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Precision Fermentation: Applications in the Food and Beverage Industry

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

Deadline for manuscript submissions: 30 September 2025 | Viewed by 14545

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Prof. Dr. Tiago Lima de Albuquerque

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Department of Food Engineering, Center for Agricultural Sciences, Federal University of Ceará, Fortaleza 60020-181, CE, Brazil
Interests: food engineering; bioprocesses; waste valorization; agro-industrial residues; enzymes immobilization
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Dear Colleagues,

We are pleased to announce a Special Issue titled "Precision Fermentation: Applications in the Food and Beverage Industry", which will explore the latest advancements in this cutting-edge field. Precision fermentation is transforming the food and beverage sector by offering unprecedented control over product characteristics such as flavor, texture, and nutritional profiles. This technology enables the development of sustainable, high-quality products that meet the growing consumer demand for healthier and more environmentally friendly options.

We invite researchers, academics, and industry professionals to submit their original research, reviews, and case studies on innovative applications of precision fermentation. Contributions should explore new methods, technological advancements, and industrial-scale applications that push the boundaries of food and beverage production.

Topics of interest include, but are not limited to, the following:

Development of novel food ingredients through precision fermentation;
Fermentation for enhancing flavor, texture, and nutritional value;
Sustainable production processes using precision fermentation;
Role of microbial engineering and synthetic biology in fermentation;
Industrial applications of precision fermentation in dairy, plant-based, and cultured products;
Case studies on scaling up precision fermentation technologies.

We look forward to your contributions that will advance this exciting area of research.

Prof. Dr. Tiago Lima de Albuquerque
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

precision fermentation
food and beverage industry
microbial engineering
flavor optimization
nutritional enhancement
sustainable food production
synthetic biology
fermented food ingredients
textural improvements
fermentation technologies
industrial fermentation
protein alternatives

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Published Papers (10 papers)

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Research

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14 pages, 3431 KiB

Open AccessArticle

A Response Surface Methodology for Sustainable Production of GABA from Black Soybean Okara Using Solid-State Collaborative Fermentation of Rhizopus oligosporus and Yarrowia lipolytica

by Yi-Chung Lai, Chien-Cheng Yeh, Bang-Yuan Chen, Jung-Feng Hsieh, Chia-I Chang, Cheng Huang, Meng-I Kuo and Chun-Ping Lu

Fermentation 2025, 11(6), 296; https://doi.org/10.3390/fermentation11060296 - 22 May 2025

Viewed by 574

Abstract

Black soybean okara is a common food byproduct in Asia. This study conducted collaborative fermentation with Rhizopus oligosporus and Yarrowia lipolytica to produce a GABA-enriched okara product. Two black soybean varieties, TN3 and TN5, were used, and optimal fermentation conditions were predicted using response surface methodology (RSM). After 24 h of Rhizopus oligosporus incubation, Yarrowia lipolytica was inoculated under 20 trial conditions with variations in temperature, incubation time, and inoculation size. The model predicted that the highest GABA content would be achieved at 34–35 °C, 47–49 h incubation, and 3–4 log CFU/mL inoculation. Under these optimal conditions, the maximum GABA yields achieved were 868.3 µg/g for TN3 and 853.1 µg/g for TN5. Fermentation conditions had minimal influence on protease activity, which may be attributed to the distinct roles of Rhizopus oligosporus and Yarrowia lipolytica in the fermentation process. The solid-state collaborative fermentation technology supports food waste recycling and enhances product functionality, contributing to the circular economy. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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18 pages, 1559 KiB

Open AccessArticle

Evaluation of the Impact of Fermentation Conditions, Scale Up and Stirring on Physicochemical Parameters, Antioxidant Capacity and Volatile Compounds of Green Tea Kombucha

by Raniele Oliveira Alves, Rodrigo Lira de Oliveira, Marcílio Martins de Moraes, Wallysson Wagner Vilela Santos, Cláudio Augusto Gomes da Câmara, Suzana Pedroza da Silva, Camila Souza Porto and Tatiana Souza Porto

Fermentation 2025, 11(4), 201; https://doi.org/10.3390/fermentation11040201 - 9 Apr 2025

