Positive and Negative Aspects of Bacteriophages in the Food Chain PDF

www.nature.com/npjscifood REVIEW ARTICLE OPEN Positive and negative aspects of bacteriophages and their immense role in the food chain Soniya Ashok Ranveer1, Vaishali Dasriya1, Md Faruque Ahmad2, Harme...

www.nature.com/npjscifood REVIEW ARTICLE OPEN Positive and negative aspects of bacteriophages and their immense role in the food chain Soniya Ashok Ranveer1, Vaishali Dasriya1, Md Faruque Ahmad2, Harmeet Singh Dhillon1, Mrinal Samtiya 3, Eman Shama2, Taruna Anand4, Tejpal Dhewa3, Vishu Chaudhary5, Priya Chaudhary6, Pradip Behare1, Chand Ram1, Dharun Vijay Puniya7, Gulab D. Khedkar 8, António Raposo 9 ✉, Heesup Han10 ✉ and Anil Kumar Puniya1 ✉ Bacteriophages infect and replicate inside a bacterial host as well as serve as natural bio-control agents. Phages were once viewed as nuisances that caused fermentation failures with cheese-making and other industrial processes, which lead to economic losses, but phages are now increasingly being observed as being promising antimicrobials that can fight against spoilage and pathogenic bacteria. Pathogen-free meals that fulfil industry requirements without synthetic additives are always in demand in the food sector. This study introduces the readers to the history, sources, and biology of bacteriophages, which include their host ranges, absorption mechanisms, lytic profiles, lysogenic profiles, and the influence of external factors on the growth of phages. Phages and their derivatives have emerged as antimicrobial agents, biodetectors, and biofilm controllers, which have been comprehensively discussed in addition to their potential applications in the food and gastrointestinal tract, and they are a feasible and safe option for preventing, treating, and/or eradicating contaminants in various foods and food processing environments. Furthermore, phages 1234567890():,; and phage-derived lytic proteins can be considered potential antimicrobials in the traditional farm-to-fork context, which include phage-based mixtures and commercially available phage products. This paper concludes with some potential safety concerns that need to be addressed to enable bacteriophage use efficiently. npj Science of Food (2024)8:1 ; https://doi.org/10.1038/s41538-023-00245-8 INTRODUCTION temperature component of phage fitness should remain critical Phages have been discovered in every environment where when considering the use of viruses in order to manage bacterial bacteria can grow, but there hasn’t been much research into infections in agriculture and/ or the environment because these their ecological importance in the biosphere1. Phages eliminate phage-based products may have inconsistent activity on the same approximately 40% of bacterial biomass daily2. Studies on the disease, which is due to differences in climatic conditions, such as effects of phages on cohabiting microorganisms remain rare and temperatures. Phages can act as allies and enemies in human undervalued, even in the most complex ecosystems. The most activities, and bacteria may evolve phage resistance via different studied environments, which include food processing, human defense mechanisms5. The release of substances that prevent guts, and plant crops, have a lot to learn in terms of their phage attachment to the bacterial pathogen, hiding, modifying, or environmental phages and their impact in various contexts. Also, a removing the receptor, blocking phage DNA injection into a cell, lot of work is still needed to employ phages in medical and altering or removing the receptor, and blocking phage replication biotechnological applications. The prevention and treatment of and release are all examples of inhibiting phage replication and infectious diseases in humans, animals, and plants remain the release. Antibiotic resistance genes (ARGs) may spread as a result primary objectives of bacterial virus research3. The rise of of the horizontal gene transfer activities, which is due to their multidrug-resistant human infections and the emerging concerns involvement in these processes. The bacteriophage poses a of antibiotic resistance among pathogenic bacteria have renewed challenge to the fermentation economy since phage contamina- interest in phage therapy. Viruses could be used alone or in tion can cause it to lyse an entire batch6. Bacteriophages can be combination with other viruses in order to reduce infections in employed to make food safer, and they can be used as an situ. These studies focus on pathogenic and spoilage-causing adversary in specific stages of food production. Disinfecting bacteria4. A phage is a promising new weapon in the fight against equipment and surfaces used in the food industry with antibiotic-resistant, pathogenic, and biofilm-forming bacteria. bacteriophage biocontrol is an intriguing possibility7. The novel There are several growth limitations to consider when using a applications of phages in the food and allied industries and the bio-control approach regarding pH, temperature, and ion currently available mixtures that describe the applications of these concentration. The virus heat stability is critical when using phages represent a significant gap in the literature about this phages to control harmful microorganisms in food products. The topic, which is explained in this study in a detailed perspective. 