Advances in Fermentation Technology: A Focus on Health and Safety

Abstract

Fermentation represents a pivotal bioconversion process that enhances foodstuffs’ nutritional and sensory attributes while playing a crucial role in global food systems. Nevertheless, concerns about safety issues associated with microbial contamination and the production of biogenic amines are often understated. This review appraised recent advancements in fermentation technology, emphasising their association with the health and safety of fermented foods. Key advances include predictive microbiology models, in some cases achieving up to 95% accuracy in predicting microbial behaviour, and high-throughput sequencing (HTS) for microbial enrichment. In addition, advanced detection methods such as biosensors and PCR-based assays enable the rapid identification of contaminants, improving manufacturing processes and preserving product integrity. Advanced bioreactor technologies equipped with real-time monitoring systems have been shown to increase fermentation efficiency. Moreover, innovative packaging, artificial intelligence, machine learning models, and sensor technologies have optimised fermentation processes and contributed to tracking quality and safety in the blockchain technology supply chain, potentially reducing spoilage rates and showing a decrease in production times. This study also addresses regulatory frameworks essential for establishing robust safety protocols. Integrating advanced fermentation technologies is imperative to meet the growing global demand for safe fermented foods. Continuous research and innovation are needed to address safety challenges and promote industry practices prioritising health and quality, ensuring public safety and building consumer confidence in fermented products.

1. Introduction

Fermentation is a bioconversion process of significant scientific, local, and industrial importance. The metabolic activities of microorganisms, such as lactic acid bacteria, yeasts, and moulds, convert organic substrates into bioactive sub-stances [1]. Historically, fermentation has been used to enhance the organoleptic properties, nutritional content, and shelf life of foods, resulting in the development of numerous dietary staples, such as yoghurt, cheese, kimchi, tempeh, and kombucha in various global cultures [2]. These fermented foods are characterised by their unique sensory attributes and physiological benefits, including improved gastrointestinal health and immunomodulatory effects that are increasingly recognised in research [3].

The global market for fermented foods has experienced substantial expansion, driven by consumer demand for functional and minimally processed products. A recent projection study conducted by cognitive market research indicated that the market will reach a valuation of USD 890.8 billion by 2031, with a compound annual growth rate (CAGR) of 6.20% from 2024 to 2031 [4]. Such growth trajectory highlights the increasing integration of fermented foods into contemporary diets, with these products currently estimated to constitute approximately one-third of global food consumption. However, this expansion in consumption also necessitates more attention to critical safety concerns associated with these foods. Although fermentation is generally considered a natural process that inhibits pathogenic microorganisms, inadequate fermentation practices and insufficient hygiene measures, conversely, have been identified as the primary causes, alongside various other concerns, of the accumulation of biogenic amines, mycotoxins production, and the proliferation of harmful bacteria [5,6].

Foodborne illnesses are a significant global concern, as the World Health Organisation (WHO) indicates that there are more than 600 million infection cases each year and approximately 420,000 deaths, with over 30% of these instances associated with contaminated foods, some of which involve fermented foods [7]. As a result, regulatory authorities globally have implemented rigorous safety protocols and risk management frameworks.

Recent advances in fermentation technology have significantly improved approaches to ensuring the safety and quality of fermented foods. These innovations have transformed manufacturing methods, quality control protocols, and overall safety assurance of fermented produce. Among them are high-throughput sequencing (HTS), new predictive microbiology models, or novel contamination detection method such as biosensors and polymerase chain reaction (PCR)-based approaches [8,9,10]. Advancements in food fermentation technology are crucial for meeting the rising global demand for these foods, requiring a thorough examination of their health and safety implications to improve product integrity.

This review objectively provides a comprehensive evaluation of recent advancements in fermentation technology and control, taking into account the health and safety of fermented foods, with a focus on cutting-edge microbial control strategies, contamination detection methodologies, and preservation techniques. It addresses critical safety issues like pathogen control and product integrity, highlighting novel solutions like biosensor technology, PCR-based diagnostics, and innovative preservation methods. Moreover, the regulatory framework was addressed for its vital role in guiding stakeholders to advance safer and higher-quality products and scrutinizing innovative strategies within a rapidly evolving landscape.

2. Microbial Control of the Pathogens’ Growth—Biocontrol Strategies

2.1. Potential Health Hazards in Traditional Fermentation

Fermented food’s health and safety benefits largely depend on effective microbial management of pathogens during fermentation. Insufficient oversight and regulation can lead to significant health risks despite the many advantages of consuming these foods. Key risks associated with traditional fermentation include pathogenic bacteria growth, antibiotic resistance development, and toxic metabolite production, as illustrated in Figure 1. The characteristics of unsafe fermented foods and their associated health risks highlight the need for enhanced fermentation techniques and strict safety regulations to reduce these hazards. This underlines the importance of raising awareness and implementing monitoring measures to ensure fermented products’ microbiological safety and quality.

2.1.1. Pathogenic Contamination

Pathogenic contamination remains a significant concern in traditional fermentation practices, mainly through foodborne outbreaks with varying incidence rates influenced by regional factors, production practices, and food types. In 2021, 28 multistate foodborne outbreaks in the United States were specifically attributed to contaminated fermented, primarily involving Shiga toxin-producing E. coli (STEC, 14%), Listeria (29%), and Salmonella (57%), causing 15 deaths, 496 hospitalizations, surprisingly 1740 illnesses [11]. An outbreak of Shiga toxin-producing E. coli (STEC) O157 associated with kimchi in Canada involved 14 confirmed cases, with 91% of affected individuals (10 out of 11 interviewed) reporting consumption of a single brand (Kimchi Brand A), strongly implicating that product as the outbreak source [12]. The European Food Safety Authority (EFSA) reported that from 2018 to 2022, fermented foods represented approximately 1.2% of foodborne outbreak incidents in the EU [13].

Specific fermented foods that are particularly susceptible to microbial contamination include animal products (meat and dairy products), cereal-based fermentations, and fermented fruits and vegetables (kimchi, sauerkraut). The risk of outbreaks is heightened by factors such as inadequate hygiene practices, unregulated fermentation conditions, and the use of contaminated raw materials, all of which can significantly promote the growth of pathogenic bacteria in ready-to-eat foods [14]. Studies have indicated the high prevalence rates of S. aureus (46.3%), Salmonella (26.0%), and E. coli (33.8%) [15]. Recent studies have reported that traditionally fermented dairy products have substantial issues with microbiological safety, highlighting the need for improved techniques and regulations to ensure their safety and quality. For instance, a study in Iran revealed that 65% of traditional dairy samples were contaminated with at least one pathogenic bacteria, including Listeria monocytogenes (27.5%) and Staphylococcus aureus (59.5%) [16]. Similarly, research in Zambia identified pathogens in raw milk used for Mabisi production, although the final products met safety limits [17]. In Portugal, L. monocytogenes and coagulase-positive staphylococci, exceeding 10⁴ CFU/g, were detected in 15.6% and 16.9% of cured raw milk cheeses, respectively [18]. Additionally, an Ethiopian study found S. aureus in 24.6% of raw milk samples and 17.5% of yoghurt samples, with 38.5% of methicillin-resistant isolates [19]. Pathogenic bacteria, such as L. monocytogenes and Staphylococcus aureus, have been reported in Portuguese fermented sausages. Factors contributing to their proliferation include delayed fermentation processes and insufficient acidification [20].

