Fermentação Microbiana em Alimentos

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Academic Editor: Spiros Paramithiotis
Received: 30 October 2024
Revised: 31 December 2024
Accepted: 1 January 2025
Published: 2 January 2025
Citation: Sawant, S.S.; Park, H.-Y.;
Sim, E.-Y.; Kim, H.-S.; Choi, H.-S.
Microbial Fermentation in Food:
Impact on Functional Properties and
Nutritional Enhancement—A Review
of Recent Developments. Fermentation
2025, 11, 15. https://doi.org/10.3390/
fermentation11010015
Copyright: © 2025 by the authors.
Licensee MDPI, Basel, Switzerland.
This article is an open access article
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conditions of the Creative Commons
Attribution (CC BY) license
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licenses/by/4.0/).
Review
Microbial Fermentation in Food: Impact on Functional Properties
and Nutritional Enhancement—A Review of
Recent Developments
Shailesh S. Sawant, Hye-Young Park, Eun-Young Sim, Hong-Sik Kim and Hye-Sun Choi *
National Institute of Crop Science, Rural Development Administration, Suwon 16613, Republic of Korea;
shailesh@korea.kr (S.S.S.); phy0316@korea.kr (H.-Y.P.); silvery1225@korea.kr (E.-Y.S.);
kimhongs@korea.kr (H.-S.K.)
* Correspondence: choihs9587@korea.kr; Tel.: +82-31-695-0623
Abstract: The escalating global demand for nutritious and sustainable food sources has
heightened interest in microbial biotransformation in food, a process in which microor-
ganisms chemically modify food components to enhance their functional properties and
nutritional content. This review provides a comprehensive overview of recent advance-
ments in microbial fermentation, focusing on its impact on food quality, nutritional en-
hancement, and public health. Emphasizing both traditional fermentation practices and
modern biotechnological innovations, this review highlights how beneficial microorgan-
isms transform raw food substrates into products with superior nutrient bioavailability
and functional benefits. Key developments include the synthesis of bioactive compounds,
reduction of anti-nutritional factors, and improvement of sensory attributes, all of which col-
lectively contribute to disease prevention, gut health, and overall well-being. Additionally,
this review addresses safety concerns and challenges in microbial fermentation, including
microbiological hazards, chemical contaminants, and strategies for their management. It
also explores the difficulties in scaling up these processes for industrial applications and
discusses future directions for sustainable food production. By consolidating current knowl-
edge and identifying emerging trends, this review provides a comprehensive resource for
researchers, industry professionals, and policymakers, offering insights into leveraging
microbial biotransformation to create nutritionally enriched and functionally enhanced
food products.
Keywords: food; biotransformation; microbial; health; gut
1. Introduction
Existing food systems are currently in crisis, struggling to meet the increasing demand
for nutrition and protein amid growing populations [1]. Agriculture, animal farming, and
aquaculture, all components of our food system, are facing significant challenges owing to
land degradation, climate change, and the increasing frequency of climate-related disas-
ters [2,3]. Although shifting toward plant-based diets is more environmentally sustainable,
it still relies on seasonal conditions and requires the substantial use of land, water, and
chemicals [4]. In contrast, microorganisms are more ecological and resilient food sources
than traditional protein sources, such as meat [5,6]. Therefore, there is now an opportunity
for a microbial revolution in food production, as microorganisms have the potential to
enhance, improve, or even replace current alternatives [7,8].
Fermentation 2025, 11, 15 https://doi.org/10.3390/fermentation11010015
https://doi.org/10.3390/fermentation11010015
https://doi.org/10.3390/fermentation11010015
https://creativecommons.org/licenses/by/4.0/
https://creativecommons.org/licenses/by/4.0/
https://www.mdpi.com/journal/fermentation
https://www.mdpi.com
https://doi.org/10.3390/fermentation11010015
https://www.mdpi.com/article/10.3390/fermentation11010015?type=check_update&version=2
Fermentation 2025, 11, 15 2 of 29
Microbial biotransformation, a term encompassing both fermentation and broader
microbial metabolic processes, is a key driver in this revolution. This refers to the process
by which microorganisms chemically modify food components through their metabolic
activities, leading to the formation of new compounds or the enhancement of existing
compounds. Microbial biotransformation plays a pivotal role in the production and im-
provement of a wide range of food products, particularly fermented food products [9]. By
employing various beneficial species of bacteria, yeasts, and fungi, microbial biotransfor-
mation through fermentation can significantly alter the nutritional and sensory properties
of food, thereby enhancing its value and functionality [2]. The significance of microbial
biotransformation extends beyond food production; it is central to the complex interplay
between diet, microbiota, and human health and has garnered considerable interest in
recent years [10,11]. Through fermentation, a core aspect of this process, beneficial microor-
ganisms transform raw food substrates into products with enhanced nutrient bioavailability
and functional properties. This capability to convert basic food components such as milk,
cereals, vegetables, legumes, and meat into a diverse array of fermented products under-
scores the profound impact of microbial biotransformation on human nutrition and health.
Figure 1 provides a comprehensive overview of how diverse food substrates, including
milk, cereals, vegetables, legumes, fruits, meat, and fish, undergo beneficial microbe-
facilitated fermentation, resulting in their transformation into nutritious products that have
a positive impact on human health. This age-old practice has been indispensable not only
for food processing and preservation but also for enriching the nutritional value of foods,
resulting in a diverse range of fermented products that are still staples in many cultures
and offering significant health benefits.
Fermentation 2025, 11, x FOR PEER REVIEW 2 of 30 
 
 
Microbial biotransformation, a term encompassing both fermentation and broader 
microbial metabolic processes, is a key driver in this revolution. This refers to the process 
by which microorganisms chemically modify food components through their metabolic 
activities, leading to the formation of new compounds or the enhancement of existing 
compounds. Microbial biotransformation plays a pivotal role in the production and im-
provement of a wide range of food products, particularly fermented food products [9]. By 
employing various beneficial species of bacteria, yeasts, and fungi, microbial biotransfor-
mation through fermentation can significantly alter the nutritional and sensory properties 
of food, thereby enhancing its value and functionality [2]. The significance of microbial 
biotransformation extends beyond food production; it is central to the complex interplay 
between diet, microbiota, and human health and has garnered considerable interest in 
recent years [10,11]. Through fermentation, a core aspect of this process, beneficial micro-
organisms transform raw food substrates into products with enhanced nutrient bioavail-
ability and functional properties. This capability to convert basic food components such 
as milk, cereals, vegetables, legumes, and meat into a diverse array of fermented products 
underscores the profound impact of microbial biotransformation on human nutrition and 
health. Figure 1 provides a comprehensive overview of how diverse food substrates, in-
cluding milk, cereals, vegetables, legumes, fruits, meat, and fish, undergo beneficial mi-
crobe-facilitated fermentation, resulting in their transformation into nutritious products 
that have a positive impact on human health. This age-old practice hasincluding
dietary fiber and resistant starch [122]. SCFAs can regulate systemic inflammation by mod-
Fermentation 2025, 11, 15 18 of 29
ulating pro-inflammatory and anti-inflammatory interleukin secretion and enhancing the
expression of epithelial tight junctions [123]. Furthermore, SCFAs are believed to prevent
neuroinflammation by promoting neurogenesis and improving neuronal function and
homeostasis [124].
Vitamin deficiency is a concern in many population groups, including the elderly,
pregnant women, and immunocompromised individuals. Fermentation offers an effective
strategy to enhance the consumption of essential vitamins, such as riboflavin (vitamin B2),
folate (vitamin B9), cobalamin (vitamin B12), and vitamin K. Several LAB strains have
been shown to increase B-vitamin and vitamin K content in dairy products and plant-
based milk alternatives compared to their unfermented counterparts [125]. Co-culturing
R. oryzae with Propionibacterium freudenreichii and using different strains of P. freudenreichii
enabled the production of B12-enriched lupin tempeh [126–128]. In addition, high levels of
K-group vitamins have been reported in natto fermented with B. subtilis [98]. Recent studies
have also elucidated the molecular mechanisms underlying the enhanced production of
vitamin B2 by LAB, thereby providing insights into the development of vitamin B2-enriched
foods [129].
In addition to the bioactive metabolites produced during fermentation, the beneficial
effects of fermented foods can be attributed to the probiotic properties of the live microor-
ganisms found in these foods and their interactions with the host [99]. Probiotics contribute
to the repair and regeneration of damaged tissues in the digestive system, thereby enhanc-
ing digestion and nutrient absorption, stimulating the immune system, and preventing
colonization by harmful pathogens [130].
For probiotics to exert their health benefits, live microorganisms must be consumed
in adequate amounts. However, they encounter several challenges during their journey
through the digestive system. These include enzymes and antimicrobial substances in the
saliva, the low pH of the stomach, digestive enzymes, and bile salts in the small intestine,
all of which can reduce the survival rates of these microorganisms [131]. Despite these
challenges, there is evidence that microorganisms in fermented foods can survive digestion
and reach the gastrointestinal tract intact [132–134]. For instance, Veiga et al. [135] detected
Bifidobacterium animalis in the fecal samples of patients with irritable bowel syndrome after
consuming yogurt-like fermented milk containing this strain. Similarly, Bifidobacterium and
Lactobacillus species were recovered from ileal samples following the intake of fermented
foods [136]. The presence of these fermentation-associated microorganisms has also been
observed in the fecal samples of individuals who consumed kimchi, sauerkraut, and other
fermented products [136,137].
Echresh et al. [132] investigated the probiotic potential of L. rhamnosus CWKu-12, fo-
cusing on its ability to withstand gastrointestinal conditions, including resistance to acidic
environments and bile salts. This strain demonstrated high auto-aggregation (36.60%) and
hydrophobicity (52.60%), suggesting strong adherence to the gut lining. Its co-aggregation
(29.10%) with other bacteria further enhanced its ability to form beneficial microbial com-
munities within the gut.
Similarly, Zheng et al. [134] examined B. animalis subsp. lactis strains and identified
a specific strain, BB18, with notable probiotic potential. This strain showed resilience to
gastric juice conditions, which is an essential trait for targeting stomach infections. In both
in vitro and in vivo studies, BB18 exhibited significant efficacy against Helicobacter pylori.
The administration of BB18 to H. pylori-infected Mongolian gerbils reduced their pathogen
load, as demonstrated by the rapid urease test. Moreover, BB18 alleviated H. pylori-induced
gastric mucosal damage and lowered inflammatory cytokine levels, suggesting that it not
only combats infection but also helps reduce inflammation and protects the stomach lining.
Fermentation 2025, 11, 15 19 of 29
As research continues to explore specific strains and their effects, it has become in-
creasingly clear that the benefits of fermented foods extend beyond their nutritional value
and encompass significant probiotic contributions. The ability of these microorganisms to
survive digestion and interact with the host microbiota holds promise for the development
of functional foods aimed at improving gut health, boosting the immune system, and pro-
tecting against gastrointestinal infections. Further studies are essential to fully understand
the mechanisms through which these probiotic strains exert their health effects, as well as
their long-term impacts on human health. Continued research in this area may pave the
way for more targeted probiotic therapies and personalized nutrition, ultimately helping to
prevent and manage a range of chronic diseases.
6. Health Risks Associated with Fermented Foods and
Their Management
Fermented foods are widely recognized for their health-promoting properties such as
enhancing gut health, improving nutrient bioavailability, and supporting immune function.
However, as with any food production process, fermentation carries inherent risks if not
properly controlled. These risks primarily stem from microbiological and chemical hazards
that can affect the safety of the final product. A balanced approach that emphasizes both
the potential health benefits and risks of fermented foods is essential to protect consumers,
particularly vulnerable populations, and guide public health recommendations.
6.1. Microbiological Hazards
One of the primary concerns regarding fermented foods is the risk of contamination
with harmful microorganisms. Although fermentation relies on beneficial microbes such as
LAB to outcompete harmful organisms, there remains a risk of pathogenic bacteria such as
Listeria monocytogenes, Escherichia coli, Salmonella, and Clostridium botulinum, which survive
if optimal conditions are not maintained [138]. For instance, the Listeria contamination of
soft cheeses and C. botulinum in improperly fermented fish or vegetable products have
been reported to cause serious illnesses. Strict hygiene practices and fermentation control
are critical for mitigating these risks. Maintaining the correct temperature, acidity, and
anaerobic conditions can prevent undesirable microbial growth. Additionally, the use of
starter cultures with proven safety records and standardized production processes can help
reduce microbial contamination. Consumer education on the proper storage and handling
of fermented products, especially homemade varieties, is vital for reducing the risk of
foodborne illnesses.
6.2. Chemical Contaminants
The chemical hazards in fermented foods arise primarily from the formation of bio-
genic amines during fermentation. Biogenic amines such as histamine, tyramine, cadaver-
ine, and putrescine are produced by the microbial decarboxylation of amino acids present
in the food matrix. High levels of these compounds can lead to adverse health effects,
including headaches, hypertension, nausea, and allergic reactions, particularly in individu-
als with impaired abilities to metabolize these amines [138,139]. For instance, histamine
poisoning is commonly linked to the consumption of fermented fish products such as
dried or salted fish, where improper fermentation or storage can result in toxic histamine
levels [139]. Similarly, tyramine, which is often found in fermented cheeses and some
alcoholic beverages, can trigger hypertensive crises in individuals taking monoamine oxi-
dase inhibitors. The accumulation of these amines poses health risks, as well as creating
significant challenges for food safety regulations. Managing these risks involves the careful
monitoring and control of fermentationconditions to limit biogenic amine production.
Fermentation 2025, 11, 15 20 of 29
One key strategy is to use specific microbial strains that are known to produce lower
levels of these compounds. Additionally, controlling factors such as fermentation duration,
temperature, and pH is essential for reducing the formation of harmful amines. Proper
post-fermentation storage is equally important for preventing the further accumulation of
these contaminants, particularly in products that are sensitive to spoilage. To further protect
consumers, regulatory bodies have established guidelines that set maximum allowable
limits for biogenic amines in fermented foods. These limitations, combined with consistent
quality control and monitoring throughout production, are critical for ensuring the safety of
these products. Regulatory frameworks, especially for high-risk items, such as fermented
fish and cheese, need to evolve alongside innovative fermentation practices to address
emerging risks. Ultimately, by integrating microbial control, optimized fermentation pro-
cesses, and compliance with regulatory standards, manufacturers can reduce the risks
associated with biogenic amines and enhance the safety of fermented foods for consumers.
6.3. Vulnerable Populations
Certain populations are more vulnerable to the risks posed by fermented foods. Preg-
nant women, immunocompromised individuals, infants, and the elderly are at an increased
risk of severe illness from foodborne pathogens, such as L. monocytogenes and Salmonella.
For example, pregnant women are often advised to avoid certain fermented soft cheeses,
such as Brie or Camembert, because of the risk of listeriosis, which can lead to miscarriage,
stillbirth, or severe infection in newborns [138]. Similarly, individuals with compromised
immune systems may experience health complications, even from normally safe strains
of LAB or probiotics found in fermented foods, because their immune responses to po-
tential pathogens are diminished. For these populations, close attention must be paid to
both the type of fermented food consumed and the conditions under which it is prepared
and stored.
6.4. Regulatory and Safety Practices
Given the rising popularity of fermented foods, managing their risks is crucial to en-
sure their safety for consumers. Global regulatory bodies such as the European Food Safety
Authority and the U.S. Food and Drug Administration provide guidelines on fermentation
processes and permissible levels of contaminants in food. A key part of these guidelines in-
volves setting microbial standards and implementing Hazard Analysis and Critical Control
Points to monitor and control risks during the production of fermented foods. However,
existing regulatory frameworks for fermented foods, particularly those outside the realm
of fermented dairy products, are generally underdeveloped [140]. These frameworks are
often not mature enough to address the wide variety of fermented foods emerging in the
market, making it difficult to adequately regulate their production and safety. As new types
of fermented foods and novel production methods are introduced, regulatory agencies
face the challenge of keeping pace with innovation while ensuring consumer protection.
To address these gaps, initiatives such as Promoting Innovation in Fermented Foods, as
outlined by Todorovic et al. [138], advocate a more systematic approach for evaluating the
health risks of fermented foods. This approach integrates human studies, detailed food
characterization, and mechanistic data to develop a comprehensive risk–benefit framework.
Such a framework aims to provide better guidance for both manufacturers and consumers,
while encouraging ongoing research to improve safety standards and assess the health
impacts of novel fermented foods. In addition, there is a growing need for the clear and
transparent labeling of fermented food products, especially regarding potential allergens,
amine content, and storage instructions. This will help consumers make informed choices
and further reduce their health risks.
Fermentation 2025, 11, 15 21 of 29
Public awareness and education are vital for mitigating the risks associated with
fermented foods. Consumers, especially those preparing fermented foods at home, should
be informed about proper handling, fermentation times, and storage conditions to minimize
the risk of contamination or foodborne illness. By strengthening both regulatory oversight
and consumer education, the industry can effectively manage the safety challenges posed
by the growing diversity of fermented foods.
