Bacteriophages on dairy foods

Dynamics of the viral community on the surface of a French smear-ripened cheese during maturation and persistence across production years

The surface of smear-ripened cheeses constitutes a dynamic microbial ecosystem resulting from the successive development of different microbial groups such as lactic acid bacteria, fungi, and ripening bacteria. Recent studies indicate that a viral community, mainly composed of bacteriophages, also represents a common and substantial part of the cheese microbiome. However, the composition of this community, its temporal variations, and associations between bacteriophages and their hosts remain poorly characterized. Here, we studied a French smear-ripened cheese by both viral metagenomics and 16S metabarcoding approaches to assess both the succession of phages and bacterial communities on the cheese surface during cheese ripening and their temporal variations in ready-to-eat cheeses over the years of production. We observed a clear transition of the phage community structure during ripening with a decreased relative abundance of viral species (vOTUs) associated with Lactococcus phages, which were replaced by vOTUs associated with phages infecting ripening bacteria such as Brevibacterium, Glutamicibacter, Pseudoalteromonas, and Vibrio. The dynamics of the phage community was strongly associated with bacterial successions observed on the cheese surface. Finally, while some variations in the distribution of phages were observed in ready-to-eat cheeses produced at different dates spanning more than 4 years of production, the most abundant phages were detected throughout. This result revealed the long-term persistence of the dominant phages in the cheese production environment. Together, these findings offer novel perspectives on the ecology of bacteriophages in smear-ripened cheese and emphasize the significance of incorporating bacteriophages in the microbial ecology studies of fermented foods.IMPORTANCEThe succession of diverse microbial populations is critical for ensuring the production of high-quality cheese. We observed a temporal succession of phages on the surface of a smear-ripened cheese, with new phage communities showing up when ripening bacteria start covering this surface. Interestingly, the final phage community of this cheese is also consistent over large periods of time, as the same bacteriophages were found in cheese products from the same manufacturer made over 4 years. This research highlights the importance of considering these bacteriophages when studying the microbial life of fermented foods like cheese.

Whole genome analysis, thermal and UV-tolerance of Lactococcus phage BIM BV-114 isolated from cheese brine

Lactococcus phages that belong to the genus Ceduovirus are among the three most frequently isolated phage groups infecting Lactococcus lactis starter strains in dairy plants. In this study, we characterized virulent Lactococcus phage BIM BV-114 isolated from industrial cheese brine in Belarus and identified as Ceduovirus. The bacteriophage demonstrated a relatively short lytic cycle (latent period of 23 ± 5 min, lysis time of 90 ± 5 min), high thermal stability (inactivation after 7 min at 95 °C in skimmed milk) and tolerance to UV radiation (inactivation time - 15 min), indicating adaptation for better persistence in dairy facilities. The genome of the phage BIM BV-114 (21 499 bp; 37 putative open reading frames) has a similar organization to that of other Ceduovirus phages. RLf1_00140 and RLf_00050 gene products, found in the early genes region, may be involved in the sensitivity of phage to the lactococcal abortive infection mechanisms AbiV and AbiQ, respectively. Furthermore, nucleotide deletion, observed in the middle region of the gene encoding putative tape measure protein (RLf1_00300), is possibly responsible for increased thermal tolerance of phage BIM BV-114. Together, these findings will contribute to a better knowledge of virulent Lactococcus phages and the development of effective methods of their control for dairy technologies.

Shotgun metagenomic analysis of microbiota dynamics during long-term backslopping fermentation of traditional fermented milk in a controlled laboratory environment

Traditional fermented milks are produced through an inoculation process that involves the deliberate introduction of microorganisms that have been adapted and perpetuated across successive generations. However, the changes in the microbiota of traditional fermented milk during long-term inoculation fermentation in a laboratory environment remain unclear. In this study, we collected 5 samples of traditional fermented milk samples from 5 different counties in Tibet (3 kurut products) and Xinjiang (2 tarag products) of China, which served as starter cultures for a 9-mo continuous inoculation fermentation experiment. We analyzed the inter- and intra-population variations in the microbial communities of the collected samples, representing their macrodiversity and microdiversity, using shotgun metagenomic sequencing. Across all samples, we obtained a total of 186 high-quality metagenomic-assembled genomes, including 7 genera and 13 species with a relative abundance of more than 1%. The majority of these genomes were annotated as Lactobacillus helveticus (60.46%), Enterococcus durans (9.52%), and Limosilactobacillus fermentum (6.23%). We observed significant differences in species composition and abundance among the 5 initial inoculants. During the long-term inoculation fermentation, we found an overall increasing trend in species diversity, composition, and abundances of carbohydrate metabolism module-encoding genes in the fermented milk bacterial metagenome, while the fermented milk virome exhibited a relatively narrow range of variation. Lactobacillus helveticus, a dominant species in traditional fermented milk, displayed high stability during the long-term inoculation fermentation. Our study provides valuable insights for the industrial production of traditional fermented milk.