Pathogenic contamination is a significant concern in dairy and other fermented products, including soy products, fruits, and vegetables. For instance, research has indicated that contaminants are particularly prevalent in fermented soy products, highlighting the need for effective control measures. These measures should encompass rigorous screening of raw materials, the optimization of fermentation processes, and the incorporation of specific inhibitors during fermentation to reduce contaminant levels significantly. Several enteric pathogens, such as Clostridium botulinum and E. coli, have been identified in traditional fermented foods from Northeast India [21]. In addition, Bacillus cereus has shown significant prevalence in Korean fermented soybean products, with detection rates reaching up to 73.1% in the fermented paste known as doenjang [22].

A study that evaluated the microbiological hazards in fermented vegetables sold in wet markets in Cambodia revealed alarming rates of contamination of Enterococcus spp. (34%), followed by Bacillus spp. (31%), other coliform bacteria (24%), and E. coli (10%). Furthermore, fermented mixed vegetables showed an even higher contamination rate of coliform bacteria (50%) than single-type fermented vegetables (13%). These contamination issues have been attributed to inadequate hygiene practices [23]. Alcoholic beverages are generally considered as microbiologically safe due to their intrinsic physical and chemical properties, including high carbon dioxide, high alcohol content, low oxygen, low pH, and antimicrobial agents [24]. Nonetheless, some foodborne pathogens can survive within these environments, with studies showing that bacteria like Listeria, E. coli, and Salmonella can persist in low-pH products like apple cider and juice concentrates for several weeks [25]. Pathogens inoculated in beetroot or watermelon juice were effectively controlled through combined treatments with organic acid or lemon (Citrus limon) extract and mild heat. Heating the juices to 55 °C for 5 min resulted in log reductions of less than 2.0 for E. coli O157:H7, Salmonella typhimurium, and L. monocytogenes populations. However, the addition of 1.0% organic acid or 20% lemon extract, along with mild heat, significantly enhanced the effectiveness of the treatment, achieving further log reductions of 2.2 to 5.0 logs for E. coli O157:H7, 4.5 to 5.0 logs for S. Typhimurium, and 1.5 to 5.0 logs for L. monocytogenes [26]. The chemical compounds produced during the fermentation process of these beverages provide a partially favourable environment for microbial survival despite their inherent antibacterial properties. A comprehensive investigation into the survival of pathogenic bacteria and their spores in fermented alcoholic beverages, including beer and rice wine, is crucial for accurately assessing potential health risks associated with these products [25]. Therefore, a comparative analysis of contamination rates in different regions and types of fermented products is essential as it provides a comprehensive framework for understanding the global implications of microbial safety in fermentation practices.

2.1.2. Biogenic Amine Formation

Another potential health hazard in fermented foods is the formation of biogenic amines (BAs), particularly histamine, tyramine, and putrescine, which are produced through amino acid decarboxylation pathways during fermentation [27]. This biochemical process is catalysed by substrate-specific decarboxylase enzymes produced by certain bacteria, fungi, or yeasts; recent studies have identified that typical genes for decarboxylases targeting histidine, tryptophan, arginine, and ornithine are prevalent in fermented foods. Primary histamine production has also been linked to the Lactococcus, Enterococcus, and Lactobacillus genera, while tyramine production is predominantly associated with Bacillus and other specific genera [28]. The accumulation of BAs depends on multiple factors, including the substrate availability (free amino acids from proteolysis), the presence of decarboxylase-positive microorganisms (Staphylococcus, Enterobacteriaceae, and some lactic acid bacteria [LAB]), and environmental conditions such as temperature, pH, and oxygen levels. Elevated temperatures (25–37 °C) and anaerobic conditions typically promote BA-producing LAB; on the other hand, acidic environments (pH < 5.0) can induce microbial decarboxylase activity as a mechanism for pH regulation [29,30,31]. For example, fish sauce fermentation studies reported histamine levels exceeded the FDA limit of 50 mg/kg after 12 months, reaching 55.59 mg/kg. Notably, the accumulation of BAs is primarily attributed to dominant bacteria, such as Tetragenococcus and Halomonas, present in fish sauce [32]. Another research on Cambodian fermented fish products revealed that some samples contained histamine levels above the FDA guideline [33]. Elevated BA concentrations characterize meat sausages and fish sauces. Research has demonstrated that tyramine levels are particularly significant in luncheon meats, while high levels of cadaverine have been detected in corned beef. The biogenic amine index (BAI) serves as a vital criterion for assessing the quality of meat products, categorizing them as follows: spoiled (BAI > 50 mg/kg), poor quality (BAI 20–50 mg/kg), acceptable (BAI 5–20 mg/kg), and good quality (BAI < 5 mg/kg) [34].

Furthermore, a study conducted by Kandasamy et al. [35] revealed that domestically ripened cheeses exhibit notable total BA levels, with cheddar reaching 257.71 mg/kg and semi-hard Gouda ranging from 292.79 to 384.33 mg/kg. In stark contrast, imported ripened cheeses demonstrate even more concerning BA concentrations; for instance, Pecorino Romano showed a frightening total BA level of 1889.75 mg/kg, while Grana Padano recorded 1237.80 mg/kg, both surpassing the 1000 mg/kg threshold. In these imported varieties, histamine constituted approximately 86% of the total BA content in Pecorino Romano and 77% in Grana Padano. Another study further identified considerable variability in the average BA levels in fermented vegetables available in the Polish retail market, with the total BAs measured ranging from 30.29 ± 16.43 mg/kg in fermented olives to 612.1 ± 359.33 mg/kg in fermented Brussels sprouts. The BA profiles were predominantly composed of putrescine (42%), tyramine (20%), cadaverine (18%), and histamine (8%), cumulatively accounting for 88% of the nine studied BAs. Consequently, excessive BA consumption can lead to adverse reactions such as migraines, tachycardia, cardiovascular issues, respiratory problems, gastrointestinal disturbances, headaches, and allergic responses in sensitive individuals [36]. To address this issue, studies have identified potential starter cultures with high BA reduction capabilities to mitigate these risks, including Staphylococcus nepalensis and S. xylosus and a selection of strains of microorganisms that do not produce or have a low probability of synthesizing biogenic amines [32]. Traditional microbiological strategies for controlling BA production primarily focus on the suppression of BA-producing microorganisms through rigorous hygienic practices, such as pasteurization, and the use of starter cultures that are devoid of decarboxylase genes [37]. In this regard, acidification (pH < 4.5) and salt (NaCl > 10%) have proven effective in inhibiting decarboxylase activity, especially in fermented meats, fish, and cereal-based products [38]. Moreover, promising advanced technologies have introduced innovative solutions, including bacteriophage that specifically targets BA-producing pathogens without affecting beneficial LAB; for example, bacteriophage 156 reduced tyramine by over 95% and putrescine by 77.85% in cheese [39]. Non-thermal technologies, including high-pressure processing (HPP) and pulsed electric fields (PEF), have been shown to inactivate decarboxylase enzymes and spoilage microbes while preserving food quality [40].

