Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota

Microbiological quality and native lactic acid bacteria diversity of artisanal Mexican cheeses: A review

This review aims to provide an overview of artisanal Mexican cheeses microbiota focused on microbiological quality and safety, as well as native Lactic acid Bacteria (LAB) diversity. For the search, key words of artisanal Mexican cheeses varieties was carried out through several online databases and original articles were screened and data about populations of indicator microorganisms, presence of pathogens, and native LAB identified were extracted. Several artisanal Mexican cheeses exceeded the permissible limit established in Mexican regulation (NOM-243-SSA1-2010) for indicator microorganisms, as well as in some types of cheese, the presence of pathogens was confirmed. However, other varieties of artisanal Mexican cheeses possess unique physicochemical characteristics, and during their manufacturing particular steps are used that contribute to ensuring their quality and safety. Additionally, strains able to control the growth of pathogenic and spoilage bacteria are part of the microbiota of some artisanal Mexican cheeses. About native LAB diversity, it is composed by species of Lactobacillus, Enterococcus, Streptococcus, Leuconostoc, Weisella, Lactococcus, Pediococus, Aerococus, Carnobacterium, Tetragenococus, among others genera. Otherwise, artisanal Mexican cheeses represent an important source of specific LAB with several approaches within human health because they showed potential for the development of functional foods, nutraceutical, and bioprotective cultures.

Microbiological Evaluation of Two Mexican Artisanal Cheeses: Analysis of Foodborne Pathogenic Bacteria in Cotija Cheese and Bola de Ocosingo Cheese by qPCR

Cotija and Bola de Ocosingo are artisanal ripened cheeses produced in Mexico. Both are made with raw bovine milk from free-grazing cows and with no starter cultures. Unlike culture-based techniques, molecular methods for pathogen detection in food allow a shorter turnaround time, higher detection specificity, and represent a lower microbiological risk for the analyst. In the present investigation, we analyzed 111 cheese samples (95 Cotija and 16 Bola de Ocosingo) by qPCR (TaqMan®) after an enrichment-culture step specific to each foodborne bacterium. The results showed that 100% of the samples were free of DNA from Listeria monocytogenes, Brucella spp., Escherichia coli enterotoxigenic (ETEC), and O157:H7; 9% amplified Salmonella spp. DNA; and 11.7%, Staphylococcus aureus DNA. However, the threshold cycle (Ct) values of the amplified targets ranged between 23 and 30, indicating DNA from non-viable microorganisms. Plate counts supported this assumption. In conclusion, 100% of the cheeses analyzed were safe to consume, and the enrichment step before DNA extraction proved essential to discern between viable and non-viable microorganisms. Hygienic milking, milk handling, cheese manufacturing, and ripening are crucial to achieve an adequate microbiological quality of cheeses made with raw milk.

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome

Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.

Extraction of Proteins from Fermented Food

The metaproteomic approach allows a deep microbiome characterization in different complex systems. Based on metaproteome data, microbial communities' composition, succession, and functional role in different environmental conditions can be established.The main challenge in metaproteomic studies is protein extraction, and although many protocols have been developed, a few are focused on the protein extraction of fermented foods. In this chapter, a reproducible and efficient method for the extraction of proteins from a traditionally fermented starchy food is described. The method can be applied to any fermented food and aims to enrich the extraction of proteins from microorganisms for their subsequent characterization.

Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia

Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.

The Weissella and Periweissella genera: up-to-date taxonomy, ecology, safety, biotechnological, and probiotic potential

Bacteria belonging to the genera Weissella and Periweissella are lactic acid bacteria, which emerged in the last decades for their probiotic and biotechnological potential. In 2015, an article reviewing the scientific literature till that date on the taxonomy, ecology, and biotechnological potential of the Weissella genus was published. Since then, the number of studies on this genus has increased enormously, several novel species have been discovered, the taxonomy of the genus underwent changes and new insights into the safety, and biotechnological and probiotic potential of weissellas and periweissellas could be gained. Here, we provide an updated overview (from 2015 until today) of the taxonomy, ecology, safety, biotechnological, and probiotic potential of these lactic acid bacteria.

A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes

Biological control agents (BCAs), beneficial organisms that reduce the incidence or severity of plant disease, have been expected to be alternatives to replace chemical pesticides worldwide. To date, BCAs have been screened by culture-dependent methods from various environments. However, previously unknown BCA candidates may be buried and overlooked because this approach preferentially selects only easy-to-culture microbial lineages. To overcome this limitation, as a small-scale test case, we attempted to explore novel BCA candidates by employing the shotgun metagenomic information of the activated sludge (AS) microbiome, which is thought to contain unutilized biological resources. We first performed genome-resolved metagenomics for AS taken from a municipal sewage treatment plant and obtained 97 nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS)-related gene sequences from 43 metagenomic assembled bins, most of which were assigned to the phyla Proteobacteria and Myxococcota. Furthermore, these NRPS/PKS-related genes are predicted to be novel because they were genetically dissimilar to known NRPS/PKS gene clusters. Of these, the condensation domain of the syringomycin-related NRPS gene cluster was detected in Rhodoferax- and Rhodocyclaceae-related bins, and its homolog was found in previously reported AS metagenomes as well as the genomes of three strains available from the microbial culture collections, implying their potential BCA ability. Then, we tested the antimicrobial activity of these strains against phytopathogenic fungi to investigate the potential ability of BCA by in vitro cultivation and successfully confirmed the actual antifungal activity of three strains harboring a possibly novel NRPS gene cluster. Our findings provide a possible strategy for discovering novel BCAs buried in the environment using genome-resolved metagenomics.

