The Life Cycle Transitions of Temperate Phages: Regulating Factors and Potential Ecological Implications

Salinity as a key factor affects viral structure, function, and life strategies in lakes from arid and semi-arid regions

Salinity impacts lake microorganisms in arid and semiarid zones, affecting climate change. Viruses regulate community structure, facilitate gene transfer, and mediate nutrient cycling. However, studies on the diversity and functional differences of viruses in lakes of varying salinity are limited. Thus, we investigated metagenomic data from 20 lakes in Xinjiang Province, China, to determine viral distribution, virus-host linkage, function, and drivers in lakes of varying salinity. The results showed that salinity shaped the distribution of viral community composition, and Hafunaviridae was the dominant virus in high-salinity lakes. All the metagenome-assembled genomes (MAGs) belonging to Halobacteriota were predicted as hosts, with a lysogenic lifestyle predominating the life strategy, implying their potential protection in salt lakes. Moreover, some auxiliary metabolic genes (AMGs), such as cpeT and PTOX, were related to antioxidant and stress responses, which might help the host survive high salinity stress-induced peroxidation. Notably, the main antibiotic resistance genes (ARGs) carried by viruses, which conferred resistance to polymyxin and trimethoprim, related to the local use of veterinary antibiotics, suggesting that they are potential vehicles for the transmission of ARGs. Overall, these findings suggest that lake systems include unique viral varieties that may influence microbial ecosystems and host metabolism related to environmental adaptability.

Description of two novel bacteriophages of the class Caudoviricetes that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum

Here, we describe the isolation and characterization of two novel phages from Brazilian soil that infect Ralstonia solanacearum and Ralstonia pseudosolanacearum, which we have named "RS phage AB1 and RS phage CA1. Genome sequencing and phylogenetic analysis revealed that RS phage AB1 is a novel member of the family Peduoviridae, while RS phage CA1 could not be classified as part of any established family. Thus, we propose a new viral family, "Anamaviridae", with two subfamilies, "Kantovirinae" and "Mascarenevirinae", with the latter including RS phage CA1. We propose the species names "Cocadavirus alagoinhas" and "Acarajevirus bahia" for RS phage CA1 and RS phage AB1, respectively. These findings increase our understanding of the diversity of phages infecting plant pathogens of the genus Ralstonia.

Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages

Extensive use of antibiotics in human healthcare as well as in agricultural and environmental settings has led to the emergence and spread of antibiotic-resistant bacteria, rendering many infections increasingly difficult to treat. Coupled with the limited development of new antibiotics, the rise of antimicrobial resistance (AMR) has caused a major health crisis worldwide, which calls for immediate action. Strengthening AMR surveillance systems is, therefore, crucial to global and national efforts in combating this escalating threat. This review explores the potential of metagenomics, a sequenced-based approach to analyze entire microbial communities without the need for cultivation, as a transformative and rapid tool for improving AMR surveillance strategies as compared to traditional cultivation-based methods. We emphasize the importance of monitoring mobile genetic elements (MGEs), such as integrons, transposons, plasmids, and bacteriophages (phages), in relation to their critical role in facilitating the dissemination of genetic resistance determinants via horizontal gene transfer (HGT) across diverse environments and clinical settings. In this context, the strengths and limitations of current bioinformatic tools designed to detect AMR-associated MGEs in metagenomic datasets, including the emerging potential of predictive machine learning models, are evaluated. Moreover, the controversial role of phages in AMR transmission is discussed alongside the potential of phage therapy as a promising alternative to conventional antibiotic treatment.

Should I stay or should I go: transmission trade-offs in phages and plasmids

Mobile genetic elements (MGEs), like temperate bacteriophages and conjugative plasmids, are major vectors of virulence and antibiotic resistance in bacterial populations. For reproductive success, MGEs must balance horizontal and vertical transmission. Yet, the cost of horizontal transmission (metabolic burden or host death) puts these transmission modes at odds. Using virulence-transmission trade-off (VTT) theory, we identify three groups of environmental variables affecting the balance between horizontal and vertical transmission: host density, host physiology, and competitors. We find that general theoretical predictions of the optimal response to environmental cues align with experimental evidence on the regulation of transmission by phages and plasmids. We further highlight gaps between theory and experiments, differences between phages and plasmids, and suggest areas for future research.