Characterization of Salmonella phages isolated from poultry coops and its effect with nisin on food bio-control

Salmonella is a bacterium associated with food contaminated by various animals, primarily poultry. Interest and research on bacteriophages are increasing because they can be used as an alternative against increasing antibiotic resistance. In our study, eight Salmonella-specific lytic bacteriophages were isolated from chicken feces. Two of the isolated phages (AUFM_Sc1 and AUFM_Sc3) were chosen for their characterization due to their broader host range. Based on morphological and genomic analysis, AUFM_Sc1 was identified to be close to similar Enterobacteria spp. CC31 (Myoviridae) and AUFM_Sc3 was identified to be close to Salmonella phage vB_Sen_I1 (Demerecviridae (formerly Siphoviridae)). Although these phages have shown promise for use in phage therapy applications for chickens, further studies are needed on their suitability. When a cocktail of these phages (AUFM_Sc1 + AUFM_Sc3) and nisin combination was applied on chicken breast meat, it was determined that it was effective against Salmonella contamination and while a good inhibitory effect was observed on the food, especially during the first 48 h, the effect decreased later, but the bacterial concentration was still low compared to the control group. Therefore, it is considered that the combination of AUFM_Sc1 + AUFM_Sc3 + nisin can be used as a food preservative against Salmonella.

Thermal and Chemical Inactivation of Bacillus Phage BM-P1

Bacillus spp. are often used as probiotics; however, they can be infected by phages, leading to significant economic losses. Biocidal and thermal treatments are considered rapid and effective methods for controlling microbial contamination. To prevent viral contamination in industrial dairy production, the impact of temperature and biocides on the viability of Bacillus methylotrophic phage BM-P1 was assessed. The results demonstrated that reconstituted skim milk (RSM) as a medium showed the most effective protective effect on phage BM-P1. Treatment at 90°C for 5 min or 72°C for 10 min inactivated it to nondetectable levels from the initial titer of 7.19 ± 0.11 log, regardless of the culture medium. Sodium hypochlorite exhibited the best inactivating effect, which could reduce the phage titer below the detection level in 4 min at 50 ppm. Additionally, treatment with 75% ethanol for 20 min or 50% isopropanol for 30 min could achieve inactivation to nondetectable levels. The inactivating effect of peracetic acid was limited; even when treated at the highest concentration (0.45%) for 60 min, only a 2.47 ± 0.17 log reduction was observed. This study may provide some theoretical basis and data support for establishing measures against Bacillus spp. phages.

Bacteriophage Challenges in Industrial Processes: A Historical Unveiling and Future Outlook

Humans have used fermentation processes since the Neolithic period, mainly to produce beverages. The turning point occurred in the 1850s, when Louis Pasteur discovered that fermentation resulted from the metabolism of living microorganisms. This discovery led to the fast development of fermented food production. The importance of industrial processes based on fermentation significantly increased. Many branches of industry rely on the metabolisms of bacteria, for example, the dairy industry (cheese, milk, yogurts), pharmaceutical processes (insulin, vaccines, antibiotics), or the production of chemicals (acetone, butanol, acetic acid). These are the mass production processes involving a large financial outlay. That is why it is essential to minimize threats to production. One major threat affecting bacteria-based processes is bacteriophage infections, causing substantial economic losses. The first reported phage infections appeared in the 1930s, and companies still struggle to fight against phages. This review shows the cases of phage infections in industry and the most common methods used to prevent phage infections.

Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu

Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.

Inactivation of Lactobacillus Bacteriophages by Dual Chemical Treatments

Phage contamination is one of the significant problems in the food fermentation industry, which eventually causes economic losses to the industry. Here, we investigated the viability of Lactobacillus plantarum phage P1 and P2 using various biocides treatments (ethanol, isopropanol, sodium hypochlorite and peracetic acid). Results indicated that phage P1 and P2 could be completely inactivated by treatment with 75% ethanol for 5 min, followed by 400 ppm of sodium hypochlorite treatment for 5 min. Phage P2 could be completely inactivated in the reverse sequence, while 800 ppm of sodium hypochlorite was required to achieve a similar effect for phage P1. Moreover, 100% isopropanol could increase the inactivating effect of 75% ethanol. This study may provide basic information on using multiple antimicrobials for phage control in laboratories and food plants.