2.1.3. Mycotoxin Contamination

Mycotoxins pose another critical safety concern, particularly in grain and soybean-based products [41]. Specifically, common mycotoxins found in Southeast Asian fermented foods include ochratoxin, citrinin, and aflatoxins [42]. Among these, aflatoxin B1 is particularly problematic; indeed, studies have documented its presence across various fermented products [41,43]. Several strategies have been proposed to address mycotoxin risks, including the use of appropriate starter cultures and stringent control measures during the pre-harvest, harvest, and post-harvest stages [42,43]. More importantly, LAB, particularly Lactiplantibacillus plantarum, has demonstrated promise in reducing free aflatoxin B1 levels by up to 90% during fermentation [43]. Furthermore, novel eco-friendly biocontrol approaches were explored to prevent mycotoxin contamination in fermented foods [41]. Consequently, discussing and making decisions regarding the regulatory frameworks governing mycotoxin levels in fermented products could provide a more comprehensive understanding of the current safety measures.

2.1.4. Antimicrobial Resistance

Fermented foods can serve as reservoirs for antimicrobial resistance genes (ARGs), particularly in spontaneously fermented plant-based foods, which cause added risks due to the lack of controlled starter cultures [44,45]. ARGs, such as those conferring resistance to tetracyclines, penicillins, chloramphenicol, and macrolides, have been identified in LAB and coagulase-negative staphylococci [44]. Although many resistance traits in LAB are intrinsic, horizontal gene transfer remains a potential risk [46]. Furthermore, the food supply chain offers multiple pathways for ARG transfer, causing direct risks to humans from resistant microbes in fermented foods and raising safety concerns about a farm-to-gut antimicrobial resistance pipeline [44,47].

Despite these inherent risks, LAB also produces bacteriocins, which are natural antimicrobial compounds effective against foodborne pathogens. These compounds present viable alternatives to conventional preservatives, especially amid the increasing consumer demand for clean labels and natural antimicrobials [48,49]. Thus, monitoring ARGs throughout fermentation becomes essential as LAB can act as conduits and barriers for the spread of antimicrobial resistance (AR). Therefore, careful strain selection and continual monitoring during fermentation are crucial in mitigating the risks associated with AR [50]. Consequently, the standardization of ARG monitoring protocols and the development of comprehensive risk assessment frameworks represent urgent research priorities within the domain of fermented foods.

In summary, effectively controlling microbial control through targeted biocontrol strategies is critical for maintaining the safety and quality of fermented foods. A more profound comprehension of the associated microbial risks and the implementation of suitable prevention measures is essential to safeguarding public health while allowing consumers to reap the benefits of fermented products.

2.2. Detection and Biopreservation for Food Fermentation and Safety

The safety and quality of fermented foods are critical due to the risk of contamination by harmful pathogens and toxins during production. Recent advancements in detection techniques, as presented in Table 1, have markedly improved the identification of these contaminants in diverse fermented food products. Recent advancements in real-time PCR assays have significantly improved the detection of foodborne pathogens in fermented and ready-to-eat foods. Multiplex PCR methods have been developed to simultaneously detect multiple pathogens, including Salmonella spp., Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli O157 [51]. These assays demonstrate high sensitivity, with detection limits as low as 10–100 CFU/mL or CFU/g, and can provide results within 4–8 h [51,52]. Combining enrichment steps with multiplex PCR has further enhanced the reliability and effectiveness of pathogen detection in diverse fermented food samples. Ngamwongsatit et al. [53] developed a multiplex PCR assay that can simultaneously identify six common foodborne pathogens: Salmonella spp., Escherichia coli, Klebsiella pneumoniae, Shigella spp., Yersinia enterocolitica, and Yersinia pseudotuberculosis in different food matrices. The assay demonstrated a sensitivity threshold of 100 fg, corresponding to roughly 20 bacterial cells. Additionally, novel molecular targets have been identified for specific detection of Staphylococcus species, enabling rapid and accurate monitoring in various food matrices [54]. These advanced monitoring technologies offer significant potential for improving quality control processes in the food industry.

Advances in multi-omics approaches have revolutionised our understanding of fermented foods and biopreservation strategies. These techniques provide comprehensive insights into microbial communities, their interactions, and metabolic processes during fermentation [55,56]. Multi-omics analyses offer more accurate identification of microbial and molecular features than single-omics approaches, including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. This integration allows for better elucidation of flavour formation mechanisms and fermentation processes in various food matrices [56]. In biopreservation, omics techniques have contributed to the selection of biopreservation agents and improved understanding of their mechanisms of action within food ecosystems [57]. These advancements emphasise the importance of considering food as a complex, dynamic microbiome requiring integrated engineering strategies to address safety, environmental, and economic challenges in the agri-food sector.

Implementing blockchain technology in the fermented food supply chain can significantly enhance traceability and transparency. This technology allows for real-time tracking of products from farm to table, which is crucial for quickly addressing safety concerns. The integration of blockchain can provide consumers with detailed information about the origins and handling of fermented foods, thereby increasing trust and accountability within the industry [58]. The NUTRIA project employed blockchain technology within the Swiss dairy supply chain, effectively developing a decentralized application that streamlines data collection while bolstering consumer confidence by providing immutable information [59]. In a related effort, Casino et al. proposed a blockchain-based framework to enhance traceability within food supply chains, utilizing smart contracts for automation. They detailed its implementation through a real-world case study involving a local private dairy company, demonstrating its practical applications [60]. Furthermore, Tan and Ngan, introduced a blockchain-based traceability system specifically designed to combat food fraud and safety concerns in the Vietnamese dairy sector. This system addresses various challenges, including adulteration, contamination, and forgery, enhancing overall food safety [61]. In a separate but noteworthy study, Cocco et al. developed a decentralized application that integrates radio-frequency identification (RFID) and near-field communication technologies with blockchain in the bread supply chain [62]. Their innovative solution offers significant advantages for supply chain participants, including improved operational efficiency, cost reductions, time savings, and better resource optimization. As the demand for transparency in food production continues to grow, blockchain technology presents a viable solution to enhance safety and quality in the fermented food sector.

