The quality of fermented foods is governed by the composition, function, and interactions of their microbial communities. However, fermentations carried out using traditional approaches are often variable with respect to their composition and are difficult to control, thereby limiting industrial reproducibility. Recent advances in omics technologies-including metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics-have greatly enhanced our ability to analyze and reconstruct the microbial ecosystems in fermented foods. This review first highlights the importance of omics analyses for characterizing microbial composition, metabolic potential, and functional interactions. It then discusses the bipartite structure of defined microbial consortia (DMCs), distinguishing between the core microbiome, comprising taxa consistently associated with fermentation performance, and the supplementary microbiome, consisting of variable species that influence flavor diversity and system stability. Finally, we describe a multi-omics-guided strategy for the design and refinement of DMCs, framed within the Assembly-Assessment-Redesign (A-A-R) workflow, which enables iterative optimization of microbial consortia for reproducible and desirable fermentation outcomes. Integrating omics insights with DMC engineering provides a systematic approach for precision fermentation, paving the way for next-generation fermented food production.

There is a growing appreciation of the health benefits of fermented foods, including their potential ability to modulate the microbiota-gut-brain axis. Such foods contain diverse microbial communities that can influence host phenotypes, although the mechanisms are poorly understood, especially in terms of modulating the central nervous system. Here, we analysed 820 fermented food microbial metagenomes for their potential to produce neuromodulatory metabolites. We identified health-associated functional diversity to be driven by abiotic factors such as food substrate categories and fermentation strategy, which critically influence fermented food production. We identified food substrates including brine, cereal, root, tuber and seed along with their food-associated microbial species to be rich in pathways pertaining to the production of neuromodulatory metabolites. Overall, we unravel key factors that shape the functional potential of fermented foods that will be an important resource for the development of optimised fermented foods and beverages to enhance brain health.

Consortia of microbial isolates, also known as synthetic communities (SynComs), are increasingly used to study and harness microbe-microbe and microbe-host interactions. Since “synthetic” potentially evokes negative connotations, we propose adopting the term “Defined Microbial Community” for practical applications.

The increasing generation of fruit waste represents a major environmental and economic challenge for the agri-food sector, while also offering significant opportunities for sustainable valorisation within the framework of the circular economy. Fruits rejected for cosmetic reasons, together with processing by-products, are rich sources of dietary fibre, sugars and bioactive compounds that can be converted into value-added products. This review aims to provide a comprehensive overview of microbial fermentation as a sustainable strategy for fruit waste valorisation, with particular emphasis on the role of lactic acid bacteria, acetic acid bacteria, yeasts and microbial consortia in improving the nutritional, technological and functional properties of fruit-derived substrates. Current evidence demonstrates that microbial fermentation not only preserves fruit biomass but also enhances its value through the degradation of complex carbohydrates, the biotransformation of phenolic compounds, the production of bioactive metabolites and the generation of functional ingredients. This review further discusses the contribution of viable microorganisms and postbiotic components to product functionality, as well as the importance of microbial viability, processing conditions and storage stability for the development of safe and functional fermented foods. In addition, it highlights recent advances in the use of microbial consortia and identifies the mechanisms governing microorganism-plant matrix interactions as a key area requiring further investigation. Overall, the available literature supports fermentation as a versatile and effective strategy for transforming fruit waste into high-value food products. By integrating current knowledge on microbial metabolism, functionality and processing challenges, this review identifies the main scientific and technological gaps and outlines future research priorities, including microbial consortium design, process scale-up, regulatory considerations and life cycle assessment, to facilitate the industrial implementation of sustainable fruit waste biorefineries.