Recombinant anti-HIV MAP30, a ribosome inactivating protein: against plant virus and bacteriophage

The ribosome inactivating proteins (RIPs) efficiently decrease the microbial infections in plants. Momordica charantia MAP30 is a type I RIP that has not been investigated against plant viruses or bacteriophages. To evaluate of these activities, the recombinant MAP30 (rMAP30) was produced in the hairy roots of Nicotiana tabacum. Inoculation of 3 μg of transgenic total protein or 0.6 μg of rMAP30 against 0.1 μg of TMV reduced the leaf necrotic spots to 78.23% and 82.72%, respectively. The treatment of 0.1 μg of CMV with rMAP30 (0.6 μg) showed the reduction in the leaf necrotic spots to 85.8%. While the infection was increased after rMAP30 dilution. In the time interval assays, the leaves were first inoculated with 1 μg of rMAP30 or 0.1 μg of purified TMV or CMV agent for 6 h, then virus or protein was applied in order. This led the spot reduction to 35.22% and 67% for TMV, and 38.61% and 55.31% for CMV, respectively. In both the pre- and co-treatments of 1:10 or 1:20 diluted bacteriophage with 15 μg of transgenic total protein, the number and diameter of the plaques were reduced. The results showed that the highest inhibitory effect was observed in the pre-treatment assay of bacteriophage with transgenic total protein for 24 h. The decrease in the growth of bacteriophage caused more growth pattern of Escherichia coli. The results confirm that rMAP30 shows antibacterial activity against Streptococcus aureus and E. coli, antifungal activity against Candida albicans, and antiviral activity against CMV and TMV. Moreover, rMAP30 exhibits anti-phage activity for the first time. According to our findings, rMAP30 might be a valuable preservative agent in foods and beverages in the food industry as well as an antiviral and antimicrobial mixture in agriculture.

Functional genomics of the lactic acid bacterium Limosilactobacillus fermentum LAB-1: metabolic, probiotic and biotechnological perspectives

A genome-based systematic analysis was conducted to characterize the metabolic, probiotic, fitness, and safety properties of Limosilactobacillus fermentum LAB-1, a lactic acid bacterium demonstrating strong antimicrobial effects against clinical pathogens. Gene functional characterization revealed a large number of genes for carbohydrate metabolism and a heterofermentative system for carbon dissimilation. Genes for intact pyruvate oxidation, pentose phosphate, and PRPP biosynthetic pathways were identified. Substantial carbohydrate-active enzymes and transporters were also predicted. Metabolic reconstruction revealed complete sets of enzymes for arginine, lysine, methionine, threonine, proline, and ornithine biosynthesis. The bacterium harbors a diverse range of peptidases, and a large variety of peptide and amino acid uptake systems. It encodes restriction-modification and CRISPR-Cas systems for protection against phage infections and carries a wide spectrum of stress proteins for adaptation in the gut and industrial conditions. Genes related to the biosynthesis of B-group and K vitamins were identified allowing its application for novel bio-enriched food production. Other beneficial traits of probiotic and industrial importance such as production of flavor compounds, exopolysaccharide, acetoin, and butanediol were identified. Three antimicrobial peptides were predicted which showed >98% sequence-identity to experimentally validated bacteriocins. Negative traits such as transmissible antibiotic resistance, pathogenicity or virulence appeared to be absent suggesting the strain to be considered safe. The genome analysis will allow precisely targeted laboratory research and full exploitation of the probiotic potentials towards functional-food, biotechnology and health-related applications.

Bacteriophages and Food Production: Biocontrol and Bio-Preservation Options for Food Safety

Food safety and sustainable food production is an important part of the Sustainable Development goals aiming to safeguard the health and wellbeing of humans, animals and the environment. Foodborne illness is a major cause of morbidity and mortality, particularly as the global crisis of antimicrobial resistance proliferates. In order to actively move towards sustainable food production, it is imperative that green biocontrol options are implemented to prevent and mitigate infectious disease in food production. Replacing current chemical pesticides, antimicrobials and disinfectants with green, organic options such as biopesticides is a step towards a sustainable future. Bacteriophages, virus which infect and kill bacteria are an area of great potential as biocontrol agents in agriculture and aquaculture. Lytic bacteriophages offer many advantages over traditional chemical-based solutions to control microbiological contamination in the food industry. The innate specificity for target bacterial species, their natural presence in the environment and biocompatibility with animal and humans means phages are a practical biocontrol candidate at all stages of food production, from farm-to-fork. Phages have demonstrated efficacy as bio-sanitisation and bio-preservation agents against many foodborne pathogens, with activity against biofilm communities also evident. Additionally, phages have long been recognised for their potential as therapeutics, prophylactically and metaphylactically. Further investigation is warranted however, to overcome their limitations such as formulation and stability issues, phage resistance mechanisms and transmission of bacterial virulence factors.