7. Challenges and Future Perspectives
7.1. Challenges
Although microbial biotransformation holds great promise for enhancing the func-
tional and nutritional properties of foods, several challenges must be addressed to fully
realize its potential. One significant hurdle is the variability in microbial activity, which
is influenced by factors such as the substrate type, fermentation conditions, and strain
specificity. This variability can lead to inconsistencies in product quality, making it dif-
ficult to scale biotransformation processes from the laboratory to industrial production.
Optimizing fermentation conditions for large-scale operations and maintaining microbial
stability under varying environmental conditions remains challenging. The scaling up of
fermentation technologies involves intricate interactions within biological systems, often
resulting in unexpected difficulties in ensuring product consistency and quality.
From an economic standpoint, the scale-up process requires significant financial
investment, whereas the technical aspect demands meticulous control over multiple factors.
Additionally, regulatory hurdles add to the complexity of introducing biotransformed
products to the market, along with the lengthy approval processes necessary to ensure safety
and compliance [141]. As microbial fermentation is scaled up, maintaining a consistent
product quality becomes increasingly difficult, leading to potential variations in flavor,
texture, and nutritional content, which can affect consumer satisfaction. Ensuring uniform
conditions, such as nutrient availability, temperature, pH, and oxygen levels, becomes
more complex at larger production scales. Proper heat and oxygen transfer, which are
critical for supporting microbial growth and metabolism, require a deep understanding of
thermodynamics and precise process control. Additionally, rapid and controlled freezing
techniques are essential during scale-up to preserve the product’s quality and integrity
from production to final packaging. These coordinated efforts are key to addressing the
inherent challenges of scaling fermentation processes, while ensuring high-quality results.
Scaling microbial fermentation also requires a substantial initial investment in pro-
duction facilities, along with the ongoing costs of raw materials and maintenance. These
economic challenges make it difficult for companies to increase their output, while man-
aging expenses and adhering to sustainable practices. Balancing these considerations is
critical during scale-up activities, underscoring the need to integrate economic and environ-
mental factors into the expansion of fermentation processes. This comprehensive approach
ensures that scalability does not compromise efficiency or sustainability, thus facilitating a
smoother transition from the laboratory to commercial-scale production [142].
7.2. Future Perspectives
Future research on food fermentation should focus on promoting the production
of sustainable food. A key area of exploration is the selection of crop substrates that
yield fermented products rich in health-promoting bioactive compounds. When fermented,
certain crops produce bioactive peptides, antioxidants, and other beneficial compounds that
positively influence health outcomes. By prioritizing substrates with a high potential for
bioactive generation, researchers can maximize the health benefits of biotransformedfoods.
Fermentation 2025, 11, 15 22 of 29
The development of novel fermented foods is an exciting field. New fermented
foods with improved functional properties and health benefits can be created by making
informed choices regarding raw materials and starter cultures. Innovations may stem
from the use of nontraditional substrates, novel microbial strains, or a combination of both.
For instance, selecting new species as starter cultures or combining unique raw materials
with specific microbial consortia can unlock new health-promoting properties in foods.
However, ensuring the safety and consumer acceptance of these novel fermented foods is
crucial for their market success.
There should be a significant emphasis on developing innovative fermentation tech-
niques that leverage synthetic biology to produce high-quality, nutritious, and environ-
mentally friendly foods, including plant-based alternatives. Advances in synthetic biology
and metagenomics offer promising tools for future innovations in microbial biotransfor-
mation. These technologies enable the design of engineered strains or microbial consortia
tailored to specific functional needs, thereby enhancing both the efficiency and scalability
of biotransformation processes. Interdisciplinary collaboration among food scientists, mi-
crobiologists, and regulatory bodies is essential to navigate the complexities of integrating
these technologies into food production.
Gene editing and advancements in microbial capabilities are critical for improving
fermentation processes. Modern biotechnological approaches, such as genome editing
using CRISPR/Cas9, have been explored for their potential to enhance fermentation [12].
The advent of next-generation sequencing techniques and meta-omics tools have expanded
our understanding of the microbiomes involved in food fermentation and their functional
roles. These technologies can refine the metabolic pathways of microorganisms, thereby
increasing their efficiency and capacity to produce specific compounds. Gene editing not
only boosts production rates but also aids in developing strains with customized charac-
teristics. Additionally, efforts are underway to create microbial strains that demonstrate
improved resistance to environmental stressors such as temperature variations and pH
fluctuations. This enhanced resilience can significantly increase fermentation yields and
stabilize the end products, ensuring consistent and reliable production outcomes across
various industrial applications [12].
Another area requiring attention is the efficient use of raw materials. Utilizing crop
waste and byproducts in microbial biotransformation presents an exciting opportunity
to produce nutrient-fortified products while promoting sustainability. Crop residues,
which are often discarded, can serve as substrates for microbial fermentation, helping to
reduce agricultural waste while generating value-added products. Exploring low-cost
and alternative crops, particularly those that thrive in resource-limited environments,
could make biotransformation more economically viable and accessible in regions facing
agricultural constraints.
Research on the use of agricultural byproducts such as crop residues and food waste
as substrates in fermentation processes is gaining traction as a strategy to reduce costs and
enhance sustainability [143]. By leveraging these byproducts, which are often viewed as
waste, the fermentation industry can reduce its dependence on traditional raw materials,
which tend to be more expensive and less environmentally friendly. This approach not
only improves the management of agricultural waste but also supports the development
of more sustainable and cost-effective production cycles. Such innovative applications of
waste materials align with global initiatives aimed at reducing environmental impacts and
promoting circular economic principles within industrial processes.
Finally, based on the potential of agricultural byproducts and alternative crops for
microbial biotransformation, future research should emphasize precision fermentation,
particularly in advancing bioengineering techniques to optimize production processes.
Fermentation 2025, 11, 15 23 of 29
The key areas of focus include enhancing the synthesis of bioengineered microbes and
enzymes using tools such as synthetic biology, gene editing, and bioinformatics. Precision
fermentation allows for the controlled production of high-value proteins, with the aim
of maximizing yields while reducing costs. However, the challenges, such as scaling up
production, navigating regulatory approvals, and achieving market acceptance, remain
unresolved. Innovative approaches such as solid-state precision fermentation and cell-free
systems are being explored to address these hurdles, with an emphasis on sustainability
and safety. The ultimate goal is to further refine fermentation processes by incorporating
cost-effective substrates, aligning with global efforts toward sustainable and eco-friendly
production practices.
Author Contributions: Conceptualization, funding acquisition, and review and editing: H.-S.C. and
S.S.S.; investigation: H.-Y.P., E.-Y.S. and H.-S.K.; writing of original draft: S.S.S. and H.-S.C.; review,
editing, and supervision: S.S.S. and H.-S.C. All authors have read and agreed to the published version
of the manuscript.
Funding: This research was funded by the Rural Development Administration (RDA) of the Republic
of Korea (PJ017413042024).
Acknowledgments: This study was supported by 2024 the RDA Fellowship Program of the National
Institute of Crop Science (PJ017413042024), Rural Development Administration (RDA), Republic
of Korea.
Conflicts of Interest: The authors declare no conflicts of interest.
References
1. Rockström, J.; Edenhofer, O.; Gaertner, J.; DeClerck, F. Planet-Proofing the Global Food System. Nat. Food 2020, 1, 3–5. [CrossRef]
2. Graham, A.E.; Ledesma-Amaro, R. The Microbial Food Revolution. Nat. Commun. 2023, 14, 2231. [CrossRef]
3. Choi, K.R.; Jung, S.Y.; Lee, S.Y. From Sustainable Feedstocks to Microbial Foods. Nat. Microbiol. 2024, 9, 1167–1175. [CrossRef]
4. Sun, Z.; Scherer, L.; Tukker, A.; Spawn-Lee, S.A.; Bruckner, M.; Gibbs, H.K.; Behrens, P. Dietary Change in High-Income Nations
Alone Can Lead to Substantial Double Climate Dividend. Nat. Food 2022, 3, 29–37. [CrossRef] [PubMed]
5. Järviö, N.; Maljanen, N.-L.; Kobayashi, Y.; Ryynänen, T.; Tuomisto, H.L. An Attributional Life Cycle Assessment of Microbial
Protein Production: A Case Study on Using Hydrogen-Oxidizing Bacteria. Sci. Total Environ. 2021, 776, 145764. [CrossRef]
6. Humpenöder, F.; Bodirsky, B.L.; Weindl, I.; Lotze-Campen, H.; Linder, T.; Popp, A. Projected Environmental Benefits of Replacing
Beef with Microbial Protein. Nature 2022, 605, 90–96. [CrossRef] [PubMed]
7. Lv, X.; Wu, Y.; Gong, M.; Deng, J.; Gu, Y.; Liu, Y.; Li, J.; Du, G.; Ledesma-Amaro, R.; Liu, L.; et al. Synthetic Biology for Future
Food: Research Progress and Future Directions. Future Foods 2021, 3, 100025. [CrossRef]
8. Choi, K.R.; Yu, H.E.; Lee, S.Y. Microbial Food: Microorganisms Repurposed for Our Food. Microb. Biotechnol. 2022, 15, 18–25.
[CrossRef]
9. Gomathy, M.; Sabarinathan, K.G.; Rajakumar, D.; Manoj, M.; Bhimani, H.D.; John, P.; Wijayaratne, T.; Ekanayake, S.; Maheswari,
U.; Rajan, A.S.; et al. Fermented Foods of South Asia. In Microbial Fermentations in Nature and as Designed Processes; Hurst, C.J., Ed.;
Wiley: Hoboken, NJ, USA, 2023; pp. 323–351. ISBN 9781119849971.
10. Li, Y.; Cao, H.; Wang, X.; Guo, L.; Ding, X.; Zhao, W.; Zhang, F. Diet-Mediated Metaorganismal Relay Biotransformation: Health
Effects and Pathways. Crit. Rev. Food Sci. Nutr. 2023, 63, 4599–4617. [CrossRef] [PubMed]
11. Nurmilah, S.; Frediansyah, A.; Cahyana, Y.; Utama, G.L. Biotransformation and Health Potential of Isoflavones by Microorganisms
in Indonesian Traditional Fermented Soy Products: A Review. J. Agric. Food Res. 2024, 18, 101365. [CrossRef]
12. Mannaa, M.; Han, G.; Seo, Y.-S.;Park, I. Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering
the Roles of the Microbiota. Foods 2021, 10, 2861. [CrossRef] [PubMed]
13. Pan, M.; Barrangou, R. Combining Omics Technologies with CRISPR-Based Genome Editing to Study Food Microbes. Curr. Opin.
Biotechnol. 2020, 61, 198–208. [CrossRef] [PubMed]
14. Akamine, I.T.; Mansoldo, F.R.P.; Vermelho, A.B. Probiotics in the Sourdough Bread Fermentation: Current Status. Fermentation
2023, 9, 90. [CrossRef]
15. Rusu, A.V.; Trif, M.; Rocha, J.M. Microbial Secondary Metabolites via Fermentation Approaches for Dietary Supplementation
Formulations. Molecules 2023, 28, 6020. [CrossRef] [PubMed]
https://doi.org/10.1038/s43016-019-0010-4
https://doi.org/10.1038/s41467-023-37891-1
https://doi.org/10.1038/s41564-024-01671-4
https://doi.org/10.1038/s43016-021-00431-5
https://www.ncbi.nlm.nih.gov/pubmed/37118487
https://doi.org/10.1016/j.scitotenv.2021.145764
https://doi.org/10.1038/s41586-022-04629-w
https://www.ncbi.nlm.nih.gov/pubmed/35508780
https://doi.org/10.1016/j.fufo.2021.100025
https://doi.org/10.1111/1751-7915.13911
https://doi.org/10.1080/10408398.2021.2004993
https://www.ncbi.nlm.nih.gov/pubmed/34802351
https://doi.org/10.1016/j.jafr.2024.101365
https://doi.org/10.3390/foods10112861
https://www.ncbi.nlm.nih.gov/pubmed/34829140
https://doi.org/10.1016/j.copbio.2019.12.027
https://www.ncbi.nlm.nih.gov/pubmed/32035346
https://doi.org/10.3390/fermentation9020090
https://doi.org/10.3390/molecules28166020
https://www.ncbi.nlm.nih.gov/pubmed/37630272
Fermentation 2025, 11, 15 24 of 29
16. Jahn, L.J.; Rekdal, V.M.; Sommer, M.O.A. Microbial Foods for Improving Human and Planetary Health. Cell 2023, 186, 469–478.
[CrossRef]
17. Gupta, R.; Gupta, N. (Eds.) Glycolysis and Gluconeogenesis. In Fundamentals of Bacterial Physiology and Metabolism; Springer:
Singapore, 2021; pp. 267–287. ISBN 9789811607233.
18. Cha, J.; Kim, Y.B.; Park, S.-E.; Lee, S.H.; Roh, S.W.; Son, H.-S.; Whon, T.W. Does Kimchi Deserve the Status of a Probiotic Food?
Crit. Rev. Food Sci. Nutr. 2024, 64, 6512–6525. [CrossRef] [PubMed]
19. Gunawardena, S.; Nadeeshani, H.; Amarasinghe, V.; Liyanage, R. Bioactive Properties and Therapeutic Aspects of Fermented
Vegetables: A Review. Food Prod. Process Nutr. 2024, 6, 31. [CrossRef]
20. Marsh, A.J.; Hill, C.; Ross, R.P.; Cotter, P.D. Fermented Beverages with Health-Promoting Potential: Past and Future Perspectives.
Trends Food Sci. Technol. 2014, 38, 113–124. [CrossRef]
21. Vinicius De Melo Pereira, G.; De Carvalho Neto, D.P.; Junqueira, A.C.D.O.; Karp, S.G.; Letti, L.A.J.; Magalhães Júnior, A.I.; Soccol,
C.R. A Review of Selection Criteria for Starter Culture Development in the Food Fermentation Industry. Food Rev. Int. 2020, 36,
135–167. [CrossRef]
22. Sionek, B.; Szydłowska, A.; Küçükgöz, K.; Kołożyn-Krajewska, D. Traditional and New Microorganisms in Lactic Acid Fermenta-
tion of Food. Fermentation 2023, 9, 1019. [CrossRef]
23. Yassunaka Hata, N.N.; Surek, M.; Sartori, D.; Serrato, R.V.; Spinosa, W.A. Role of Acetic Acid Bacteria in Food and Beverages.
Food Technol. Biotechnol. 2023, 61, 85–103. [CrossRef] [PubMed]
24. Han, J.; Kong, T.; Wang, Q.; Jiang, J.; Zhou, Q.; Li, P.; Zhu, B.; Gu, Q. Regulation of Microbial Metabolism on the Formation of
Characteristic Flavor and Quality Formation in the Traditional Fish Sauce during Fermentation: A Review. Crit. Rev. Food Sci.
Nutr. 2023, 63, 7564–7583. [CrossRef]
25. Kumar, V.; Naik, B.; Kumar, A.; Khanduri, N.; Rustagi, S.; Kumar, S. Probiotics Media: Significance, Challenges, and Future
Perspective—A Mini Review. Food Prod. Process Nutr. 2022, 4, 17. [CrossRef]
26. Lin, X.; Tang, Y.; Hu, Y.; Lu, Y.; Sun, Q.; Lv, Y.; Zhang, Q.; Wu, C.; Zhu, M.; He, Q.; et al. Sodium Reduction in Traditional
Fermented Foods: Challenges, Strategies, and Perspectives. J. Agric. Food Chem. 2021, 69, 8065–8080. [CrossRef] [PubMed]
27. Wang, T.; Li, R.; Liu, K.; Chen, Q.; Bo, N.; Wang, Q.; Xiao, Y.; Sha, G.; Chen, S.; Lei, X.; et al. Changes in Sensory Characteristics,
Chemical Composition and Microbial Succession during Fermentation of Ancient Plants Pu-Erh Tea. Food Chem. X 2023, 20,
101003. [CrossRef] [PubMed]
28. Ai, C.; Tong, A.; Wen, J.; Chen, R.; Huang, Y.; Zhao, C. Variations in the Substrate Composition and Microbial Community
Structure in the Anaerobic Fermentation Process Using the Green Algae Enteromorpha prolifera. Food Prod. Process Nutr. 2022, 4, 32.
[CrossRef]
29. Fu, H.; Pan, L.; Wang, J.; Zhao, J.; Guo, X.; Chen, J.; Lu, S.; Dong, J.; Wang, Q. Sensory Properties and Main Differential Metabolites
Influencing the Taste Quality of Dry-Cured Beef during Processing. Foods 2022, 11, 531. [CrossRef]
30. You, C.; Zhang, Y.-H.P. Cell-Free Biosystems for Biomanufacturing. In Future Trends in Biotechnology; Zhong, J.-J., Ed.; Springer:
Berlin/Heidelberg, Germany, 2013; pp. 89–119. ISBN 9783642365089.
31. Horecker, B.L. The Pentose Phosphate Pathway. J. Biol. Chem. 2002, 277, 47965–47971. [CrossRef] [PubMed]
32. Bartowsky, E.J.; Pretorius, I.S. Microbial Formation and Modification of Flavor and Off-Flavor Compounds in Wine. In Biology of
Microorganisms on Grapes, in Must and in Wine; König, H., Unden, G., Fröhlich, J., Eds.; Springer: Berlin/Heidelberg, Germany,
2009; pp. 209–231. ISBN 9783540854630.