Bifidobacteria are common members of the human gut microbiota and are associated with host health. Bifidobacterium longum subsp. longum (B. longum) is prevalent across host ages and can utilise diverse plant-derived glycans, including xylooligosaccharides (XOS), that are indigestible by humans. Here, we show that XOS utilisation is strain specific among members of B. longum. In B. longum NCIMB 8809, growth on XOS induced transcription of genes encoding three glycoside hydrolases (XouA, XouB, and XouC), together with adjacent genes (xouDEF) predicted to encode an ABC-type carbohydrate uptake system. Biochemical analyses demonstrated that XouA and XouC are β-xylosidases, whereas XouB is an α-arabinofuranosidase. Genetic disruption and complementation experiments showed that XouA and the XouDEF uptake system are required for growth on XOS. Together, these findings identify the genetic and enzymatic basis of XOS utilisation in B. longum and highlight how strain-level variation in carbohydrate metabolism may inform the design of targeted prebiotic and synbiotic strategies to promote gut health.

The increasing generation of fruit waste represents a major environmental and economic challenge for the agri-food sector, while also offering significant opportunities for sustainable valorisation within the framework of the circular economy. Fruits rejected for cosmetic reasons, together with processing by-products, are rich sources of dietary fibre, sugars and bioactive compounds that can be converted into value-added products. This review aims to provide a comprehensive overview of microbial fermentation as a sustainable strategy for fruit waste valorisation, with particular emphasis on the role of lactic acid bacteria, acetic acid bacteria, yeasts and microbial consortia in improving the nutritional, technological and functional properties of fruit-derived substrates.Current evidence demonstrates that microbial fermentation not only preserves fruit biomass but also enhances its value through the degradation of complex carbohydrates, the biotransformation of phenolic compounds, the production of bioactive metabolites and the generation of functional ingredients. This review further discusses the contribution of viable microorganisms and postbiotic components to product functionality, as well as the importance of microbial viability, processing conditions and storage stability for the development of safe and functional fermented foods. In addition, it highlights recent advances in the use of microbial consortia and identifies the mechanisms governing microorganism–plant matrix interactions as a key area requiring further investigation.Overall, the available literature supports fermentation as a versatile and effective strategy for transforming fruit waste into high-value food products. By integrating current knowledge on microbial metabolism, functionality and processing challenges, this review identifies the main scientific and technological gaps and outlines future research priorities, including microbial consortium design, process scale-up, regulatory considerations and life cycle assessment, to facilitate the industrial implementation of sustainable fruit waste biorefineries.

Listeria monocytogenes is an important foodborne pathogen and is a common contaminant of raw milk and meat products. It is also found in many sources such as soil, water, and vegetables. Pathogenic L. monocytogenes is the etiological agent of listeriosis that mainly affects certain risk groups such as the elderly, pregnant women, neonates, and immunocompromised patients. Of note, L. monocytogenes is almost exclusively transmitted to humans through food. New biological and environmental tools are needed to inhibit the proliferation of foodborne pathogens and to prevent spoilage microorganisms that contribute to food waste and the negative environmental sustainability impacts of food production and processing. These include biopreservation, which could be defined as a biological and effective method that involves the use of lactic acid bacteria strains and/or their metabolites, such as bacteriocins, to ensure the food safety of fermented foods without altering their organoleptic properties. Here, we discuss how lactic acid bacteria and their bacteriocins affect the proliferation of foodborne L. monocytogenes and spoilage microorganisms in cold-smoked salmon (CSS), dairy and meat products, and vegetables, when used as protective cultures or natural food additives. Thus, relevant cases of lactic acid bacteria and bacteriocins applications are presented as promising agents in agrifood industries.

Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.