To sum up, integrating modern biotechnology methods, including efficient starter cultures and sophisticated omics technologies, can positively enhance fermentation processes while reducing dangers associated with pathogenic microbes and biogenic amine production. This not only helps with the safety of fermented food but also retains the sensory variety and nutritional advantages that traditional techniques provide. Prioritizing food safety in fermentation techniques may enhance public health outcomes and increase customer confidence in fermented products.

Table 1. Examples of advanced contamination detection techniques for fermented foods.

Technology	Food	Contamination Type	Detection Limit	Application	Cost	References
HPLC with Fluorescence Detection	Fermented soybean products (ganjang, doenjang, gochujang)	Aflatoxins	Not detected to 6.06 μg/kg	Detection of aflatoxins in complex food matrices	Moderate	[63]
Multiplex PCR with Macroarray	Milk, meat products	Pathogenic bacteria (E. coli, Listeria, Salmonella)	100 cells/mL or g	Accurate and time-saving simultaneous detection of multiple bacteria	Moderate	[64]
MALDI-TOF MS	Dairy products, fermented beverages, seafood, pork	Bacteria, fungi, yeasts	Not specified	Rapid and accurate identification of microorganisms	Moderate to high	[65]
Dispersive Liquid-Liquid Microextraction with HPLC	Fermented fish, wine, beer	Biogenic amines	0.0010 to 0.0026 mg/L	Simultaneous determination of multiple biogenic amines	Low	[66]
CdTe Quantum Dots/Nano-TPP-OCH3 Fluorescence Sensor	Chinese spirits, yellow rice wine, Pu-erh tea, soy sauce	Toxic carcinogen (ethyl carbamate)	7.14 μg/L	Sensitive and accurate detection of ethyl carbamate	Low to moderate	[9]
Potentiometric Stripping Analysis (PSA)	Dairy products	Heavy metals (Pb, Cd, Cu)	Pb: 1.7 μg/L, Cd: 0.30 μg/L, Cu: 3.8 μg/L	Direct determination of heavy metals	Low	[67]

Table 1. Examples of advanced contamination detection techniques for fermented foods.

Technology	Food	Contamination Type	Detection Limit	Application	Cost	References
HPLC with Fluorescence Detection	Fermented soybean products (ganjang, doenjang, gochujang)	Aflatoxins	Not detected to 6.06 μg/kg	Detection of aflatoxins in complex food matrices	Moderate	[63]
Multiplex PCR with Macroarray	Milk, meat products	Pathogenic bacteria (E. coli, Listeria, Salmonella)	100 cells/mL or g	Accurate and time-saving simultaneous detection of multiple bacteria	Moderate	[64]
MALDI-TOF MS	Dairy products, fermented beverages, seafood, pork	Bacteria, fungi, yeasts	Not specified	Rapid and accurate identification of microorganisms	Moderate to high	[65]
Dispersive Liquid-Liquid Microextraction with HPLC	Fermented fish, wine, beer	Biogenic amines	0.0010 to 0.0026 mg/L	Simultaneous determination of multiple biogenic amines	Low	[66]
CdTe Quantum Dots/Nano-TPP-OCH3 Fluorescence Sensor	Chinese spirits, yellow rice wine, Pu-erh tea, soy sauce	Toxic carcinogen (ethyl carbamate)	7.14 μg/L	Sensitive and accurate detection of ethyl carbamate	Low to moderate	[9]
Potentiometric Stripping Analysis (PSA)	Dairy products	Heavy metals (Pb, Cd, Cu)	Pb: 1.7 μg/L, Cd: 0.30 μg/L, Cu: 3.8 μg/L	Direct determination of heavy metals	Low	[67]

3. The Effectiveness of Innovative Methods in Fermented Food Safety Assurance

3.1. Biological and Technological Approaches

Recent advancements in managing pathogenic and spoilage microorganisms highlight the transition from traditional to modern safety protocols. Despite their historical significance, labour-intensive and time-consuming processes sometimes differentiate conventional systems. These methods often lack the accuracy and sensitivity necessary for successful microbiological safety monitoring [68,69]. Conversely, modern procedures use swift and automated analytical techniques that enhance operating efficiency and increase accuracy and sensitivity, ultimately advancing global food safety. Traditional methods are advantageous for their cost-efficiency and accessibility. Still, despite elevated initial expenses, modern approaches provide significant long-term economic gains, particularly in extensive industrial and food production environments [70,71]. This paradigm shift underscores a substantial revolution in the food sector, emphasizing the increasing need for novel technological solutions to tackle the intricate challenges of microbiological safety in fermented foods.

Generally, traditional fermentation methods rely on manipulating factors such as temperature and time and utilizing selective and non-selective starter cultures (LAB, yeasts, and moulds) associated with natural preservation techniques like curing, pickling, and smoking. However, these methods can sometimes overlook subtle shifts in microbial populations. Nevertheless, challenges such as batch variations, the production of undesirable compounds, and the necessity for prolonged fermentation periods are common due to the mixed-culture fermentation approach. In contrast, modern techniques, non-thermal processing technologies (e.g., pulsed electric fields and high-pressure processing), enzymatic monitoring of chemical markers, and precisely selected starter cultures to ensure a tightly controlled fermentation process aimed at enhancing the flavour and quality of fermented foods often face obstacles, as consumers increasingly demand safe, healthy, and functional foods with superior quality [72,73,74]. Functional microorganisms play a crucial role in enhancing the safety and quality of fermented products, as they significantly influence both the microbial community and metabolic processes during fermentation [75]. A comparison of traditional and modern methods for microbial safety in fermented foods is summarized in Table 2.

Furthermore, strategies to enhance the safety of fermented foods have focused on both technological and biological approaches (Table 3). High-pressure processing (HPP) has shown promise in reducing pathogenic and spoilage organisms while maintaining the beneficial microbiota. Recent studies have explored innovative approaches to control Listeria monocytogenes in fermented sausages while maintaining product quality. HPP at 600 MPa for 5 min, combined with bioprotective starter cultures, effectively reduced L. monocytogenes populations by over 4 log CFU/g in dry-fermented sausages [76,77]. A novel multi-hurdle approach combining mild HPP (300 MPa), bacteriophage P100, and bacteriocinogenic Pediococcus acidilactici achieved a 5-log reduction of L. monocytogenes in traditional fermented sausages [78]. This HPP-assisted biocontrol method enhanced safety and preserved the product’s physicochemical, organoleptic, and microbiological characteristics throughout storage [79]. These studies demonstrate that HPP, especially when combined with bioprotective cultures or other antimicrobial agents, can significantly improve the safety of fermented sausages without compromising their quality or sensory attributes.