Enhancing the Stability of Bacteriophages Using Physical, Chemical, and Nano-Based Approaches: A Review

Phages are efficient in diagnosing, treating, and preventing various diseases, and as sensing elements in biosensors. Phage display alone has gained attention over the past decade, especially in pharmaceuticals. Bacteriophages have also found importance in research aiming to fight viruses and in the consequent formulation of antiviral agents and vaccines. All these applications require control over the stability of virions. Phages are considered resistant to various harsh conditions. However, stability-determining parameters are usually the only additional factors in phage-related applications. Phages face instability and activity loss when preserved for extended periods. Sudden environmental changes, including exposure to UV light, temperature, pH, and salt concentration, also lead to a phage titer fall. This review describes various formulations that impart stability to phage stocks, mainly focusing on polymer-based stabilization, encapsulation, lyophilization, and nano-assisted solutions.

Bacteriocin-phage interaction (BaPI): Phage predation of Lactococcus in the presence of bacteriocins

Bacteriophages infecting dairy starter bacteria are a leading cause of milk fermentation failure and strategies to reduce the risk of phage infection in dairy settings are demanded. Along with dairy starters, bacteriocin producers (protective cultures) or the direct addition of bacteriocins as biopreservatives may be applied in food to extend shelf-life. In this work, we have studied the progress of infection of Lactococcus cremoris MG1363 by the phage sk1, in the presence of three bacteriocins with different modes of action: nisin, lactococcin A (LcnA), and lactococcin 972 (Lcn972). We aimed to reveal putative bacteriocin-phage interactions (BaPI) that could be detrimental and increase the risk of fermentation failure due to phages. Based on infections in broth and solid media, a synergistic effect was observed with Lcn972. This positive sk1-Lcn972 interaction could be correlated with an increased burst size. sk1-Lcn972 BaPI occurred independently of a functional SOS and cell envelope stress response but was lost in the absence of the major autolysin AcmA. Furthermore, BaPI was not exclusive to the sk1-Lcn972 pairing and could be observed with other phages and lactococcal strains. Therefore, bacteriocins may facilitate phage predation of dairy lactococci and their use should be carefully evaluated.

Use of the European standardization framework established by CEN/TC 216 for effective disinfection strategies in human medicine, veterinary medicine, food hygiene, industry, and domestic and institutional use - a review

The SARS-CoV-2 pandemic illustrates the necessity of effective preventive measures for existing and newly emerging pathogens. When confronted with pathogens or spoilage agents, especially if they are not yet well studied, effective hygiene protocols are needed immediately. In the medical field, effective preventive measures are key to prevent vulnerable patients from infections. In production areas, effective hygiene measures are needed to protect goods from spoilage or microbial contamination. The European standardization framework established by the European Committee for Standardization (CEN) ensures that effective hygiene measures are available and can be immediately implemented when needed. Based on a broad portfolio of standards/laboratory tests, activity claims specifically addressing the special features of applications of antimicrobial formulations are substantiated. In this review, the concept of using standardized surrogate test organisms is explained, and the European standardized test approach to claim microbicidal and virucidal efficacy, the specificity of claims and their relevance for infection prevention measures is illustrated. Furthermore, relevance of the European Norm test methods is elucidated in the light of legal requirements. Finally, the review explains the systematics of the standardized methodological portfolio of CEN, Technical Committee 216, which is very useful when effective strategies for fighting or preventing microbial and viral induced infections, contaminations or spoilage are needed on an immediate basis.

Antibiotic resistance in the viral fraction of dairy products and a nut-based milk

Phages, the most abundant biological entities in the biosphere, can carry different bacterial genes, including those conferring antibiotic resistance. In this study, dairy products were analyzed by qPCR for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Eleven ARGs were identified in 50 samples of kefir, yogurt, milk, fresh cheese and nut-based milk (horchata), purchased from local retailers in Barcelona. Propagation experiments showed that at least some of the phages isolated from these samples infected Escherichia coli WG5, which was selected as the host strain because it does not contain prophages or ARGs in its genome. Electron microscopy revealed that the phage particles showed morphologies compatible with the Myoviridae and Siphoviridae families. Our results show that dairy products contain ARGs within infectious phage particles and may therefore serve as a reservoir of ARGs that can be mobilized to susceptible hosts, both in the food matrix and in the intestinal tract after ingestion.

Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods

Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.

Characterization and Genome Study of Novel Lytic Bacteriophages against Prevailing Saprophytic Bacterial Microflora of Minimally Processed Plant-Based Food Products

The food industry is still searching for novel solutions to effectively ensure the microbiological safety of food, especially fresh and minimally processed food products. Nowadays, the use of bacteriophages as potential biological control agents in microbiological food safety and preservation is a promising strategy. The aim of the study was the isolation and comprehensive characterization of novel bacteriophages with lytic activity against saprophytic bacterial microflora of minimally processed plant-based food products, such as mixed leaf salads. From 43 phages isolated from municipal sewage, four phages, namely Enterobacter phage KKP 3263, Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 have lytic activity against Enterobacter ludwigii KKP 3083, Citrobacter freundii KKP 3655, Enterobacter cloacae KKP 3082, and Serratia fonticola KKP 3084 bacterial strains, respectively. Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) identified Enterobacter phage KKP 3263 as an Autographiviridae, and Citrobacter phage KKP 3664, Enterobacter phage KKP 3262, and Serratia phage KKP 3264 as members of the Myoviridae family. Genome sequencing revealed that these phages have linear double-stranded DNA (dsDNA) with sizes of 39,418 bp (KKP 3263), 61,608 bp (KKP 3664), 84,075 bp (KKP 3262), and 148,182 bp (KKP 3264). No antibiotic resistance genes, virulence factors, integrase, recombinase, or repressors, which are the main markers of lysogenic viruses, were annotated in phage genomes. Serratia phage KKP 3264 showed the greatest growth inhibition of Serratia fonticola KKP 3084 strain. The use of MOI 1.0 caused an almost 5-fold decrease in the value of the specific growth rate coefficient. The phages retained their lytic activity in a wide range of temperatures (from -20 °C to 50 °C) and active acidity values (pH from 4 to 11). All phages retained at least 70% of lytic activity at 60 °C. At 80 °C, no lytic activity against tested bacterial strains was observed. Serratia phage KKP 3264 was the most resistant to chemical factors, by maintaining high lytic activity across a broader range of pH from 3 to 11. The results indicated that these phages could be a potential biological control agent against saprophytic bacterial microflora of minimally processed plant-based food products.

Genome Sequences of Bacteriophages cd2, cd3, and cd4, which Specifically Target Carnobacterium divergens

Carnobacteria have been implicated in food spoilage, but also in protection against pathogenic bacteria. We report the isolation and complete genome sequences of three bacteriophages (phages cd2, cd3, and cd4) that specifically target Carnobacterium divergens. The genome sizes are approximately 57 kbp and have limited homology to known enterococcal and streptococcal phages.

Bacteriophages in dairy plants

Bacteriophages represent the main microbiological threat for the manufacture of fermented foods. The dairy industry is the most affected by this problem, as phages are naturally present in raw milk, surfaces, vats, tanks, floors, and distributed by air displacements. Cheese whey may also contain high phage concentrations. Prophages harbored by lysogenic strains could be induced, generating new lytic phages. In this context, where phages cannot be eradicated from dairies, methods of phage monitoring are mandatory. These are mainly based in microbiological features, like classical methods, that are the most used, economic and simple to carry out. Phage DNA detection and quantification by PCR and qPCR, more complex and expensive, are faster, although not able to discern between viable and non-viable virions. Electron microscopy allows direct visualization and characterization of phage morphology, but the apparatus is expensive. Alternative methods based in other phage traits also exist, though less studied and not applicable on a daily basis. Recognition of contamination sources and correct phage monitoring in dairy factories allow a correct application of control measures. These include general measures such as proper factory design, efficient programs of sanitization, good treatment of raw materials, especially milk, and careful handling of by-products. Additionally, the use of starts cultures should be adequate, with application of rotation schemes when possible. Finally, the selection of bacteriophage insensitive mutants (BIM) is essential, and can be achieved simply and empirically, though the study of CRISPR-Cas and other newly discovered mechanisms provide a more rational basis to obtain BIMs with optimized features.

