Lysogenic Bacteria Research Articles

The Isolation and Characterization of Novel Caulobacter and Non-Caulobacter Lysogenic Bacteria from Soil and the Discovery of Broad-Host-Range Phages Infecting Multiple Genera.

To explore how microbial interactions within the rhizosphere influence the diversity and functional roles of bacterial communities, we isolated 21 bacterial strains from soil samples collected near Rocky Branch Creek on the University of South Carolina campus. Our findings revealed that a significant proportion of the isolated bacterial strains are lysogenic. Contrary to predictions of a narrow host range, most of the bacteriophages derived from these lysogenic bacteria demonstrated the ability to infect a broad range of bacterial strains. These results suggest that the bacterial community shares a complex phage community, creating an intricate web of interactions. This study enhances our understanding of the relationships between phages and their bacterial hosts in soil ecosystems, with implications for ecological balance and agricultural practices aimed at improving plant health through microbial management strategies.

Characterization of Mu-Like Yersinia Phages Exhibiting Temperature Dependent Infection.

Yersinia pestis is the etiological agent of plague. Marmota himalayana of the Qinghai-Tibetan plateau is the primary host of flea-borne Y. pestis. This study is the report of isolation of Mu-like bacteriophages of Y. pestis from M. himalayana. The isolation and characterization of four Mu-like phages of Y. pestis were reported, which were named as vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 according to their morphology. Comparative genome analysis revealed that vB_YpM_3, vB_YpM_5, vB_YpM_6, and vB_YpM_23 are phylogenetically closest to Escherichia coli phages Mu, D108 and Shigella flexneri phage SfMu. The role of LPS core structure of Y. pestis in the phages' receptor was pinpointed. All the phages exhibit "temperature dependent infection," which is independent of the growth temperature of the host bacteria and dependent of the temperature of phage infection. The phages lyse the host bacteria at 37°C, but enter the lysogenic cycle and become prophages in the chromosome of the host bacteria at 26°C. IMPORTANCE Mu-like bacteriophages of Y. pestis were isolated from M. himalayana of the Qinghai-Tibetan plateau in China. These bacteriophages have a unique temperature dependent life cycle, follow a lytic cycle at the temperature of warm-blooded mammals (37°С), and enter the lysogenic cycle at the temperature of its flea-vector (26°С). A switch from the lysogenic to the lytic cycle occurred when lysogenic bacteria were incubated from lower temperature to higher temperature (initially incubating at 26°C and shifting to 37°C). It is speculated that the temperature dependent lifestyle of bacteriophages may affect the population dynamics and pathogenicity of Y. pestis.

Characterization of Temperate LPS-Binding Bordetella avium Phages That Lack Superinfection Immunity.

Bordetella avium causes a highly infectious upper respiratory tract disease in turkeys and other poultry with high economic losses. Considering the antimicrobial resistance crisis, bacteriophages (phages) may be an alternative approach for treating bacterial infections such as bordetellosis. Here, we describe seven B. avium phages, isolated from drinking water and feces from chicken and turkey farms. They showed strong bacteriolytic activity with a broad host range and used lipopolysaccharides (LPS) as a host receptor for their adsorption. All phages are myoviruses based on their structure observed by transmission electron microscopy. Genome sequence analyses revealed genome assembly sizes ranging from 39,087 to 43,144 bp. Their permutated genomes were organized colinearly, with a conserved module order, and were packed according to a predicted headful packing strategy. Notably, they contained genes encoding putative markers of lysogeny, indicative of temperate phages, despite their lytic phenotype. Further investigation revealed that the phages could indeed undergo a lysogenic life cycle with varying frequency. However, the lysogenic bacteria were still susceptible to superinfection with the same phages. This lack of stable superinfection immunity after lysogenization appears to be a characteristic feature of B. avium phages, which is favorable in terms of a potential therapeutic use of phages for the treatment of avian bordetellosis. IMPORTANCE To maintain the effectiveness of antibiotics over the long term, alternatives to treat infectious diseases are urgently needed. Therefore, phages have recently come back into focus as they can specifically infect and lyse bacteria and are naturally occurring. However, there is little information on phages that can infect pathogenic bacteria from animals, such as the causative agent of bordetellosis of poultry, B. avium. Therefore, in this study, B. avium phages were isolated and comprehensively characterized, including whole-genome analysis. Although phenotypically the phages were thought to undergo a lytic cycle, we demonstrated that they undergo a lysogenic phase, but that infection does not confer stable host superinfection immunity. These findings provide important information that could be relevant for potential biocontrol of avian bordetellosis by using phage therapy.

