides, Papiliotrema terrestris, and Saccharomyces cerevisiae on Dough Fermentation and Final Bread Characteristics
by Enrico Viola, Giuliana Garofalo, Marcella Barbera, Daniela Piazzese, Davide Palmieri, Sabrina Di Giorgi, Antonio Alfonzo, Raimondo Gaglio and Luca Settanni
Appl. Sci. 2024, 14(24), 11581; https://doi.org/10.3390/app142411581 - 11 Dec 2024
Cited by 1 | Viewed by 845
Abstract
The integration of yeast and lactic acid bacteria (LAB) in bakery products is currently trending, which aims to enhance the taste and quality to satisfy consumer preferences. This study explored the interaction of Leuconostoc mesenteroides, Saccharomyces cerevisiae, and Papiliotrema terrestris during [...] Read more.
The integration of yeast and lactic acid bacteria (LAB) in bakery products is currently trending, which aims to enhance the taste and quality to satisfy consumer preferences. This study explored the interaction of Leuconostoc mesenteroides, Saccharomyces cerevisiae, and Papiliotrema terrestris during dough fermentation. Yeasts and LAB were monitored every three hours over a twelve-hour period. The chemical parameters and quality characteristics of both the dough and bread were analyzed. The highest level of S. cerevisiae was observed in the control treatment (9.30 log CFU/g, after 9 h) and in the treatment with co-inoculation of S. cerevisiae and P. terrestris (9.30 log CFU/g, after 12 h). Non-Saccharomyces yeasts peaked in the treatment with P. terrestris and L. mesenteroides, showing 7.77 log CFU/g after three hours. Doughs with L. mesenteroides achieved the fastest acidification. Treatments involving all three strains showed the highest increase in volume and CO₂ emissions. The profiles of volatile organic compounds emitted from bread varied depending on the inoculum combination. These findings underscore the need for further research into the interactions between this unconventional yeast and other microorganisms typically used in baking. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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17 pages, 3051 KiB  
Article
Microbiome Evolution of Brewer’s Spent Grain and Spent Coffee Ground Solid Sidestreams Under Industrial Storage Conditions
by Christian Hermansen, Qi Kang Chong, Sherilyn Ho, Federica Natali, Melanie Weingarten and Eric Charles Peterson
Appl. Sci. 2024, 14(21), 9759; https://doi.org/10.3390/app14219759 - 25 Oct 2024
Viewed by 1675
Abstract
Brewer’s spent grain (BSG) and spent coffee ground (SCG) are solid sidestreams from beverage production increasingly being upcycled into food, feed and other value-added products. These solid sidestreams are prone to microbial spoilage, negatively impacting their upcycling potential. Three samples each of BSG [...] Read more.
Brewer’s spent grain (BSG) and spent coffee ground (SCG) are solid sidestreams from beverage production increasingly being upcycled into food, feed and other value-added products. These solid sidestreams are prone to microbial spoilage, negatively impacting their upcycling potential. Three samples each of BSG and SCG were obtained from generators and recycling facilities in Singapore, and their chemical, elemental, and microbial composition was characterized. The spoilage mechanisms were investigated during storage under anaerobic and aerobic conditions. Bacterial loads of sidestreams were low from craft brewery and café sources (<1 and 3.53 ± 0.03 log10 CFU/g) and high from recycling facilities (>6 log10 CFU/g). The microbiome of BSG from recycling facilities was dominated by Bacilli, and B. coagulans was identified as the most prevalent species. SCG from recycling facilities was dominated by lactic acid bacteria, with L. panis being the most prevalent species. Storage up to 14 days under anaerobic conditions led to further bacterial proliferation mainly by Bacilli, lactic acid bacteria, and acetic acid bacteria, while aerobic storage led to extensive fungal contamination, including potential aflatoxin-producing Aspergillus flavus. The results shed light on the spoilage mechanisms, while highlighting the short shelf-life and food safety risks of BSG and SCG to inform valorization strategies. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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13 pages, 1064 KiB  
Article
Improved Functions of Fermented Coffee by Lactic Acid Bacteria
by Seon-Gyu Kim, Aoun Abbas and Gi-Seong Moon
Appl. Sci. 2024, 14(17), 7596; https://doi.org/10.3390/app14177596 - 28 Aug 2024
Cited by 2 | Viewed by 2462
Abstract
Coffee is one of the most popular beverages in the world, and at present, specialty coffees are developing for better tastes, flavors, or functions. Fermented coffees also reflect this trend and some brands are commercialized. Unlike general fermented coffees, we tried to ferment [...] Read more.