Moreover, sensor-integrated systems are increasingly being applied to optimise fermented food production and other manufacturing processes. Electronic noses and tongues can monitor fermentation in real-time, while gas chromatography and nuclear magnetic resonance technologies analyse flavour metabolism [80]. Combining online sensors with machine learning enables predictive modelling for various food manufacturing applications, improving resource efficiency [81]. Internet of Things (IoT) technologies allow real-time monitoring of fermentation parameters, remote process control, and predictive analysis of fermented products [82]. Sensor integration in machining equipment provides deep process insights, enabling condition monitoring, model fitting, and real-time control [83]. These advancements in sensor technology and data analysis allow manufacturers to enhance product quality, optimise processes, and reduce operational risks across various industries, including food fermentation and machining processes.

Generally, the progress in fermentation technology, especially with the incorporation of real-time monitoring and sophisticated biotechnological techniques, offers considerable potential to improve the safety of fermented foods (Figure 2). Using modern methods for pathogen detection alongside multi-omics strategies can significantly enhance the quality control processes within the food industry, leading to a deeper understanding of microbial communities. Producers should also prioritize adopting these innovative technologies to effectively mitigate risks associated with pathogenic microbes and biogenic amine production. Moreover, blockchain technology for traceability can enhance consumer trust by offering clear information regarding product origins and safety handling practices. Implementing these strategies enhances food safety while maintaining traditional fermentation methods’ sensory and nutritional advantages. This, in turn, positively impacts public health and boosts consumer confidence in fermented products.

Table 2. Selected studies and safety implications of the latest developments in fermentation technology.

Aspect	Traditional Methods	Modern Methods	References
Detection techniques	Culture-based methods using selective and non-selective enrichment; sensory evaluation by humans	High-throughput “omics” technologies; molecular profiling (e.g., DNA sequencing); biosensor and nanosensor-based techniques; instrumental techniques (e.g., E-nose, HPLC, gas chromatography–mass spectrometry).	[84,85,86]
Microbial control	Conditions such as temperature and time; use of starter cultures such as LAB, yeasts, and moulds; controlled Fermentation	Non-thermal processing technologies (e.g., pulsed electric fields, high-pressure processing); enzymatic approaches for monitoring chemicals; starter cultures for controlled fermentation.	[87,88,89,90]
Safety and quality assurance	Natural preservation methods (pickling, curing, and smoking); traditional disinfection methods (e.g., heat, chemical preservatives); good manufacturing practices (GMP) and hazard analysis	Intelligent bionic sensing technologies (e.g., visual, olfactory, tactile, gustatory); hurdle technologies combining multiple methods; advanced disinfection technologies (e.g., UV-light, cold plasma); quality assurance protocols.	[91,92,93,94,95]

Table 2. Selected studies and safety implications of the latest developments in fermentation technology.

Aspect	Traditional Methods	Modern Methods	References
Detection techniques	Culture-based methods using selective and non-selective enrichment; sensory evaluation by humans	High-throughput “omics” technologies; molecular profiling (e.g., DNA sequencing); biosensor and nanosensor-based techniques; instrumental techniques (e.g., E-nose, HPLC, gas chromatography–mass spectrometry).	[84,85,86]
Microbial control	Conditions such as temperature and time; use of starter cultures such as LAB, yeasts, and moulds; controlled Fermentation	Non-thermal processing technologies (e.g., pulsed electric fields, high-pressure processing); enzymatic approaches for monitoring chemicals; starter cultures for controlled fermentation.	[87,88,89,90]
Safety and quality assurance	Natural preservation methods (pickling, curing, and smoking); traditional disinfection methods (e.g., heat, chemical preservatives); good manufacturing practices (GMP) and hazard analysis	Intelligent bionic sensing technologies (e.g., visual, olfactory, tactile, gustatory); hurdle technologies combining multiple methods; advanced disinfection technologies (e.g., UV-light, cold plasma); quality assurance protocols.	[91,92,93,94,95]

Table 3. Key development and safety implications of the latest developments in selected fermented food.

Food Product	Key Development	Key Findings and Safety Implications	References
Fermented beverages	Isolation and application of beneficial microorganisms	- Isolation of Clavispora lusitaniae for ethyl carbamate degradation. - Effective reduction of carcinogenic compounds in beverages, enhancing safety.	[96]
Fermented mullet fish	Application of controlled fermentation processes	- Using Lactiplantibacillus plantarum and Saccharomyces cerevisiae for improved safety and quality. - Enhanced safety through controlled fermentation, reducing spoilage risks.	[97]
Korean traditional soybean paste	Use of selected starter cultures	- Comparing microbial contamination with and without starter cultures. - Starter cultures significantly improved safety by controlling microbial populations.	[98]
Buffalo fermented milk	Using next-Generation 16S rRNA Amplicon Sequencing	- Use of Lactobacillus fermentum NMCC-14. - Higher protein content, water-holding capacity, and dynamic viscosity; safe for consumption with no histological dysfunctions in mice.	[99]
Fermented fruits		- Bacterial community structure and functional prediction using sequencing. - Improved understanding of beneficial microbial diversity enhances safety assessments. - The results showed that fermentation is a safe and reliable process since pathogenic bacteria were absent in the fermentation products.	[100]
Cattle and poultry feed	XPC™ (pathogen mitigation tool)	- Use of Saccharomyces cerevisiae fermentation products. - Reduced prevalence, load, virulence, and antibiotic resistance of Salmonella and E. coli O157:H7; enhanced immunocyte killing of Salmonella.	[101]
Kefir	Novel functional starter development	- Development of non-yeast kefir using Lactobacillus acidophilus KCNU and Lactobacillus brevis Bmb6. - Stable microbial composition, improved disease activity index score in mice, and enhanced sensory properties.	[102]
Traditional Chinese fermented vegetables (Jiangshui)		- Isolation and safety assessment of Lactiplantibacillus plantarum WYH. - Inhibition of Aspergillus flavus growth, no hemolysin activity, absence of antimicrobial resistance genes, and no toxicity in mice.	[103]
Fermented soy products	Microbiome analysis using shotgun metagenomics	- Identified harmful bacteria (e.g., Klebsiella) and antibiotic resistance gene transfer risks.	[104]
Sausage	Application of PCR, plasmid profiling and sequencing to identify antibiotic resistance genes	- Antibiotic resistance in sausages showed a very moderate risk in Staphylococcus xylosus. - Staphylococcus xylosus was recommended to be considered as a European QPS approach.	[105]
Low-Salt Fermented Chilies	Using high-throughput sequencing, controlled fermentation	- Reduced spoilage bacteria and biogenic amines; improved flavour and safety through LAB interactions. - The inhibition rate of Enterobacter hormaechei has increased by 80.31%.	[106]
Traditional Chinese Pu-erh tea	Integrated meta-omics approaches for characterizing the microbiome	- The analysis showed that microbiota played an essential part in fermentation by producing enzymes involved in polysaccharide degradation and phenolic compound metabolism, resulting in changes in metabolite content, which impacted the safety and quality of Pu-erh tea.	[107]

Table 3. Key development and safety implications of the latest developments in selected fermented food.