Cited by 1 | Viewed by 925

Abstract

This study evaluated the influence of tea, sucrose, and inoculum concentrations on green tea kombucha’s physicochemical properties and antioxidant capacity to optimize its production. The highest total phenolic content (98.61 mg GAE/100 mL) and radical scavenging activity for ABTS (9647.14 μmol/mL) and DPPH (6640.00 μmol/mL) were observed with 8 g/L of tea, 80 g/L of sucrose, and 30% inoculum. Principal Component Analysis highlighted inoculum as the key factor influencing these parameters. Following this, fermentation was scaled up in 6.5 L bioreactors operating under static and stirred conditions. Monitoring physicochemical properties, antioxidant capacity, and volatile compounds revealed the impact of agitation on fermentation, with the kombucha obtained by static cultivation presenting higher biological activity. Eleven volatile compounds were identified, including carboxylic acids, terpenes, esters, alcohols, and phenols. Notably, α-terpinolene, dodecanoic acid, and 2,4-di-tert-butylphenol, found in kombucha, exhibit antioxidant properties linked to health benefits. Differences in volatile compound profiles were observed between static and stirred processes. This study concluded that kombucha maintains its physicochemical characteristics and bioactivity during scale-up, contributing to a better understanding of large-scale production. It also suggests stirred cultivation as an alternative for kombucha production. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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23 pages, 5248 KiB

Open AccessArticle

Functional Component Production Capabilities in Milk Fermentation of Some Featured Lactic Acid Bacteria Species for Use in Different Food Processes

by Tuğba Kök Taş, Fatma Ecemnur Duran, Nilgün Özdemir and Ebru Çubuk Demiralay

Fermentation 2025, 11(4), 165; https://doi.org/10.3390/fermentation11040165 - 24 Mar 2025

Viewed by 974

Abstract

This study examines the fermentation performance of featured bacteria (Lactobacillus acidophilus-ATCC-4356, Lactobacillus helveticus-ATCC-15009, Lactobacillus delbrueckii subsp. bulgaricus-ATCC-11842, Lacticaseibacillus casei-ATCC-393, Streptococcus thermophilus-ATCC-19258 (ST), and Bifidobacterium bifidum-ATCC-29521 (BB)) used in fermented dairy products and their impact on product quality. The main focus is on evaluating the metabolic activities, organic acid production, viscosity values, and sensory properties of probiotic strains such as L. acidophilus, L. bulgaricus, L. casei, L. helveticus, B. bifidum, and S. thermophilus. The strains were activated in a sterile milk medium and incubated until they reached a pH of 4.6. Then, pH, microbial enumeration, organic acid, sugar composition, vitamins A, D, E, K1, and K2 (menaquinone-7), and viscosity values were measured in the bacteria. Organic acid, sugar composition, and vitamins A, D, E, K1, and K2 (menaquinone-7) were analyzed with the HPLC method. Additionally, sensory analyses were performed, and volatile compounds were examined. L. casei demonstrated superiority in lactic acid production, while L. helveticus showed high lactose consumption. L. bulgaricus stood out in galactose metabolism. The highest viscosity was observed in products produced by B. bifidum. Differences in viscosity were attributed to exopolysaccharide (EPS) production and acid production capacity. A total of 62 volatile compounds were identified, with the highest levels of aromatic components found in products containing B. bifidum. The most preferred product, based on panel evaluations, was the fermented dairy product produced with L. acidophilus. As for aroma profiles, it was determined that the phenethyl alcohol, 3-methyl-1 butanol, and ethanol compounds are associated with B. bifidum, the hexanoic acid and 2-methylbutanal compounds are associated with the L. acidophilus, the hexanoic acid, 2-methylbutanal, 2-furanmethanol, and acetaldehyde compounds are associated with the L. bulgaricus, and the hexanoic acid, 2-methylbutanal, 2-heptanone, acetoin, and d-limonene are associated with the L. casei. On the other hand, the L. helveticus strain is associated with the hexanoic acid, 2-methylbutanal, and 2-heptanone, and the S. termophilus strain is associated with the hexanoic acid, hexanol, acetoin, 2,3-pentanedione, 1-butanol, and 3-methyl-2-butanone volatile aroma compounds. The determination of fat-soluble vitamins is particularly important for vitamin K1 and vitamin K2. In this study, the bacterial sources of these vitamins were compared for the first time. The menaquinone-7 production by L. helveticus was determined to be the highest at 0.048 µg/mL. The unique metabolic capacities of these prominent cultures have been revealed to play an important role in determining the aroma, organic acid content, viscosity, and overall quality of the products as a whole. Therefore, the findings of this study will provide the right strain selection for a fermented dairy product or a different non-dairy-based fermented product according to the desired functional properties. It also provides a preliminary guide for inoculation in the right ratios as an adjunct culture or co-culture for a desired property. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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17 pages, 1259 KiB