33. Singhania, R.R.; Adsul, M.; Pandey, A.; Patel, A.K. 4—Cellulases. In Current Developments in Biotechnology and Bioengineering;
Pandey, A., Negi, S., Soccol, C.R., Eds.; Elsevier: Amsterdam, The Netherlands, 2017; pp. 73–101. ISBN 9780444636621.
34. Kashyap, D.R.; Vohra, P.K.; Chopra, S.; Tewari, R. Applications of Pectinases in the Commercial Sector: A Review. Bioresour.
Technol. 2001, 77, 215–227. [CrossRef] [PubMed]
35. Contesini, F.J.; Melo, R.R.D.; Sato, H.H. An Overview of Bacillus Proteases: From Production to Application. Crit. Rev. Biotechnol.
2018, 38, 321–334. [CrossRef]
36. Xu, D.; Pan, L.; Zhao, H.; Zhao, M.; Sun, J.; Liu, D. Breeding and Identification of Novel Koji Molds with High Activity of
Acid Protease by Genome Recombination between Aspergillus oryzae and Aspergillus niger. J. Ind. Microbiol. Biotechnol. 2011, 38,
1255–1265. [CrossRef]
37. Gupta, R.; Gupta, N.; Rathi, P. Bacterial Lipases: An Overview of Production, Purification and Biochemical Properties. Appl.
Microbiol. Biotechnol. 2004, 64, 763–781. [CrossRef]
38. Bhan, C.; Singh, J. Role of Microbial Lipases in Transesterification Process for Biodiesel Production. Environ. Sustain. 2020, 3,
257–266. [CrossRef]
39. Gupta, R.; Kumari, A.; Syal, P.; Singh, Y. Molecular and Functional Diversity of Yeast and Fungal Lipases: Their Role in
Biotechnology and Cellular Physiology. Prog. Lipid Res. 2015, 57, 40–54. [CrossRef] [PubMed]
40. Samtiya, M.; Aluko, R.E.; Puniya, A.K.; Dhewa, T. Enhancing Micronutrients Bioavailability through Fermentation of Plant-Based
Foods: A Concise Review. Fermentation 2021, 7, 63. [CrossRef]
https://doi.org/10.1016/j.cell.2022.12.002
https://doi.org/10.1080/10408398.2023.2170319
https://www.ncbi.nlm.nih.gov/pubmed/36718547
https://doi.org/10.1186/s43014-023-00176-7
https://doi.org/10.1016/j.tifs.2014.05.002
https://doi.org/10.1080/87559129.2019.1630636
https://doi.org/10.3390/fermentation9121019
https://doi.org/10.17113/ftb.61.01.23.7811
https://www.ncbi.nlm.nih.gov/pubmed/37200796
https://doi.org/10.1080/10408398.2022.2047884
https://doi.org/10.1186/s43014-022-00098-w
https://doi.org/10.1021/acs.jafc.1c01687
https://www.ncbi.nlm.nih.gov/pubmed/34269568
https://doi.org/10.1016/j.fochx.2023.101003
https://www.ncbi.nlm.nih.gov/pubmed/38144832
https://doi.org/10.1186/s43014-022-00110-3
https://doi.org/10.3390/foods11040531
https://doi.org/10.1074/jbc.X200007200
https://www.ncbi.nlm.nih.gov/pubmed/12403765
https://doi.org/10.1016/S0960-8524(00)00118-8
https://www.ncbi.nlm.nih.gov/pubmed/11272008
https://doi.org/10.1080/07388551.2017.1354354
https://doi.org/10.1007/s10295-010-0904-5
https://doi.org/10.1007/s00253-004-1568-8
https://doi.org/10.1007/s42398-020-00119-9https://doi.org/10.1016/j.plipres.2014.12.001
https://www.ncbi.nlm.nih.gov/pubmed/25573113
https://doi.org/10.3390/fermentation7020063
Fermentation 2025, 11, 15 25 of 29
41. Kumari, M.; Platel, K. Impact of Soaking, Germination, Fermentation, and Thermal Processing on the Bioaccessibility of Trace
Minerals from Food Grains. J. Food Process. Preserv. 2020, 44, e14752. [CrossRef]
42. Ferruzzi, M.G.; Kruger, J.; Mohamedshah, Z.; Debelo, H.; Taylor, J.R.N. Insights from in Vitro Exploration of Factors Influencing
Iron, Zinc and Provitamin A Carotenoid Bioaccessibility and Intestinal Absorption from Cereals. J. Cereal Sci. 2020, 96, 103126.
[CrossRef]
43. Gupta, R.K.; Gangoliya, S.S.; Singh, N.K. Reduction of Phytic Acid and Enhancement of Bioavailable Micronutrients in Food
Grains. J. Food Sci. Technol. 2015, 52, 676–684. [CrossRef]
44. Nkhata, S.G.; Ayua, E.; Kamau, E.H.; Shingiro, J. Fermentation and Germination Improve Nutritional Value of Cereals and
Legumes through Activation of Endogenous Enzymes. Food Sci. Nutr. 2018, 6, 2446–2458. [CrossRef] [PubMed]
45. Ahmed, M.I.; Xu, X.; Sulieman, A.A.; Na, Y.; Mahdi, A.A. The Effect of Fermentation Time on in Vitro Bioavailability of Iron,
Zinc, and Calcium of Kisra Bread Produced from Koreeb (Dactyloctenium aegyptium) Seeds Flour. Microchem. J. 2020, 154, 104644.
[CrossRef]
46. Day, C.N.; Morawicki, R.O. Effects of Fermentation by Yeast and Amylolytic Lactic Acid Bacteria on Grain Sorghum Protein
Content and Digestibility. J. Food Qual. 2018, 2018, 3964392. [CrossRef]
47. Hajimohammadi, A.; Mottaghitalab, M.; Hashemi, M. Effects of Microbial Fermented Sesame Meal and Enzyme Supplementation
on the Intestinal Morphology, Microbiota, pH, Tibia Bone and Blood Parameters of Broiler Chicks. Ital. J. Anim. Sci. 2020, 19,
457–467. [CrossRef]
48. Liang, J.; Han, B.-Z.; Nout, M.J.R.; Hamer, R.J. Effects of Soaking, Germination and Fermentation on Phytic Acid, Total and in
Vitro Soluble Zinc in Brown Rice. Food Chem. 2008, 110, 821–828. [CrossRef] [PubMed]
49. Sarvani, B.H.; Suvarna, V.C.; Kumar, K.H.; Ranadev, P.; Girisha, H.C. Effect of Processing and Fermentation on Functional
Properties and on Anti-Nutritional Factors in Horse Gram (Macrotyloma uniflorum). CJAST 2020, 39, 38–45. [CrossRef]
50. Castro-Alba, V.; Lazarte, C.E.; Perez-Rea, D.; Sandberg, A.; Carlsson, N.; Almgren, A.; Bergenståhl, B.; Granfeldt, Y. Effect of
Fermentation and Dry Roasting on the Nutritional Quality and Sensory Attributes of Quinoa. Food Sci. Nutr. 2019, 7, 3902–3911.
[CrossRef] [PubMed]
51. Rekha, C.R.; Vijayalakshmi, G. Bioconversion of Isoflavone Glycosides to Aglycones, Mineral Bioavailability and Vitamin B
Complex in Fermented Soymilk by Probiotic Bacteria and Yeast: Biotransformation of Isoflavones. J. Appl. Microbiol. 2010, 109,
1198–1208. [CrossRef]
52. Bahaciu, G.V.; Nicolae, C.G.; S, uler, A.D.; Segal, R. Germinated and Lactic Fermented Soybean Seeds, a Natural Alternative for
Healthy Bones. A Scientific Approach. Bull. UASVM Food Sci. Technol. 2018, 75, 8. [CrossRef] [PubMed]
53. Makokha, A.O.; Oniang’o, R.K.; Njoroge, S.M.; Kamar, O.K. Effect of Traditional Fermentation and Malting on Phytic Acid and
Mineral Availability from Sorghum (Sorghum bicolor) and Finger Millet (Eleusine coracana) Grain Varieties Grown in Kenya. Food
Nutr. Bull. 2002, 23, 241–245. [CrossRef] [PubMed]
54. Valencia, S.; Svanberg, U.; Sandberg, A.-S.; Ruales, J. Processing of Quinoa (Chenopodium Quinoa, Willd): Effects on in Vitro Iron
Availability and Phytate Hydrolysis. Int. J. Food Sci. Nutr. 1999, 50, 203–211. [CrossRef]
55. Chiş, M.S.; Păucean, A.; Man, S.M.; Bonta, V.; Pop, A.; Stan, L.; Beldean, B.V.; Pop, C.R.; Mureşan, V.; Muste, S. Effect of Rice
Flour Fermentation with Lactobacillus spicheri DSM 15429 on the Nutritional Features of Gluten-Free Muffins. Foods 2020, 9, 822.
[CrossRef]
56. Cizeikiene, D.; Juodeikiene, G.; Bartkiene, E.; Damasius, J.; Paskevicius, A. Phytase Activity of Lactic Acid Bacteria and Their
Impact on the Solubility of Minerals from Wholemeal Wheat Bread. Int. J. Food Sci. Nutr. 2015, 66, 736–742. [CrossRef] [PubMed]
57. Xu, Y.; Hlaing, M.M.; Glagovskaia, O.; Augustin, M.A.; Terefe, N.S. Fermentation by Probiotic Lactobacillus gasseri Strains Enhances
the Carotenoid and Fibre Contents of Carrot Juice. Foods 2020, 9, 1803. [CrossRef] [PubMed]
58. Pérez–Velasco, R.; Gómez-Gil, B.; Martínez-Montaño, E.; González-Córdova, A.F.; Hernández, C. Nutritional Attributes and
Microbial Metagenomic Profile during Solid-state Fermentation of Soybean Meal Inoculated with Lactobacillus acidophilus under
Non-sterile Conditions. J. Sci. Food Agric. 2024, 104, 8219–8229. [CrossRef] [PubMed]
59. Curiel, J.A.; Coda, R.; Centomani, I.; Summo, C.; Gobbetti, M.; Rizzello, C.G. Exploitation of the Nutritional and Functional
Characteristics of Traditional Italian Legumes: The Potential of Sourdough Fermentation. Int. J. Food Microbiol. 2015, 196, 51–61.
[CrossRef] [PubMed]
60. Chen, X.; Lu, Y.; Zhao, A.; Wu, Y.; Zhang, Y.; Yang, X. Quantitative Analyses for Several Nutrients and Volatile Components
during Fermentation of Soybean by Bacillus subtilis natto. Food Chem. 2022, 374, 131725. [CrossRef]
61. Asensio-Grau, A.; Calvo-Lerma, J.; Heredia, A.; Andrés, A. Enhancing the Nutritional Profile and Digestibility of Lentil Flour by
Solid State Fermentation with Pleurotus ostreatus. Food Funct. 2020, 11, 7905–7912. [CrossRef]
62. Cao, Y.; Lu, J.; Cai, G. Quality Improvement of Soybean Meal by Yeast Fermentation Based on the Degradation of Anti-nutritional
Factors and Accumulation of Beneficial Metabolites. J. Sci. Food Agric. 2024, 104, 1441–1449. [CrossRef] [PubMed]
63. Fang, L.; Wang, W.; Dou, Z.; Chen, J.; Meng, Y.; Cai, L.; Li, Y. Effects of Mixed Fermentation of Different Lactic Acid Bacteria and
Yeast on Phytic Acid Degradation and Flavor Compounds in Sourdough. LWT 2023, 174, 114438. [CrossRef]
https://doi.org/10.1111/jfpp.14752
https://doi.org/10.1016/j.jcs.2020.103126
https://doi.org/10.1007/s13197-013-0978-y
https://doi.org/10.1002/fsn3.846
https://www.ncbi.nlm.nih.gov/pubmed/30510746
https://doi.org/10.1016/j.microc.2020.104644
https://doi.org/10.1155/2018/3964392
https://doi.org/10.1080/1828051X.2020.1755378
https://doi.org/10.1016/j.foodchem.2008.02.064
https://www.ncbi.nlm.nih.gov/pubmed/26047266
https://doi.org/10.9734/cjast/2020/v39i3731086
https://doi.org/10.1002/fsn3.1247
https://www.ncbi.nlm.nih.gov/pubmed/31890168
https://doi.org/10.1111/j.1365-2672.2010.04745.x
https://doi.org/10.15835/buasvmcn-fst:0010
https://www.ncbi.nlm.nih.gov/pubmed/39105138
https://doi.org/10.1177/15648265020233S147
https://www.ncbi.nlm.nih.gov/pubmed/12362804
https://doi.org/10.1080/096374899101247
https://doi.org/10.3390/foods9060822
https://doi.org/10.3109/09637486.2015.1088939
https://www.ncbi.nlm.nih.gov/pubmed/26397032
https://doi.org/10.3390/foods9121803
https://www.ncbi.nlm.nih.gov/pubmed/33291830
https://doi.org/10.1002/jsfa.13657
https://www.ncbi.nlm.nih.gov/pubmed/38873977
https://doi.org/10.1016/j.ijfoodmicro.2014.11.032
https://www.ncbi.nlm.nih.gov/pubmed/25522057
https://doi.org/10.1016/j.foodchem.2021.131725
https://doi.org/10.1039/D0FO01527J
https://doi.org/10.1002/jsfa.13041
https://www.ncbi.nlm.nih.gov/pubmed/37822013
https://doi.org/10.1016/j.lwt.2023.114438
Fermentation 2025, 11, 15 26 of 29
64. Xu, R.; Han, J.; Tian, T.; Zhu, N.; Chen, Y.; Wangkahart, E.; Zhang, Z.; Liu, J.; Yu, D.; Wei, J.; et al. Comparative Study of Solid-state
Fermentation with Lactobacillus plantarum versus Saccharomycopsis fibuligera on Anti-nutritional Factors, Nutritional Values and
Antioxidant Activity of Faba Bean (Vicia Faba L.) Meal. Int. J. Food Sci. Technol. 2024, 59, 288–298. [CrossRef]
65. Idate, A.; Shah, R.; Gaikwad, V.; Kumathekar, S.; Temgire, S. A Comprehensive Review on Antinutritional Factors of Chickpea
(Cicer arietinum L.). Pharma Innov. 2021, 10, 816–823. [CrossRef]
66. Yegrem, L. Nutritional Composition, Antinutritional Factors, and Utilization Trends of EthiopianChickpea (Cicer arietinum L.).
Int. J. Food Sci. 2021, 2021, 5570753. [CrossRef]
67. Samtiya, M.; Aluko, R.E.; Dhewa, T. Plant Food Anti-Nutritional Factors and Their Reduction Strategies: An Overview. Food Prod.
Process Nutr. 2020, 2, 6. [CrossRef]
68. Yarlina, V.P.; Djali, M.; Andoyo, R.; Lani, M.N.; Rifqi, M. Effect of Soaking and Proteolytic Microorganisms Growth on the Protein
and Amino Acid Content of Jack Bean Tempeh (Canavalia ensiformis). Processes 2023, 11, 1161. [CrossRef]
69. Xing, Q.; Dekker, S.; Kyriakopoulou, K.; Boom, R.M.; Smid, E.J.; Schutyser, M.A.I. Enhanced Nutritional Value of Chickpea
Protein Concentrate by Dry Separation and Solid State Fermentation. Innov. Food Sci. Emerg. Technol. 2020, 59, 102269. [CrossRef]
70. Cressey, P.; Saunders, D.; Goodman, J. Cyanogenic Glycosides in Plant-Based Foods Available in New Zealand. Food Addit.
Contam. Part. A 2013, 30, 1946–1953. [CrossRef] [PubMed]
71. Obafemi, Y.D.; Oranusi, S.U.; Ajanaku, K.O.; Akinduti, P.A.; Leech, J.; Cotter, P.D. African Fermented Foods: Overview, Emerging
Benefits, and Novel Approaches to Microbiome Profiling. npj Sci. Food 2022, 6, 15. [CrossRef] [PubMed]
72. Timothy, B.; Iliyasu, A.H.; Anvikar, A.R. Bacteriocins of Lactic Acid Bacteria and Their Industrial Application. Curr. Top. Lact.
Acid. Bact. Probiotics 2021, 7, 1–13. [CrossRef]
73. Zhang, D.; Wang, Q.; Li, Z.; Shen, Z.; Tan, B.; Zhai, X. Changing the Polyphenol Composition and Enhancing the Enzyme Activity
of Sorghum Grain by Solid-state Fermentation with Different Microbial Strains. J. Sci. Food Agric. 2024, 104, 6186–6195. [CrossRef]
[PubMed]
74. Pulido-Mateos, E.C.; Lessard-Lord, J.; Desjardins, Y.; Roy, D. Biotransformation of Camu–Camu Galloylated Ellagitannins by
Lactiplantibacillus plantarum with Extracellular Tannase Activity. Food Funct. 2024, 15, 7189–7199. [CrossRef]
75. Mendes, H.C.; Kelbert, M.; Michels, C.; Soares, H.M. Exploring Sustainable Pathways for Cyanide Biodegradation in Cassava
Waste: Insights into Methodologies, Microbial Degradation, and Emerging Technologies. J. Water Process Eng. 2024, 64, 105594.