BACKGROUND:Fermented foods can confer benefits to human health and modulate the microbiota-gut-brain axis. Fermented foods are gaining popularity in Western cultures, with increasing calls for their inclusion in national dietary guidelines. As no specific validated measure to capture fermented food intake exists, this study aimed to develop and validate a fermented food intake questionnaire (FFIQ) to assess habitual intake in adults from the United States, Canada, the United Kingdom, Ireland, Australia and New Zealand, aged 18-60 years. METHODS:A 32-item self-administered FFIQ, informed by available international food consumption data for adults, was developed and subsequently validated in an online sample of 167 adults using six online 24-h automated dietary recalls (intake24.com) as the reference method. Correlation and Bland-Altman analyses were used to assess agreement and bias between the FFIQ and the 24-h dietary recalls. RESULTS:The most frequently consumed fermented foods were cheeses, yoghurt, kefir and kombucha. Median (Interquartile range) intake of total fermented food was 85.4 (42.3, 143.0) g/day for the FFIQ and 54.9 (20.8, 112.1) g/day for the average of the 24-h dietary recalls, respectively and showed good agreement for total fermented food consumption (r = 0.56, p < 0.001) and for most individual fermented foods and food categories. The FFIQ classified 93.4% of participants in the same or adjacent tertile of total fermented food intake. Bland-Altman plots for total intake of fermented food demonstrated good agreement between the FFIQ and the 24 h recalls. The FFIQ also showed good to excellent reliability upon re-administration for most fermented foods as indicated by the intraclass correlation coefficients. CONCLUSIONS:The FFIQ provides a robust estimate of fermented food consumption among adults from English-first language countries. This will be a valuable resource with potential applications in clinical and epidemiological research aimed at exploring associations between fermented foods and health outcomes.

Artisanal raw milk cheeses harbour complex microbial communities that drive cheese making and shape sensory quality. Previous work on Idiazabal cheese identified rennet as a major microbial source, although all reservoirs contributed to varying degrees. However, their impact in terms of enzyme-encoding genes related to technological quality of cheese remained unexplored. Building on that, this study draws on metagenome-assembled genomes (MAGs) from cheeses and dairy environments to comprehensively identify enzyme-encoding genes involved in key biochemical processes. In cheese MAGs (Lacticaseibacillus paracasei), protease-encoding genes were dominated by ATP-dependent metalloproteases (M41), carbohydrate-active enzyme-encoding genes (CAZymes) by glycoside hydrolases (GH) and glycosyltransferases (GT), while esterase, lipase, and related-enzyme-encoding genes were restricted to sparse 'GDXG', type-B and esterase D families. Dairy environments emerged as major reservoirs of enzyme-encoding genes, with notable differences among sample types (p <= 0.001). The richest sources of protease-encoding genes were grass (610 genes), linked primarily to Pantoea agglomerans, and rennet (318), mainly related to Basfia sp. and Moraxella sp., dominated by metalloproteases (M23, M38) and serine proteases (S15). The largest reservoirs of CAZyme-encoding genes were food contact surfaces (1550), associated mainly with Salinisphaera sp. and Dietzia sp., and rennet (1505), related to, e.g., Bacteroides pyogenes, Alloprevotella sp., and Lentilactobacillus buchneri. Food contact surfaces were also the richest source of esterase, lipase and related-enzyme-encoding genes (1209), mainly linked to Dietzia sp., Corynebacterium sp., and Brevibacterium aurantiacum. Similarly, aroma-related enzyme-encoding genes (e.g., oppA, pepA, GH13, esterase D) were consistently detected in environmental matrices. These results provide novel insights into dairy microbiomes as functional reservoirs of aroma precursors, revealing their relevance for artisanal PDO cheese production and future biotechnological applications.

BACKGROUND:Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL. METHODS:In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500). RESULTS:Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia. CONCLUSIONS:MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.

Over the past two decades, scientific understanding of the composition and function of the human gut microbiome has expanded substantially. The recent surge in human gut microbiota-related studies has unveiled the profound influence of the gut microbiota on host nutrition, health, and behavior, bridging biology, medicine, and ecology, among others. The dynamic interaction between daily lifestyle choices, life events, and the gut microbiota makes it understandably, a topic of interest among the lay public. Communicating scientific insights from the laboratory to the population effectively, however, can be challenging, and might involve adapting the delivery of knowledge to different audiences, using precise language in corresponding settings and the use of more accessible concepts in public forums such as science festivals or social media. With the growing interest in gut microbiota beyond academic circles, there is also an increased risk of disseminating information lacking scientific rigor. The current study aimed to assess the general knowledge regarding the gut microbiota among an exploratory pool of participants, primarily accessed via academic and social networks, and evaluate healthcare professionals’ understanding of its links to various health conditions, ultimately informing better communication strategies for both groups. Our findings from this exploratory survey indicate that while most participants were familiar with the gut microbiota, instances of partial and even complete misconceptions persisted. The results from our survey further underlined the need for targeted scientific communication to emphasize the microbial diversity of the gut microbiota, the factors influencing it, its links to health conditions, and the realistic scope of current microbiota analyses.