The Controversial Nature of Some Non-Starter Lactic Acid Bacteria Actively Participating in Cheese Ripening

This mini review deals with some controversial non-starter lactic acid bacteria (NSLAB) species known to be both human and animal pathogens but also health-promoting and probiotic. The focus is on Lactococcus garvieae, two Streptococcus species (S. uberis and S. parauberis), four Weissella species (W. hellenica, W. confusa, W. paramesenteroides, and W. cibaria), and Mammalicoccus sciuri, which worldwide, are often found within the microbiotas of different kinds of cheese, mainly traditional artisanal cheeses made from raw milk and/or relying on environmental bacteria for their ripening. Based on literature data, the virulence and health-promoting effects of these bacteria are examined, and some of the mechanisms of these actions are reviewed. Additionally, their possible roles in cheese ripening are also discussed. The analysis of the literature data available so far showed that, in general, the pathogenic and the beneficial strains, despite belonging to the same species, show somewhat different genetic constitutions. Yet, when the safety of a given strain is assessed, genomic analysis on its own is not enough, and a polyphasic approach including additional physiological and functional tests is needed.

Application of multi-functional lactic acid bacteria strains in a pilot scale feta cheese production

Feta cheese is the most recognized Greek Protected Designation of Origin (PDO) product in the world. The addition of selected autochthonous lactic acid bacteria (LAB) strains to cheese milk as adjunct cultures is gaining more attention, since they can impact the nutritional, technological and sensory properties of cheeses, as well as improve the safety of the product. The aim of this study was to produce Feta cheese with enhanced quality and safety, and distinctive organoleptic characteristics by applying autochthonous lactic acid bacteria (LAB) with multi-functional properties as adjunct cultures. Feta cheeses were produced with the commercial lactococcal starter culture and the addition of 9 LAB strains (Lactococcus lactis SMX2 and SMX16, Levilactobacillus brevis SRX20, Lacticaseibacillus paracasei SRX10, Lactiplantibacillus plantarum FRX20 and FB1, Leuconostoc mesenteroides FMX3, FMX11, and FRX4, isolated from artisanal Greek cheeses) in different combinations to produce 13 cheese trials (12 Feta trials with the adjunct LAB isolates and the control trial). In addition, Feta cheese manufactured with FMX3 and SMX2 and control Feta cheese were artificially inoculated (4 log CFU/g) with Listeria monocytogenes (a cocktail of 4 acid or non-acid adapted strains). Cheese samples were monitored by microbiological and physicochemical analyses during ripening, and microbiological, physicochemical, molecular and sensory analyses during storage at 4°C. The results showed that after manufacture, the LAB population was ca. 9.0 log CFU/g at all samples, whereas during storage, their population declined to 6.5-7.0 log CFU/g. In the Listeria inoculated samples, Listeria was absent after 60 days (end of ripening) and after 90 days in the adjunct culture, and in the control trials, respectively. Moreover, the addition of selected strains, especially Lcb. paracasei SRX10, led to cheeses with desirable and distinctive organoleptic characteristics. Furthermore, randomly amplified polymorphic PCR (RAPD-PCR) molecular analysis confirmed that the multi-functional LAB strains were viable by the end of storage. Overall, the results of this study are promising for the use of autochthonous strains in various combinations with the commercial starter culture to satisfy industry requirements and consumer demands for traditional and high added value fermented products.

Metagenomic Insights into the Microbiome and Resistance Genes of Traditional Fermented Foods in Arabia

This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods-mish, jibneh, zabadi, and pickles-were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were sequenced using 16S amplicons and shotgun metagenomics. Alpha and beta diversity indicated inter- and intra-variation in the studied fermented foods' bacterial communities. In the case of mish, the replicates were clustered. Twenty-one genera were found to be significantly different (FDR < 0.05) in abundance in pairwise comparison of fermented foods. Five high-quality, metagenome-assembled genomes (MAGs) of Lactococcus lactis, Lactobacillus helveticus, Pseudoalteromonas nigrifaciens, Streptococcus thermophiles, and Lactobacillus acetotolerans were retrieved from the shotgun sequencing representing the dominant taxa in the studied fermented foods. Additionally, 33 genes that cause antimicrobial resistance (ARGs) against ten different antibiotic classes were detected. Metabolic pathways were abundant in the studied metagenomes, such as amino acid metabolism, carbohydrate metabolism, cofactors, and vitamin biosynthesis. Metagenomic evaluation of Arabian fermented foods, including the identification of probiotics, pathogenic bacteria, and ARGs, illustrates the importance of microbiological analysis in evaluating their health effects.

Characterization of the Bacterial Communities in Cichorium intybus According to Cultivation and Storage Conditions

Chicory leaves (Cichorium intybus) are widely consumed due to their health benefits. They are mainly consumed raw or without adequate washing, which has led to an increase in food-borne illness. This study investigated the taxonomic composition and diversity of chicory leaves collected at different sampling times and sites. The potential pathogenic genera (Sphingomonas, Pseudomonas, Pantoea, Staphylococcus, Escherichia, and Bacillus) were identified on the chicory leaves. We also evaluated the effects of various storage conditions (enterohemorrhagic E. coli contamination, washing treatment, and temperature) on the chicory leaves' microbiota. These results provide an understanding of the microbiota in chicory and could be used to prevent food-borne illnesses.