Massive Survey on Bacterial-Bacteriophages Biodiversity and Quality of Natural Whey Starter Cultures in Trentingrana Cheese Production

This study focused on the microbial and bacteriophages identification and characterization in cheese-production facilities that use natural whey starter (NWS) cultures for Trentingrana production. Bacterial and phage screening was carried out on cooked not acidified whey and NWS samples isolated from six dairy factories, for 4 consecutive days in four different months. By means of a combined approach, using plate counts, bacterial isolation, and metataxonomic analysis Lactobacillus helveticus was found occurring as the dominant species in NWS cultures and Levilactobacillus brevis as codominant in the cheese factories where the temperature of NWS production was mainly lower than 40°C, suggesting that the variability in the parameters of the NWS culture preparation could differently modulate the bacterial species in NWS cultures. Using turbidity test approach on 303 bacterial isolates from the NWS cultures, 120 distinct phages were identified. L. helveticus phage contamination of NWS cultures was revealed in most of the analyzed samples, but despite the great recovery of bacteriophage contamination cases, the microbial quality of NWS cultures was high. Our results support the presence of natural bacteriophage resistance mechanisms in L. helveticus. The use of NWS cultures probably creates an ideal environment for the proliferation of different L. helveticus strains balanced with their phages without a clear dominance. It is evident, from this study, that the presence of a high biodiversity of NWS bacterial strains is relevant to avoid phages dominance in NWS cultures and consequently to keep a good acidification ability.

Viruses in fermented foods: are they good or bad? Two sides of the same coin

The emergence of Coronavirus disease 2019 as a global pandemic has increased popular concerns about diseases caused by viruses. Fermented foods containing high loads of viable fungi and bacteria are potential sources for virus contamination. The most common include viruses that infect bacteria (bacteriophage) and yeasts reported in fermented milks, sausages, vegetables, wine, sourdough, and cocoa beans. Recent molecular studies have also associated fermented foods as vehicles for pathogenic human viruses. Human noroviruses, rotavirus, and hepatitis virus have been identified in different fermented foods through multiple routes. No severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus or close members were found in fermented foods to date. However, the occurrence/persistence of other pathogenic viruses reveals a potential vulnerability of fermented foods to SARS-CoV-2 contamination. On the other side of the coin, some bacteriophages are being suggested for improving the fermentation process and food safety, as well as owing potential probiotic properties in modern fermented foods. This review will address the diversity and characteristics of viruses associated with fermented foods and what has been changed after a short introduction to the most common next-generation sequencing platforms. Also, the risk of SARS-CoV-2 transmission via fermented foods and preventive measures will be discussed.

Bacillus subtilis natto as a potential probiotic in animal nutrition

The growing global demand for animal products and processed meat has created a challenge for the livestock sector to enhance animal productivity without compromising product quality. The restriction of antibiotics in animal feeds as growth promoters makes the use of probiotics a natural and safe alternative to obtain functional foods that provide animal health and quality and to maintain food safety for consumers. To incorporate these additives into the diet, detailed studies are required, in which in vitro and in vivo assays are used to prove the efficacy and to ensure the safety of probiotic candidate strains. Studies on the use of Bacillus subtilis natto as a spore-forming probiotic bacterium in animal nutrition have shown no hazardous effects and have demonstrated the effectiveness of its use as a probiotic, mainly due to its proven antimicrobial, anti-inflammatory, antioxidant, enzymatic, and immunomodulatory activity. This review summarizes the recent scientific background on the probiotic effects of B. subtilis natto in animal nutrition. It focuses on its safety assessment, host-associated efficacy, and industrial requirements.

Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture

Undefined strain starters are used for the production of many traditional and artisanal cheeses. Composition of undefined starters depends on several factors, and the diversity in strains and species significantly affects cheese quality and features. Culture-dependent approaches have long been used for the microbial profiling and functionalities of undefined cultures but underestimate their diversity due to culturability biases. Recently, culture-independent methods, based on high-throughput sequencing (HTS), have been preferred, with a significant boost in resolution power and sensitivity level. Amplicon targeted (AT) metagenomics, based on 16S rRNA sequencing, returned a larger microbiota diversity at genus and, sometimes, at species levels for artisanal starters of several PDO cheeses, but was inappropriate for populations with high strain diversity, and other gene targets were tested in AT approaches. Shotgun metagenomics (total DNA) and metatranscriptomics (total RNA), although are more powerful in depicting diversity and functionality of undefined cultures, have been rarely applied because of some limitations (e.g., high costs and laboriousness, need for bioinformatics skills). The advantages of HTS technologies are undoubted, but some hurdles need to be still overcame (e.g., resolution power, discrepancy between active and inactive cells, robust analytic pipelines, cost and time reduction for integrated approaches) so that HTS become routinary and convenient for defining complexity, microbial interactions (including host-phage relationships) and evolution in cheeses of undefined starters.