Plant-derived pentose sugars represent a major nutrient source in the gut, yet their metabolism remains incompletely defined. Strains of the human gut commensal Bifidobacterium longum subsp. longum utilise arabinose- and xylose-containing glycans, which are found in the pectin and hemicellulose layers of plant cell walls. To gain insight into the metabolism of these two pentoses as well as ribose, a naturally occurring sugar and a component of RNA and ATP, we identified and analysed the genes responsible for their uptake and subsequent catabolism. Based on transcriptomic data and mutant phenotype analyses, we show that these three pentoses share a common, ABC-type uptake system encoded by penABCD. Furthermore, we identify a gene cluster, araBDA, and two genes, xylA and xylB, that are required for conversion of arabinose and xylose, respectively, into xylulose-5-phosphate, and rbsK, which converts ribose into ribose-5-phosphate. These intermediate metabolic products enter the bifid shunt, an energy-generating fermentative pathway typical of bifidobacteria. We also show that arabinose and xylose are co-metabolized, while xylose is preferentially utilised before ribose. This study provides molecular insights using a multi-omics approach, including comparative genomics and transcriptomics combined with mutational analysis, into how B. longum subsp. longum metabolizes pentose-containing plant glycans, common yet indigestible components of the adult human diet.

Effective cleaning and sanitation are essential in cheese manufacturing to control microbial contamination and prevent biofilm formation. A multi-step approach was undertaken to assess microbial persistence and cleaning-in-place (CIP) strategies at an industrial Cheddar cheese facility with a production capacity of similar to 40,000 tonnes. Pre- and post-CIP environmental swabs were analysed using plate counts and high-throughput (16S rRNA amplicon and shotgun) sequencing to identify microbial hotspots. Traditional CIP was broadly effective, however residual contamination persisted in critical zones such as the Alfomatic weir, curd distribution tank (CDT), and block formers. Industrial-scale trials comparing caustic and acid-based CIP with an enzymatic alternative revealed complete microbial elimination post traditional CIP, while enzymatic CIP left DNA signatures at one site, culturable cells were not detected. Sequencing identified Pseudomonas fluorescens as the dominant non-starter bacterium, suggesting possible biofilm formation. Parallel laboratory-scale studies of P. fluorescens biofilm removal using a CDC Biofilm Reactor (R) coupled with Scanning Electron Microscopy (SEM) compared caustic and enzymatic CIP. Caustic treatment completely removed the biofilm matrix but left adherent cells, while enzymatic treatments degraded the matrix but showed residual matrix fragments and adherent cells. Plate counts confirmed significant differences in residual biofilm populations, with average reductions of 3.75 log, 2.56 log, and 1.87 log after caustic, enzyme cocktail, and protease treatments, respectively (p < 0.0001), underscoring the incomplete nature of these approaches. Caustic CIP improves microbial reduction, while enzymes disrupt biofilm matrices. However, neither alone achieves complete removal, supporting combined strategies to enhance cleaning efficacy and sustainability in dairy processing.