Role of Feeding and Novel Ripening System to Enhance the Quality and Production Sustainability of Curd Buffalo Cheeses

The buffalo dairy sector is extending its boundaries to include new buffalo cheese productions beyond mozzarella, overcoming some barriers that make cheeses expensive and unsustainable. This study aimed to evaluate the effects of both the inclusion of green feed in the diet of Italian Mediterranean buffaloes and an innovative ripening system on buffalo cheese quality, providing solutions capable of guaranteeing the production of nutritionally competitive and sustainable products. For this purpose, chemical, rheological, and microbiological analyses were carried out on cheeses. Buffaloes were fed with or without the inclusion of green forage. Their milk was used to produce dry ricotta and semi-hard cheeses, ripened according to both respective traditional (MT) and innovative methods (MI); these are based on automatic adjustments of climatic recipe guided by the continuous control of pH. Green feed enhances the nutritional profile of the final products (high content of MUFAs and PUFAs). As far as the ripening method is concerned, to our knowledge, this is the first study that tests aging chambers, commonly used for meat, for the maturing of buffalo cheeses. Results pointed out the MI validity also in this field of application, as it shortens the ripening period without negatively compromising any of desirable physicochemical properties and the safety and hygiene of the final products. Conclusively, this research highlights the benefits of diets rich in green forage on productions and provides support for the ripening optimization of buffalo semi-hard cheeses.

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Lactic Acid Bacteria (LAB) exert a fundamental activity in cheese production, as starter LAB in curd acidification, or non-starter LAB (NSLAB) during ripening, in particular in flavor formation. NSLAB originate from the farm and dairy environment, becoming natural contaminants of raw milk where they are present in very low concentrations. Afterward, throughout the different cheesemaking processes, they withstand chemical and physical stresses becoming dominant in ripened cheeses. However, despite a great body of knowledge is available in the literature about NSLAB effect on cheese ripening, the investigations regarding their presence and abundance in raw milk are still poor. With the aim to answer the initial question: "which and how many LAB are present in cow raw milk used for cheese production?," this review has been divided in two main parts. The first one gives an overview of LAB presence in the complex microbiota of raw milk through the meta-analysis of recent taxonomic studies. In the second part, we present a collection of data about LAB quantification in raw milk by culture-dependent analysis, retrieved through a systematic review. Essentially, the revision of data obtained by plate counts on selective agar media showed an average higher concentration of coccoid LAB than lactobacilli, which was found to be consistent with meta-taxonomic analysis. The advantages of the impedometric technique applied to the quantification of LAB in raw milk were also briefly discussed with a focus on the statistical significance of the obtainable data. Furthermore, this approach was also found to be more accurate in highlighting that microorganisms other than LAB are the major component of raw milk. Nevertheless, the variability of the results observed in the studies based on the same counting methodology, highlights that different sampling methods, as well as the "history" of milk before analysis, are variables of great importance that need to be considered in raw milk analysis.

Lactic Bacteria in Artisanal Cheese: Characterization through Metagenomics

Artisanal cheese, produced with raw milk by a predominantly manual approach, has a historical and cultural tradition related to the region of origin. Given its economic and cultural importance, the main objective of this study was to investigate and characterize the diversity of lactic acid bacteria (LAB) of artisanal cheeses produced and traded by family agro-industries in a region of southern Brazil. The LAB composition of artisanal cheese samples, belonging to different municipalities of the Region of Vale do Taquari, were characterized by the next-generation sequencing (NGS) method, amplifying the V3/V4 region of the 16S rRNA gene. A total of 35 LAB species, distributed in seven genera, were identified, and rarefaction analysis suggested that the total diversity assessed by 16S rRNA analysis was high in the analyzed samples. The average Ph ranged from 4.6 to 6.6, and a correlation with the genus Lactococcus (r = 0.62) was the most expressive. The LAB genera identified in the cheese samples were Bavariicococcus, Enterococcus, Lactobacillus, Lactococcus, Leuconostoc, Marinillactibacillus, and Pediococcus. Lactococcus lactis was the most predominant species, present in all samples. Although some species have been identified in the three altitudes studied, the abundance varied according to geographic environments. Enterococcus italicus is more present at high altitudes, unlike Lactococcus plantarum and Lactococcus raffinolactis at low altitudes. Lactococcus lactis was present in the three geographic environments evaluated, but the highest abundance was observed at high altitudes. The identification of LAB present in fermented cheeses is essential to understand the organoleptic quality during the maturation process as well as to establish the shelf life, including the safety and the overall quality of the cheese. This specific microbiota contributes to the flavor and unique characteristics of the regional dairy products, and on the other hand can be a source of specific starter cultures that guarantee the product’s identity.