Open AccessArticle

Fermentation of Light and Dark Bean Coffee Brews with SCOBY and Lactic Acid Bacteria

by Rusen Metin Yildirim

Fermentation 2025, 11(3), 158; https://doi.org/10.3390/fermentation11030158 - 20 Mar 2025

Viewed by 789

Abstract

This study investigated the effects of fermentation with a SCOBY (symbiotic culture of bacteria and yeast) and lactic acid bacteria (LAB) on the physicochemical and sensory properties of coffee brews prepared from light-roasted (LR) and dark-roasted (DR) coffee beans, with and without the addition of spent coffee grounds (SC). Total phenolic content (TPC), total flavonoid content (TFC), antioxidant activities (DPPH and FRAP), caffeine, and individual phenolic acids were analyzed. Fermentation significantly increased TPC and the concentrations of chlorogenic acids (CGAs), particularly in LR samples, with 5-caffeoylquinic acid (5-CQA) as the most abundant phenolic acid. The addition of spent coffee grounds further enhanced TPC and CGA levels, with total CGA concentrations increasing from 1412.32 to 2458.57 mg/L in LR samples and from 519.77 to 586.37 mg/L in DR samples. Fermentation also led to the isomerization of 5-CQA into 3-CQA and 4-CQA, as well as the release of caffeic acid in LAB-fermented samples. Acetic acid production was exclusive to SCOBY-fermented samples, with higher levels in LR samples (6658 mg/L) compared to DR samples (4331 mg/L). In contrast, lactic acid production was observed only in LAB-fermented samples, reaching 6559 mg/L in LR samples with spent coffee grounds. Antioxidant activity varied depending on the assay, with FRAP values decreasing in fermented samples, while DPPH values remained largely unchanged. Sensory evaluation identified the dark-roasted SCOBY-fermented sample with spent coffee grounds (SK) as the most preferred, characterized by balanced flavor and high overall acceptability. These findings highlight the influence of roasting degree, fermentation type, and substrate composition on the bioactive and sensory properties of fermented coffee, providing insights for the development of novel coffee-based fermented beverages with enhanced functional and sensory profiles. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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17 pages, 5030 KiB

Open AccessArticle

Novel Malolactic Fermentation Starter Formulated Using Native Lactic Acid Bacteria Strains from a Re-Emerging Wine-Growing Region of Argentina—A Pilot Scale Vinification

by Gabriel Alejandro Rivas, Naiquen Elizabeth Flores, Natalia Soledad Brizuela, Andrea Cecilia Guillade, Liliana Carmen Semorile and Lucrecia Delfederico

Fermentation 2025, 11(3), 140; https://doi.org/10.3390/fermentation11030140 - 13 Mar 2025

Cited by 1 | Viewed by 855

Abstract

Argentina ranks worldwide among the top ten wine producers, known for its diverse terroirs and Malbec as its emblematic varietal. Typically, the winemaking process involves alcoholic fermentation, led by yeasts, and malolactic fermentation (MLF), primarily driven by lactic acid bacteria (LAB). Oenococcus oeni and Lactiplantibacillus plantarum are recognised as the best-adapted LAB species for this process. Our previous research focused on a winery located in the southwest of Buenos Aires Province, a scarcely studied re-emerging region of Argentina, which showed a low relative abundance of LAB and incomplete MLF in various vintages. The current study involved the isolation, identification, typing, and use of native strains from the above-mentioned region to formulate a malolactic fermentation starter (MLFS) and to evaluate the strains’ malolactic performance at pilot-scale, implantation capacity and impact on wine aromatic profiles using HS-SPME-GC-FID/MS. Two selected autochthonous strains (Lpb. plantarum UNQLp1001 and a O. oeni UNQOe1101) from the re-emerging region successfully implanted in Malbec wine, achieving faster and more efficient MLF compared to spontaneous MLF. Moreover, the MLFS seems to have influenced the aromatic profile, reducing relative concentrations of alcohols, contributing to the decrease in the bitter and herbaceous notes, and increasing some esters (ethyl acetate, 2-phenethyl acetate, ethyl octanoate), that could enhance floral and fruity, notes. Expanding the availability of candidate strains to formulate native MLFS is a crucial technological tool for the wine industry. Thus, we propose the use of Lpb. plantarum UNQLp1001 and O. oeni UNQOe1101 as potential MLFS in Malbec wines from somewhat similar wine-producing regions. Additionally, the local winery can access a cost-effective MLFS with native LAB strains, enabling a more controlled MLF that preserves regional typicity. Moreover, these strains could enable technology transfer, potentially becoming the first malolactic starters in the region. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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23 pages, 2690 KiB