Characterization of the First Virulent Phage Infecting Oenococcus oeni, the Queen of the Cellars

There has been little exploration of how phages contribute to the diversity of the bacterial community associated with winemaking and may impact fermentations and product quality. Prophages of Oenococcus oeni, the most common species of lactic acid bacteria (LAB) associated with malolactic fermentation of wine, have been described, but no data is available regarding phages of O. oeni with true virulent lifestyles. The current study reports on the incidence and characterization of the first group of virulent oenophages named Vinitor, isolated from the enological environment. Vinitor phages are morphologically very similar to siphoviruses infecting other LAB. Although widespread during winemaking, they are more abundant in musts than temperate oenophages. We obtained the complete genomic sequences of phages Vinitor162 and Vinitor27, isolated from white and red wines, respectively. The assembled genomes shared 97.6% nucleotide identity and belong to the same species. Coupled with phylogenetic analysis, our study revealed that the genomes of Vinitor phages are architecturally mosaics and represent unique combinations of modules amongst LAB infecting-phages. Our data also provide some clues to possible evolutionary connections between Vinitor and (pro)phages associated to epiphytic and insect-related bacteria.

Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants

Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.

Application of Bacteriophages in Nanotechnology

Bacteriophages (phages for short) are viruses, which have bacteria as hosts. The single phage body virion, is a colloidal particle, often possessing a dipole moment. As such, phages were used as perfectly monodisperse systems to study various physicochemical phenomena (e.g., transport or sedimentation in complex fluids), or in the material science (e.g., as scaffolds). Nevertheless, phages also execute the life cycle to multiply and produce progeny virions. Upon completion of the life cycle of phages, the host cells are usually destroyed. Natural abilities to bind to and kill bacteria were a starting point for utilizing phages in phage therapies (i.e., medical treatments that use phages to fight bacterial infections) and for bacteria detection. Numerous applications of phages became possible thanks to phage display-a method connecting the phenotype and genotype, which allows for selecting specific peptides or proteins with affinity to a given target. Here, we review the application of bacteriophages in nanoscience, emphasizing bio-related applications, material science, soft matter research, and physical chemistry.

A Proof of Principle for the Detection of Viable Brucella spp. in Raw Milk by qPCR Targeting Bacteriophages

Brucellosis is still a global health issue, and surveillance and control of this zoonotic disease in livestock remains a challenge. Human outbreaks are mainly linked to the consumption of unpasteurized dairy products. The detection of human pathogenic Brucella species in food of animal origin is time-consuming and laborious. Bacteriophages are broadly applied to the typing of Brucella isolates from pure culture. Since phages intracellularly replicate to very high numbers, they can also be used as specific indicator organisms of their host bacteria. We developed a novel real-time PCR (qPCR) assay targeting the highly conserved helicase sequence harbored in all currently known Brucella-specific lytic phages. Quality and performance tests determined a limit of detection of <1 genomic copy/µL. In raw milk artificially contaminated with Brucella microti, Iz_v phages were reliably detected after 39 h of incubation, indicating the presence of viable bacteria. The qPCR assay showed high stability in the milk matrix and significantly shortened the time to diagnosis when compared to traditional culture-based techniques. Hence, our molecular assay is a reliable and sensitive method to analyze phage titers, may help to reduce the hands-on time needed for the screening of potentially contaminated food, and reveals infection risks without bacterial isolation.

Prophage in Phage Manufacturing: Is the Risk Overrated Compared to Other Therapies or Food?

The rehabilitation of lytic bacteriophages, as living and replicative biological therapeutic agents, is only 2 decades old in western countries, compared to other therapeutic approaches using chemicals and inactivated or alive biologicals. This paper attempts to provide arguments to address prophage content issues in phage pharmaceutical preparations from a regulatory perspective. The author rebalances the risk associated with the presence of prophages in their pharmaceutical preparations in comparison (i) to lysogenic phages and prophages contained in various therapeutic anti-infective treatments, as well as in food or probiotics, (ii) to adventitious whole retroviruses or fragments contained in vaccines, and (iii) to the massive release of lysogenic phages and prophages induced by antibiotics usage.