Competition between lysogenic and sensitive bacteria is determined by the fitness costs of the different emerging phage-resistance strategies.

Many bacterial genomes carry prophages whose induction can eliminate competitors. In response, bacteria may become resistant by modifying surface receptors, by lysogenization, or by other poorly known processes. All these mechanisms affect bacterial fitness and population dynamics. To understand the evolution of phage resistance, we co-cultivated a phage-sensitive strain (BJ1) and a polylysogenic Klebsiella pneumoniae strain (ST14) under different phage pressures. The population yield remained stable after 30 days. Surprisingly, the initially sensitive strain remained in all populations and its frequency was highest when phage pressure was strongest. Resistance to phages in these populations emerged initially through mutations preventing capsule biosynthesis. Protection through lysogeny was rarely observed because the lysogens have increased death rates due to prophage induction. Unexpectedly, the adaptation process changed at longer time scales: the frequency of capsulated cells in BJ1 populations increased again because the production of the capsule was fine-tuned, reducing the ability of phage to absorb. Contrary to the lysogens, these capsulated-resistant clones are pan-resistant to a large panel of phages. Intriguingly, some clones exhibited transient non-genetic resistance to phages, suggesting an important role of phenotypic resistance in coevolving populations. Our results show that interactions between lysogens and sensitive strains are shaped by antagonistic co-evolution between phages and bacteria. These processes may involve key physiological traits, such as the capsule, and depend on the time frame of the evolutionary process. At short time scales, simple and costly inactivating mutations are adaptive, but in the long term, changes drawing more favorable trade-offs between resistance to phages and cell fitness become prevalent.

The book of Lambda does not tell us that naturally occurring lysogens of Escherichia coli are likely to be resistant as well as immune

The most significant difference between bacteriophages functionally and ecologically is whether they are purely lytic (virulent) or temperate. Virulent phages can only be transmitted horizontally by infection, most commonly with the death of their hosts. Temperate phages can also be transmitted horizontally, but upon infection of susceptible bacteria, their genomes can be incorporated into that of their host's as a prophage and be transmitted vertically in the course of cell division by their lysogenic hosts. From what we know from studies with the temperate phage Lambda and other temperate phages, in laboratory culture, lysogenic bacteria are protected from killing by the phage coded for by their prophage by immunity; where upon infecting lysogens, the free temperate phage coded by their prophage is lost. Why are lysogens not only resistant but also immune to the phage coded by their prophage since immunity does not confer protection against virulent phages? To address this question, we used a mathematical model and performed experiments with temperate and virulent mutants of the phage Lambda in laboratory culture. Our models predict and experiments confirm that selection would favor the evolution of resistant and immune lysogens, particularly if the environment includes virulent phage that shares the same receptors as the temperate. To explore the validity and generality of this prediction, we examined 10 lysogenic Escherichia coli from natural populations. All 10 were capable of forming immune lysogens, but their original hosts were resistant to the phage coded by their prophage.