Diabetes mellitus (DM), which encompasses Type 1, Type 2 and gestational diabetes, affects approximately 537 million adults, with prevalence continuing to rise. In addition to pregnancy, factors such as dietary choices, lifestyle and infections can lead to the development of DM. Given the increasing prevalence of DM, it is necessary to continue to identify approaches to control the release of insulin. Emerging evidence indicates that the gut microbiota plays a central role in mediating the metabolic effects of diet on the host, including the regulation of insulin secretion. Dietary interventions have been proven to be successful in this regard, but identifying foods and food components that influence insulin secretion is challenging due to the complexity of diet-microbiota-host interactions and the lack of fast and standardised screening tools. We have developed a novel screening framework based on the β-cell insulin response, using the human cell line EndoC-βH1 to assess candidate foods and ingredients with insulinotropic properties. As an initial proof-of-concept, we applied the framework to food ingredients, i.e., dairy-derived fermentates, which had first undergone simulated digestion followed by addition to an ex vivo colon model, allowing us to mimic the metabolic transformations taking place in the human gut. The processed colonic fermentation supernatants were then evaluated using a static and microfluidic platform, respectively, to capture dynamic insulin release profiles. Distinct fermentate compositions were associated with varying levels of insulin secretion. Our results suggest that this framework could be applied broadly to screen foods and food components for insulinotropic potential, providing an affordable approach for the development for anti-diabetic dietary applications.

IntroductionCheddar cheese is a nutritionally dense food matrix containing nutrients and bioactives with the potential to influence gut microbial characteristics. Food matrices influence nutrient absorption and digestibility, therefore the dairy matrix may affect gut microbial responses to dairy food intake. This research aims to identify gut microbial responses to Cheddar cheese consumption, considering aspects of the dairy matrix.MethodsSecondary analysis was conducted on a subset (n = 69) of participants’ data collected during a 6-week parallel 3-armed intervention study. Interventions involved daily consumption of one of the following: (A) 120 g unmelted Cheddar cheese; (B) 120 g melted Cheddar cheese; (C) butter (49 g), calcium caseinate powder (30 g), and Ca supplement (500 mg). Demographics, anthropometry, dietary intake and fecal samples were collected at baseline (V1) and post-intervention (V2). Fecal samples underwent 16S rRNA gene sequencing, followed by bioinformatic processing and statistical analysis.ResultsAt V1, 52% were female, mean age was 58.2 ± 5.4 years, with no significant differences between groups or timepoints. Following sequencing, 12,098 unique bacterial taxa in total were identified. Under a False Discovery Rate (FDR) cutoff of 0.1, Dorea (W = 0.568, FDR = 0.079) and Erysipelotrichaceae UCG-003 (W = 0.887, FDR = 0.097) were significantly increased from V1 to V2 in the unmelted cheese group. At V2, Bacteroides was differentially more abundant in the unmelted cheese group, relative to the melted group (W = 0.587, FDR = 0.034). Bacterial alpha diversity (Shannon, Simpson) significantly increased in the unmelted cheese group only from V1 to V2 (p < 0.05). Beta diversity analysis showed a significant group effect considering both timepoints (F = 1.505, p < 0.01). Considering V2 only, Principal Coordinate Analysis showed the unmelted group clustered more closely relative to the other groups, although the effect was not significant.DiscussionUnmelted Cheddar cheese modulated the gut microbiome by increasing alpha diversity and abundance of several fermenting bacteria. Overall community structure also became more similar following consumption of unmelted cheese, relative to the other groups. Heating cheese and altering its physical structure disrupts the dairy matrix, potentially influencing downstream gut-nutrient interactions and subsequent gut microbial response.