[CrossRef]
76. Zhang, K.; Zhang, T.-T.; Guo, R.-R.; Ye, Q.; Zhao, H.-L.; Huang, X.-H. The Regulation of Key Flavor of Traditional Fermented
Food by Microbial Metabolism: A Review. Food Chem. X 2023, 19, 100871. [CrossRef]
77. Zheng, X.; Shi, X.; Wang, B. A Review on the General Cheese Processing Technology, Flavor Biochemical Pathways and the
Influence of Yeasts in Cheese. Front. Microbiol. 2021, 12, 703284. [CrossRef]
78. Ou, M.; Lou, J.; Lao, L.; Guo, Y.; Pan, D.; Yang, H.; Wu, Z. Plant-Based Meat Analogue of Soy Proteins by the Multi-Strain
Solid-State Mixing Fermentation. Food Chem. 2023, 414, 135671. [CrossRef] [PubMed]
79. Hui, C.; Wei, R.; Jiang, H.; Zhao, Y.; Xu, L. Characterization of the Ammonification, the Relevant Protease Production and Activity
in a High-Efficiency Ammonifier Bacillus amyloliquefaciens DT. Int. Biodeterior. Biodegrad. 2019, 142, 11–17. [CrossRef]
80. Wang, R.; Dong, P.; Zhu, Y.; Yan, M.; Liu, W.; Zhao, Y.; Huang, L.; Zhang, D.; Guo, H. Bacterial Community Dynamics Reveal
Its Key Bacterium, Bacillus amyloliquefaciens ZB, Involved in Soybean Meal Fermentation for Efficient Water-Soluble Protein
Production. LWT 2021, 135, 110068. [CrossRef]
81. Yang, J.; Wu, X.; Chen, H.; Sun-waterhouse, D.; Zhong, H.; Cui, C. A Value-Added Approach to Improve the Nutritional Quality
of Soybean Meal Byproduct: Enhancing Its Antioxidant Activity through Fermentation by Bacillus amyloliquefaciens SWJS22. Food
Chem. 2019, 272, 396–403. [CrossRef]
82. Nedele, A.-K.; Gross, S.; Rigling, M.; Zhang, Y. Reduction of Green Off-Flavor Compounds: Comparison of Key Odorants during
Fermentation of Soy Drink with Lycoperdon Pyriforme. Food Chem. 2021, 334, 127591. [CrossRef]
83. El Youssef, C.; Bonnarme, P.; Fraud, S.; Péron, A.-C.; Helinck, S.; Landaud, S. Sensory Improvement of a Pea Protein-Based
Product Using Microbial Co-Cultures of Lactic Acid Bacteria and Yeasts. Foods 2020, 9, 349. [CrossRef]
84. Shi, Y.; Singh, A.; Kitts, D.D.; Pratap-Singh, A. Lactic Acid Fermentation: A Novel Approach to Eliminate Unpleasant Aroma in
Pea Protein Isolates. LWT 2021, 150, 111927. [CrossRef]
85. Galli, V.; Venturi, M.; Pini, N.; Guerrini, S.; Granchi, L. Exploitation of Sourdough Lactic Acid Bacteria to Reduce Raffinose Family
Oligosaccharides (RFOs) Content in Breads Enriched with Chickpea Flour. Eur. Food Res. Technol. 2019, 245, 2353–2363. [CrossRef]
86. Bintsis, T. Lactic Acid Bacteria as Starter Cultures: An Update in Their Metabolism and Genetics. AIMS Microbiol. 2018, 4, 665–684.
[CrossRef] [PubMed]
87. Liu, L.; Chen, X.; Hao, L.; Zhang, G.; Jin, Z.; Li, C.; Yang, Y.; Rao, J.; Chen, B. Traditional Fermented Soybean Products: Processing,
Flavor Formation, Nutritional and Biological Activities. Crit. Rev. Food Sci. Nutr. 2022, 62, 1971–1989. [CrossRef]
88. Cichońska, P.; Kostyra, E.; Piotrowska, A.; Ścibisz, I.; Roszko, M.; Ziarno, M. Enhancing the Sensory and Nutritional Properties of
Bean-Based and Lentil-Based Beverages through Fermentation and Germination. LWT 2024, 199, 116140. [CrossRef]
https://doi.org/10.1111/ijfs.16808
https://doi.org/10.22271/tpi.2021.v10.i5k.6306
https://doi.org/10.1155/2021/5570753
https://doi.org/10.1186/s43014-020-0020-5
https://doi.org/10.3390/pr11041161
https://doi.org/10.1016/j.ifset.2019.102269
https://doi.org/10.1080/19440049.2013.825819
https://www.ncbi.nlm.nih.gov/pubmed/23984870
https://doi.org/10.1038/s41538-022-00130-w
https://www.ncbi.nlm.nih.gov/pubmed/35181677
https://doi.org/10.35732/ctlabp.2021.7.1.1
https://doi.org/10.1002/jsfa.13454
https://www.ncbi.nlm.nih.gov/pubmed/38459923
https://doi.org/10.1039/D4FO00149D
https://doi.org/10.1016/j.jwpe.2024.105594
https://doi.org/10.1016/j.fochx.2023.100871
https://doi.org/10.3389/fmicb.2021.703284
https://doi.org/10.1016/j.foodchem.2023.135671
https://www.ncbi.nlm.nih.gov/pubmed/36809723
https://doi.org/10.1016/j.ibiod.2019.04.009
https://doi.org/10.1016/j.lwt.2020.110068
https://doi.org/10.1016/j.foodchem.2018.08.037
https://doi.org/10.1016/j.foodchem.2020.127591
https://doi.org/10.3390/foods9030349
https://doi.org/10.1016/j.lwt.2021.111927
https://doi.org/10.1007/s00217-019-03353-6
https://doi.org/10.3934/microbiol.2018.4.665
https://www.ncbi.nlm.nih.gov/pubmed/31294241
https://doi.org/10.1080/10408398.2020.1848792
https://doi.org/10.1016/j.lwt.2024.116140
Fermentation 2025, 11, 15 27 of 29
89. Spaccasassi, A.; Utz, F.; Dunkel, A.; Aragao Börner, R.; Ye, L.; De Franceschi, F.; Bogicevic, B.; Glabasnia, A.; Hofmann, T.;
Dawid, C. Screening of a Microbial Culture Collection: Empowering Selection of Starters for Enhanced Sensory Attributes of
Pea-Protein-Based Beverages. J. Agric. Food Chem. 2024, 72, 15890–15905. [CrossRef] [PubMed]
90. Nouska, C.; Hatzikamari, M.; Matsakidou, A.; Biliaderis, C.G.; Lazaridou, A. Enhancement of Textural and Sensory Characteristics
of Wheat Bread Using a Chickpea Sourdough Fermented with a Selected Autochthonous Microorganism. Foods 2023, 12, 3112.
[CrossRef]
91. Boukid, F.; Hassoun, A.; Zouari, A.; Tülbek, M.Ç.; Mefleh, M.; Aït-Kaddour, A.; Castellari, M. Fermentation for Designing
Innovative Plant-Based Meat and Dairy Alternatives. Foods 2023, 12, 1005. [CrossRef] [PubMed]
92. Diez-Ozaeta, I.; Astiazaran, O.J. Fermented Foods: An Update on Evidence-Based Health Benefits and Future Perspectives. Food
Res. Int. 2022, 156, 111133. [CrossRef] [PubMed]
93. Valentino, V.; Magliulo, R.; Farsi, D.; Cotter, P.D.; O’Sullivan, O.; Ercolini, D.; De Filippis, F. Fermented Foods, Their Microbiome
and Its Potential in Boosting Human Health. Microb. Biotechnol. 2024, 17, e14428. [CrossRef] [PubMed]
94. Mukherjee, A.; Breselge, S.; Dimidi, E.; Marco, M.L.; Cotter, P.D. Fermented Foods and Gastrointestinal Health: Underlying
Mechanisms. Nat. Rev. Gastroenterol. Hepatol. 2024, 21, 248–266. [CrossRef]
95. Wang, Z.; Neupane, A.; Vo, R.; White, J.; Wang, X.; Marzano, S.-Y.L. Comparing Gut Microbiome inMothers’ Own Breast Milk-
and Formula-Fed Moderate-Late Preterm Infants. Front. Microbiol. 2020, 11, 891. [CrossRef]
96. Feng, R.; Chen, L.; Chen, K. Fermentation Trip: Amazing Microbes, Amazing Metabolisms. Ann. Microbiol. 2018, 68, 717–729.
[CrossRef]
97. Melini, F.; Melini, V.; Luziatelli, F.; Ficca, A.G.; Ruzzi, M. Health-Promoting Components in Fermented Foods: An Up-to-Date
Systematic Review. Nutrients 2019, 11, 1189. [CrossRef]
98. Tarvainen, M.; Fabritius, M.; Yang, B. Determination of Vitamin K Composition of Fermented Food. Food Chem. 2019, 275, 515–522.
[CrossRef]
99. Marco, M.L.; Heeney, D.; Binda, S.; Cifelli, C.J.; Cotter, P.D.; Foligné, B.; Gänzle, M.; Kort, R.; Pasin, G.; Pihlanto, A.; et al. Health
Benefits of Fermented Foods: Microbiota and Beyond. Curr. Opin. Biotechnol. 2017, 44, 94–102. [CrossRef] [PubMed]
100. Bhanwar, S.; Bamnia, M.; Ghosh, M.; Ganguli, A. Use of Lactococcus lactis to Enrich Sourdough Bread with γ-Aminobutyric Acid.
Int. J. Food Sci. Nutr. 2013, 64, 77–81. [CrossRef]
101. Zhou, Y.; Cui, Y.; Qu, X. Exopolysaccharides of Lactic Acid Bacteria: Structure, Bioactivity and Associations: A Review. Carbohydr.
Polym. 2019, 207, 317–332. [CrossRef] [PubMed]
102. Beltrán-Barrientos, L.M.; Hernández-Mendoza, A.; González-Córdova, A.F.; Astiazarán-García, H.; Esparza-Romero, J.; Vallejo-
Córdoba, B. Mechanistic Pathways Underlying the Antihypertensive Effect of Fermented Milk with Lactococcus lactis NRRL
B-50571 in Spontaneously Hypertensive Rats. Nutrients 2018, 10, 262. [CrossRef]
103. Kim, H.J.; Noh, J.S.; Song, Y.O. Beneficial Effects of Kimchi, a Korean Fermented Vegetable Food, on Pathophysiological Factors
Related to Atherosclerosis. J. Med. Food 2018, 21, 127–135. [CrossRef]
104. Dimidi, E.; Cox, S.R.; Rossi, M.; Whelan, K. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and
Effects on Gastrointestinal Health and Disease. Nutrients 2019, 11, 1806. [CrossRef]
105. Chen, L.; Wang, L.; Shu, G.; Yuan, J.; Zhang, J.; Qin, S.; Li, J. Enhanced Antihypertensive Potential of Fermented Pomegranate Juice:
The Contribution of Phenolic Compounds Biotransformation and the Resultant Angiotensin-I-Converting Enzyme Inhibition
Mechanism. Food Chem. 2023, 404, 134745. [CrossRef] [PubMed]
106. Rendon-Rosales, M.Á.; Torres-Llanez, M.J.; González-Córdova, A.F.; Hernández-Mendoza, A.; Mazorra-Manzano, M.A.; Vallejo-
Cordoba, B. In Vitro Antithrombotic and Hypocholesterolemic Activities of Milk Fermented with Specific Strains of Lactococcus
lactis. Nutrients 2019, 11, 2150. [CrossRef]
107. Singh, B.P.; Vij, S.; Hati, S. Functional Significance of Bioactive Peptides Derived from Soybean. Peptides 2014, 54, 171–179.
[CrossRef]
108. Tung, Y.; Chen, H.; Wu, H.; Ho, M.; Chong, K.; Chen, C. Kefir Peptides Prevent Hyperlipidemia and Obesity in High-Fat-Diet-
Induced Obese Rats via Lipid Metabolism Modulation. Mol. Nutr. Food Res. 2018, 62, 1700505. [CrossRef] [PubMed]
109. Rocchetti, G.; Miragoli, F.; Zacconi, C.; Lucini, L.; Rebecchi, A. Impact of Cooking and Fermentation by Lactic Acid Bacteria on
Phenolic Profile of Quinoa and Buckwheat Seeds. Food Res. Int. 2019, 119, 886–894. [CrossRef] [PubMed]
110. Lorusso, A.; Verni, M.; Montemurro, M.; Coda, R.; Gobbetti, M.; Rizzello, C.G. Use of Fermented Quinoa Flour for Pasta Making
and Evaluation of the Technological and Nutritional Features. LWT 2017, 78, 215–221. [CrossRef]
111. Mantzourani, I.; Terpou, A.; Alexopoulos, A.; Kimbaris, A.; Bezirtzoglou, E.; Koutinas, A.A.; Plessas, S. Production of a Potentially
Synbiotic Pomegranate Beverage by Fermentation with Lactobacillus plantarum ATCC 14917 Adsorbed on a Prebiotic Carrier. Appl.
Biochem. Biotechnol. 2019, 188, 1096–1107. [CrossRef] [PubMed]
112. Bujna, E.; Farkas, N.A.; Tran, A.M.; Dam, M.S.; Nguyen, Q.D. Lactic Acid Fermentation of Apricot Juice by Mono- and Mixed
Cultures of Probiotic Lactobacillus and Bifidobacterium Strains. Food Sci. Biotechnol. 2018, 27, 547–554. [CrossRef]
https://doi.org/10.1021/acs.jafc.4c02316
https://www.ncbi.nlm.nih.gov/pubmed/38953212
https://doi.org/10.3390/foods12163112
https://doi.org/10.3390/foods12051005
https://www.ncbi.nlm.nih.gov/pubmed/36900522
https://doi.org/10.1016/j.foodres.2022.111133
https://www.ncbi.nlm.nih.gov/pubmed/35651092
https://doi.org/10.1111/1751-7915.14428
https://www.ncbi.nlm.nih.gov/pubmed/38393607
https://doi.org/10.1038/s41575-023-00869-x
https://doi.org/10.3389/fmicb.2020.00891
https://doi.org/10.1007/s13213-018-1384-5
https://doi.org/10.3390/nu11051189
https://doi.org/10.1016/j.foodchem.2018.09.136
https://doi.org/10.1016/j.copbio.2016.11.010
https://www.ncbi.nlm.nih.gov/pubmed/27998788
https://doi.org/10.3109/09637486.2012.700919
https://doi.org/10.1016/j.carbpol.2018.11.093
https://www.ncbi.nlm.nih.gov/pubmed/30600013
https://doi.org/10.3390/nu10030262
https://doi.org/10.1089/jmf.2017.3946
https://doi.org/10.3390/nu11081806
https://doi.org/10.1016/j.foodchem.2022.134745
https://www.ncbi.nlm.nih.gov/pubmed/36444086
https://doi.org/10.3390/nu11092150
https://doi.org/10.1016/j.peptides.2014.01.022
https://doi.org/10.1002/mnfr.201700505
https://www.ncbi.nlm.nih.gov/pubmed/29178253
https://doi.org/10.1016/j.foodres.2018.10.073
https://www.ncbi.nlm.nih.gov/pubmed/30884729
https://doi.org/10.1016/j.lwt.2016.12.046
https://doi.org/10.1007/s12010-019-02977-4
https://www.ncbi.nlm.nih.gov/pubmed/30790224
https://doi.org/10.1007/s10068-017-0269-x
Fermentation 2025, 11, 15 28 of 29
113. Kaprasob, R.; Kerdchoechuen, O.; Laohakunjit, N.; Thumthanaruk, B.; Shetty, K. Changes in Physico-Chemical, Astringency,
Volatile Compounds and Antioxidant Activity of Fresh and Concentrated Cashew Apple Juice Fermented with Lactobacillus
plantarum. J. Food Sci. Technol. 2018, 55, 3979–3990. [CrossRef] [PubMed]
114. Yang, X.; Zhou, J.; Fan, L.; Qin, Z.; Chen, Q.; Zhao, L. Antioxidant Properties of a Vegetable–Fruit Beverage Fermented with Two
Lactobacillus plantarum Strains. Food Sci. Biotechnol. 2018, 27, 1719–1726. [CrossRef] [PubMed]
115. Sun, Y.; Xu, J.; Zhao, H.; Li, Y.; Zhang, H.; Yang, B.; Guo, S. Antioxidant Properties of Fermented Soymilk and Its Anti-Inflammatory
Effect on DSS-Induced Colitis in Mice. Front. Nutr. 2023, 9, 1088949. [CrossRef]
116. Nampoothiri, K.M.; Beena, D.J.; Vasanthakumari, D.S.; Ismail, B. Chapter 3—Health Benefits of Exopolysaccharides in Fermented
Foods. In Fermented Foods in Health and Disease Prevention; Frias, J., Martinez-Villaluenga, C., Peñas, E., Eds.; Academic Press:
Boston, MA, USA, 2017; pp. 49–62. ISBN 9780128023099.