Viral involvement in microbial anaerobic methane oxidation-mediated arsenic mobilization in paddy soil

Anaerobic oxidation of methane (AOM) facilitates arsenic (As) mobilization, posing a significant environmental risk. Soil viruses potentially participate in the microbial AOM process, yet their roles in methane-mediated As mobilization of paddy soil remain elusive. Here, an anaerobic microcosm study was conducted by inoculating microbial suspension with extracellular free virus and mitomycin C (MC)-induced virus, along with 13CH4 injection. The results showed that extracellular free virus enhanced while MC-induced virus suppressed 13CH4-mediated As mobilization. During the AOM process, both viruses inhibited 13CH4 oxidation to 13CO2. However, the extracellular free virus suppressed whereas the MC-induced virus enhanced 13CH4 consumption, likely attributed to the viral influence on the ANME-2d abundance. The methane consumption differences were inferred to influence As reduction, as evidenced by a strong correlation between As(III) and 13CH4 consumption concentrations. Moreover, virus-mediated methane assimilation into microbial biomass carbon influenced the overall microbial population. An increased abundance of Geobacter in the extracellular free virus treatment elevated net As(III) concentrations (up to 260 %) relative to treatment without virus in the presence of 13CH4. In contrast, MC-induced virus led to a net 122 % reduction in As(III) concentration due to decreased Geobacter abundance. These findings provide new insights into soil viruses in microbial AOM-driven As mobilization, highlighting their crucial functions in soil ecosystems.

Genomic Analysis of 'Candidatus Liberibacter africanus' Strain from Zimbabwe Reveals Unique Virulence and Prophage Characteristics Compared with 'Ca. L. asiaticus'

Citrus Huanglongbing (HLB) is caused by the phloem-limited α-proteobacterium 'Candidatus Liberibacter spp.', among which 'Ca. L. africanus' (CLaf) has posed a significant threat to citrus production in Africa for nearly a century. CLaf is closely related to the globally prevalent 'Ca. L. asiaticus' (CLas), whereas little is known about the virulence of CLaf, primarily because of limited genome resources. In this study, we completed the whole-genome assembly and annotation of the CLaf strain Zim (from Zimbabwe). Compared with CLas, a total of 102 CLaf unique genes were identified, including 14 potential Sec-dependent effector (SDE) genes, 29 phage-associated genes, and 59 genes with hypothetical function. Among 14 SDEs, V9J15_03810 was able to induce a significant hypersensitive response in Nicotiana benthamiana, indicating its potential as a virulence factor for CLaf. Genome analysis showed that the CLaf strain Zim genome harbored a complete prophage region (named P-Zim-1, 42,208 bp). P-Zim-1 retained two immunosuppressive peroxidase genes (V9J15_02125 and V9J15_02130) homologous to CLas prophage SC1/SC2, whereas the lysogen-associated genes encoding integrase (V9J15_01970) and repressor (V9J15_02080) were homologous to the prophage of 'Ca. L. solanacearum', the causal agent of potato zebra chip disease. In addition, P-Zim-1 carried a novel CRISPR/Cas system, including a CRISPR array (located within V9J15_02040, ranging from 443,643 to 443,897) and five CRISPR-related Cas proteins (V9J15_02005, V9J15_02010, V9J15_02015, V9J15_02025, and V9J15_02035). This study first characterized the unique genomic feature of CLaf related to virulence and prophage, which will facilitate future research on CLaf biology and African HLB management.

Standardization of the Agar Plate Method for Bacteriophage Production

The growing threat of antimicrobial resistance (AMR), exacerbated by the COVID-19 pandemic, highlights the urgent need for alternative treatments such as bacteriophage (phage) therapy. Phage therapy offers a targeted approach to combat bacterial infections, particularly those resistant to conventional antibiotics. This study aimed to standardize an agar plate method for high-mix, low-volume phage production, suitable for personalized phage therapy. Plaque assays were conducted with the double-layer agar method, and plaque sizes were precisely measured using image analysis tools. Regression models developed with Minitab software established correlations between plaque size and phage production, optimizing production while minimizing resistance development. The resulting Plaque Size Calculation (PSC) model accurately correlated plaque size with inoculum concentration and phage yield, establishing specific plaque-forming unit (PFU) thresholds for optimal production. Using phages targeting pathogens such as Escherichia, Salmonella, Staphylococcus, Pseudomonas, Chryseobacterium, Vibrio, Erwinia, and Aeromonas confirmed the model's accuracy across various conditions. The model's validation showed a strong inverse correlation between plaque size and minimum-lawn cell clearing PFUs (MCPs; R² = 98.91%) and identified an optimal inoculum density that maximizes yield while minimizing the evolution of resistant mutants. These results highlight that the PSC model offers a standardized and scalable method for efficient phage production, which is crucial for personalized therapy and AMR management. Furthermore, its adaptability across different conditions and phages positions it as a potential standard tool for rapid and precise phage screening and propagation in both clinical and industrial settings.

Beyond antibiotics: mesenchymal stem cells and bacteriophages-new approaches to combat bacterial resistance in wound infections

Wound management is a major global health problem. With the rising incidence of diabetic wounds, accidents, and other injuries, the demand for prompt wound treatment has become increasingly critical. Millions of people suffer from serious, large wounds resulting from major accidents, surgeries, and wars. These wounds require considerable time to heal and are susceptible to infection. Furthermore, chronic wounds, particularly in elderly and diabetic patients, often require frequent medical interventions to prevent complications. Consequently, wound management imposes a significant economic burden worldwide. The complications arising from wound infections can vary from localized issues to systemic effects. The most severe local complication of wound infection is the non-healing, which results from the disruption of the wound-healing process. This often leads to significant pain, discomfort, and psychological trauma for the patient. Systemic complications may include cellulitis, osteomyelitis, and septicemia. Mesenchymal stem cells are characterized by their high capacity for division, making them suitable candidates for the treatment of tissue damage. Additionally, they produce antimicrobial peptides and various cytokines, which enhance their antimicrobial activity. Evidence shows that phages are effective in treating wound-related infections, and phage therapy has proven to be highly effective for patients when administered correctly. The purpose of this article is to explore the use of bacteriophages and mesenchymal stem cells in wound healing and infection management.