Fungal community and physicochemical profiles of ripened cheeses from the Canastra of Minas Gerais, Brazil

Canastra's Minas artisanal cheese [QMA (Minas artisanal cheese)] is a protected geographical indication traditional food. The influence of fungi on the cheese ripening process is of great importance. This study aimed to apply culture-dependent and -independent methods to determine the mycobiota of QMA produced in the Canastra region, as well as to determine its physicochemical characteristics. Illumina-based amplicon sequencing and matrix-assisted laser desorption ionization time-of-flight mass spectrometry were the culture-independent methods used. The physicochemical analysis results showed that the QMA has a moisture content ranging 18.4-28.2%, fat content ranging 20.5-40%, sodium chloride percentage of approximately 0.9%, and pH ranging 5.2-5.5. The population of fungi ranged between 6.3 and 8 log colony-forming unit/g. Fusarium spp., Geotrichum candidum, Paecilomyces spp., Trichosporon coremiiforme, Candida catenulata, Aspergillus spp., Trichosporon japonicum, Aspergillus oryzae, Kluyveromyces spp., Torulaspora spp., and Debaryomyces spp. were the most prevalent fungi. The methods used to evaluate the mycobiota provide a better understanding of which species are present in the final product and eventually contribute to the characteristics of QMA. Geotrichum candidum and C. catenulata were identified as promising species for future studies on product quality.

Grape Pomace in Ewes Diet Affects Metagenomic Profile, Volatile Compounds and Biogenic Amines Contents of Ripened Cheese

The main objective of this research was to evaluate the development of volatile organic compounds (VOCs) and the accumulation of biogenic amines (BAs) in relation to the dynamic of microbial population composition in fresh and ripened cheese produced from raw milk of ewes fed a diet containing grape pomace (GP+) and fed a standard diet (Ctrl). Genomic DNA was extracted from the cheeses at 2 (T2), 60 (T60), 90 (T90) and 120 (T120) days of ripening and prepared for 16S rRNA-gene sequencing to characterize the cheese microbiota; furthermore, VOCs were determined via solid-phase microextraction combined with gas chromatography-mass spectrometry and biogenic amines by HPLC analyses. Diet did not affect the relative abundance of the main phyla identified, Proteobacteria characterized T2 samples, but the scenario changed during the ripening. At genus level, Pseudomonas, Chryseobacterium and Acinetobacter were the dominant taxa, however, a lower percentage of Pseudomonas was detected in GP+ cheeses. Enterococcus became dominant in ripened cheeses followed in Ctrl cheeses by Lactobacillus and in GP+ cheeses by Lactococcus. The diet affected the development of carboxylic acids and ketones but not of aldehydes. Low levels of esters were identified in all the samples. In total, four biogenic amines were determined in cheeses samples and their levels differed between the two groups and during ripening time. In 60, T90 and T120 GP+ cheeses, a lower amount of 2-phenylethylamine was found compared to Ctrl. Putrescine was detected only in GP+ samples and reached the highest level at 120 days. Conversely, the amount of cadaverine in GP+ samples was invariable during the ripening. The concentration of tyramine in GP+ samples was compared to Ctrl during the ripening. Overall, significant positive correlations between some families of bacteria and the formation of VOCs and BAs were found.

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage

Adjuevan is an Ivorian traditional fermented fish used as a condiment. However, the fermentation process and storage conditions may lead to the production of biogenic amines (BA) which can induce severe human toxicological effects. Thus, this study aimed to reveal the bacterial community diversity and the BA contents during the storage. Samples of adjuevan from the fish species Chloroscombrus chrysurus, Galeoides decadactylus, and Thunnus thynnus were collected from local producers, stored at ambient temperature (28-30 °C) and in a refrigerator (4 °C) over a period of 8 weeks. At 2-week intervals, BA were determined by HPLC and the bacterial communities analyzed using high-throughput sequencing (NGS) of the V3-V4 region of the 16S rRNA gene. Results showed that histamine, cadaverine, putrescine, and tyramine were the major compounds. In adjuevan from T. thynnus, the level of histamine was over the maximum level of 200 mg/kg determined by Codex Alimentarius. For the other amines, no safety concerns are related. In total, 21 bacterial genera with a relative abundance ≥ 1% and belonging to 14 families and 5 phyla were detected. The Bacillaceae family was the most found at ambient temperature while Staphylococcaceae and Enterococcaceae were the most abundant in a refrigerator. The analysis of correlation showed that the increase of Lentibacillus leads to a decrease of the major BA at ambient temperature. On the contrary, the increase of Staphylococcus, Lactobacillus, Psychrobacter, Peptostreptococcus, and Fusobacterium leads to an increase of these biogenic compounds. Thus, Lentibacillus acted as BA-oxidizing bacteria while the others were found as BA-producing bacteria during adjuevan storage.

Elucidation of the initial bacterial community of Ezine PDO cheese using next-generation sequencing

This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.

Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities

BACKGROUND

Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.

RESULTS

We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.

CONCLUSIONS

Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.

Metataxonomic sequencing to assess microbial safety of Turkish white cheeses

High-throughput sequencing has provided a way to monitor the large diversity of microorganisms in fermented foods that have complex microbiota. Up to date, many kinds of cheese have been characterized with the metataxonomic approach, but the safety of unpacked Turkish white cheeses, which are widely consumed in Turkey, has not been assessed. In this study, fifteen unpacked white cheeses sold in public bazaars in Ankara province have been collected and subjected to microbial enumeration as well as physicochemical analysis. Five white cheeses, which have relatively the highest foodborne pathogens, out of fifteen white cheeses, have been analyzed by next-generation sequencing and metataxonomic analysis. According to the results, abundant families were Lactobacillaceae, Oceanospirillaceae, Enterococcaceae, Pseudomonadaceae, and Vibrionaceae. Staphylococcus aureus, E. coli, and Salmonella, which are indicators of bad hygiene and sanitation conditions, were found in cheeses. In conclusion, culture-independent methods such as metataxonomic can be important to evaluate the safety of foods.