Coffee is one of the most popular beverages in the world, and at present, specialty coffees are developing for better tastes, flavors, or functions. Fermented coffees also reflect this trend and some brands are commercialized. Unlike general fermented coffees, we tried to ferment coffee extract with several lactic acid bacteria. Finally, we selected three strains that persisted in the coffee extract, and show strong antimicrobial activity, for the fermentation starters. The strains were identified as Pediococcus pentosaceus (KNUT 0384), Lacticaseibacillus paracasei (CJNU 1840), and Lactiplantibacillus plantarum (CJNU 0441) based on 16S rRNA gene sequences. During the fermentation process, the total acidities (p < 0.05 vs. the control, non-fermented coffee extract) and cell masses increased, which indicates that the bacteria metabolized properly in the extract. Furthermore, the fermented coffee extracts showed increased antimicrobial activities against Listeria monocytogenes (p < 0.05 vs. the control) and Streptococcus mutans (p < 0.05 vs. the control), increased anti-oxidative activities (p < 0.05 vs. the control, except for the KNUT 0384 sample), decreased caffeine content (p < 0.05 vs. the control, except for the KNUT 0384 sample), and increased chlorogenic acid content (p < 0.05 vs. the control). Taken together, the fermented coffee extracts with the selected lactic acid bacteria could be specialty coffees where several functions are improved when compared with a control coffee extract. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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Review

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29 pages, 1828 KiB  
Review
Advances in Fermentation Technology: A Focus on Health and Safety
by Theoneste Niyigaba, Kübra Küçükgöz, Danuta Kołożyn-Krajewska, Tomasz Królikowski and Monika Trząskowska
Appl. Sci. 2025, 15(6), 3001; https://doi.org/10.3390/app15063001 - 10 Mar 2025
Cited by 1 | Viewed by 1776
Abstract
Fermentation represents a pivotal bioconversion process that enhances foodstuffs’ nutritional and sensory attributes while playing a crucial role in global food systems. Nevertheless, concerns about safety issues associated with microbial contamination and the production of biogenic amines are often understated. This review appraised [...] Read more.
Fermentation represents a pivotal bioconversion process that enhances foodstuffs’ nutritional and sensory attributes while playing a crucial role in global food systems. Nevertheless, concerns about safety issues associated with microbial contamination and the production of biogenic amines are often understated. This review appraised recent advancements in fermentation technology, emphasising their association with the health and safety of fermented foods. Key advances include predictive microbiology models, in some cases achieving up to 95% accuracy in predicting microbial behaviour, and high-throughput sequencing (HTS) for microbial enrichment. In addition, advanced detection methods such as biosensors and PCR-based assays enable the rapid identification of contaminants, improving manufacturing processes and preserving product integrity. Advanced bioreactor technologies equipped with real-time monitoring systems have been shown to increase fermentation efficiency. Moreover, innovative packaging, artificial intelligence, machine learning models, and sensor technologies have optimised fermentation processes and contributed to tracking quality and safety in the blockchain technology supply chain, potentially reducing spoilage rates and showing a decrease in production times. This study also addresses regulatory frameworks essential for establishing robust safety protocols. Integrating advanced fermentation technologies is imperative to meet the growing global demand for safe fermented foods. Continuous research and innovation are needed to address safety challenges and promote industry practices prioritising health and quality, ensuring public safety and building consumer confidence in fermented products. Full article
(This article belongs to the Special Issue Current Progress in Fermentation Technology and Microbial Biotechnology: A Comprehensive Overview of Recent Developments and Innovations)
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