Open AccessArticle

Apple and Grape Waste Pomace Fermentation and Co-Ferment Product Chemistry

by Zhuoyu Wang, Andrej Svyantek and Zachariah Miller

Fermentation 2025, 11(3), 126; https://doi.org/10.3390/fermentation11030126 - 5 Mar 2025

Viewed by 1178

Abstract

The pomace from apple and grape processing is usually treated as waste. Nowadays, pomace has attracted increasing interest due to its potential value as a nutrient source, as a raw ingredient for fermented products, and as a health beneficial product. Hence, from the perspective of a circular economy, this study incorporated different ratios of grape pomace from ‘Frontenac gris’ and apple pomace from ‘McIntosh’ to develop novel fermented beverages. This study provides knowledge of the fundamental characteristics, fermentation dynamics, and final fermented product chemistries. The results indicated different amounts of apple and grape pomace influenced sugar content, tartaric acids, and yeast nutrients in the fermentation must. The dynamic color changes indicated that grape pomace contributed to the wine’s red color, whereas apple pomace mainly contributed to the yellow coloration in the fermented products. Apple and grape pomace also contributed differently to the phenolic compounds, ethanol, and volatile acids. Different pomace contributed different phenolic components in the final wine. This fermentation study indicated the potential application of grape and apple pomace in the wine industry. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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20 pages, 2098 KiB

Open AccessArticle

The Impact of Grape Maceration on Quality and Biogenic Amine Formation in Slovak Tokaj Wines: Examination of Microbial, Chemical and Sensory Properties

by Boris Semjon, Martin Bartkovský, Peter Očenáš, Ivana Regecová, Zuzana Megyesy Eftimová, Jana Výrostková, Lýdia Mesarčová, Mariana Kováčová, Matúš Várady, Lucia Šuľáková and Slavomír Marcinčák

Fermentation 2025, 11(1), 27; https://doi.org/10.3390/fermentation11010027 - 10 Jan 2025

Cited by 2 | Viewed by 1101

Abstract

Grape maceration is essential in modulating the quality of Tokaj wines. The aim of this research was to analyse the effect of two maceration practices—one utilizing the application of a Saccharomyces cerevisiae culture and the other being maceration without a yeast culture in experimental Lipovina (Vitis vinifera L.) white wine from the Slovak part of the Tokaj region. Multiple factor analysis was used for the examination of wine quality regarding the formation of biogenic amines (BAs), and chemical, microbial and sensory variables were analysed over three months of wine production. The formation of bioactive components in wine was affected by maceration and maceration with the addition of a yeast culture, which resulted in a significantly increased antioxidant activity, as well as total phenolic and flavonoid content (p < 0.001). The wine samples that underwent maceration scored significantly lower in their appearance, aroma and taste (p < 0.05), which could be caused by a higher phenolic content and specific taste. The dynamics of BA formation in wine, evaluated using multiple factor analysis, highlighted that the maceration and maceration with an added yeast culture significantly affected these processes (p < 0.05). Microbiological examination promoted stable yeast counts during the maceration process, ensuring their longer presence during fermentation. Future research should aim to optimize maceration time in order to enhance the sensory quality of macerated wines without increasing the BA concentration, especially that of histamine. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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12 pages, 978 KiB

Open AccessArticle

Development of Starter Cultures for Precision Fermentation of Kombucha with Enriched Gamma-Aminobutyric Acid (GABA) Content

by Geun-Hyung Kim, Kwang-Rim Baek, Ga-Eun Lee, Ji-Hyun Lee, Ji-Hyun Moon and Seung-Oh Seo

Fermentation 2025, 11(1), 17; https://doi.org/10.3390/fermentation11010017 - 2 Jan 2025