Use of Autochthonous Lactic Acid Bacteria as Starter Culture of Pasteurized Milk Adobera Cheese

Adobera, a genuine, brick-shaped, lightly ripened, unstretched pasta filata-like cheese from Western México, is one of the most important market-share wise but is usually made with raw milk and prepared following artisanal procedures. A pasteurized milk cheese is needed to assess its safety and guarantee standardized quality features. However, no commercial Adobera cheese culture is available, as specific lactic acid bacteria relevant for its production have not been thoroughly identified. This study is aimed at comparing the technological and quality features of Adobera cheeses made with pasteurized milk inoculated with a mixture of autochthonous lactic acid bacteria (Lactobacillus and Leuconostoc strains) to those of traditional raw milk cheeses, hypothesizing that no significant differences would be found between them. Milk pasteurization promoted water retention into the cheese matrix, impacting its texture and color profiles. Raw milk cheeses were harder, more cohesive, and less elastic than pasteurized milk cheeses. Ripening markers were significantly higher in raw milk cheeses at all sampling times, although its evolution over time showed that the starter culture could exhibit similar proteolytic activity than that of native milk microbiota under favorable ripening conditions. The principal component analysis revealed apparent overall differences between raw Adobera cheeses and those made with pasteurized cheese milk.

Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms

Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.

Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation

Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.

Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening

Vorarlberger Bergkäse (VB) is an artisanal Austrian washed-rind hard cheese produced from alpine cows' raw milk without the addition of ripening cultures. Ripening time is a key factor in VB, as it strongly influences the microbial communities present in the cheeses and the organoleptic properties of the product. In this study, the microbial and metabolic transcriptional profiles in VB rinds at different ripening times were investigated. VB products before (30 days of ripening) and after (90 days of ripening) selling were selected, RNA was extracted and subjected to shotgun metatranscriptomic sequencing. The analysis revealed some of the previously described abundant bacterial taxa of Brevibacterium, Corynebacterium, Halomonas, Psychrobacter, and Staphylococcus to be highly active in VB rinds. Additionally, the investigation of most important metabolic pathways in cheese ripening clearly showed differences in the gene transcription profiles and the active microbiota between the two ripening points investigated. At 30 days of ripening, metabolic events related with the degradation of residual lactose, lactate, citrate, proteolysis, and lipolysis were significantly more transcribed and mainly associated with Staphylococcus. On the other hand, genes involved in the degradation of smaller compounds derived from previous metabolism (i.e., metabolism of free amino acids and fatty acids) were significantly more expressed in VB rinds with 90 of ripening, and mainly associated with Brevibacterium and Corynebacterium. These latter metabolic activities are responsible of the generation of compounds, such as methanethiol and 2,3-butanediol, that are very important for the flavor and aroma characteristics of cheeses. This study shows the dynamic changes in the gene transcriptional profiles associated with energy substrates metabolism and the generation of organoleptic compounds during VB ripening and uncovers bacterial taxa as key drivers of the ripening process. These taxa might be the target for future studies toward an accelerated cheese ripening and the enhancement of its organoleptic properties.

A review on the application of bioinformatics tools in food microbiome studies

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.

Omics Approaches to Assess Flavor Development in Cheese

Cheese is characterized by a rich and complex microbiota that plays a vital role during both production and ripening, contributing significantly to the safety, quality, and sensory characteristics of the final product. In this context, it is vital to explore the microbiota composition and understand its dynamics and evolution during cheese manufacturing and ripening. Application of high-throughput DNA sequencing technologies have facilitated the more accurate identification of the cheese microbiome, detailed study of its potential functionality, and its contribution to the development of specific organoleptic properties. These technologies include amplicon sequencing, whole-metagenome shotgun sequencing, metatranscriptomics, and, most recently, metabolomics. In recent years, however, the application of multiple meta-omics approaches along with data integration analysis, which was enabled by advanced computational and bioinformatics tools, paved the way to better comprehension of the cheese ripening process, revealing significant associations between the cheese microbiota and metabolites, as well as their impact on cheese flavor and quality.

Evolution of Food Fermentation Processes and the Use of Multi-Omics in Deciphering the Roles of the Microbiota

Food fermentation has been practised since ancient times to improve sensory properties and food preservation. This review discusses the process of fermentation, which has undergone remarkable improvement over the years, from relying on natural microbes and spontaneous fermentation to back-slopping and the use of starter cultures. Modern biotechnological approaches, including genome editing using CRISPR/Cas9, have been investigated and hold promise for improving the fermentation process. The invention of next-generation sequencing techniques and the rise of meta-omics tools have advanced our knowledge on the characterisation of microbiomes involved in food fermentation and their functional roles. The contribution and potential advantages of meta-omics technologies in understanding the process of fermentation and examples of recent studies utilising multi-omics approaches for studying food-fermentation microbiomes are reviewed. Recent technological advances in studying food fermentation have provided insights into the ancient wisdom in the practice of food fermentation, such as the choice of substrates and fermentation conditions leading to desirable properties. This review aims to stimulate research on the process of fermentation and the associated microbiomes to produce fermented food efficiently and sustainably. Prospects and the usefulness of recent advances in molecular tools and integrated multi-omics approaches are highlighted.