From forgotten cure to modern medicine: The resurgence of bacteriophage therapy

OBJECTIVES

The unregulated use of antibiotics has led to the rise of antibiotic-resistant bacterial strains. This study explores bacteriophage therapy as an alternative treatment, highlighting its history, significance, and advancements in Europe, the United States, and the Middle East.

METHODS

A comprehensive literature review on bacteriophage therapy was conducted, focusing on its development, clinical trials, and patient treatment applications. The study also examined challenges, limitations, criteria for ideal phage selection, and manipulation techniques.

RESULTS

The United States and several European countries have advanced in phage therapy, progressing from clinical trials to patient treatment, whereas Middle Eastern countries are still in the early stages. Bacteriophages offer specificity, abundance, and minimal side effects, but challenges like safety concerns and potential resistance limit their widespread use.

CONCLUSION

Bacteriophage therapy shows promise as an antibiotic alternative but faces safety and resistance challenges. Continued research and better regulatory frameworks, especially in the Middle East, are needed to realize its potential.

Prevention and Modern Strategies for Managing Methicillin-Resistant Staphylococcal Infections in Prosthetic Joint Infections (PJIs)

Periprosthetic joint infections (PJIs) are a dangerous complication of joint replacement surgeries which have become much more common in recent years (mostly hip and knee replacement surgeries). Such a condition can lead to many health issues and often requires reoperation. Staphylococci is a bacterial group most common in terms of the pathogens causing PJIs. S. aureus and coagulase-negative staphylococci are found in around two-thirds of PJI cases. Recently, the numbers of staphylococci that cause such infections and that are methicillin-resistant are increasing. This trend leads to difficulties in the treatment and prevention of such infections. That is why MRSA and MRSE groups require extraordinary attention when dealing with PJIs in order to successfully treat them. Controlling carriage, using optimal prosthetic materials, and implementing perioperative antimicrobial prophylaxis are crucial strategies in infection prevention and are as essential as quick diagnosis and effective targeted treatment. The comprehensive professional procedures presented in this review show how to deal with such cases.

Phage Therapy Against Antibiotic-Resistant and Multidrug-Resistant Infections Involving Nonhealing Wounds and Prosthetic Joint Infections Associated With Biofilms: A Mini-Review

Chronic wounds and prosthetic joint infections are difficult to treat and are associated with a high burden of disease and economic cost. The rise of antibiotic resistance and the understanding of biofilm formation has inflamed an already challenging situation. Bacteriophage therapy has been used throughout the last century to treat bacterial infections. However, in the last 10 years, there has been a resurgence in phage therapy as a novel innovative treatment for nonhealing wounds. This mini systemic review assesses relevant clinical studies, case series and trials over 5 years associated with safety, treatment and success rates of phage therapy concerning nonhealing and prosthetic joint infections. A search of PubMed, Web of Science, Cochrane and Clinical Trials.gov databases resulted in 3151 studies, 27 met the criteria, and a total of 152 bacterial infections were treated from 130 individuals. Most common pathogen isolated in wounds was P. aeruginosa, and S. aureus was mostly associated with prosthetic joint infections. Treatment modalities differed across studies, adverse effects were limited, and success rate was deemed to be 91%.

Microhabitat influences on phage-bacteria dynamics in an abandoned mine for ecorestoration

Understanding the complex interactions between bacteriophages (phages) and bacteria within varied environmental niches is critical yet underexplored for improving microbe-assisted ecological restoration. This study investigates the influence of microhabitat heterogeneity within an abandoned mine on phage-bacteria interaction patterns, focusing on Pseudomonas-enriched bacterial communities. By isolating viral communities and purifying bacteria from soils of three distinct microhabitats, we assessed the regulatory role of environmental factors on these interactions, crucial for bacterial success in environmental applications. We characterized microhabitat variability by analyzing soil particle size fractions, minerals composition, and elemental content using X-ray diffraction and energy-dispersive X-ray analyses. 16S rRNA sequencing and cross-infection assays revealed that although bacterial communities across different microhabitats are taxonomically similar, their interaction patterns with phages are distinct. Phage communities showed nonselective infectivity across soil types, while bacterial communities exhibited selective adaptation, facilitating colonization across diverse microhabitats. Minerals such as mica, kaolinite, and hematite were found to increase phage infectivity, whereas mixed-layer clay correlated with early lysis. Additionally, higher levels of iron (Fe) and potassium (K) were linked to bacterial resistance strategies. Our findings highlight the importance of understanding asymmetric adaptive strategies between bacteria and phages, driven by microhabitat heterogeneity, for enhancing microbial-mediated nature-based restoration of degraded ecosystems.