117. Afreen, A.; Ahmed, Z.; Khalid, N.; Ferheen, I.; Ahmed, I. Optimization and Cholesterol-Lowering Activity of Exopolysaccharide
from Lactiplantibacillus paraplantarum NCCP 962. Appl. Microbiol. Biotechnol. 2023, 107, 1189–1204. [CrossRef]
118. Lindström, C.; Xu, J.; Öste, R.; Holst, O.; Molin, G. Oral Administration of Live Exopolysaccharide-Producing Pediococcus parvulus,
but Not Purified Exopolysaccharide, Suppressed Enterobacteriaceae without Affecting Bacterial Diversity in Ceca of Mice. Appl.
Env. Microbiol. 2013, 79, 5030–5037. [CrossRef]
119. Mårtensson, O.; Biörklund, M.; Lambo, A.M.; Dueñas-Chasco, M.; Irastorza, A.; Holst, O.; Norin, E.; Welling, G.; Öste, R.; Önning,
G. Fermented, Ropy, Oat-Based Products Reduce Cholesterol Levels and Stimulate the Bifidobacteria Flora in Humans. Nutr. Res.
2005, 25, 429–442. [CrossRef]
120. Dahiya, P.; Kumari, S.; Behl, M.; Kashyap, A.; Kumari, D.; Thakur, K.; Devi, M.; Kumari, N.; Kaushik, N.; Walia, A.; et al.
Guardians of the Gut: Harnessing the Power of Probiotic Microbiota and Their Exopolysaccharides to Mitigate Heavy Metal
Toxicity in Human for Better Health. Probiotics Antimicro. Prot. 2024, 16, 1937–1953. [CrossRef]
121. Salazar, N.; Gueimonde, M.; De Los Reyes-Gavilán, C.G.; Ruas-Madiedo, P. Exopolysaccharides Produced by Lactic Acid Bacteria
and Bifidobacteria as Fermentable Substrates by the Intestinal Microbiota. Crit. Rev. Food Sci. Nutr. 2016, 56, 1440–1453. [CrossRef]
[PubMed]122. Silva, Y.P.; Bernardi, A.; Frozza, R.L. The Role of Short-Chain Fatty Acids From Gut Microbiota in Gut-Brain Communication.
Front. Endocrinol. 2020, 11, 25. [CrossRef] [PubMed]
123. Sun, H.; Ni, X.; Song, X.; Wen, B.; Zhou, Y.; Zou, F.; Yang, M.; Peng, Z.; Zhu, H.; Zeng, Y.; et al. Fermented Yupingfeng
Polysaccharides Enhance Immunity by Improving the Foregut Microflora and Intestinal Barrier in Weaning Rex Rabbits. Appl.
Microbiol. Biotechnol. 2016, 100, 8105–8120. [CrossRef] [PubMed]
124. Chen, T.; Noto, D.; Hoshino, Y.; Mizuno, M.; Miyake, S. Butyrate Suppresses Demyelination and Enhances Remyelination.
J. Neuroinflamm. 2019, 16, 165. [CrossRef] [PubMed]
125. Tangyu, M.; Muller, J.; Bolten, C.J.; Wittmann, C. Fermentation of Plant-Based Milk Alternatives for Improved Flavour and
Nutritional Value. Appl. Microbiol. Biotechnol. 2019, 103, 9263–9275. [CrossRef]
126. Chamlagain, B.; Sugito, T.A.; Deptula, P.; Edelmann, M.; Kariluoto, S.; Varmanen, P.; Piironen, V. In Situ Production of Active
Vitamin B12 in Cereal Matrices Using Propionibacterium freudenreichii. Food Sci. Nutr. 2018, 6, 67–76. [CrossRef] [PubMed]
127. Signorini, C.; Carpen, A.; Coletto, L.; Borgonovo, G.; Galanti, E.; Capraro, J.; Magni, C.; Abate, A.; Johnson, S.K.; Duranti, M.; et al.
Enhanced Vitamin B12 Production in an Innovative Lupin Tempeh Is Due to Synergic Effects of Rhizopus and Propionibacterium in
Cofermentation. Int. J. Food Sci. Nutr. 2018, 69, 451–457. [CrossRef] [PubMed]
128. Wolkers-Rooijackers, J.C.M.; Endika, M.F.; Smid, E.J. Enhancing Vitamin B12 in Lupin Tempeh by in Situ Fortification. LWT 2018,
96, 513–518. [CrossRef]
129. Ripa, I.; Ruiz-Masó, J.Á.; De Simone, N.; Russo, P.; Spano, G.; Del Solar, G. A Single Change in the Aptamer of the Lactiplantibacillus
plantarum Rib. Operon Riboswitch Severely Impairs Its Regulatory Activity and Leads to a Vitamin B2—Overproducing Phenotype.
Microb. Biotechnol. 2022, 15, 1253–1269. [CrossRef]
130. Bock, H.-J.; Lee, H.-W.; Lee, N.-K.; Paik, H.-D. Probiotic Lactiplantibacillus plantarum KU210152 and Its Fermented Soy Milk
Attenuates Oxidative Stress in Neuroblastoma Cells. Food Res. Int. 2024, 177, 113868. [CrossRef]
131. Castro-López, C.; Romero-Luna, H.E.; García, H.S.; Vallejo-Cordoba, B.; González-Córdova, A.F.; Hernández-Mendoza, A. Key
Stress Response Mechanisms of Probiotics During Their Journey Through the Digestive System: A Review. Probiotics Antimicro.
Prot. 2023, 15, 1250–1270. [CrossRef] [PubMed]
132. Echresh, S.; Alizadeh Behbahani, B.; Falah, F.; Noshad, M.; Ibrahim, S.A. Assessment of the Probiotic, Anti-Bacterial, and Anti-
Biofilm Characteristics of Lacticaseibacillus rhamnosus CWKu-12, along with Its Potential Impact on the Expression of Virulence
Genes in Listeria monocytogenes ATCC 19115. LWT 2024, 203, 116391. [CrossRef]
133. Alizadeh Behbahani, B.; Jooyandeh, H.; Taki, M.; Falah, F. Evaluation of the Probiotic, Anti-Bacterial, Anti-Biofilm, and Safety
Properties of Lacticaseibacillus paracasei B31-2. LWT 2024, 207, 116676. [CrossRef]
134. Zheng, Y.; Zhang, S.; Zhang, T.; Teng, X.; Ling, X.; Li, B.; Xiao, G.; Huang, S. A Bifidobacterium animalis Subsp. Lactis Strain That
Can Suppress Helicobacter pylori: Isolation, in Vitro and in Vivo Validation. Lett. Appl. Microbiol. 2024, 77, ovae005. [CrossRef]
https://doi.org/10.1007/s13197-018-3323-7
https://www.ncbi.nlm.nih.gov/pubmed/30228396
https://doi.org/10.1007/s10068-018-0411-4
https://www.ncbi.nlm.nih.gov/pubmed/30483436
https://doi.org/10.3389/fnut.2022.1088949
https://doi.org/10.1007/s00253-023-12372-z
https://doi.org/10.1128/AEM.01456-13
https://doi.org/10.1016/j.nutres.2005.03.004
https://doi.org/10.1007/s12602-024-10281-9
https://doi.org/10.1080/10408398.2013.770728
https://www.ncbi.nlm.nih.gov/pubmed/25675369
https://doi.org/10.3389/fendo.2020.00025
https://www.ncbi.nlm.nih.gov/pubmed/32082260
https://doi.org/10.1007/s00253-016-7619-0
https://www.ncbi.nlm.nih.gov/pubmed/27260288
https://doi.org/10.1186/s12974-019-1552-y
https://www.ncbi.nlm.nih.gov/pubmed/31399117
https://doi.org/10.1007/s00253-019-10175-9
https://doi.org/10.1002/fsn3.528
https://www.ncbi.nlm.nih.gov/pubmed/29387363
https://doi.org/10.1080/09637486.2017.1386627
https://www.ncbi.nlm.nih.gov/pubmed/29041832
https://doi.org/10.1016/j.lwt.2018.05.062
https://doi.org/10.1111/1751-7915.13919
https://doi.org/10.1016/j.foodres.2023.113868
https://doi.org/10.1007/s12602-022-09981-x
https://www.ncbi.nlm.nih.gov/pubmed/36001271
https://doi.org/10.1016/j.lwt.2024.116391
https://doi.org/10.1016/j.lwt.2024.116676
https://doi.org/10.1093/lambio/ovae005
Fermentation 2025, 11, 15 29 of 29
135. Veiga, P.; Pons, N.; Agrawal, A.; Oozeer, R.; Guyonnet, D.; Brazeilles, R.; Faurie, J.-M.; van Hylckama Vlieg, J.E.T.; Houghton,
L.A.; Whorwell, P.J.; et al. Changes of the Human Gut Microbiome Induced by a Fermented Milk Product. Sci. Rep. 2014, 4, 6328.
[CrossRef] [PubMed]
136. Han, K.; Bose, S.; Wang, J.; Kim, B.; Kim, M.J.; Kim, E.; Kim, H. Contrasting Effects of Fresh and Fermented Kimchi Consumption
on Gut Microbiota Composition and Gene Expression Related to Metabolic Syndrome in Obese Korean Women. Mol. Nutr. Food
Res 2015, 59, 1004–1008. [CrossRef] [PubMed]
137. Kok, C.R.; Hutkins, R. Yogurt and Other Fermented Foods as Sources of Health-Promoting Bacteria. Nutr. Rev. 2018, 76, 4–15.
[CrossRef] [PubMed]
138. Todorovic, S.; Akpinar, A.; Assunção, R.; Bär, C.; Bavaro, S.L.; Berkel Kasikci, M.; Domínguez-Soberanes, J.; Capozzi, V.; Cotter,
P.D.; Doo, E.-H.; et al. Health Benefits and Risks of Fermented Foods—The PIMENTO Initiative. Front. Nutr. 2024, 11, 1458536.
[CrossRef]
139. Saha Turna, N.; Chung, R.; McIntyre, L. A Review of Biogenic Amines in Fermented Foods: Occurrence and Health Effects.
Heliyon 2024, 10, e24501. [CrossRef] [PubMed]
140. Mukherjee, A.; Gómez-Sala, B.; O’Connor, E.M.; Kenny, J.G.; Cotter, P.D. Global Regulatory Frameworks for Fermented Foods:
A Review. Front. Nutr. 2022, 9, 902642. [CrossRef]
141. Smanski, M.J.; Aristidou, A.; Carruth, R.; Erickson, J.; Gordon, M.; Kedia, S.B.; Lee, K.H.; Prather, D.; Schiel, J.E.; Schultheisz, H.;
et al. Bioindustrial Manufacturing Readiness Levels (BioMRLs) as a Shared Framework for Measuring and Communicating the
Maturity of Bioproduct Manufacturing Processes. J. Ind. Microbiol. Biotechnol. 2022, 49, kuac022. [CrossRef] [PubMed]
142. Melchor-Moncada, J.J.; García-Barco, A.; Zuluaga-Vélez, A.; Veloza, L.A.; Sepúlveda-Arias, J.C. Scale-Up of the Fermentation
Process for the Production and Purification of Serratiopeptidase Using Silkworm Pupae as a Substrate. Methods Protoc. 2024, 7, 19.
[CrossRef] [PubMed]
143. Sawant, S.S.; Bhapkar, S.R.; Song, J.; Seo, H.J. Sustainable Bioplastics: Harnessing Pear Agro-Industrial Waste for Polyhydrox-
yalkanoates Production: A Review. Int. J. Environ. Sci. Technol. 2024, 21, 7341–7352. [CrossRef]
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual
author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to
people or property resulting from any ideas, methods, instructions or products referred to in the content.
https://doi.org/10.1038/srep06328
https://www.ncbi.nlm.nih.gov/pubmed/25209713
https://doi.org/10.1002/mnfr.201400780
https://www.ncbi.nlm.nih.gov/pubmed/25688926
https://doi.org/10.1093/nutrit/nuy056
https://www.ncbi.nlm.nih.gov/pubmed/30452699
https://doi.org/10.3389/fnut.2024.1458536
https://doi.org/10.1016/j.heliyon.2024.e24501
https://www.ncbi.nlm.nih.gov/pubmed/38304783
https://doi.org/10.3389/fnut.2022.902642
https://doi.org/10.1093/jimb/kuac022
https://www.ncbi.nlm.nih.gov/pubmed/36150719
https://doi.org/10.3390/mps7020019
https://www.ncbi.nlm.nih.gov/pubmed/38525777
https://doi.org/10.1007/s13762-024-05493-z
	Introduction 
	Microbial Fermentation: Mechanisms and Classification Based on End Products 
	Microbial Metabolism in Biotransformation 
	Impact on NutritionalEnhancement 
	Bioavailability of Nutrients Post-Fermentation 
	Reduction in Anti-Nutritional Factors 
	Functional Properties of Fermented Foods 
	Development and Enhancement of Sensory Attributes 
	Probiotic Enrichment and Health Benefits 
	Health Risks Associated with Fermented Foods and Their Management 
	Microbiological Hazards 
	Chemical Contaminants 
	Vulnerable Populations 
	Regulatory and Safety Practices 
	Challenges and Future Perspectives 
	Challenges 
	Future Perspectives 
	Referencesbeen indispensable 
not only for food processing and preservation but also for enriching the nutritional value 
of foods, resulting in a diverse range of fermented products that are still staples in many 
cultures and offering significant health benefits. 
 
Figure 1. Microbial fermentation in food: a comprehensive overview of the fermentation process, 
substrates, products, and associated health benefits. Created with BioRender.com. 
However, microbial biotransformation encompasses more than fermentation. Mod-
ern biotechnological approaches are expanding the scope by exploring enzymatic modifi-
cations, metabolic engineering, and novel microbial pathways that enable targeted trans-
formations of food components into bioactive and functional compounds. Although fer-
mentation remains the cornerstone of microbial biotransformation and has been utilized 
for centuries as a natural method of food preservation and flavor enhancement [12], the 
potential of microbial biotransformation extends far beyond traditional practices. Modern 
advances in microbiology and biotechnology have revealed the extensive capability of 
microorganisms to synthesize bioactive compounds, reduce anti-nutritional factors, and 
improve the bioavailability of essential nutrients [2,12,13]. These transformations are 
driven by the enzymatic machinery of microorganisms, which catalyzes a variety of bio-
chemical reactions, leading to the modification of carbohydrates, proteins, lipids, and 
other food constituents [14]. 
Figure 1. Microbial fermentation in food: a comprehensive overview of the fermentation process,
substrates, products, and associated health benefits. Created with BioRender.com.
However, microbial biotransformation encompasses more than fermentation. Modern
biotechnological approaches are expanding the scope by exploring enzymatic modifications,
metabolic engineering, and novel microbial pathways that enable targeted transformations
of food components into bioactive and functional compounds. Although fermentation
remains the cornerstone of microbial biotransformation and has been utilized for centuries
as a natural method of food preservation and flavor enhancement [12], the potential of
microbial biotransformation extends far beyond traditional practices. Modern advances
in microbiology and biotechnology have revealed the extensive capability of microorgan-
isms to synthesize bioactive compounds, reduce anti-nutritional factors, and improve
the bioavailability of essential nutrients [2,12,13]. These transformations are driven by
the enzymatic machinery of microorganisms, which catalyzes a variety of biochemical
reactions, leading to the modification of carbohydrates, proteins, lipids, and other food
constituents [14].
BioRender.com
Fermentation 2025, 11, 15 3 of 29
In recent years, the evolution of microbial capabilities has led to significant shifts in
the global food industry and consumer preferences [3]. There is an increasing demand
for foods that not only satisfy basic nutritional needs but also contribute to overall health
and well-being [15,16]. This shift has fueled a growing interest in the development of
functional foods that offer additional health benefits beyond their inherent nutritional
value. As a result, enhancing the nutritional properties and functional benefits of food
has become crucial, particularly in addressing public health challenges and improving the
quality of life. One of the primary drivers for enhancing nutritional properties is the need
to combat various forms of malnutrition, including micronutrient deficiencies, that affect
millions of people worldwide [15]. Microbial biotransformation plays a crucial role in this
process by improving the bioavailability and concentration of essential nutrients, such as
vitamins, minerals, and amino acids, in food products. For example, through fermentation,
microorganisms can increase the levels of B-vitamins or convert precursors into bioactive
forms of nutrients, making them more readily absorbed by the human body [15].
In addition to addressing nutritional deficiencies, enhancing the functional benefits
of foods through microbial biotransformation has significant potential for disease pre-
vention and health promotion. For example, foods enriched with probiotics have been
shown to improve gut health, boost the immune system, and reduce the risk of chronic
diseases [17,18]. Similarly, the synthesis of bioactive compounds such as antioxidants, pep-
tides, and polyphenols during microbial fermentation can contribute to the prevention of
oxidative stress, inflammation, and other conditions associated with aging and lifestyle
diseases [19]. Furthermore, the enhancement of functional properties also encompasses
the improvement of sensory attributes such as taste, texture, and aroma, which are critical
to consumer acceptance. Foods that are both nutritious and appealing are more likely to
be incorporated into regular diets, thereby maximizing their health benefits [11,20]. The
development of novel flavors and textures through microbial biotransformation not only
increases the diversity of food choices but also supports cultural and culinary innovation.