1 Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal 132001, India. 2Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan 45142, Saudi Arabia. 3Department of Nutrition Biology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh 123031, India. 4ICAR-National Research Centre on Equines, Sirsa Road, Hisar 125001, India. 5University Institute of Biotechnology, Chandigarh University, Sahibzada Ajit Singh Nagar 140413, India. 6Microbiology Department, VCSG Government Institute of Medical Science and Research, Ganganali Srikot, Srinagar Pauri Garhwal 246174, India. 7Centre of One Health, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, India. 8Paul Hebert Centre for DNA Barcoding and Biodiversity Studies, Dr. Babasaheb Ambedkar Marathwada University, Aurangabad, India. 9CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal. 10College of Hospitality and Tourism Management, Sejong University, 98 Gunja-Dong, Gwanjin-gu, Seoul 143-747, Republic of Korea. ✉email: [email protected]; [email protected]; [email protected]; [email protected] Published in partnership with Beijing Technology and Business University  S.A. Ranveer et al. 2 This will attract the readers and researchers working on Host range of phages bacteriophages and the related fields, because this review The host range of a phage is a challenging attribute to assess presents a broad overview of the topics, which are not previously when determining its utility regarding phage therapy. The host comprehensively explained elsewhere. A summary of the busi- range is defined by Hyman,13 as bacteria that are capable of nesses and commodities that use bacteriophages for food-safety supporting phage infections that stimulate the spread of new purposes is also included. phage virions. The wider the host range within a target pathogen, the more probable a particular phage will be exploited by that same target pathogen in order to cause a specific disease. A HISTORY, SOURCES, AND BIOLOGY OF PHAGES phage should not infect other species because it may kill non- Bacteriophages were first studied and independently character- pathogenic commensal bacteria and dilute the phage’s optimum ized by Felix d’Herelle in 1917, and Hankin and co- workers dosage toward the targeted bacteria. However, the condition will discovered that bacteriophages have a bactericidal effect on be much more composite if the non-target bacteria’s disease is bacteria1,8. d’Herelle wrote several papers in the 1920s on productive. Other limits on the host’s range include bacterial anti- bacteriophage biology, and he was credited with helping in phage defenses, such as toxin-antitoxin systems, CRISPR and regards to establish the International Bacteriophage Institute in restriction enzymes are sometimes assumed to be a function of Tbilisi, Georgia in 19239. Phages are viruses that can only infect the precise receptor that is present in the targeted bacteria13,17. bacteria and are nearly 50 times smaller than bacteria Phage systems are contradictory, and they also have a host range, (20–200 nm). Also, they can be found in soil, water, and a range a dynamic attribute that can alter over time18. There are various of food products. Phages are categorized into various classes ways to determine the host range. Some of them are more precise based on their size and morphology. Most of them have tails, but and realistic than others. This approach is used to assess the host filamentous and pleomorphic phages can also be found in some range using individual host species in groups for each phage that phage families. Bacteriophage virion has the two most important is being tested19. Diverse host range bacteriophages have been components. They include nucleic acid, which is double-stranded isolated and characterized, which can potentially prevent diarrhea or single-stranded DNA or RNA, and the protein envelope. Lipids in cattle20. 