Food Product	Key Development	Key Findings and Safety Implications	References
Fermented beverages	Isolation and application of beneficial microorganisms	- Isolation of Clavispora lusitaniae for ethyl carbamate degradation. - Effective reduction of carcinogenic compounds in beverages, enhancing safety.	[96]
Fermented mullet fish	Application of controlled fermentation processes	- Using Lactiplantibacillus plantarum and Saccharomyces cerevisiae for improved safety and quality. - Enhanced safety through controlled fermentation, reducing spoilage risks.	[97]
Korean traditional soybean paste	Use of selected starter cultures	- Comparing microbial contamination with and without starter cultures. - Starter cultures significantly improved safety by controlling microbial populations.	[98]
Buffalo fermented milk	Using next-Generation 16S rRNA Amplicon Sequencing	- Use of Lactobacillus fermentum NMCC-14. - Higher protein content, water-holding capacity, and dynamic viscosity; safe for consumption with no histological dysfunctions in mice.	[99]
Fermented fruits		- Bacterial community structure and functional prediction using sequencing. - Improved understanding of beneficial microbial diversity enhances safety assessments. - The results showed that fermentation is a safe and reliable process since pathogenic bacteria were absent in the fermentation products.	[100]
Cattle and poultry feed	XPC™ (pathogen mitigation tool)	- Use of Saccharomyces cerevisiae fermentation products. - Reduced prevalence, load, virulence, and antibiotic resistance of Salmonella and E. coli O157:H7; enhanced immunocyte killing of Salmonella.	[101]
Kefir	Novel functional starter development	- Development of non-yeast kefir using Lactobacillus acidophilus KCNU and Lactobacillus brevis Bmb6. - Stable microbial composition, improved disease activity index score in mice, and enhanced sensory properties.	[102]
Traditional Chinese fermented vegetables (Jiangshui)		- Isolation and safety assessment of Lactiplantibacillus plantarum WYH. - Inhibition of Aspergillus flavus growth, no hemolysin activity, absence of antimicrobial resistance genes, and no toxicity in mice.	[103]
Fermented soy products	Microbiome analysis using shotgun metagenomics	- Identified harmful bacteria (e.g., Klebsiella) and antibiotic resistance gene transfer risks.	[104]
Sausage	Application of PCR, plasmid profiling and sequencing to identify antibiotic resistance genes	- Antibiotic resistance in sausages showed a very moderate risk in Staphylococcus xylosus. - Staphylococcus xylosus was recommended to be considered as a European QPS approach.	[105]
Low-Salt Fermented Chilies	Using high-throughput sequencing, controlled fermentation	- Reduced spoilage bacteria and biogenic amines; improved flavour and safety through LAB interactions. - The inhibition rate of Enterobacter hormaechei has increased by 80.31%.	[106]
Traditional Chinese Pu-erh tea	Integrated meta-omics approaches for characterizing the microbiome	- The analysis showed that microbiota played an essential part in fermentation by producing enzymes involved in polysaccharide degradation and phenolic compound metabolism, resulting in changes in metabolite content, which impacted the safety and quality of Pu-erh tea.	[107]

Advanced fermentation technologies are increasingly emerging as a sustainable solution for food production as they use microbial and enzymatic systems to convert renewable resources into valuable food products effectively, as illustrated in Figure 3. Specifically, these methods incorporate agricultural waste and non-food feedstocks, such as cheese whey and other by-products, to produce high-value compounds, including lactic acid, proteins, and bioplastics [108]. This approach, therefore, reduces reliance on traditional agricultural inputs and helps mitigate environmental impacts. Moreover, the fermentation of agricultural waste directly addresses waste management issues while simultaneously promoting a circular economy by transforming low-value materials into protein-rich biomass suitable for human consumption and animal feed [109]. Furthermore, recent advancements in synthetic biology have enabled the engineering of microbes, which enhance the efficiency and yield of specific food components, such as flavourings and colourants, through environmentally sustainable methods that effectively replace conventional chemical synthesis [110].

3.2. Advanced Bioreactor Technologies with Real-Time Monitoring

Recent advancements in bioreactor technology have significantly improved fermentation processes through integrated sensors for real-time monitoring and control. These sensors continuously measure critical parameters such as pH, temperature, dissolved oxygen, and biomass concentration without sample requiring removal, reducing contamination risks and enhancing batch consistency [111]. Novel sensing technologies, including fluorescence and turbidimetry, have been developed to directly measure cell mass, substrate, and product concentrations [112]. Portable, multiplexed thread-based sensing microprobes have been demonstrated for continuous pH and ammonium ion monitoring during biofermentation [113].

Furthermore, integrating advanced sensors with software models has shown promise for process fingerprinting, smart control, and outcome prediction in biopharmaceutical manufacturing. These innovations drive the industry towards automation and smart manufacturing, improving understanding and outcomes in cell culture processes [10]. For instance, a study by Kreß et al. [114] demonstrated that bioreactors equipped with sensor-integrated monitoring systems significantly increased product consistency and reduced contamination risks. Integrating advanced online monitoring technologies within bioreactors allows for real-time adjustments to critical parameters, thereby enhancing the stability and reliability of cell cultures. This capability is crucial for maintaining optimal growth conditions and minimising the risk of contamination, which is often a significant concern in bioprocessing environments [114]. These innovations improved the overall efficiency of bioprocesses and contributed to producing high-quality biological products, aligning with industry demands for consistency and safety.

3.3. Smart Packaging and Sensor Technology for Supply Chain Monitoring

Smart packaging significantly advances food supply chain management by improving safety and quality through integrated sensors, indicators, and communication systems for real-time monitoring during transit and storage [115]. Benefits include enhanced traceability, reduced food waste, and improved consumer satisfaction, which is particularly crucial for perishable items like fermented foods. Continuous monitoring helps ensure safety throughout the supply chain [116,117,118]. As the field continues to evolve, smart packaging is poised to revolutionise food preservation and distribution practices.