As the field of food science continues to evolve in response to growing consumer
demand for healthier and more sustainable options, understanding the intricate mecha-
nisms by which microorganisms transform food components is essential for advancing
both academic knowledge and industrial applications. This review aims to consolidate the
current knowledge in the field, highlight key developments, and identify emerging trends
that could shape the future of functional food production. By covering these areas, this
review aims to provide a holistic understanding of microbial biotransformation and its
potential to revolutionize the food industry. This review aims to bridge the gap between
traditional fermentation practices and modern biotechnological approaches by providing a
detailed analysis of how microbial biotransformation can be harnessed to improve food
quality and health outcomes. In addition to these core objectives, this review discusses the
challenges in scaling up microbial biotransformation for industrial applications, ensuring
quality control, and gaining consumer acceptance. It also explores future directions and
innovations in the field, particularly in the context of sustainable food production and the
potential for waste reduction. In addition, this review aims to provide a valuable resource
for researchers, food industry professionals, and policymakers by offering insights into
how microbial biotransformation can be leveraged to create nutritionally enhanced and
functionally superior food products. By synthesizing the current knowledge and identi-
fying areas for future research, this review will contribute to ongoing efforts to improve
global food security and public health.
Fermentation 2025, 11, 15 4 of 29
2. Microbial Fermentation: Mechanisms and Classification Based on
End Products
Fermentation is one of the oldest and most extensively used food preservation meth-
ods. This process relies on the biological activity of microorganisms to alter the flavor
and appearance of foods, thereby extending their shelf life. With progress in scientific
understanding and technological advancements, fermentation processes have significantly
improved. This evolution has transformed local small-scale fermentation into large-scale
controlled industrial processes [21]. A pivotal development in fermentation is the use of
selected microbial cultures to improve processing efficiency and ensure the safety and
quality of the final product. These scientific advancements have resulted in the availability
on the market of a diverse array of high-quality fermented products with superior sen-
sory attributes and nutritional benefits. Fundamentally, fermentation can be described
as the oxidation of carbohydrates into various products, such as organic acids, alcohols,
and carbon dioxide, throughchemical reactions facilitated by microorganisms under spe-
cific conditions. These microorganisms are naturally present in the environment or are
intentionally added. Based on the predominant end product and the main biochemical
pathways involved, fermentation can be categorized into lactic, acetic, alcoholic, and al-
kaline fermentation (Figure 2). During lactic acid fermentation, sugars are transformed
into lactic acid, a process that is characteristic of products such as yogurt, kimchi, and
fermented cereals. This type of fermentation is primarily driven by lactic acid bacteria
(LAB) [22]. Kimchi, a typical fermented vegetable food, contains a variety of LAB, includ-
ing homofermentative types like Lactobacillus plantarum (now known as Lactiplantibacillus
plantarum), which produce organic acids, and heterofermentative types like Leuconostoc
mesenteroides, which simultaneously produce carbon dioxide, acids, and weak alcohols.
These bacteria play a major role in controlling the flavor (taste and aroma) of the product.
Acetic fermentation involves the conversion of organic compounds, such as alcohols and
sugars, into acetic acid, predominantly by bacteria of the genus Acetobacter. This process
is integral for the production of water kefir, kombucha, cocoa, and vinegar [23]. During
alcoholic fermentation, sugars are converted into alcohol and carbon dioxide, and yeast
is the primary microorganism responsible for this process. This type of fermentation is
used to produce bread, beer, and wine. Alkaline fermentation, on the other hand, involves
the hydrolysis of proteins into amino acids and peptides, accompanied by the release
of ammonia, which raises the pH to around 8–9, thereby inhibiting spoilage organisms.
Ammonia is also responsible for the distinct umami flavor and aroma associated with
products such as Japanese nattu and African fermented legumes and eggs. The microor-
ganisms involved in alkaline fermentation are mainly Bacillus spp. and coagulase-negative
Staphylococcus, which produce extracellular proteinases that facilitate protein hydrolysis [9].
Considering the various fermentation processes described above, combining simple and
complex fermentation technologies could enable the development of a range of fermented
food products with the desired characteristics.
Fermentation 2025, 11, 15 5 of 29Fermentation 2025, 11, x FOR PEER REVIEW 5 of 30 
 
 
 
Figure 2. Overview of common fermentation types, associated microorganisms, and resulting end 
products. 
3. Microbial Metabolism in Biotransformation 
During microbial biotransformation, various microorganisms proliferate within the 
food system and gradually establish a stable and unique microbial community. Under 
specific conditions, these microorganisms alter the nutritional and sensory properties of 
food by producing desired compounds through complex metabolic activities [24,25]. Tra-
ditional fermented foods exemplify this process, as they experience a dynamic succession 
of microbial communities that not only include beneficial bacteria essential for fermenta-
tion but also spoilage and pathogenic bacteria that need to be inhibited [26]. The key mi-
crobial genera responsible for changes in sensory characteristics and the production of 
bioactive molecules differ depending on the stage of fermentation [27]. The predominant 
bacteria differ across various fermented foods, reflecting the unique symbiotic and alter-
nating relationships among microorganisms that can significantly influence metabolic 
pathways [28]. These pathways, including amino acid, fatty acid, and carbohydrate me-
tabolisms, are intricate, interdependent, and collectively contribute to the nutritional en-
hancement of fermented foods [29]. Through these metabolic processes, microflora not 
only contribute to taste but also significantly enhance the nutritional profile of food by 
increasing the bioavailability of nutrients, fortifying vitamins, and producing bioactive 
compounds, as illustrated in Figure 3. 
Microbial metabolism is essential for the development of functional properties in 
food systems. Microbial communities within food systems perform a range of metabolic 
processes that produce various metabolites that contribute significantly to the sensory 
qualities of food. These processes involve several metabolic pathways, such as glycome-
tabolism, polysaccharide degradation, proteolysis, and lipid and fatty acid breakdown. 
Glycometabolism encompasses several key pathways, including the Embden–Meyerhof–
Parnas (EMP), Hexose Monophosphate (HMP), Entner–Doudoroff (ED), and Pentose 
Phosphate Ketolase (PK) pathways. The EMP pathway, commonly referred to as glycoly-
sis, is a fundamental metabolic route through which glucose is initially converted to 1,6-
diphosphate fructose and then split into two three-carbon molecules by fructose-bisphos-
phate aldolase, resulting in the formation of two pyruvate molecules [30]. Together with 
the tricarboxylic acid cycle, this pathway is central to the synthesis and degradation of 
various compounds within microbial cells. The HMP pathway, also known as the Pentose 
Phosphate pathway, involves the dehydrogenation of glucose through phosphorylation, 
leading to the production of 6-phosphogluconic acid, which is further degraded by 6-
phosphogluconic acid dehydrogenase into pentose phosphate and carbon dioxide, even-
tually forming pyruvate after a series of reactions [31]. This pathway typically operates 
Figure 2. Overview of common fermentation types, associated microorganisms, and resulting
end products.
3. Microbial Metabolism in Biotransformation
During microbial biotransformation, various microorganisms proliferate within the
food system and gradually establish a stable and unique microbial community. Under spe-
cific conditions, these microorganisms alter the nutritional and sensory properties of food
by producing desired compounds through complex metabolic activities [24,25]. Traditional
fermented foods exemplify this process, as they experience a dynamic succession of micro-
bial communities that not only include beneficial bacteria essential for fermentation but also
spoilage and pathogenic bacteria that need to be inhibited [26]. The key microbial genera
responsible for changes in sensory characteristics and the production of bioactive molecules
differ depending on the stage of fermentation [27]. The predominant bacteria differ across
various fermented foods, reflecting the unique symbiotic and alternating relationships
among microorganisms that can significantly influence metabolic pathways [28]. These
pathways, including amino acid, fatty acid, and carbohydrate metabolisms, are intricate,
interdependent, and collectively contribute to the nutritional enhancement of fermented
foods [29]. Through these metabolic processes, microflora not only contribute to taste but
also significantly enhance the nutritional profile of food by increasing the bioavailability
of nutrients, fortifying vitamins, and producing bioactive compounds, as illustrated in
Figure 3.
Microbial metabolism is essential for the development of functional properties in
food systems. Microbial communities within food systems perform a range of metabolic
processes that produce various metabolites that contribute significantly to the sensory
qualities of food. These processes involve several metabolic pathways, such as gly-
cometabolism, polysaccharide degradation, proteolysis, and lipid and fatty acid break-
down. Glycometabolism encompasses several key pathways, including the Embden–
Meyerhof–Parnas (EMP), Hexose Monophosphate (HMP), Entner–Doudoroff (ED), and
Pentose Phosphate Ketolase (PK) pathways. The EMP pathway, commonly referred to as
glycolysis, is a fundamental metabolic route through which glucose is initially converted
to 1,6-diphosphate fructose and then split into two three-carbon molecules by fructose-
bisphosphate aldolase, resulting in the formation of two pyruvate molecules [30]. Together
with the tricarboxylic acidcycle, this pathway is central to the synthesis and degrada-
tion of various compounds within microbial cells. The HMP pathway, also known as the
Pentose Phosphate pathway, involves the dehydrogenation of glucose through phospho-
rylation, leading to the production of 6-phosphogluconic acid, which is further degraded
by 6-phosphogluconic acid dehydrogenase into pentose phosphate and carbon dioxide,
eventually forming pyruvate after a series of reactions [31]. This pathway typically oper-
Fermentation 2025, 11, 15 6 of 29
ates along the EMP pathway during microbial metabolism. The ED pathway involves the
cleavage of 6-phosphogluconic acid into pyruvate and 3-phosphoglyceraldehyde by 2-keto-
3-deoxy-6-phosphogluconate aldolase, and the resulting products are further processed
into pyruvate through the EMP pathway [17]. The ED pathway functions anaerobically
and is frequently associated with the HMP pathway. The PK pathway, which is less com-
mon and found in select microorganisms, enables the conversion of monosaccharides into
pyruvate, which can subsequently be transformed into various organic acids, alcohols, and
carbonyl compounds, thereby contributing to the production of bioactive compounds [32].
Fermentation 2025, 11, x FOR PEER REVIEW 6 of 30 
 
 
along the EMP pathway during microbial metabolism. The ED pathway involves the 
cleavage of 6-phosphogluconic acid into pyruvate and 3-phosphoglyceraldehyde by 2-
keto-3-deoxy-6-phosphogluconate aldolase, and the resulting products are further pro-
cessed into pyruvate through the EMP pathway [17]. The ED pathway functions anaero-
bically and is frequently associated with the HMP pathway. The PK pathway, which is 
less common and found in select microorganisms, enables the conversion of monosaccha-
rides into pyruvate, which can subsequently be transformed into various organic acids, 
alcohols, and carbonyl compounds, thereby contributing to the production of bioactive 
compounds [32]. 
 
Figure 3. Overview of microbial metabolism and the accumulation of bioactive compounds. 
The microbial metabolism of polysaccharides includes processes such as starch deg-
radation, cellulose breakdown, and pectin hydrolysis. Because microorganisms cannot di-
rectly absorb large polysaccharide molecules, these need to be broken down into smaller, 
more absorbable units. Starch decomposition is facilitated by amylases produced by var-
ious bacteria, molds, and actinomycetes. Cellulose degradation, on the other hand, is car-
ried out by cellulase-producing microorganisms such as Trichoderma viride, Trichoderma 
reesei, and certain actinomycetes and bacteria [33]. Pectinases found in plants, bacteria, 
molds, and yeasts such as Aspergillus wentii and Aspergillus niger play crucial roles in the 
microbial decomposition of pectin, leading to the generation of bioactive compounds such 
as acids and alcohols [34]. 
Proteins are complex macromolecules composed of amino acids that undergo micro-
bial degradation into smaller peptides and amino acids. Microorganisms, including bac-
teria, molds, and actinomycetes, produce proteases that break down proteins. Different 
strains produce various proteases, with bacteria such as Bacillus being the major producers 
of alkaline proteases and molds such as Aspergillus niger and Aspergillus oryzae predomi-
nantly producing acid proteases [35,36]. Following protein breakdown, amino acids are 
further metabolized by microorganisms through transamination, deamination, and decar-
boxylation, resulting in the formation of bioactive compounds such as aldehydes, acids, 
and alcohols. 
Figure 3. Overview of microbial metabolism and the accumulation of bioactive compounds.
The microbial metabolism of polysaccharides includes processes such as starch degra-
dation, cellulose breakdown, and pectin hydrolysis. Because microorganisms cannot
directly absorb large polysaccharide molecules, these need to be broken down into smaller,
more absorbable units. Starch decomposition is facilitated by amylases produced by various
bacteria, molds, and actinomycetes. Cellulose degradation, on the other hand, is carried
out by cellulase-producing microorganisms such as Trichoderma viride, Trichoderma reesei,
and certain actinomycetes and bacteria [33]. Pectinases found in plants, bacteria, molds,
and yeasts such as Aspergillus wentii and Aspergillus niger play crucial roles in the microbial
decomposition of pectin, leading to the generation of bioactive compounds such as acids
and alcohols [34].
Proteins are complex macromolecules composed of amino acids that undergo mi-
crobial degradation into smaller peptides and amino acids. Microorganisms, including
bacteria, molds, and actinomycetes, produce proteases that break down proteins. Dif-
ferent strains produce various proteases, with bacteria such as Bacillus being the major
producers of alkaline proteases and molds such as Aspergillus niger and Aspergillus oryzae
predominantly producing acid proteases [35,36]. Following protein breakdown, amino
acids are further metabolized by microorganisms through transamination, deamination,
and decarboxylation, resulting in the formation of bioactive compounds such as aldehydes,
acids, and alcohols.
Fermentation 2025, 11, 15 7 of 29
Lipid metabolism in microorganisms, facilitated by lipases, results in the breakdown of
lipids into glycerols and fatty acids. Bacteria, molds, and yeasts are key producers of lipases,
with notable bacterial sources including Bacillus, Pseudomonas, and Staphylococcus [37].
Lipases are also derived from molds, such as Rhizopus oryzae and Aspergillus niger, as well as
yeasts, such as Candida [38,39]. Unsaturated fatty acids released during lipid degradation
are prone to auto-oxidation, leading to the formation of bioactive compounds, such as
ketones, aldehydes, and alkanes. Aldehydes can be further metabolized into alcohols and
acids, which may then esterify to form esters, thereby significantly affecting the bioactive
profile and sensory properties of food.
Microbial metabolism plays a pivotal role in the shaping of food systems. Through
their diverse metabolic functions, microbial communities in various food environments
generate a wide array of metabolites that contribute to their distinct sensory properties.
Therefore, understanding these metabolic pathways is essential for analyzing changes in
the bacterial community composition and microbial diversity in food. By revealing the
specific metabolic pathways of microorganisms and studying the characteristics of different
microbial strains in fermented foods, researchers can better understand how these processes
result in the production of bioactive compounds with distinct sensory properties. This
knowledge is vital for identifying key microbial strains responsible for producing beneficial
bioactive compounds that can enhance the nutritional value of food and contribute to
health benefits. Additionally, controlling and optimizing microbial metabolic pathways
can improve the sensory properties of food, ensuring consistency in texture, taste, and
aroma, while reducing food safety risks. Ultimately, this study supports the industrial
standardized production of fermented foods with enhanced bioactive properties and
desirable sensory qualities.
4. Impact on Nutritional Enhancement
Microbial biotransformation significantly enhances the nutritional value of foods via
fermentation by modifying their biochemical composition. This process improves nutrient
bioavailability, reduces anti-nutritional factors, and changes the overall nutritional content
and profile of food products [40]. These aspects are crucial for understanding how microbial
activity can be leveraged to develop functional foods with greater health benefits.
4.1. Bioavailability of Nutrients Post-Fermentation
Bioavailability refers to the proportion of nutrients absorbed and utilized by the body
after consumption. During fermentation, microorganisms, such as bacteria, yeast, and
molds, produce enzymes that break downcomplex molecules into simpler forms that
are more easily absorbed by the human digestive system. For example, fermentation
can convert proteins into amino acids, carbohydrates into simple sugars, and lipids into
free fatty acids [41]. Food crops, particularly cereals and legumes, contain phytic acid, a
compound that binds to minerals such as iron, zinc, calcium, and magnesium, thereby
reducing their bioavailability [42]. During fermentation, microorganisms such as LAB
produce phytases that degrade phytic acid, thereby releasing these bound minerals and
making them more accessible for absorption in the human gastrointestinal tract [43]. For
example, the fermentation of soybeans, a common practice in Asian cuisines, increases the
bioavailability of iron and zinc, which are typically low because of the high phytic acid
content of raw soybeans [40].
The low bioavailability of minerals in plant-based foods is often due to their binding
to non-digestible compounds, which form complexes that the human digestive system
struggles to break down. Fermentation offers a solution by degrading these complexes,
thereby freeing minerals and making them more accessible [44]. For example, fermentation
Fermentation 2025, 11, 15 8 of 29
has been found to increase the levels of minerals, such as zinc, calcium, iron, and magne-
sium, in certain fermented foods, largely due to the reduction of phytates [45]. However,
the apparent increase in mineral content during fermentation may also result from the loss
of dry matter as fermenting microorganisms break down proteins and carbohydrates [46].