Correlation: Between Autochthonous Microbial Diversity and Volatile Metabolites During the Fermentation of Nongxiang Daqu

Daqu is an important saccharifying and fermenting agent. It provides various microorganisms and enzymes for the fermentation of Baijiu and plays a vital role in the formation of Baijiu flavor. However, it is difficult to obtain information on microbial growth and metabolism in time for Daqu production. Therefore, the “Qu Xiang” obtained by smelling is an important index in the traditional production process to evaluate the microbial fermentation in the process of Daqu-making, “Qu Xiang” mainly represents the volatile flavor compounds in Daqu. The microbial diversity and volatile metabolites on 0, 6, 16, and 29 days of the fermentation process were measured using high-throughput sequencing and gas chromatography–mass spectrometry. Significant differences were found in the composition of the microbial community. Pseudomonas, Weissella, Bacillus, and Pelomonas were the main bacterial genera. Alternaria, Rhizopus, and Pichia are the main fungal genera. A total of 32 differential volatile metabolites were detected in samples at four time points using differential metabolic analysis. The correspondence of prevailing microorganisms with differential metabolites distinguished by Spearman correlation and two-way orthogonal partial least square analysis show that Saccharopolyspora exhibited a significant connection for the 12 differential metabolites. A significant positive correlation was observed between Rhizomucor and 13 different metabolites. These findings further understanding of the metabolism of microorganisms in Daqu fermentation and also help to control the microorganisms in the Daqu-making process, to obtain more stable Baijiu products.

Microbiome Studies from Saudi Arabia over the Last 10 Years: Achievements, Gaps, and Future Directions

In the past ten years, microbiome studies have shown tremendous potentiality for implementation of understanding microbiome structures and functions of various biomes and application of this knowledge for human betterment. Saudi Arabia is full of geographical, ecological, ethnical, and industrial diversities and scientific capacities. Therefore, there is a great potential in Saudi Arabia to conduct and implement microbiome-based research and applications. However, there is no review available on where Saudi Arabia stands with respect to global microbiome research trends. This review highlights the metagenome-assisted microbiome research from Saudi Arabia compared to the global focuses on microbiome research. Further, it also highlights the gaps and areas that should be focused on by Saudi microbiome researchers and the possible initiatives to be taken by Saudi government and universities. This literature review shows that the global trends of microbiome research cover a broad spectrum of human and animal health conditions and diseases, environmental and antimicrobial resistance surveillance, surveillance of food and food processing, production of novel industrial enzymes and bioactive pharmaceutical products, and space applications. However, Saudi microbiome studies are mostly confined to very few aspects of health (human and animal) and environment/ecology in last ten years, without much application. Therefore, Saudi Arabia should focus more on applied microbiome research through government, academic, and industry initiatives and global cooperation to match the global trends.

Serra da Estrela PDO Cheese Microbiome as Revealed by Next Generation Sequencing

Serra da Estrela PDO cheese is the oldest traditional cheese manufactured in Portugal. In this work, its microbiome as well as the main raw materials used in cheese production, raw ewes’ milk and thistle flowers (Cynara cardunculus L.), were characterized using next generation sequencing. Samples were accordingly retrieved from a local producer over two consecutive production campaigns and at different time periods within each campaign. The bacterial and fungi communities associated with each matrix were accessed through sequencing of V3–V4 and Internal Transcribed Spacer 2 regions of rRNA gene amplicons, respectively. A high microbial diversity was found associated to each matrix, differing significantly (p < 0.05) from each other. Over 500 taxa were identified in each analyzed matrix, ranging from dominant (relative abundance > 1%), sub-dominant (0.01–1%) and rare taxa (<0.01%). Specifically, in cheese, 30 taxa were present in all analyzed samples (core taxa), including species of Leuconostoc spp. and Lactococcus spp. for bacteria and Candida spp., Debaryomyces spp. and Yarrowia spp. for fungi, that were cumulatively the most prevalent genera in Serra da Estrela PDO cheese (average relative abundance ≥10%). Ultimately, this characterization study may contribute to a better understanding of the microbial dynamics of this traditional PDO product, namely the influence of raw materials on cheese microbiome, and could assist producers interested in preserving the identity, quality and safety of Serra da Estrela PDO cheese.

Microbiological Characteristics and Behavior of Staphylococcus aureus, Salmonella spp., Listeria monocytogenes and Staphylococcal Toxin during Making and Maturing Cotija Cheese

Cotija cheese is an artisanal matured Mexican cheese from unpasteurized milk. This work determined the microbiological characteristics and behavior of Staphylococcus aureus, Salmonella spp., Listeria monocytogenes and staphylococcal toxin during cheese elaboration and ripening. Sixteen 20-kg cheeses were used, eight inoculated with 6 log CFU/mL of each pathogen, and eight uninoculated, and samples were taken at each stage of the process. In the uninoculated samples, the survival of S. aureus and L. monocytogenes decreased after 30 days of ripening. The average counts of S. aureus in milk, curd, and serum were 7 log MPN /mL, and 8.7 log MPN /g in cheese, decreasing from day 15. Salmonella spp. counts (initial inoculum: 7.2 log MPN /mL) decreased after 24 h, and L. monocytogenes counts (8.7 log MPN/g at 24 h) decreased from day 15 in the cheese. Salmonella spp. and L. monocytogenes were not detected in any sample after 60 days of ripening, unlike S. aureus, which was detected at the end of the study. Lactic acid bacteria counts were 9 log CFU/mL in milk and whey and 7.2 log CFU/g in cheese. Pathogens behavior during the ripening process reduces the health risks by consuming products made with unpasteurized milk when subjected to ripening.