Fermented foods (FF) have long been integral to human diets, originally serving as a natural means of food preservation. Recently, they have gained renewed attention for their potential health benefits. This study, within the PIMENTO COST Action CA20128, aimed to map FF diversity, production volumes, fermentation technologies, challenges, and innovation trends across Europe and neighboring regions. Data were collected from 16 countries, including Northern, Southern, Western and Eastern Europe, as well as Türkiye and Morocco, via a structured questionnaire covering production and certification, fermentation technologies, limitations and innovation trends. Information was obtained from EU or national databases and direct consultations with associations, companies and producers. Results showed that dairy products dominate FF across all countries, followed by meat-, cereal- and plant-based products. Lactic fermentation was most prevalent, followed by alcoholic, acetic and mixed fermentations, depending on the raw material. Northern and Western European countries primarily use commercial starter cultures and standardized industrial processes, while Southern and Eastern regions maintain strong artisanal traditions relying on spontaneous or back-slopping fermentations. Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) certifications are concentrated in Southern Europe. Emerging innovation trends include low-fat, low-salt, hybrid (plant-animal) FF and probiotic-enriched products, aligned with several Sustainable Development Goals (SDGs). Key limitations include raw material scarcity, financial constraints for small producers and limited technology transfer. The diversity of FF, combined with a shared gastronomic heritage, underscores Europe's strong potential for sustainable innovation, sectoral growth and global leadership in fermented foods.

Mammals have species-specific adaptations to sustain growth during the suckling stage of life. These include species-specific milk composition and associated whey protein (WP)-to-casein (CN) ratio. Consuming milk (proteins) from other species may therefore cause different growth outcomes during early life. This systematic review examined the effect of intake of feeds with a high bovine WP-to-CN ratio on growth outcomes in infants, piglets, and rodent pups, focusing on milk and/or protein intake, body weight, and gut morphology and its cellular activity. The relevant studies were identified from PUBMedR using the keywords, "whey," "infant formula," and "growth" for infant studies and "whey" and "suckling stage" for animal studies. Of the original research articles reviewed (280 in total), 16 infant (with 3207 participants) and 13 animal studies met the imposed inclusion criteria and were independently reviewed by the authors. Data show that consumption of infant formula with bovine whey-to-casein ratio equal to or exceeding that of human milk (60:40), and with proteins supplying ≥8% of total energy, is associated with a discordance between energy intake and weight gain, consistent with net nutrient loss. Data from porcine and rodent models further indicate that the nutrient loss occurs because of reduced nutrient absorption through the gut, and that the effect appears to be driven primarily by bovine WP. We present further evidence supporting a role for gut microbiota in mediating the reduced nutrient absorption and that hydrolysis of bovine WP mitigates, at least some of, this effect and increases growth compared with formulas with intact proteins. We envisage that these findings, based on proteins sourced from cow's milk, will inform improvements in infant formula that increases nutrient absorption and support healthier growth using a protein content much lower than the current regulatory threshold of 1.8 g/100 kcal.

Water Kefir is a plant-based fermented beverage, traditionally produced on a small scale by fermenting a sucrose solution with fresh or dried fruits, using water kefir grains as inoculum. The grains are relatively simple communities that consist of both eukaryotes and prokaryotes, rendering them a paradigm for studying microbial ecology and interspecies interactions. Recently, water kefir has attracted growing research and industrial interest due to its potential and perceived health benefits. Owing to its increasing popularity, there is a growing demand for controlled and standardised production on an industrial scale. However, industrial-scale production remains a challenge due to the limited knowledge of the biological interactions of the microbial consortia and the lack of defined starter cultures. This review examines the current understanding of microbial and metabolic complexity of water kefir obtained from various omics studies. It further investigates the potential of an integrated multi-omics approach to elucidate mechanisms of microbial interactions and provides a roadmap for conducting multi-omics studies on fermented foods using water kefir as an example. This review also explores the potential application of genome-scale metabolic modelling in the development of functional and defined microbial communities for food fermentation. It identifies key challenges associated with such modelling and provides perspectives to address them. Finally, this review briefly discusses the regulatory challenges associated with the use of defined communities in food systems.

Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study found chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for chlorate mitigation. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4°C and after 24 hours when incubated at 25°C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4°C and 25°C, respectively. High abundances of ydeP and narG genes were observed for 4°C samples and were attributed to Pseudomonas and various low abundance genera, respectively. High abundances of the napA gene were noted in 25°C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterised genes, such as ydeP, belonging to the dimethyl sulfoxide (DMSO) reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasising the need for further biochemical characterisation of these genes to better understand the pathways involved in chlorate reduction in milk.