1234567890():,; are the constituents of the envelope or a specialized lipid wall in some cases10. Absorption mechanism Phages have a high degree of selectivity when infecting the The main phase in bacteriophage (phage) infection on a host bacteria. Phages are divided into two types: lytic, which is competent host cell is the attachment of phage virions. Mass- virulent, and lysogenic, which is temperate phages. The host cell is action kinetics, which assume an influential effect of the host disrupted by lysis during the lytic cycle, which results in the cell’s density and adsorption speed on the adsorption process, are death. Lytic phages are absorbed outside the host at a specific commonly used in order to describe this adsorption mechanism. receptor site, later followed by a permanent attachment. The As a result, a high host density environment may be considered ability of a bacteriophage to effectively recognize and bind to the comparable to a phage capable of a high adsorption rate and vice receptor molecules on the cell’s surface determines its host versa. Phage strains with a greater adsorption rate will have a spectrum. Phages enter the bacteria’s cell walls with the help of smaller optimal lysis period and vice versa. their tails, which causes phage DNA to be inserted into the host cytoplasm. Unique enzymes encode the phage genome within the Lytic cycle bacterial cell in order to produce a new phage particle and Only lytic viruses are used in phage therapy because these attack diversify the host cell’s DNA and protein production. It comprises a cell from the outside and do not integrate their genomic the structural and enzymatic phage proteins that are necessary for material into the host cell’s DNA, which is due to their shorter cell lysis and the release of progeny phage. New phage particles replication cycle. Lytic viruses change their hosts’ genomes so are phage-encoded structural elements, and newly replicated viral they can multiply and spread new viruses by bursting or lysing the genomes are bundled into phage heads11. Temperate phages are cell membrane after a certain amount of time. These new viruses phages that can choose between the lytic and lysogenic growth infect and propagate quickly in order to infect the nearby cells21. pathways. These viruses can facilitate the transfer of genomic (Fig. 1). material from one bacterial cell to another, so these viruses are normally avoided as direct-use treatments. Temperate phages use Lysis profile lysogenic conversion, which is the transmission of genes that The isolated phages are examined for their ability to infect host improve the pathogenicity of the host cell. As a result, these viral bacterial cells in order to assess their infectivity range or lysis viruses are unable to kill the host that they infect. Furthermore, efficacy. The ability of the phage to form a clear plaque, a muddy super-infection immunity occurs when a bacterial cell protects a plaque, or no lysis against a given host cell is used to make this prophage within its genome and develops a resistance to determination. Bacterial cultures are cultivated on a special agar infection by comparable or nearly related phages12,13. medium, and phage lysates are used to pattern the lawns. Plaques Pathogens are entered into the food system by non-food are detected by incubating the plates at certain temperatures and resources, such as wastewater from municipalities, faeces, soil, periods. Liquefaction profiles, plaque clarity, and size are used in farms, and effluent processing facilities in food manufacturing order to determine the most efficient phages with the zones of plants. Pathogenic phages in food have been shown to be a lot lysis indicating bacteriophage lysis patterns22. more important than coliform phages and psychrotrophic spoilage phages14. Lysogenic cycle Isolating phages against various foodborne spoilage bacteria Viruses that infect the cells and incorporate their genetic material and indicator species is a lot more common than isolating phages into the host genome cause eternal association as a prophage with against specific infection-causing bacteria15. Pattern-based studies the cell and all its progeny. Its genome is retrieved in intervals that analyze the phage types of bacterial pathogens should be from the host and starts replication, and as a final point, it breaks periodically conducted to identify and detect the changes in the open the cell and sets free the new viruses (lysis). The lysogenic phage biotypes16. cycle extends the infection of the virus over several replications of npj Science of Food (2024) 1 Published in partnership with Beijing Technology and Business University  S.A. Ranveer et al. 3 Fig. 1 Life cycle of phages. the infected host cell. The parts of the bacterial DNA are inactivates phages in dewatered sludge and raw sewage. The sometimes carried along through