Smart packaging equipped with time-temperature indicators and gas sensors enables ongoing feedback on product quality, facilitating early detection of spoilage or microbial growth. These materials monitor temperature, humidity, microbial growth, oxygen levels, pH, and chemical composition within packaged food, ensuring food safety throughout storage and transit. Active functions include ethylene and oxygen absorption and humidity control. In fruits and vegetables crucial for fermentation, smart technologies utilize freshness sensors and active strategies to minimize decay [119,120,121]. These innovations aim to minimise food losses, reduce waste in fruits and vegetables by monitoring environmental conditions in real-time, improve food quality and safety, and extend shelf life during distribution and storage, which is especially significant due to fermented foods’ often limited shelf life. However, challenges remain, including cost considerations, consumer acceptance, and regulatory aspects, which need to be addressed for commercial sustainability [122].

Incorporating agents like oxygen scavengers and moisture absorbers, these systems also employ phase change materials to maintain optimal temperatures. Smart applications enhance consumer understanding of expiration dates and inventory management [123]. Although various sensing systems based on food quality indicators are proposed, commercial application challenges remain. Future research should address safety concerns, legal regulations, and cost management to promote the broader adoption of intelligent packaging technologies specifically designed for the fermentation industry.

3.4. Artificial Intelligence and Machine Learning in Smart Fermentation Systems

Smart fermentation systems leverage machine learning (ML) and Internet of Things (IoT) technologies to optimise fermentation processes. ML applications in metabolic engineering systems enable efficient strain development and optimisation of metabolic flux [124]. These systems use advanced algorithms to analyse and optimise fermentation parameters, including temperature, humidity, and microbial composition. IoT technologies allow real-time monitoring of critical parameters and remote automation of production processes. Integrating constraint-based modelling with ML enhances predictability and efficiency in fermentation analysis [82,125]. Furthermore, ML techniques are increasingly applied across various biorefinery systems, including fermentation, to handle complex scientific tasks and support resource efficiency in the circular bioeconomy [126]. These advancements in smart fermentation systems represent a significant leap forward, offering greater control and efficiency in fermentation.

Integrating artificial intelligence (AI) and ML in food fermentation has significantly improved quality control and process optimisation. AI-based systems can enhance operational efficiency, predict sales, and improve food safety [127]. For example, an in-line monitoring strategy employing Raman spectroscopy to assess ethanol production through yeast fermentation (Saccharomyces cerevisiae) was introduced. By applying machine learning techniques for feature selection, this study effectively reduced the dimensionality of the Raman spectral data. The results demonstrated a significant decrease in model training time, exceeding 90%, while also improving the predictive accuracy for glycerol and cell concentration by 14.20% and 17.10%, respectively, measured at the root mean square error (RMSE) level. Additionally, the refined model, following hyperparameter optimization, shows enhancements in RMSE for ethanol, glycerol, glucose, and biomass, with 9.73%, 4.33%, 22.22%, and 13.79%, respectively [128].

In beer production, AI technologies like electronic noses and robotics have shown high accuracy in identifying fermentation types and predicting consumer acceptability. The research discussed the incorporation and application of AI technology utilising low-cost sensor networks in the form of an electronic nose (e-nose), robotics, and ML. The findings from the machine learning models demonstrated impressive accuracy (97%) in distinguishing between fermentation types (Model 1) based on data from the e-nose. Moreover, the models successfully predicted consumer acceptability using near-infrared data (Model 2; R = 0.90) and e-nose data (Model 3; R = 0.95) and analysed the physicochemical properties and colour metrics of beers sourced from e-nose data. Integrating RoboBEER with an electronic nose and advanced AI provides brewers with a sophisticated yet accessible solution for assessing the fermentation process. This approach enables precise evaluation of beer quality, pinpointing defects, ensuring traceability, and confirming product authenticity while maintaining cost-effectiveness [129]. The IoT enables real-time monitoring of fermentation parameters, remote automation, and predictive analysis of fermented food products [82]. Omics tools and bioinformatics approaches can characterise and trace fermented foods, predict metabolic outcomes, and enhance nutritional value while preserving traditional methods [130]. These technologies offer opportunities for improving food quality, safety, and production efficiency across various food industry sectors, from smart farming to restaurant management [127].

Predictive microbiology models integrated with sensor technologies offer promising advancements in food safety and fermentation control. These models can accurately predict microbial growth in various food products, enabling timely interventions and optimised processing conditions [131,132]. ML algorithms, particularly Random Forest, have shown high accuracy (>95%) in predicting foodborne pathogen presence [132]. As a matter of fact, one study explored the use of machine learning algorithms to assess the presence of Salmonella in ground chicken meat. Their findings indicated that the semi-supervised Random Forest model achieved the highest accuracy at 94%, along with a Kappa value of 82% and an 87% prediction rate. The model successfully identified virulence-associated genes, suggesting potential contributions to predictive modelling in food safety, including identifying pathogen sources, predicting antibiotic resistance, and evaluating foodborne pathogens [133]. Another study investigated the growth and inhibition limits of L. monocytogenes under various preservatives commonly used in the meat industry, along with pH as a control factor. They created a multifactorial logistic regression model to estimate the likelihood of growth, establishing two thresholds to define growth limits. At the first threshold (p = 0.0104), their model achieved a classification accuracy of 68.6%, with a true positive rate of 77.6% and a true negative rate of 45.5% for growth detected on PALCAM agar. The second threshold (p = 0.04) yielded an improved accuracy of 82.6%, with a true positive rate of 95.5% and a true negative rate of 80%. These insights can inform the development of ready-to-eat products that inhibit L. monocytogenes growth when stored at optimal temperatures [134]. Real-time environmental sensors and predictive models can significantly improve supply chain management and food safety [135]. However, limitations exist in modelling complex microbial interactions under dynamic conditions, necessitating ongoing research and development [136,137].

AI has shown the potential to enhance the management of microbial communities in fermentation processes, creating environments that support beneficial microorganisms and suppress harmful pathogens. Nonetheless, dependence on AI-driven algorithms could foster an excessive trust in automated systems, possibly neglecting the subtle human judgment essential in quality control. ML algorithms have become potent instruments in food safety, especially in forecasting microbiological behaviours that provide considerable public health hazards. With the incorporation of extensive datasets, these algorithms may exceed the restrictions of classic culture-dependent approaches. Supervised machine learning can enhance production processes by enhancing conventional microbiological testing rather than serving as an alternative. By anticipating microbial activity at critical production phases, these models may serve as proactive tools for food safety, allowing early intervention and better results.

3.5. Precision Fermentation for Targeted Compound Production

Precision fermentation involves using genetically engineered microorganisms to produce specific compounds and has raised essential safety considerations. While this technology has the potential to create high-quality fermented products with tailored health benefits, it also necessitates rigorous safety assessments to evaluate the potential risks associated with genetically modified organisms (GMOs) [138]. Recent studies have highlighted the importance of thorough testing to ensure these microorganisms do not introduce harmful traits, such as antibiotic resistance, into the food supply [139]. Regulatory frameworks are evolving to address these concerns, ensuring precision fermentation can safely be integrated into food production systems.