Moreover, by breaking down anti-nutrients such as phytates and oxalates that form com-
plexes with minerals, fermentation further enhances the bioavailability of minerals such as
iron, phosphorus, and calcium [47]. As shown in Table 1, these effects are highly influenced
by the specific strains of microorganisms used, the fermentation conditions, and the type of
food matrix.
Table 1. Effects of microbial fermentation on nutrient bioavailability in various food substrates.
Food
Substrate
Fermentation
Method Microorganisms/Strains
Lactobacillus
Species (New
Name)
Effect on
Nutrient
Bioavailability
Effect on
Anti-Nutrients Reference
Fish
Fermentation
with Bacillus,
LAB, yeast
Aerococcus NJ-20,
Bacillus subtilis JM-3,
Pediococcus pentosaceus
NP6
-
Antioxidant
activity,
bioactive
peptides
Bioactive
peptides [24]
Koreeb seeds Natural
fermentation - -
Enhanced
bioavailability
of minerals (Fe,
Zn, Ca)
Reduced phytic
acid and oxalic
acid
[45]
Sorghum Yeast
fermentation Saccharomyces cerevisiae - Increase in
protein content
Reduced phytic
acid [46]
Rice Natural
fermentation - -
Enhanced
bioavailability
of Zn
Reduced phytic
acid [48]
Horse gram Natural
fermentation - -
Enhanced
utilization in
functional
foods
Reduction of
tannins and
phytates
[49]
Quinoa Fermentation
with LAB Lactobacillus plantarum
Lactiplantibacillus
plantarum
299v®
Enhanced
bioavailability
of minerals (Fe,
Zn, Ca)
Reduced phytic
acid [50]
Soybean Fermentation
with LAB
Lactobacillus fermentum
B4655, L. plantarum
B4495, Lactobacillus casei
B1922, Lactobacillus
acidophilus B4496,
Lactobacillus bulgaricus
CFR2028
Limosilactobacillus
fermentum
B4655, Lactiplan-
tibacillus
plantarum
B4495,
Lacticaseibacillus
casei B1922,
Lactobacillus
delbrueckii
CFR2028
Enhanced
bioavailability
of minerals
(Mg, Ca, Zn)
Reduced phytic
acid, increased
mineral content
[51]
Soybean Fermentation
with LAB Lactobacillus -
Enhanced
bioavailability
of minerals (Fe,
Mg, Zn, Ca)
- [52]
Sorghum Natural
fermentation - -
Increased
calcium,
manganese,
iron
Reduced phytic
acid [53]
Fermentation 2025, 11, 15 9 of 29
Table 1. Cont.
Food
Substrate
Fermentation
Method Microorganisms/Strains
Lactobacillus
Species (New
Name)
Effect on
Nutrient
Bioavailability
Effect on
Anti-Nutrients Reference
Quinoa Fermentation
with LAB L. plantarum Lactiplantibacillus
plantarum
Increased iron
content,
reduced phytic
acid
Iron [54]
Rice Fermentation
with LAB
Lactobacillus spicheri DSM
15429
Levilactobacillus
spicheri DSM
15429
Increased
mineral
bioavailability
(Fe, Zn, Mg)
Iron, zinc,
magnesium [55]
Whole wheat
flour
Fermentation
with
Pediococcus
strain
P. pentosaceus -
Enhanced
mineral
solubility (Ca,
Mg)
Calcium,
magnesium [56]
Carrot juice Fermentation
with LAB
Lactobacillus gasseri DSM
20604, DSM 20077 No change
Increased
polysaccha-
rides, decreased
monosaccha-
rides
Decreaseed
monosaccha-
rides
[57]
Soybean
(legume)
Fermentation
with LAB Lactobacillus -
Enhanced
protein
digestibility
Reduced tannin
levels [58]
Italian
legumes
Fermentation
with LAB
L. plantarum C48 and
Lactobacillus brevis AM7
Lactiplantibacillus
plantarum C48,
Levilactobacillus
brevis AM7
Increased FAAs,
soluble fibers,
and total
phenols
Decreased
tannins [59]
Soybean Fermentation
with Bacillus Bacillus subtilis natto -
Significant
increase in
isoflavone
aglycone levels,
increased
SCFAs
Polysaccharide
content was
significantly
decreased
[60]
Lentils
Fermentation
with edible
fungus
Pleurotus ostreatus -
Increased
digestible
protein and
polyphenol
content
Change in
protein [61]
Soybean meal Yeast
fermentation S. cerevisiae -
Increased crude
protein and
essential amino
acid content
Amino acids,
protein [62]
Wheat flour
Mixed
fermentation
of LAB and
yeast
L. paracasei LG0260,
L. plantarum LG1034,
Lactococcus lactis LG0827,
S.cerevisiae J2815 and
S. cerevisiae J8202
Lacticaseibacillus
paracasei
LG0260, Lacti-
plantibacillus
plantarum
LG1034
Increased acids,
aldehydes,
esters
Decreased
polyphenol and
phytic acid
[63]
Faba bean
Fermentation
with LAB and
yeast
L. plantarum,
Saccharomycopsis
fibuligera
Lactiplantibacillus
plantarum
Improved
antioxidant
activity,
increased
phenols and
flavonoids
Reduced
tannins and
phytates
[64]
Note: Species names have been updated to reflect the recent reclassification of the Lactobacillus genus. For clarity,
the new nomenclature is provided in a ‘Lactobacillus species (new name)’ column alongside the old names where
applicable, as shown in the table.
Fermentation 2025, 11, 15 10 of 29
Enzymes such as α-amylase and phytase, which are produced during fermentation,
help degrade starch and phytate, respectively, breaking down the complexes that limit
mineral absorption. Some fermenting microbes can also break down dietary fibers, further
loosening the food matrix and releasing bound minerals [48]. However, the effectiveness
of fermentation can be influenced by food composition; for example, fiber may reduce
the availability of specific minerals. Methods such as seed germination and incubation
with enzymes such as polyphenol oxidase or phytase (through fermentation) can enhance
mineral availability by reducing the levels of phytate or tannins [49]. Fermentation also
lowers the pH, which promotes iron absorption by converting ferric iron to the more
absorbable ferrous form and creates an optimal environment for phytase activity to de-
grade phytate. Grinding food materials before fermentation can further enhance mineral
bioavailability by breaking down the cellular structure and increasing the surface area for
phytase activity [50].
As summarized in Table 1, various studies have demonstrated that fermentation
processes, using different microorganisms, significantly enhance the bioavailability of
nutrients in various food substrates. These improvements are primarily attributed to
the breakdown of anti-nutrients such as phytic acid, as well as the conversion of complex
proteins and carbohydrates into more bioavailable forms. Studies have shown that different
fermentation methods can improve mineral bioavailability in plant-based foods. For
instance, one study demonstrated the effectiveness of five strains of LAB, Lactobacillus
fermentum B4655 (now known as Limosilactobacillus fermentum), L. plantarum B4495, L.
casei B1922 (now known as Lacticaseibacillus casei), L. bulgaricus CFR2028 (now known
as Lactobacillus delbrueckii), andL. acidophilus B4496, in enhancing mineral bioavailability
in soymilk. After 24 h of fermentation at 37 ◦C, these strains significantly reduced the
phytic acid content and increased the levels of magnesium and calcium in fermented
soymilk compared with the control sample [51]. Bahaciu et al. [52] examined the effects of
germination and fermentation using Lactobacillus on the mineral bioavailability of soybean
seeds. They found that germination for four days at 25 ◦C increased zinc, magnesium,
iron, and calcium levels by 28.04%, 15.77%, 22.31%, and 48.76%, respectively, compared to
untreated samples. Following fermentation, these levels increased even further to 40.87%,
43.41%, 59.56%, and 53.4% for zinc, magnesium, iron, and calcium, respectively.
Research has also demonstrated the positive effects of fermentation on mineral
bioavailability in other grains. Natural fermentation reduced phytic acid levels in sorghum
and finger millet by 64.8% and 72.3%, respectively, after 96 h and increased calcium, man-
ganese, and iron bioavailability [53]. Similarly, fermenting quinoa flour with L. plantarum
for 16–18 h at 30 ◦C significantly increased iron content and reduced phytic acid levels
compared to unfermented samples [54]. Recent studies have confirmed that fermentation
with specific LAB strains like L. spicheri DSM 15429 (now known as Levilactobacillus spicheri),
can enhance the levels of various minerals in rice sourdough [55]. In addition, fermentation
with phytase-producing organisms such as Pediococcus pentosaceus strains improves mineral
solubility in whole wheat flour by approximately 30% [56]. Fermentation also reduces the
number of monosaccharides by converting them into polysaccharides. This relationship
was observed in fermented carrot juice, in which 52% more polysaccharides and 27% fewer
monosaccharides were detected. This was probably due to the enzymatic conversion of
simple sugars to insulin by fructosyltransferases produced by starter microorganisms such
as L. gasseri DSM 20604 and DSM 20077 [57].
Fermentation can increase the digestibility of proteins by breaking them down into
peptides and free amino acids (FAAs). This is particularly important in legumes such as
soybeans, which are known for their high protein content, as well as for inhibitors that
affect protein absorption. For example, fermentation with Lactobacillus species enhances
Fermentation 2025, 11, 15 11 of 29
the digestibility of soy proteins, thereby improving their bioavailability [58]. In line with
this, controlled fermentation using L. plantarum C48 and L. brevis AM7 (now known as
Levilactobacillus brevis) led to an increase in FAA content across all the legumes studied
in [59], corresponding to a reduction in tannin levels. Specifically, in soybeans, the sub-
stantial protein content resulted in a notable increase in FAA concentration, from 3.74 to
64.30 µg/mL, which is likely due to the active protease produced by B. subtilis natto [60].
Similar findings were observed in fermented lentils, in which the amount of digested
protein was significantly higher [61]. Additionally, a recent study by Cao et al. [62] demon-
strated improvements in soybean meal through yeast fermentation, with the crude protein
and acid-soluble protein content reaching 542.5 g kg−1 and 117.2 g kg−1, respectively, and
an increase in essential amino acid content by 17.9%. This further supports the role of
fermentation in enhancing the nutritional quality and digestibility of legume proteins.
Studies have shown that the fermentation of grains, vegetables, etc., can reduce in-
hibitors, thereby increasing the bioavailability of these essential minerals. However, the
degree of bioavailability enhancement can be highly variable, depending on the specific
microorganisms, fermentation conditions, and the food matrix involved. This variability
poses a challenge in standardizing fermentation protocols to achieve consistent nutritional
outcomes. To address this, future research should focus on understanding the specific path-
ways and microbial actions responsible for enhancing bioavailability. Advanced analytical
techniques such as metabolomics and proteomics could help clarify the mechanisms by
which microbial biotransformation improves nutrient absorption, leading to more targeted
and reliable fermentation processes.
4.2. Reduction in Anti-Nutritional Factors
Anti-nutritional factors are compounds present in various foods that can interfere with
the digestion and absorption of nutrients. Examples of such substances include goitrogens,
phytic acid, saponins, tannins, amylase inhibitors, lectins, antivitamins, and protease
inhibitors. Plants produce these compounds as a protective strategy against predators and
to enhance their survival under adverse conditions [65]. Anti-nutritional factors in food
can be either resistant or sensitive to heat. Yegrem [66] and Samtiya et al. [67] highlighted
that proteinase inhibitors present in seeds block the activity of enzymes, such as trypsin,
pepsin, and other proteases in the digestive system, thus hindering protein digestion and
absorption [65,67]. In contrast, tannins can inhibit the activity of digestive enzymes and
reduce the absorption of key nutrients, including proteins and carbohydrates [66].
Given these challenges, methods to mitigate the impact of anti-nutritional factors are
essential for improving the nutritional quality of foods. One such method is microbial
biotransformation through fermentation, which has been proven effective in reducing
these compounds. Phytic acid is a significant anti-nutritional factor in cereals and legumes.
Microbial fermentation activates phytase production, leading to phytic acid degradation.
This process increases the bioavailability of minerals, FAAs, and proteins and decreases
the inhibitory effects of phytic acid on mineral absorption [63]. Fermented foods such as
tempeh [68] and sourdough bread [63] contain a significantly lower level of phytic acid
than their non-fermented counterparts. For example, Fang et al. [63] showed that mixed
fermentation using Lactobacillus paracasei LG0260 (now known as Lacticaseibacillus paracasei),
L. plantarum LG1034, Lactococcus lactis LG0827, and S. cerevisiae strains J2815 and J8202
could degrade up to 96.6% of the phytic acid in sourdough bread.
Additionally, a recent comparative study by Xu et al. [64] evaluated the effects of
solid-state fermentation (SSF) using L. plantarum and Saccharomycopsis fibuligera on the
anti-nutritional factors, nutritional value, and antioxidant activity of faba bean (Vicia faba L.)
meal. This study found that SSF with both S. fibuligera and L. plantarum significantly reduced
Fermentation 2025, 11, 15 12 of 29
tannin and phytic acid levels, while enhancing the nutritional quality and antioxidant
capacity of faba bean meal. Interestingly, SSF with L. plantarum was more effective in
decreasing tannins and increasing titratable acidity, trichloroacetic acid–soluble protein
content, and in vitro protein digestibility than SSF with S. fibuligera. However, fermentation
with S. fibuligera led to greater improvements in antioxidant activity, as well as higher
phenol and flavonoid contents.
Fermentation has also been shown to reduce other anti-nutritional factors in various
legumes. For example, the fermentation of chickpea sourdough using LAB strains signif-
icantly lowered the concentration of α-galactosides, which are associated with digestive
discomfort, such as flatulence and bloating. Raffinose and stachyose levels were reduced
by 88.3–92.3% and 97.7–99.1%, respectively [69]. Similarly, a 17% reduction in phytic acid
was observed in chickpea sourdough fermented with P. pentosaceus and P. acidilactici, along
with a significant decrease in stachyose and raffinose levels and the complete removal
of verbascose [69]. Comparable results were observed for other legumes such as kidney
beans, peas, lentils, and grass beans, where tannin and raffinose concentrations decreased
following fermentationwith L. brevis and L. plantarum [59].
Some legumes, such as pigeon peas, contain cyanogenic glycosides that release hy-
drogen cyanide, a toxic compound, upon enzymatic breakdown [70]. Fermentation with
bacteria such as L. plantarum has been shown to degrade these cyanogenic glycosides
into nontoxic substances [71]. In addition, the fermentation process generates beneficial
metabolites such as organic acids and bacteriocins, which inhibit the growth of undesirable
microorganisms that can produce harmful compounds [72].
In addition to reducing phytic acid and α-galactosides, fermentation also effectively
degrades tannins and certain polyphenols, further mitigating anti-nutritional factors. These
compounds, commonly present in cereals, legumes, and certain fruits, can bind to proteins
and minerals, thereby reducing their digestibility and bioavailability. Tannins also inhibit
the activity of digestive enzymes, limiting the absorption of key nutrients such as proteins
and carbohydrates. However, microbial fermentation can significantly reduce tannin
content through microbial action, improving the digestibility of proteins and increasing
the absorption of essential minerals such as iron and calcium. For example, the SSF of
sorghum, a tannin-rich grain, using L. plantarum, S. cerevisiae, R. oryzae, A. oryzae, and
Neurospora sitophila has been shown to reduce tannin and free phenolic content by 56.36%
and 23.48%, respectively. This reduction makes sorghum more nutritionally valuable
because it enhances protein digestibility and mineral bioavailability [73]. Moreover, the
biotransformation of tannins by L. plantarum strains, which produce extracellular tannase,
has been shown to significantly hydrolyze galloylated ellagitannins, releasing bioactive
phenolic metabolites such as gallic acid and pyrogallol, which enhance the nutritional and
health benefits of these compounds [74]. In addition, certain traditional fermented foods
involve the detoxification of naturally occurring toxins. For example, cassava contains
cyanogenic glycosides that release toxic cyanide upon consumption [75]. Fermentation
by microorganisms (mainly bacteria and fungi) breaks down these glycosides, thereby
reducing the risk of cyanide poisoning [75].
To maximize the benefits of microbial fermentation in mitigating anti-nutritional
factors, it is essential to refine and optimize fermentation conditions tailored to various
food matrices. Although fermentation has proven effective in reducing phytic acid, α-
galactosides, and tannins, precisely controlling factors such as the pH, temperature, and
microbial strain selection is challenging. To achieve optimal results, future research must
focus on developing tailored fermentation protocols for different food types and exploring
the potential of genetically modified or novel microbial strains that can efficiently degrade
Fermentation 2025, 11, 15 13 of 29
anti-nutritional compounds while preserving the sensory qualities and nutritional value of
the food.
5. Functional Properties of Fermented Foods
5.1. Development and Enhancement of Sensory Attributes
Fermentation not only enhances the nutritional value of food but also significantly
alters its functional properties, leading to improvements in sensory attributes, the devel-
opment of novel flavors and textures, and the enrichment of probiotic content. These
functional changes are driven by the metabolic activities of microorganisms that produce a
range of compounds that influence the taste, aroma, texture, and health-promoting qualities
of fermented food products.