Metagenomic and phytochemical analyses of kefir water and its subchronic toxicity study in BALB/c mice

BACKGROUND

In recent years, researchers are interested in the discovery of active compounds from traditional remedies and natural sources, as they reveal higher therapeutic efficacies and improved toxicological profiles. Among the various traditional treatments that have been widely studied and explored for their potential therapeutic benefits, kefir, a fermented beverage, demonstrates a broad spectrum of pharmacological properties, including antioxidant, anti-inflammation, and healing activities. These health-promoting properties of kefir vary among the kefir cultures found at the different part of the world as different media and culture conditions are used for kefir maintenance and fermentation.

METHODS

This study investigated the microbial composition and readily found bioactive compounds in water kefir fermented in Malaysia using 16S rRNA microbiome and UHPLC sequencing approaches. The toxicity effects of the kefir water administration in BALB/c mice were analysed based on the mice survival, body weight index, biochemistry profile, and histopathological changes. The antioxidant activities were evaluated using SOD, FRAP, and NO assays.

RESULTS

The 16S rRNA amplicon sequencing revealed the most abundant species found in the water kefir was Lactobacillus hilgardii followed by Lactobacillus harbinensis, Acetobacter lovaniensis, Lactobacillus satsumensis, Acetobacter tropicalis, Lactobacillus zeae, and Oenococcus oeni. The UHPLC screening showed flavonoid and phenolic acid derivatives as the most important bioactive compounds present in kefir water which has been responsible for its antioxidant activities. Subchronic toxicity study showed no toxicological signs, behavioural changes, or adverse effects by administrating 10 mL/kg/day and 2.5 mL/kg/day kefir water to the mice. Antioxidants assays demonstrated enhanced SOD and FRAP activities and reduced NO level, especially in the brain and kidney samples.

CONCLUSIONS

This study will help to intensify the knowledge on the water kefir microbial composition, available phytochemicals and its toxicological and antioxidant effects on BALB/c mice since there are very limited studies on the water kefir grain fermented in Malaysia.

Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India

Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.

Microbiomes of commercially-available pine nuts and sesame seeds

Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.

Combining Culture-Dependent and Culture-Independent Methods: New Methodology Insight on the Vibrio Community of Ruditapes philippinarum

Vibrios represent a natural contaminant of seafood products. V. alginolyticus, V. cholerae, V. parahaemolyticus and V. vulnificus are the most hazardous species to human health. Given the worldwide consumption of mollusc products, reliable detection of Vibrio species is recommended to prevent human vibriosis. In this study, culture-dependent and -independent methods were compared and integrated to implement knowledge of the Manila clam Vibrio community composition. Here, 16S and recA-pyrH metabarcoding were applied to compare the microbial communities of homogenate clam samples (culture-independent method) and their culture-derived samples plated on three different media (culture-dependent method). In addition, a subset of plated clam samples was investigated using shotgun metagenomics. Homogenate metabarcoding characterized the most abundant taxa (16S) and Vibrio species (recA-pyrH). Culture-dependent metabarcoding detected the cultivable taxa, including rare species. Moreover, marine agar medium was found to be a useful substrate for the recovery of several Vibrio species, including the main human pathogenic ones. The culture-dependent shotgun metagenomics detected all the main human pathogenic Vibrio species and a higher number of vibrios with respect to the recA-pyrH metabarcoding. The study revealed that integration of culture-dependent and culture-independent methods might be a valid approach for the characterization of Vibrio biodiversity.

Metagenomic Analysis of Microbial Composition Revealed Cross-Contamination Pathway of Bacteria at a Foodservice Facility

Bacterial contamination of food-contact surfaces can be a potential risk factor for food quality and safety. To evaluate the spatial and temporal variations of the potential cross-contamination routes, we conducted a biogeographical assessment of bacteria in a foodservice facility based on the diversity of microflora on each surface. To this end, we performed high-throughput amplicon sequencing of 13 food-contact and non-food contact surfaces in a foodservice facility throughout a year. The results showed that Bacillus, Acinetobacter, Streptophyta, Enterobacter, Pseudomonas, Serratia, Enhydrobacter, Staphylococcus, Paracoccus, and Lysinibacillus were the dominant genera found on the kitchen surfaces of the foodservice facility. Depending on the season, changes in Firmicute/Proteobacteria ratios were observed, and the fan becomes the main source of outdoor air contamination. The microbial flow associated with spoilage was also observed throughout food preparation. Taken together, our results would be a powerful reference to hygiene managers for improvement of food processes.