Unlike conventional fermentation, which relies on mixed microbial communities with broad metabolic outputs, precision fermentation offers a high degree of control over the types of compounds produced, potentially enhancing both the consistency and safety of fermented products. Fytsilis et al. [140] emphasised the need for rigorous safety assessments of precision fermentation products, particularly concerning potential allergenicity and metabolic by-products. For example, precision fermentation can be used to produce rare bioactive peptides that enhance immune response or improve gut health, thereby contributing directly to food safety. However, using genetically GMOs raises regulatory and consumer acceptance challenges. Traditional fermentation has a well-established safety profile and consumer trust, while precision fermentation, being a novel technology, requires clear regulatory oversight and transparent communication to gain broader acceptance.

4. Regulatory Frameworks and Global Standards of Fermented Foods

The regulations for food safety vary significantly among countries, but they usually try to guarantee the safe application of food cultures, which is the providers’ duty [141]. A detailed review of regulatory frameworks for fermented foods is discussed elsewhere [142]. Briefly, in Asia, governments such as Japan and South Korea have altered their regulatory methods to assess the safety of both conventional and innovative fermented foods [142]. Generally, Southeast Asia faces various challenges in fermentation, notably enhancing safety and quality without compromising the characteristic flavours and authenticity of the products [143]. To address these issues, the Japanese Ministry of Health, Labour, and Welfare has established updated guidelines for the safety evaluation of fermented foods, especially those that involve genetically modified microorganisms [144].

The enforcement of the European Union food safety regulation highlights mandating that all food products, including fermented foods, adhere to rigorous safety requirements [141]. These regulations cover all aspects of food manufacturing, from sourcing raw ingredients to distributing the end product, ensuring compliance with safety guidelines across the supply chain. Integrating hazard analysis and critical control point (HACCP) principles into the production of fermented foods significantly enhances safety protocols [145,146]. The European Food Safety Authority (EFSA) recommend compliance with stringent microbiological criteria, process hygiene standards, and risk assessment models to analyse the potential dangers associated with bacterial hazards in fermented foods, identify knowledge gaps, and prioritise future research to adapt safety standards to new challenges. Moreover, EFSA has developed the qualified presumption of safety (QPS) framework to streamline evaluating the safety of microorganisms used in food manufacturing. The recent evaluation involved 71 microorganisms reported to the EFSA between April and September 2023, of which 10 notifications pertained to 9 distinct taxonomic units assessed for their potential QPS status [147]. This regulatory method expedites the licensing process for microbial strains and bolsters customer assurance about the safety of fermented foods.

By creating a generally recognized as safe (GRAS) list, the U.S. Food and Drug Administration (FDA) has implemented specific regulations to reduce microbial hazards and maintain fermented food stability, avoiding hazardous microbial growth and preserving suitable pH levels [142]. The GRAS and the QPS system in the EU are sometimes claimed to be identical; nonetheless, they function at different levels and possess unique criteria. The GRAS approach evaluates safety at the strain level, requiring that particular strains of microorganisms be assessed and deemed safe based on scientific evidence and historical usage. As of December 2020, 736 novel food components, comprising 26 microorganisms, had been incorporated into the GRAS list, signifying an extensive procedure for strain-specific safety assessment. Conversely, the QPS method assesses safety at the species level, focusing on microorganisms that have a longstanding record of safe application in food and feed. This method requires a deep understanding of the species involved, including taxonomy, pathogenicity, and end-use factors, to ensure that the microorganisms are safe and have adequate historical evidence to support them [148].

Furthermore, the rise of innovative food sources and production methods has led regulatory authorities to confront the potential safety concerns related to emerging fermentation techniques. As plant-based fermented products gain popularity and unconventional fermentation agents are increasingly used, there is a pressing need for updated regulations to safeguard consumer health [149]. Consequently, regulatory frameworks are evolving to include a wider array of fermentation practices, reflecting the ever-changing landscape of the food industry.

5. International Harmonization of Safety Standards of Fermented Foods

The international harmonisation of food safety standards, particularly concerning fermented foods, is imperative for fostering global trade and enhancing consumer protection across national borders. The Codex Alimentarius Commission assumes a central role in formulating guidelines that nations may adopt to regulate fermented foods effectively [150]. A pertinent illustration of the positive economic implications of such standards is evident in the increase in South Korea’s kimchi exports and the rise in imports from China [151]. Additionally, the Global Food Safety Initiative (GFSI) enhances these efforts by establishing benchmarks for existing food safety standards against fundamental requirements, thereby fostering convergence and compliance among various regulatory frameworks [152].

However, divergent regulatory frameworks and varying institutional capacities across different countries impede the pursuit of harmonisation. The rapid expansion of the fermented food market has underscored the necessity for evolving regulatory frameworks; nevertheless, significant discord persists among jurisdictions [142]. To overcome these challenges, it is essential to promote international collaboration, policy harmonisation, and public-private partnerships, all vital for advancing global food safety initiatives and ensuring equitable access to safe and nutritious food [153].

The globalisation of food trade has necessitated efforts towards international harmonisation of safety standards for fermented foods. The Codex Alimentarius Commission, a joint initiative of the Food and Agriculture Organization (FAO) and the WHO, has been at the forefront of developing harmonised standards for fermented foods [154]. The Commission has recently updated its guidelines on the microbiological criteria for fermented foods, providing a framework for assessing the safety and quality of these products across different regions.

6. Conclusions

In conclusion, the rapid progress in the application of fermentation technology offers both prospects and challenges in safeguarding the health and safety of fermented foods. This review highlights the significance of understanding microbial dynamics and improving safety control measures to reduce hazards linked to foodborne pathogens in fermented products. Advanced technologies, including high-throughput sequencing, predictive microbiology models, and innovative contaminant detection tools, have greatly enhanced our ability to monitor and regulate fermentation. As consumer demand for fermented goods increases, regulatory frameworks must change concurrently, ensuring that safety requirements are maintained and updated to meet new hazards.

Future research should concentrate on several critical areas to further improve the safety and integrity of fermented foods. First, there is an urgent need for more thorough research on the long-term effects of biogenic amines and mycotoxins in fermented products to establish more precise safety thresholds and guidelines. Second, investigating microbial interactions during fermentation presents a significant opportunity to identify new microbial strains that can enhance consumer health and guarantee the stability of products. Moreover, machine learning and big data analytics for predicting fermentation results and microbial activity might transform quality and safety assurance protocols. These tools provide real-time monitoring and decision-making, optimising fermentation conditions across various production settings. However, searching for cost-effective methods involving many different analytical and IT methods should be investigated and upgraded to obtain the best results in food safety and environmentally friendly solutions. Finally, collaboration among food scientists, technologists, and regulatory agencies will promote innovation while ensuring consumer safety and health.