One of the primary contributions of fermentation is its ability to develop and refine the
taste profiles of foods by increasing their complexity. For example, LAB, which are widely
used in the fermentation of dairy, vegetables, and cereals, produce lactic acid that imparts a
mild tangy flavor. This acidity enhances flavor, while also acting as a preservative, thereby
extending the shelf life of fermented foods. The microbial breakdown of carbohydrates into
simpler sugars can lead to subtle sweetness, whereas proteolysis produces peptides and
amino acids that contribute to the umami flavor, particularly in fermented soy products
such as miso and soy sauce [76].
The production of volatile aromatic compounds such as esters, aldehydes, and ketones
is another essential aspect of fermentation [76]. These compounds are responsible for
the characteristic smell of fermented foods, ranging from the pungent aroma of kimchi
to the fruity notes in fermented dairy products. The variety of microorganisms used
in fermentation influences the type of aromatic compounds produced. During cheese
fermentation, specific molds and yeasts create distinct aromatic profiles, ranging from mild
and buttery to sharp and pungent [77].
Texture modification is a key outcome of fermentation. Microorganisms break down
large macromolecules, resulting in various textural changes. For instance, during the
fermentation of dairy into yogurt, LAB produce exopolysaccharides (EPSs) that thicken
the product, resulting in a creamy texture. Similarly, yeast fermentation during bread
production produces carbon dioxide, creating a light and airy structure in leavened bread.
Vegetable fermentation also modifies texture by breaking down plant cell walls, making
products such as sauerkraut and pickles softer, while maintaining a satisfying crunch.
Additionally, the fermentation of soy products using L. plantarum has been shown to
enhance both flavor and texture. For instance, Monascus purpureus and Rhodotorula mucilagi-
nosa have been used in soy protein fermentation to produce meat-like pigments, with the
addition of L. plantarum improving both texture and flavor [78]. Other microorganisms,
such as B. amyloliquefaciens, B. subtilis, and B. polyfermenticus, also exhibit high protease
activity, producing peptides and amino acids that enhance both color and flavor, which
makes them useful in plant-based meat analogues [79–81].
In legumes, fermentation can significantly improve flavor profiles by reducing un-
desirable odors. For example, the fermentation of a soy drink with Lycoperdon pyriforme
reduced the “green” odor derived from hexanal and related compounds, improving the
sensory quality of the product [82]. Similarly, when LAB and yeasts such as Kluyveromyces
lactis, K. marxianus, and Torulaspora delbrueckii were used to ferment pea protein, the levels
of off-putting volatiles decreased, and esters with improved flavor were generated [83].
Studies on other legume-based products, such as chickpea bread and fava beans, have
demonstrated similar improvements in flavor and reductions in off-flavors through fer-
mentation [84,85].
Fermentation 2025, 11, 15 14 of 29
Flavor development during fermentation is the result of a series of biochemical pro-
cesses in which microorganisms produce enzymes that break down complex nutrients.
Proteases, lipases, and amylases play crucial roles in releasing peptides, fatty acids, and sug-
ars, which act as precursors of flavor and aroma compounds during fermentation [86]. As
fermentation progresses, these precursors are converted into various compounds, including
organic acids, alcohols, esters, and ketones, which shape the unique sensory attributes of
the final product [86,87]. Among these processes, proteolysis is particularly important for
flavor formation during LAB fermentation [86].
However, the improvement in flavor and the reduction in off-flavors are not universal
across all fermented products. Sensory changes depend on the specific product, microbial
strains used, and fermentation conditions, underscoring the importance of individually
evaluating and optimizing each fermentation process to achieve the desired flavor profile.
Recent studies have further underscored the impact of fermentation on sensory at-
tributes. For example, Cichońska et al. [88] demonstrated that germination followed by
fermentation could enhance both the nutritional and sensory qualities ofbean- and lentil-
based beverages. However, they also found that fermentation could introduce undesirable
volatile compounds, which could be balanced by adding complementary ingredients such
as raspberry–cranberry pulp. Similarly, Spaccasassi et al. [89] showed that L. fermentum,
L. lactis, and Lacticaseibacillus rhamnosus can improve flavor by reducing bitterness and
enriching the product with umami and salty notes.
Further innovations in fermentation for sensory enhancement include the work of
Nouska et al. [90], who explored the use of chickpea flour fermentation for sourdough bread
production. Their study showed that chickpea sourdough improved both the structural
and sensory properties of bread, producing a “butter-like” flavor owing to the production
of butyric and isobutyric acids.
Overall, microbial fermentation offers an effective means of developing novel flavors
and textures that cater to consumer demand for diverse taste experiences. It is especially
valuable in plant-based food industries, where fermentation creates flavors and textures
that mimic animal-based products [91]. This transformation of traditional raw materials
into entirely new sensory experiences has broadened the culinary appeal of fermented
foods, with examples such as tempeh gaining global popularity owing to their unique
textures and flavors [68].
Despite significant advancements in fermentation technology, several limitations hin-
der its full potential for improving the sensory attributes of food products. One major
challenge is the variability in flavor and texture outcomes, which can be inconsistent owing
to differences in microbial strains, fermentation conditions (such as temperature, pH, and
oxygen levels), and the composition of raw materials [88]. These variations often lead to
unpredictable results, particularly in large-scale production where consistency is critical.
This inconsistency is evident in plant-based food products, in which it is difficult to achieve
reproducible flavors that match those of traditional animal-based products [89]. Further-
more, the development of off-flavors during fermentation remains a persistent problem.
While fermentation enhances sensory attributes, it can also introduce undesirable tastes
and aromas, as observed in bean-based beverages, where volatile alterations negatively
impact flavor [88]. Such off-flavors often require the addition of complementary ingredients
to balance the sensory profile, complicating the production process and increasing costs.
Another limitation is the lack of universal microbial strains that can enhance sensory
attributes across different food matrices. A strain that works effectively in dairy or soy
products may not perform similarly in other plant-based foods, necessitating tailored
microbial strains for each category [79,82]. This need for customization highlights the
current gap in finding all-encompassing solutions to optimize fermentation outcomes.
Fermentation 2025, 11, 15 15 of 29
Additionally, fermentation often requires the use of multiple microbial strains to achieve
the desired sensory attributes, with each strain contributing uniquely to the flavor, texture,
and aroma. Although co-cultures can lead to superior results, managing competitive
interactions between microorganisms adds complexity to the fermentation process, making
it more difficult to replicate consistent sensory outcomes, particularly on an industrial
scale [84].
In the future, precision fermentation may offer promising potential. Advances in
biotechnology enable the selection or genetic engineering of specific microbial strains to
produce targeted sensory compounds, offering a more precise control over flavor and
texture development. This precision approach can tailor products to specific consumer
preferences and address current inconsistencies [91]. Furthermore, the discovery of novel
microbial strains from unexplored environments, such as extreme ecosystems, could in-
troduce unique fermentation properties and allow the creation of innovative flavors and
textures in food [87]. Additionally, integrating fermentation with modern food engineering
techniques, such as encapsulation or bioreactors, could enhance control over fermentation
processes, ensuring consistent outcomes while refining texture, flavor, and aroma [86].
As the consumer demand for minimally processed, sustainable, and functional foods
increases, fermentation technologies are likely to play a key role in meeting these needs.
Future research should focus on minimizing the formation of off-flavors by selecting
appropriate strains, optimizing the fermentation conditions, and employing innovative
technologies [86,88]. Addressing these challenges will further unlock the potential of
microbial fermentation as an ancient yet rapidly evolving tool in food production.
5.2. Probiotic Enrichment and Health Benefits
Fermented foods have been integral to human diets for nearly 10,000 years, and
their variety has expanded significantly in the 21st century. This growing diversity has
been accompanied by extensive research on the health benefits associated with fermented
foods, particularly the identification of bioactive peptides and microbial metabolites that
can positively impact human health. Each type of fermented food contains a unique
community of microorganisms, and upon consumption, these nutrients and microbes may
interact with the gut microbiome. Advances in metagenomics have enabled scientists
to explore these interactions at the species and strain level, revealing both the transient
and long-term colonization effects of fermented food strains on the gut, as well as their
influence on native gut microorganisms.
Since the early 1900s, fermented foods have been associated with positive health
outcomes. The proposed mechanisms by which these foods contribute to health include
(i) their direct nutritional value, particularly the bioactive compounds produced during
fermentation; (ii) the support they provide for the growth of indigenous gut microbes; and
(iii) the ability of microbes within fermented foods to survive the digestive process and
potentially integrate into the gut microbiome or compete with existing members. Figure 4
provides a concise overview of the beneficial effects of fermented foods on human health.
Diverse combinations of food matrices and microbial species have led to the develop-
ment of the numerous fermented foods and beverages available today. Although extensive
reviews have highlighted the health benefits of these products [92–94], the subsequent
discussion focuses on the health-promoting compounds produced during fermentation
and their potential benefits.
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Fermentation 2025, 11, x FOR PEER REVIEW 16 of 30 
 
 
of essential nutrients, such as vitamins, amino acids, enzymes, EPSs, short-chain fatty ac-
ids (SCFAs), organic acids, phenolic compounds, and bioactive peptides. These com-
pounds significantly enhance the nutritional and functional value of fermented foods. 
 
Figure 4. Impact of microbial bioprocessing on the health benefits of food products. Created with 
BioRender.com. 
During fermentation, the content of vital vitamins, including B2 (riboflavin), B9 (fo-
late), B12 (cobalamin), and K, increases significantly [97,98]. These vitamins are crucial 
precursors of coenzymes and play key roles in nucleic acid metabolism, post-synthesis 
protein modifications, and calcium binding in the bones [99]. Additional beneficial com-
pounds formed during fermentation include γ-aminobutyric acid (GABA), which protects 
against cancer and cardiovascular diseases while regulating blood pressure [100]; EPSs, 
known for their hypocholesterolemic, antioxidant, and immunomodulatory properties 
[101]; bioactive peptides with antimicrobial, anti-diabetic, anti-tumoral, and angiotensin-
converting enzyme (ACE)-inhibitory effects [102]; and SCFAs such as acetate, propionate, 
and butyrate, which are recognized for their hepatoprotective and hypocholesterolemiceffects [103]. 
One of the most significant health-promoting compounds derived from fermentation 
is a bioactive peptide produced through protein hydrolysis, which is facilitated by prote-
ases synthesized by fermenting microorganisms. These peptides have garnered consider-
able attention because of their diverse health benefits, including anti-hypertensive, anti-
cancer, anti-inflammatory, anti-diabetic, ACE-inhibitory, antimicrobial, anti-adipogenic, 
anti-mutagenic, anti-thrombotic, and anti-atherogenic properties [104]. Among the most 
researched peptides are ACE-inhibitory peptides that help manage hypertension by low-
ering blood pressure [105]. Commonly found in fermented milk products, peptides such 
as valyl-prolyl-proline and isoleucyl-prolyl-proline have been recognized as potential 
strategies for managing hypertension [102]. Milk fermented with L. lactis strains has 
shown efficacy in reducing blood pressure both in vivo and in clinical studies [102]. 
Recently, Chen et al. [105] identified punicalagin as the most potent ACE inhibitor, 
exhibiting the highest inhibitory activity, followed by compounds such as epicatechin, 
Figure 4. Impact of microbial bioprocessing on the health benefits of food products. Created with
BioRender.com.
Food is considered one of the most significant factors influencing the gut microbiome
throughout an individual’s life [95]. Fermented foods, which contain live or inactivated
microorganisms, along with bioactive components produced during fermentation, have
the potential to modulate the gut microbiome. The human body hosts a diverse range
of microbial communities across various sites, from the skin to the intestinal tract, which
play crucial roles in health and disease. Shortly after birth, microorganisms from the
environment colonize the mouth, digestive system, respiratory and urinary tracts, and skin,
becoming integral as normal or symbiotic microorganisms [96].
In recent years, a substantial amount of research has focused on understanding the
bioactive compounds and health benefits of fermented foods. Fermentation initiates a
series of biochemical reactions facilitated by various microorganisms, leading to the release
of essential nutrients, such as vitamins, amino acids, enzymes, EPSs, short-chain fatty acids
(SCFAs), organic acids, phenolic compounds, and bioactive peptides. These compounds
significantly enhance the nutritional and functional value of fermented foods.
During fermentation, the content of vital vitamins, including B2 (riboflavin), B9 (folate),
B12 (cobalamin), and K, increases significantly [97,98]. These vitamins are crucial precur-
sors of coenzymes and play key roles in nucleic acid metabolism, post-synthesis protein
modifications, and calcium binding in the bones [99]. Additional beneficial compounds
formed during fermentation include γ-aminobutyric acid (GABA), which protects against
cancer and cardiovascular diseases while regulating blood pressure [100]; EPSs, known for
their hypocholesterolemic, antioxidant, and immunomodulatory properties [101]; bioactive
peptides with antimicrobial, anti-diabetic, anti-tumoral, and angiotensin-converting en-
zyme (ACE)-inhibitory effects [102]; and SCFAs such as acetate, propionate, and butyrate,
which are recognized for their hepatoprotective and hypocholesterolemic effects [103].
One of the most significant health-promoting compounds derived from fermenta-
tion is a bioactive peptide produced through protein hydrolysis, which is facilitated by
proteases synthesized by fermenting microorganisms. These peptides have garnered consid-
erable attention because of their diverse health benefits, including anti-hypertensive, anti-
BioRender.com
Fermentation 2025, 11, 15 17 of 29
cancer, anti-inflammatory, anti-diabetic, ACE-inhibitory, antimicrobial, anti-adipogenic,
anti-mutagenic, anti-thrombotic, and anti-atherogenic properties [104]. Among the most re-
searched peptides are ACE-inhibitory peptides that help manage hypertension by lowering
blood pressure [105]. Commonly found in fermented milk products, peptides such as valyl-
prolyl-proline and isoleucyl-prolyl-proline have been recognized as potential strategies for
managing hypertension [102]. Milk fermented with L. lactis strains has shown efficacy in
reducing blood pressure both in vivo and in clinical studies [102].
Recently, Chen et al. [105] identified punicalagin as the most potent ACE inhibitor,
exhibiting the highest inhibitory activity, followed by compounds such as epicatechin, cate-
chin, chlorogenic acid, gallic acid, and ellagic acid, all of which are released from fermented
pomegranate juice by L. plantarum subsp. 1.2437. Although numerous research on bioac-
tive peptides has concentrated on their anti-hypertensive properties, other peptides with
additional health benefits have also been discovered in various food matrices. For instance,
Rendon-Rosales et al. [106] demonstrated the anti-thrombotic and cholesterol-lowering
effects of peptide fractions derived from milk fermented with specific L. lactis strains.
Furthermore, fermented products such as soybeans, kefir, and fish have been recognized
as valuable sources of bioactive peptides with hypolipidemic and hypocholesterolemic
effects [107,108]. These peptides may reduce blood lipid and lipoprotein levels by inhibiting
lipase activity, thus preventing cholesterol accumulation in the blood vessels. The inhibition
of lipase in the gut has been associated with lower postprandial triacylglycerol and fasting
low-density lipoprotein (LDL) levels, thereby promoting weight loss and improving the
LDL/high-density lipoprotein cholesterol ratio [108].
The antioxidant properties of fermented foods are also significant, stemming from an-
tioxidant molecules released during fermentation, including GABA, isoflavones, phenolic
compounds, and bioactive peptides. These compounds exhibit free radical scavenging ac-
tivities, thereby preventing oxidative damage [64]. The antioxidant capacities of fermented
foods are typically attributable to the presence of phenolic compounds. For example, Roc-
chetti et al. [109] observed that the total phenolic content increased after the fermentation of
quinoa and buckwheat by P. pentosaceus and L. paracasei. Similarly, Lorusso et al. [110] con-
firmed that L. plantarum and Lactobacillus rossiae (now known as Furfurilactobacillus rossiae)
strains enhance the antioxidant properties of cereal-based fermented foods. The phenolic
content of fruit- and plant-derived fermented foods also increases during fermentation, and
Mantzourani et al. [111] highlighted how L. plantarum ATCC 14917 significantly increased
the total phenolic content and antioxidant properties of pomegranate juice compared to
unfermented juice. Other studies have demonstrated that various Lactobacillus and Bifidobac-
terium strains can elevate phenolic acid levels and, consequently, the antioxidant properties
of several fruit-based beverages [112–114]. Additionally, fermented soybean products show
increased antioxidant activity and DNA damage protection after fermentation, owing to
higher total phenolics and flavonoids [115].
EPSs have also attracted considerable interest owing to their diverse health bene-
fits, including antioxidant, antimicrobial, immunomodulatory, hypocholesterolemic, anti-
diabetic, and anti-tumoral properties [101,116]. EPSs have been shown to effectively lower
cholesterol levels by binding to cholesterol and reducing its absorption [116,117]. Their
hypocholesterolemic effects have been confirmed in vivo through animal studies [118] and
human trials [119]. Recently, EPSs have been referred to as “guardians of the gut” due to
their chelating properties, which help mitigate heavy metal toxicity and promote better
health [120]. Some polysaccharides also act as prebiotics, which are fermented by intestinal
microbiota to produce SCFAs [121]. SCFAs such as acetate, propionate, and butyrate are the
main products of the gut microbiota catabolism of indigestible polysaccharides,