Characterization and comparative genomic analysis of a marine Bacillus phage reveal a novel viral genus

Bacillus pumilus exhibits substantial economic significance, with its metabolism, adaptability, and ecological functions regulated by its bacteriophages. Here, we isolated and characterized a novel temperate phage vB_BpuM-ZY1 from B. pumilus derived from mangrove sediments by mitomycin C induction. Phage vB_BpuM-ZY1 is a typical myophage, which has an icosahedral head with a diameter of 43.34 ± 2.14 nm and a long contractible tail with a length of 238.58 ± 5.18 nm. Genomic analysis indicated that vB_BpuM-ZY1 encodes genes for lysogeny control, and its life cycle may be intricately regulated by multiple mechanisms. vB_BpuM-ZY1 was predicted to employ P2-like 5'-extended-cos packaging strategy. In addition, genome-wide phylogenetic tree and proteome tree analyses indicated that vB_BpuM-ZY1 belongs to the Peduoviridae family but forms a separate branch at a deeper taxonomic level. Particularly, the comparative genomic analysis showed that vB_BpuM-ZY1 has less than 70% intergenomic similarities with its most similar phages. Thus, we propose that vB_BpuM-ZY1 is a novel Bacillus phage belonging to a new genus under the Peduoviridae family. The protein-sharing network analysis identified 44 vB_BpuM-ZY1-related phages. Interestingly, these evolutionarily related myophages infect a broad range of hosts across different phyla, which may be explained by the high structural variations of the host recognition domain in their central spike proteins. Collectively, our study will contribute to our understanding of Bacillus phage diversity and Bacillus-phage interactions, as well as provide essential knowledge for the industrial application of B. pumilus.

IMPORTANCE

Although recent metagenomics research has obtained a wealth of phage genetic information, much of it is considered "dark matter" because of the lack of similarity with known sequences in the database. Therefore, the isolation and characterization of novel phages will help to interpret the vast unknown viral metagenome data and improve our understanding of phage diversity and phage-host interactions. Bacillus pumilus shows high economic relevance due to its wide applications in biotechnology, industry, biopharma, and environmental sectors. Since phages influence the abundance, metabolism, evolution, fitness, and ecological functions of bacteria through complex interactions, the significance of isolation and characterization of novel phages infecting B. pumilus is apparent. In this study, we isolated and characterized a B. pumilus phage belonging to a novel viral genus, which provides essential knowledge for phage biology as well as the industrial application of B. pumilus.

Determinants in the phage life cycle: The dynamic nature of ssDNA phage FLiP and host interactions under varying environmental conditions and growth phases

The influence of environmental factors on the interactions between phages and bacteria, particularly single-stranded DNA (ssDNA) phages, has been largely unexplored. In this study, we used Finnlakevirus FLiP, the first known ssDNA phage species with a lipid membrane, as our model phage. We examined the infectivity of FLiP with three Flavobacterium host strains, B330, B167 and B114. We discovered that FLiP infection is contingent on the host strain and conditions such as temperature and bacterial growth phase. FLiP can infect its hosts across a wide temperature range, but optimal phage replication varies with each host. We uncovered some unique aspects of phage infectivity: FLiP has limited infectivity in liquid-suspended cells, but it improves when cells are surface-attached. Moreover, FLiP infects stationary phase B167 and B114 cells more rapidly and efficiently than exponentially growing cells, a pattern not observed with the B330 host. We also present the first experimental evidence of endolysin function in ssDNA phages. The activity of FLiP's lytic enzymes was found to be condition-dependent. Our findings underscore the importance of studying phage ecology in contexts that are relevant to the environment, as both the host and the surrounding conditions can significantly alter the outcome of phage-host interactions.

Mycobacteriophages: therapeutic approach for mycobacterial infections

Tuberculosis (TB) is a significant global health threat, and cases of infection with non-tuberculous mycobacteria (NTM) causing lung disease (NTM-LD) are rising. Bacteriophages and their gene products have garnered interest as potential therapeutic options for bacterial infections. Here, we have compiled information on bacteriophages and their products that can kill Mycobacterium tuberculosis or NTM. We summarize the mechanisms whereby viable phages can access macrophage-resident bacteria and not elicit immune responses, review methodologies of pharmaceutical product development containing mycobacteriophages and their gene products, mainly lysins, in the context of drug regulatory requirements and we discuss industrially relevant methods for producing pharmaceutical products comprising mycobacteriophages, emphasizing delivery of mycobacteriophages to the lungs. We conclude with an outline of some recent case studies on mycobacteriophage therapy.