Metatranscriptomics reveals the gene functions and metabolic properties of the major microbial community during Chinese Sichuan Paocai fermentation

Chinese Sichuan Paocai (CSP) is one of the world's best-known fermented vegetables with a large presence in the Chinese market. The dynamic microbial community is the main contributor to Paocai fermentation. However, little is known about the ecological distribution and functional importance of these community members. In this study, metatranscriptomics was used to comprehensively explore the active microbial community members and key transcripts with significant functions in the Paocai fermentation process. Enterobacter, Leuconostoc, and Lactobacillus dominated the three-fermentation stages (Pre-, Mid- and Lat-), respectively. Carbon metabolism was the most abundant pathway. GH (glycoside hydrolase) and GT (lycosyl transferase) were the two most highly expressed carbohydrate-active enzymes. The most highly differentially expressed genes were grouped in the biosynthesis of amino acids, followed by glycolysis. Meta-pathways in the Sichuan Paocai fermentation ecosystem were reconstructed, Lactobacillaceae and Enterobacteriaceae were the two most important metabolic contributors. In addition, the nrfA and nirB were two genes referred to distinct nitrite reductase enzymes and 9 specialized genes, such as eclo, ron and ent were expressed to produce autoinducer 2 (AI-2) kinase in response to population density. The present study revealed functional enzymes and meta-pathways of the active microbial communities, which provide a deeper understanding of their contribution to CSP products.

Inactivation of Dairy Bacteriophages by Thermal and Chemical Treatments

This article provides information on the characteristics of diverse phages of lactic acid bacteria and highlights the incidence of their presence in different dairy fermentations. As it is known, thermal treatments on raw milk and use of sanitizers in the disinfection of surfaces and equipment are strategies usually applied in dairy to prevent bacteriophage infections. In this sense, this review mainly focuses on the existing data about the resistance against thermal treatments and sanitizers usually used in the dairy industry worldwide, and the differences found among bacteriophages of diverse genera are remarked upon. Also, we provide information concerning the problems that have arisen as a consequence of the potential presence of bacteriophages in cheese whey powder and derivatives when they are added in fermented dairy product manufacturing. Finally, some important conclusions on each topic are marked and checkpoints to be considered are suggested.

Inkjet Printed Interdigitated Biosensor for Easy and Rapid Detection of Bacteriophage Contamination: a Preliminary Study for Milk Processing Control Applications

Bacteriophages are responsible for significant material and time losses in the dairy industry. This because these viruses infect the selected lactic starter cultures used for milk fermentation, i.e., the first stage toward cheese production. Standard detection techniques are time- and labor-consuming, causing huge costs related to production plant sanitation and product wasting. A new type of biosensor for early detection of bacteriophage contamination is highly demanded by the milk processing market, and inkjet-printed electrochemical sensors could be the answer. Inkjet printing is a well-known technology that has been revisited in recent years, using silver nanoparticle (AgNP) based inks for low-cost and easy fabrication of sensing and biosensing systems on flexible and eco-compatible substrates. In this research, we studied inkjet printing for the manufacturing of both interdigitated electrodes arrays (IDEAs), and a versatile system to monitor bacterial cultures by electrochemical impedance spectroscopy (EIS). In particular, we studied this biosensing system for the detection of bacteriophages by comparing its performance with standard microbiological methods. We performed electrical and morphological characterizations of the devices produced with a consumer-use inkjet printer with commercial AgNPs ink on flexible substrates, such as office paper, polyethylene (PET), and photo paper. We used light microscopy optical analysis, profilometry, atomic force microscopy (AFM), and scanning electron microscopy (SEM) imaging to define the objects resolution, their real dimensions, and thickness. We also investigated the devices’ conductivity and layout, by EIS measurements with a standard buffer solution, i.e., phosphate buffered saline (PBS). Finally, we tested our system by monitoring Lactococcus lactis cultures and bacteriophage infection. We compared the results to those obtained by two standard microbiological methods in terms of response time, proving that our technique requires less than half the time of other methods and no specialized personnel.

Role of Bacteriophages in the Implementation of a Sustainable Dairy Chain

The growing human population is currently facing an unprecedented challenge regarding global food sustainability. Thus, it is of paramount to maintain food production and quality while avoiding a negative impact on climate change and the environment at large. Along the food chain, several practices could compromise future food safety and human health. One example is the widespread use of antibiotics and disinfectants in dairy production, which has contributed to the current antibiotic resistance crisis. Moreover, the uncontrolled release of antimicrobials to the environment poses a significant threat to natural ecosystems. For these reasons, research has recently focused on exploiting natural antimicrobials with the goal of achieving a safer and more sustainable dairy production chain. In this context, bacteriophages, viruses that infect bacteria, may become good allies to prevent and treat diseases in cattle, or be used as disinfectants in dairy facilities and as preservatives in dairy products. This review provides an overview of the current research regarding the use of phages as a global approach to reduce economic losses and food waste, while increasing food safety and reducing the environmental impact of food production. Our current understanding of progress, solutions, and future challenges in dairy production, processing, safety, waste processing, and quality assurance is also discussed.