the viral genome during the thermal resistance of somatic coliphages, which are phages cutting-out process. The spreading of this type of genome and its capable of infecting Bacteriodes fragilis, and F-specific RNA phages exchanging property may permit the transduction in the infected was discovered. This study suggests that phages are more bacterial cell, which plays the main role in the bacterial resistance resistant to thermal treatment than bacteria. The most significant properties. Hence, lysogenic phages are incompatible candidates parameter in regards to determining phage activity is the storage for phage therapy due to their elongated infection cycle23. temperature. Bacillus cereus CP-51 phages were sensitive to low temperatures and stable at room temperature, even though phage storage at room temperature is impossible. Tailed phages INFLUENCE OF EXTERNAL FACTORS ON PHAGES are the most resistant to storage and have the most extended Researchers have evaluated the impact of physical and chemical longevity. Some phages, such as T4, T5, and T7 were viable after parameters, which include temperature, acidity, and ions, on 10–20 years at 4 °C. Phages generally resist freezing and thawing, phage persistence. Phage sensitivity is an intricate issue that so repeated short-term treatments can antagonistically affect necessitates a detailed study of the involved external environ- them. Olson et al.26 discovered that 4 °C (k 40days) in wastewater mental elements. Understanding the difficulties could be bene- is the best temperature for phage storage. The temperature must ficial to people interested in phage pharmacology and agriculture be kept below −80 °C in order to retain the phage activity for a as well as to people who deal with them24. Damage to the phage’s longer period26. The phage viability is nil after 84 days in an SM internal structures, which include the envelope, head, and tail, the buffer at 42 °C, whereas no phage activity was found after loss of lipids, and/or DNA damage can render the virus inactive. 120 days at 37 °C. According to Hatch and Warren,30 phages Large capsid phages with a diameter of 100 nm will survive better should not be stored below −20 °C, because ice crystals form at than tiny capsid phages with a diameter of 60 nm. Still, there is no this temperature, which can kill phages. substantial difference in the sensitivity between contractile, non- contractile, and short tails in adverse conditions10. A phage’s pH of the environment characteristics and tolerance to external pressures may not be Another critical factor that regulates phage activity is the determined by close structural similarities or family members, and environment’s acidity. Scientists investigated the presence of they may depend on other variables25. phages in wine, particularly those associated with the lactic acid bacterium Leuconostocoenos. According to Lu et al.31 phages can Temperature grow in an acidic environment, such as in sauerkraut. After 60 and Temperature plays a vital role in a phage’s survival. The lysogenic 100 days in a sauerkraut fermentation tank, 24 phages were phase cycle is dominated by attachment, penetration, multi- identified (pH 3.5). Kerby et al.32 investigated T7 phage stability in plication, and the duration of the latent phase temperature. Only a several pH (3–11) buffers, which included citrate, phosphate, few phages genetic materials can infiltrate the host cell when the phosphate–borate, borate buffers, and citrate– phosphate, for temperature is below the optimum temperature, and only a few 1–2 weeks at 0.5–2 °C. The optimal pH for phage physical stability phages participate in phage multiplication26. Tey et al.27 for long storage is between 6 and 8. The T7 phage is most active discovered that phages that are kept at a high temperature could at pH 7, and it has the best stability in a phosphate buffer, which extend the latent stage. Furthermore, the speed, viability, and only loses 20% of its activity. It was unstable at pH 4 and lost most storage of phages are all influenced by temperature. Phages may of its infectivity after 96 h in citrate or citrate–phosphate buffers. thrive in hot springs, which are uncommon habitats with Also, it entirely lost its activity after 1 h at pH 3. T7 phages temperatures that range from 40 to 90 °C. Phages were isolated demonstrate at least 30% activity at pH 9 in alkaline conditions, from hot springs in California (USA), and they were evaluated at and their infectivity lasts for 15 days. The T7 activity was almost low and high temperatures28. eliminated after 24 h in a borate buffer with a pH >10. Their More than 75% of the phages persisted even after incubation activity was limited by a pH