Evaluating the Stability of Lytic and Lysogenic Bacteriophages in Various Protectants

Phage therapy has regained value as a potential alternative and a complementary anti-infective approach to antibiotics in the fight against bacterial pathogens. Due to their host specificity, non-pathogenic nature for humans, and low production cost, phages offer an effective opportunity for utilization in healthcare, agriculture, and food preservation. Well-defined storage conditions are essential for commercialization and dissemination of phage usage. For this purpose, in our study, after the isolation and characterization of two different phages, one lytic and the other lysogenic; storage and shelf-life studies of phages were evaluated in a presence of various protectants (glycerol, sodium azide, DMSO with chloroform) and without any protectant during 8-month period at four different temperatures. The short-time stability of the lytic P. syringae phage and lysogenic MRSA phage, which were determined by STEM analysis to belong to the Straboviridae and Siphoviridae families, respectively were also examined for the different temperatures and the pH levels ranging from 1.0 to 14.0. This study revealed the storage-model of phages that exhibit distinct lifecycles, for the first time and provided a theoretical basis for development and application of phages, has yielded valuable findings contributing to understanding of phage biology.

Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments

Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.

Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups

Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.

The role of rhizosphere phages in soil health

While the One Health framework has emphasized the importance of soil microbiomes for plant and human health, one of the most diverse and abundant groups-bacterial viruses, i.e. phages-has been mostly neglected. This perspective reviews the significance of phages for plant health in rhizosphere and explores their ecological and evolutionary impacts on soil ecosystems. We first summarize our current understanding of the diversity and ecological roles of phages in soil microbiomes in terms of nutrient cycling, top-down density regulation, and pathogen suppression. We then consider how phages drive bacterial evolution in soils by promoting horizontal gene transfer, encoding auxiliary metabolic genes that increase host bacterial fitness, and selecting for phage-resistant mutants with altered ecology due to trade-offs with pathogen competitiveness and virulence. Finally, we consider challenges and avenues for phage research in soil ecosystems and how to elucidate the significance of phages for microbial ecology and evolution and soil ecosystem functioning in the future. We conclude that similar to bacteria, phages likely play important roles in connecting different One Health compartments, affecting microbiome diversity and functions in soils. From the applied perspective, phages could offer novel approaches to modulate and optimize microbial and microbe-plant interactions to enhance soil health.

The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis

Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.

The spontaneously produced lysogenic prophage phi456 promotes bacterial resistance to adverse environments and enhances the colonization ability of avian pathogenic Escherichia coli strain DE456

In the last decade, prophages that possess the ability of lysogenic transformation have become increasingly significant. Their transfer and subsequent activity in the host have a significant impact on the evolution of bacteria. Here, we investigate the role of prophage phi456 with high spontaneous induction in the bacterial genome of Avian pathogenic Escherichia coli (APEC) DE456. The phage particles, phi456, that were released from DE456 were isolated, purified, and sequenced. Additionally, phage particles were no longer observed either during normal growth or induced by nalidixic acid in DE456Δphi456. This indicated that the released phage particles from DE456 were only phi456. We demonstrated that phi456 contributed to biofilm formation through spontaneous induction of the accompanying increase in the eDNA content. The survival ability of DE456Δphi456 was decreased in avian macrophage HD11 under oxidative stress and acidic conditions. This is likely due to a decrease in the transcription levels of three crucial genes-rpoS, katE, and oxyR-which are needed to help the bacteria adapt to and survive in adverse environments. It has been observed through animal experiments that the presence of phi456 in the DE456 genome enhances colonization ability in vivo. Additionally, the number of type I fimbriae in DE456Δphi456 was observed to be reduced under transmission electron microscopy when compared to the wild-type strain. The qRT-PCR results indicated that the expression levels of the subunit of I fimbriae (fimA) and its apical adhesin (fimH) were significantly lower in DE456Δphi456. Therefore, it can be concluded that phi456 plays a crucial role in helping bacterial hosts survive in unfavorable conditions and enhancing the colonization ability in DE456.

The interplay of low H2O2 doses, lytic cyanophage, and Microcystis aeruginosa: Implications for cyanobacterial bloom control and microcystin production/release

Low H2O2 doses can suppress cyanobacterial blooms without damaging non-target species but enable undesirable regrowth. Besides, the role of cyanophage in preventing regrowth after low H2O2 exposure remains unclear. Applying phages to cyanobacteria pre-exposed to low H2O2 in early growth stages may improve host removal and reduce microcystin (MC) production/release. Lytic cyanophage MDM-1 with a 172 PFU/cell burst size, 2-day short latent period against MCs-producing Microcystis, shows high H2O2 stability. Low H2O2 (1 to 2.5 mg/L) doses significantly (p < 0.05) inhibited Microcystis aeruginosa growth rate, biofilm and MCs concentration reduction in a dose-dependent manner but regrowth occurred at all concentrations. Phage treatment eliminated cells without H2O2 pretreatment within 3 days and reduced MC production. H2O2-pretreated M. aeruginosa cells altered the phage dynamics, affecting adsorption, latency, production, and cell lysis in response to H2O2-induced oxidative stress. At 1.5 mg H2O2/L pretreatment, cells were eliminated with reduced MC production, like untreated cells. H2O2 pretreatment with 2.0 and 2.5 mg/L resulted in an extension of the phage absorption phase and the latent period. This was accompanied by a reduction in lysis efficacy, attributed to the increased ROS production. At 2.5 mg H2O2/L, 17.10 % of phages remain un-adsorbed, with cell lysis rate dropped from 0.89 d-1 to 0.26 d-1 compared to the untreated control. The highest phage titer (70 %) was obtained with 1.5 mg/H2O2 pretreated cells. This study emphasizes that low-dose H2O2 eliminates Microcystis but severely affects phage lysis and MCs release depending on H2O2-induced ROS levels. It is a crucial consideration when using phages to control cyanobacterial blooms with H2O2-induced stress.

Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study

Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.

Bacteriophage therapy for drug-resistant Staphylococcus aureus infections

Drug-resistant Staphylococcus aureus stands as a prominent pathogen in nosocomial and community-acquired infections, capable of inciting various infections at different sites in patients. This includes Staphylococcus aureus bacteremia (SaB), which exhibits a severe infection frequently associated with significant mortality rate of approximately 25%. In the absence of better alternative therapies, antibiotics is still the main approach for treating infections. However, excessive use of antibiotics has, in turn, led to an increase in antimicrobial resistance. Hence, it is imperative that new strategies are developed to control drug-resistant S. aureus infections. Bacteriophages are viruses with the ability to infect bacteria. Bacteriophages, were used to treat bacterial infections before the advent of antibiotics, but were subsequently replaced by antibiotics due to limited theoretical understanding and inefficient preparation processes at the time. Recently, phages have attracted the attention of many researchers again because of the serious problem of antibiotic resistance. This article provides a comprehensive overview of phage biology, animal models, diverse clinical case treatments, and clinical trials in the context of drug-resistant S. aureus phage therapy. It also assesses the strengths and limitations of phage therapy and outlines the future prospects and research directions. This review is expected to offer valuable insights for researchers engaged in phage-based treatments for drug-resistant S. aureus infections.

Macroalgal virosphere assists with host-microbiome equilibrium regulation and affects prokaryotes in surrounding marine environments

The microbiomes in macroalgal holobionts play vital roles in regulating macroalgal growth and ocean carbon cycling. However, the virospheres in macroalgal holobionts remain largely underexplored, representing a critical knowledge gap. Here we unveil that the holobiont of kelp (Saccharina japonica) harbors highly specific and unique epiphytic/endophytic viral species, with novelty (99.7% unknown) surpassing even extreme marine habitats (e.g. deep-sea and hadal zones), indicating that macroalgal virospheres, despite being closest to us, are among the least understood. These viruses potentially maintain microbiome equilibrium critical for kelp health via lytic-lysogenic infections and the expression of folate biosynthesis genes. In-situ kelp mesocosm cultivation and metagenomic mining revealed that kelp holobiont profoundly reshaped surrounding seawater and sediment virus-prokaryote pairings through changing surrounding environmental conditions and virus-host migrations. Some kelp epiphytic viruses could even infect sediment autochthonous bacteria after deposition. Moreover, the presence of ample viral auxiliary metabolic genes for kelp polysaccharide (e.g. laminarin) degradation underscores the underappreciated viral metabolic influence on macroalgal carbon cycling. This study provides key insights into understanding the previously overlooked ecological significance of viruses within macroalgal holobionts and the macroalgae-prokaryotes-virus tripartite relationship.

Vibrio cyclitrophicus phage encoding gene transfer agent fragment, representing a novel viral family

Vibrio is a prevalent bacterial genus in aquatic environments and exhibits diverse metabolic capabilities, playing a vital role in marine biogeochemical cycles. This study isolated a novel virus infecting Vibrio cyclitrophicus, vB_VviC_ZQ26, from coastal waters near Qingdao, China. The vB_VviC_ZQ26 comprises a linear double-stranded DNA genome with a length of 42,982 bp and a G + C content of 43.21 %, encoding 72 putative open reading frames (ORFs). Transmission electron microscope characterization indicates a siphoviral-morphology of vB_VviC_ZQ26. Nucleic-acids-wide analysis indicates a tetranucleotide frequency deviation for genomic segments encoding putative gene transfer agent protein (GTA) and coil-containing protein, implying divergent origins occurred in different parts of viral genomes. Phylogenetic and genome-content-based analysis suggest that vB_VviC_ZQ26 represents a novel vibriophage-specific family designated as Coheviridae. From the result of biogeographic analysis, Coheviridae is mainly colonized in the temperate and tropical epipelagic zones. This study describes a novel vibriophage infecting V. cyclitrophicus, shedding light on the evolutionary divergence of different parts of the viral genome and its ecological footprint in marine environments.