Viewed by 1918

Abstract

Kombucha, a fermented tea beverage, is produced through the symbiotic interaction of several microbial strains, including acetic acid bacteria, lactic acid bacteria, and yeast, collectively known as symbiotic culture of bacteria and yeast (SCOBY). As its health benefits and distinctive flavor gain wider recognition, consumer demand and research on kombucha fermentation have increased. This study focused on developing starter cultures to produce functional kombucha through precision fermentation technology using selected microbial strains newly isolated from food sources. The isolated bacterial and yeast strains were evaluated and selected based on their fermentation characteristics. Notably, a lactic acid bacterial strain was chosen for its ability to overproduce the γ-amino butyric acid (GABA), a functional food component known to enhance cognitive function and reduce mental stress. To produce the GABA-fortified kombucha, selected single strains of Acetobacter pasteurianus, Lactiplantibacillus plantarum, and Saccharomyces cerevisiae were mixed and used as starter cultures. By optimizing the inoculation ratios and initial sugar concentration, a functional kombucha enriched with acetic acid, lactic acid, and GABA was successfully produced. The resulting kombucha demonstrated 2.2 mg/L of GABA production and 1.15 times higher antioxidant activity after the fermentation, highlighting its enhanced health-promoting properties. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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11 pages, 735 KiB

Open AccessEditor’s ChoiceArticle

Development and Large-Scale Production of High-Oleic Acid Oil by Fermentation of Microalgae

by Leon Parker, Kevin Ward, Thomas Pilarski, James Price, Paul Derkach, Mona Correa, Roberta Miller, Veronica Benites, Dino Athanasiadis, Bryce Doherty, Lucy Edy, Gawharah Alnozaili, Nina Reyes, Jon Wittenberg, Gener Eliares, Frédéric Destaillats, Walter Rakitsky and Scott Franklin

Fermentation 2024, 10(11), 566; https://doi.org/10.3390/fermentation10110566 - 6 Nov 2024

Cited by 2 | Viewed by 2281

Abstract

Our classical strain improvement began with an isolate showing 28% palmitic and 60% oleic acids. UV and chemical mutagenesis enhanced our strain’s productivity, carbon yield, and oleic acid content. The iterative methodology we used involved the creation of mutant libraries followed by clonal isolation, assessments of feedstock utilization and growth, oil titer, and the validation of oil composition. Screening these libraries facilitated the identification of isolates with the ability to produce elevated levels of oleic acid, aligning with the targets for high-oleic acid substitutes. Utilizing a classical strain improvement approach, we successfully isolated a high-oleic acid strain wherein the level of oleic acid was increased from 60 to >86% of total FA. The performance of the classically improved high oleic acid-producing strain was assessed at fermentation scales ranging from 1 L to 4000 L, demonstrating the utility of our strain and process at an industrial scale. These oils offer promise in various applications across both the food and industrial sectors, with the added potential of furthering sustainability and health-conscious initiatives. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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Review

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25 pages, 1232 KiB

Open AccessReview

Is It Possible to Produce Meat Without Animals? The Potential of Microorganisms as Protein Sources

by Alan Portal D’Almeida and Tiago Lima de Albuquerque

Fermentation 2025, 11(1), 24; https://doi.org/10.3390/fermentation11010024 - 9 Jan 2025

Cited by 4 | Viewed by 2967

Abstract

Climate change and environmental impacts from greenhouse gas emissions have spurred on efforts to reduce these emissions. Meat production, especially from cattle, is a significant contributor, releasing methane—a greenhouse gas far more potent than CO₂—and driving deforestation for pastureland. As a sustainable alternative, Single-Cell Protein (SCP), derived from microorganisms like bacteria, yeast, and algae, offers high nutritional value with a lower environmental impact. SCP production has advanced through process optimization, the use of eco-friendly substrates such as agro-industrial and food waste, and the cultivation of safe microorganisms classified as Generally Regarded as Safe (GRAS). Innovations in flavor and texture, including the use of myoglobin and natural polymers to mimic meat properties, have further improved SCP’s appeal. Despite these advances, challenges remain in optimizing production parameters, enhancing sensory acceptance, and ensuring regulatory compliance for market introduction. This review explores the potential of SCP to serve as a sustainable protein source, addressing both environmental concerns and nutritional demands. It highlights recent advancements in production techniques and sensory improvements while discussing their role in environmentally friendly and health-conscious food systems. SCP stands out as a promising solution for reducing greenhouse gas emissions, offering an efficient and sustainable alternative to conventional protein sources. Full article

(This article belongs to the Special Issue Precision Fermentation: Applications in the Food and Beverage Industry)

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