Microbial Interactions within the Cheese Ecosystem and Their Application to Improve Quality and Safety

The cheese microbiota comprises a consortium of prokaryotic, eukaryotic and viral populations, among which lactic acid bacteria (LAB) are majority components with a prominent role during manufacturing and ripening. The assortment, numbers and proportions of LAB and other microbial biotypes making up the microbiota of cheese are affected by a range of biotic and abiotic factors. Cooperative and competitive interactions between distinct members of the microbiota may occur, with rheological, organoleptic and safety implications for ripened cheese. However, the mechanistic details of these interactions, and their functional consequences, are largely unknown. Acquiring such knowledge is important if we are to predict when fermentations will be successful and understand the causes of technological failures. The experimental use of "synthetic" microbial communities might help throw light on the dynamics of different cheese microbiota components and the interplay between them. Although synthetic communities cannot reproduce entirely the natural microbial diversity in cheese, they could help reveal basic principles governing the interactions between microbial types and perhaps allow multi-species microbial communities to be developed as functional starters. By occupying the whole ecosystem taxonomically and functionally, microbiota-based cultures might be expected to be more resilient and efficient than conventional starters in the development of unique sensorial properties.

Metataxonomic Profiling of Native and Starter Microbiota During Ripening of Gouda Cheese Made With Listeria monocytogenes-Contaminated Unpasteurized Milk

Unpasteurized milk is used to produce aged artisanal cheeses, which presents a safety concern due to possible contamination with foodborne pathogens, especially Listeria monocytogenes. The objective of this study was to examine the composition of the bacterial community in unpasteurized milk used to prepare Gouda cheese artificially contaminated with L. monocytogenes (~1 log CFU/ml) and assess the community dynamics and their potential interaction with L. monocytogenes during a 90-day ripening period using targeted 16S rRNA sequencing. The diversity of bacterial taxa in three batches of unpasteurized milk was not significantly different, and the microbiomes were dominated by species of Lactococcus, Streptomyces, Staphylococcus, and Pseudomonas. The highest relative abundances were observed for Pseudomonas fluorescens (31.84-78.80%) and unidentified operational taxonomic units (OTUs) of Pseudomonas (7.56-45.27%). After manufacture, both with and without L. monocytogenes-contaminated unpasteurized milk, Gouda cheese was dominated by starter culture bacteria (including Lactococcus lactis subsp. cremoris, lactis, lactis bv. diacetylactis, and Streptococcus thermophilus), in addition to unassigned members in the taxa L. lactis and Streptococcus. During ripening there was an overall decrease in L. lactis abundance and an increase in the number of taxa with relative abundances >0.1%. After 90-day ripening, a total of 82 and 81 taxa were identified in the Gouda cheese with and without L. monocytogenes, respectively. Of the identified taxa after ripening, 31 (Gouda cheese with L. monocytogenes) and 56 (Gouda cheese without L. monocytogenes) taxa had relative abundances >0.1%; 31 were shared between the two types of Gouda cheese, and 25 were unique to the Gouda cheese without added L. monocytogenes. No unique taxa were identified in the Gouda cheese with the added L. monocytogenes. This study provides information on the dynamics of the bacterial community in Gouda cheese during ripening, both with and without the addition of L. monocytogenes.

Lifestyle, metabolism and environmental adaptation in Lactococcus lactis

Lactococcus lactis serves as a paradigm organism for the lactic acid bacteria (LAB). Extensive research into the molecular biology, metabolism and physiology of several model strains of this species has been fundamental for our understanding of the LAB. Genomic studies have provided new insights into the species L. lactis, including the resolution of the genetic basis of its subspecies division, as well as the control mechanisms involved in the fine-tuning of growth rate and energy metabolism. In addition, it has enabled novel approaches to study lactococcal lifestyle adaptations to the dairy application environment, including its adjustment to near-zero growth rates that are particularly relevant in the context of cheese ripening. This review highlights various insights in these areas and exemplifies the strength of combining experimental evolution with functional genomics and bacterial physiology research to expand our fundamental understanding of the L. lactis lifestyle under different environmental conditions.

Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter

As a widely used Asian starter culture, the quality of daqu can significantly affect the organoleptic characteristics of the final products, yet the microbial metabolic network involved in flavor development remains unclear. This study aims to investigate that network based on the dynamics of physicochemical properties, microbial community, and volatile compounds in medium-temperature daqu (MT-daqu) during spontaneous fermentation. Analyses using the metagenomic data set facilitated the gene repertoire overview of this ecosystem, indicating that Lactobacillales (mainly Weissella, Lactobacillus, and Pediococcus), Mucorales (mainly Lichtheimia), and Eurotiales (mainly Aspergillus, Rasamsonia and Byssochlamys) were the potential predominant populations successively responsible for the production of lytic enzymes and flavor precursors/compounds in MT-daqu. Flavor-relevant pathways were found to exist in multiple species, but only bacteria showed the potential to participate in butane-2,3-diol (e.g. Weissella, Lactobacillus, and Staphylococcus) and butanoate (Thermoactinomyces) metabolism, and only fungi were potentially involved in biosynthesis of guaiacol (Byssochlamys) and 4-vinylguaiacol (Aspergillus). Furthermore, a combined analysis revealed that the acidic thermal environment present in early phases was mainly due to the catabolic activities of Lactobacillales and Lichtheimia, which could contribute to the effective self-domestication of microbiota. The study helps elucidate the different metabolic roles of microorganisms and disclose the formation mechanism of daqu's partial functions, namely providing various aromatic substances/precursors and enzymes.