Characterization of a Vibriophage Infecting Pathogenic Vibrio harveyi

Bacterial diseases caused by Vibrio spp. are prevalent in aquaculture and can lead to high mortality rates among aquatic species and significant economic losses. With the increasing emergence of multidrug-resistant Vibrio strains, phage therapy is being explored as a potential alternative to antibiotics for biocontrol of infectious diseases. Here, a new lytic phage named vB_VhaS_R21Y (R21Y) was isolated against Vibrio harveyi BVH1 obtained from seawater from a scallop-farming area in Rongcheng, China. Its morphology, infection cycle, lytic profile, phage stability, and genetic features were characterized. Transmission electronic microscopy indicated that R21Y is siphovirus-like, comprising an icosahedral head (diameter 73.31 ± 2.09 nm) and long noncontractile tail (205.55 ± 0.75 nm). In a one-step growth experiment, R21Y had a 40-min latent period and a burst size of 35 phage particles per infected cell. R21Y was highly species-specific in the host range test and was relatively stable at pH 4-10 and 4-55 °C. Genomic analysis showed that R21Y is a double-stranded DNA virus with a genome size of 82,795 bp and GC content of 47.48%. Its high tolerance and lytic activity indicated that R21Y may be a candidate for phage therapy in controlling vibriosis in aquacultural systems.

Characterization of phage vB_EcoS-EE09 infecting E. coli DSM613 Isolated from Wastewater Treatment Plant Effluent and Comparative Proteomics of the Infected and Non-Infected Host

Phages influence microbial communities, can be applied in phage therapy, or may serve as bioindicators, e.g., in (waste)water management. We here characterized the Escherichia phage vB_EcoS-EE09 isolated from an urban wastewater treatment plant effluent. Phage vB_EcoS-EE09 belongs to the genus Dhillonvirus, class Caudoviricetes. It has an icosahedral capsid with a long non-contractile tail and a dsDNA genome with an approximate size of 44 kb and a 54.6% GC content. Phage vB_EcoS-EE09 infected 12 out of the 17 E. coli strains tested. We identified 16 structural phage proteins, including the major capsid protein, in cell-free lysates by protein mass spectrometry. Comparative proteomics of protein extracts of infected E. coli cells revealed that proteins involved in amino acid and protein metabolism were more abundant in infected compared to non-infected cells. Among the proteins involved in the stress response, 74% were less abundant in the infected cultures compared to the non-infected controls, with six proteins showing significant less abundance. Repressing the expression of these proteins may be a phage strategy to evade host defense mechanisms. Our results contribute to diversifying phage collections, identifying structural proteins to enable better reliability in annotating taxonomically related phage genomes, and understanding phage-host interactions at the protein level.

Safety Properties of Escherichia coli O157:H7 Specific Bacteriophages: Recent Advances for Food Safety

Shiga-toxin-producing Escherichia coli (STEC) is typically detected on food products mainly due to cross-contamination with faecal matter. The serotype O157:H7 has been of major public health concern due to the severity of illness caused, prevalence, and management. In the food chain, the main methods of controlling contamination by foodborne pathogens often involve the application of antimicrobial agents, which are now becoming less efficient. There is a growing need for the development of new approaches to combat these pathogens, especially those that harbour antimicrobial resistant and virulent determinants. Strategies to also limit their presence on food contact surfaces and food matrices are needed to prevent their transmission. Recent studies have revealed that bacteriophages are useful non-antibiotic options for biocontrol of E. coli O157:H7 in both animals and humans. Phage biocontrol can significantly reduce E. coli O157:H7, thereby improving food safety. However, before being certified as potential biocontrol agents, the safety of the phage candidates must be resolved to satisfy regulatory standards, particularly regarding phage resistance, antigenic properties, and toxigenic properties. In this review, we provide a general description of the main virulence elements of E. coli O157:H7 and present detailed reports that support the proposals that phages infecting E. coli O157:H7 are potential biocontrol agents. This paper also outlines the mechanism of E. coli O157:H7 resistance to phages and the safety concerns associated with the use of phages as a biocontrol.

The Role of Bacteriophages in the Gut Microbiota: Implications for Human Health

Bacteriophages (phages) are nano-sized viruses characterized by their inherent ability to live off bacteria. They utilize diverse mechanisms to absorb and gain entry into the bacterial cell wall via the release of viral genetic material, which uses the replication mechanisms of the host bacteria to produce and release daughter progeny virions that attack the surrounding host cells. They possess specific characteristics, including specificity for particular or closely related bacterial species. They have many applications, including as potential alternatives to antibiotics against multi-resistant bacterial pathogens and as control agents in bacteria-contaminated environments. They are ubiquitously abundant in nature and have diverse biota, including in the gut. Gut microbiota describes the community and interactions of microorganisms within the intestine. As with bacteria, parasitic bacteriophages constantly interact with the host bacterial cells within the gut system and have obvious implications for human health. However, it is imperative to understand these interactions as they open up possible applicable techniques to control gut-implicated bacterial diseases. Thus, this review aims to explore the interactions of bacteriophages with bacterial communities in the gut and their current and potential impacts on human health.

Bioprospecting the Skin Microbiome: Advances in Therapeutics and Personal Care Products

Bioprospecting is the discovery and exploration of biological diversity found within organisms, genetic elements or produced compounds with prospective commercial or therapeutic applications. The human skin is an ecological niche which harbours a rich and compositional diversity microbiome stemming from the multifactorial interactions between the host and microbiota facilitated by exploitable effector compounds. Advances in the understanding of microbial colonisation mechanisms alongside species and strain interactions have revealed a novel chemical and biological understanding which displays applicative potential. Studies elucidating the organismal interfaces and concomitant understanding of the central processes of skin biology have begun to unravel a potential wealth of molecules which can exploited for their proposed functions. A variety of skin-microbiome-derived compounds display prospective therapeutic applications, ranging from antioncogenic agents relevant in skin cancer therapy to treatment strategies for antimicrobial-resistant bacterial and fungal infections. Considerable opportunities have emerged for the translation to personal care products, such as topical agents to mitigate various skin conditions such as acne and eczema. Adjacent compound developments have focused on cosmetic applications such as reducing skin ageing and its associated changes to skin properties and the microbiome. The skin microbiome contains a wealth of prospective compounds with therapeutic and commercial applications; however, considerable work is required for the translation of in vitro findings to relevant in vivo models to ensure translatability.

Emerging applications of phage therapy and fecal virome transplantation for treatment of Clostridioides difficile infection: challenges and perspectives

Clostridioides difficile, which causes life-threatening diarrheal disease, is considered an urgent threat to healthcare setting worldwide. The current standards of care solely rely on conventional antibiotic treatment, however, there is a risk of promoting recurrent C. difficile infection (rCDI) because of the emergence of antibiotic-resistant strains. Globally, the alarming spread of antibiotic-resistant strains of C. difficile has resulted in a quest for alternative therapeutics. The use of fecal microbiota transplantation (FMT), which involves direct infusion of fecal suspension from a healthy donor into a diseased recipient, has been approved as a highly efficient therapeutic option for patients with rCDI. Bacteriophages or phages are a group of viruses that can infect and destroy bacterial hosts, and are recognized as the dominant viral component of the human gut microbiome. Accumulating data has demonstrated that phages play a vital role in microbial balance of the human gut microbiome. Recently, phage therapy and fecal virome transplantation (FVT) have been introduced as promising alternatives for the treatment of C. difficile -related infections, in particular drug-resistant CDI. Herein, we review the latest updates on C. difficile- specific phages, and phage-mediated treatments, and highlight the current and future prospects of phage therapy in the management of CDI.

Recent advances in phage defense systems and potential overcoming strategies

Bacteriophages are effective in the prevention and control of bacteria, and many phage products have been permitted and applied in the field. Because bacteriophages are expected to replace other antimicrobial agents like antibiotics, the antibacterial effect of bacteriophage has attracted widespread attention. Recently, the diversified defense systems discovered in the target host have become potential threats to the continued effective application of phages. Therefore, a systematic summary and in-depth illustration of the interaction between phages and bacteria is conducive to the development of this biological control approach. In this review, we introduce different defense systems in bacteria against phages and emphasize newly discovered defense mechanisms in recent years. Additionally, we draw attention to the striking resemblance between defense system genes and antibiotic resistance genes, which raises concerns about the potential transfer of phage defense systems within bacterial populations and its future impact on phage efficacy. Thus, attention should be given to the effects of phage defense genes in practical applications. This article is not exhaustive, but strategies to overcome phage defense systems are also discussed to further promote more efficient use of phages.

Bacteriophage Therapy as an Application for Bacterial Infection in China

Antibiotic resistance has emerged as a significant issue to be resolved around the world. Bacteriophage (phage), in contrast to antibiotics, can only kill the target bacteria with no adverse effect on the normal bacterial flora. In this review, we described the biological characteristics of phage, and summarized the phage application in China, including in mammals, ovipara, aquatilia, and human clinical treatment. The data showed that phage had a good therapeutic effect on drug-resistant bacteria in veterinary fields, as well as in the clinical treatment of humans. However, we need to take more consideration of the narrow lysis spectrum, the immune response, the issues of storage, and the pharmacokinetics of phages. Due to the particularity of bacteriophage as a bacterial virus, there is no unified standard or regulation for the use of bacteriophage in the world at present, which hinders the application of bacteriophage as a substitute for antibiotic biological products. We aimed to highlight the rapidly advancing field of phage therapy as well as the challenges that China faces in reducing its reliance on antibiotics.

Disarm The Bacteria: What Temperate Phages Can Do

In the field of phage applications and clinical treatment, virulent phages have been in the spotlight whereas temperate phages received, relatively speaking, less attention. The fact that temperate phages often carry virulent or drug-resistant genes is a constant concern and drawback in temperate phage applications. However, temperate phages also play a role in bacterial regulation. This review elucidates the biological properties of temperate phages based on their life cycle and introduces the latest work on temperate phage applications, such as on host virulence reduction, biofilm degradation, genetic engineering and phage display. The versatile use of temperate phages coupled with their inherent properties, such as economy, ready accessibility, wide variety and host specificity, make temperate phages a solid candidate in tackling bacterial infections.