Prophage induction therapy: Activation of the lytic phase in prophages for the elimination of pathogenic bacteria

The global burden of antimicrobial resistance has resulted in an unmet need to develop novel interventions targeting pathogenic bacteria. Although phage therapy employs lytic phages to cause host-specific killing of target bacteria, regulatory hurdles have impeded its development. It is interesting to note that more significant percentages of bacterial populations harbor dormant phages called prophages. This article proposes a novel approach termed prophage induction therapy to treat bacterial infections, with CI repressor as the therapeutic target. Disruption of CI repressor-operator interaction with a small molecule leads to the activation of the lytic phase in prophages. Post-induction, phages released from lysogenic bacteria can infect their non-lysogenic counterparts, leading to their elimination. A surrogate reporter assay is proposed to screen and identify inducers, followed by a demonstration of proof of principle in the pathogenic bacteria of interest. Further, eliminating a heterogeneous population of lysogenic and non-lysogenic bacteria can be demonstrated using animal models of infectious diseases. Prophage induction therapy can be potentially applied to clinical settings to target antibiotic-resistant strains of bacteria or employed as an alternative to conventional antibiotic-based treatments.

Study of the effect of bacterial-mediated legume plant growth using bacterial strain Serratia marcescens N1.14 X-45.

Soil microorganisms play an indispensable role in plant growth and are widely used to promote plant growth. However, poor microbial strains are homogeneous. The heavy application of chemical fertilizers and pesticides to agricultural soil has adversely affected the soil flora, necessitating the regulation of the soil flora to maintain soil health. In this study, X-45, a highly efficient and phosphorus-dissolving strain of the lysogenic bacterium Serratia marcescens N1.14 was isolated from bare rock slope soil samples from Yueyang Avenue, Hunan Province, China. We observed that microbial strain X-45 could release P from the rocks into solution when the sample rocks were used as the only phosphorus source. Furthermore, we observed that the P content in media increased by 3.08 X compared to the control. After applying X-45 as a bacterial fertilizer, the growth of potted Indigofera pseudotinctoria plants significantly increased, the soil physicochemical properties were significantly improved, and the relative abundance of Bradyrhizobium in the soil increased significantly from 1 to 42%. Besides, Bradyrhizobium became the most dominant genus in the soil. The indirect promotion of another beneficial microorganism by X-45 further revealed the intrinsic mechanism by which X-45 exerted its effect on plant promotion and soil improvement. Using this bacteria, the hypothesis of the superposition effect of legume plant promotion was also confirmed.

Heavy-Metal Trojan Horse: Enterobactin-Directed Delivery of Platinum(IV) Prodrugs to Escherichia coli.

The global crisis of untreatable microbial infections necessitates the design of new antibiotics. Drug repurposing is a promising strategy for expanding the antibiotic repertoire. In this study, we repurpose the clinically approved anticancer agent cisplatin into a targeted antibiotic by conjugating its Pt(IV) prodrug to enterobactin (Ent), a triscatecholate siderophore employed by Enterobacteriaceae for iron (Fe) acquisition. The l-Ent-Pt(IV) conjugate (l-EP) exhibits antibacterial activity against Escherichia coli K12 and the uropathogenic isolate E. coli CFT073. Similar to cisplatin, l-EP causes a filamentous morphology in E. coli and initiates lysis in lysogenic bacteria. Studies with E. coli mutants defective in Ent transport proteins show that Ent mediates the delivery of l-EP into the E. coli cytoplasm, where reduction of the Pt(IV) prodrug releases the cisplatin warhead, causing growth inhibition and filamentation of E. coli. Substitution of Ent with its enantiomer affords the d-Ent-Pt(IV) conjugate (d-EP), which displays enhanced antibacterial activity, presumably because d-Ent cannot be hydrolyzed by Ent esterases and thus Fe cannot be released from this conjugate. E. coli treated with l/d-EP accumulate ≥10-fold more Pt as compared to cisplatin treatment. By contrast, human embryonic kidney cells (HEK293T) accumulate cisplatin but show negligible Pt uptake after treatment with either conjugate. Overall, this work demonstrates that the attachment of a siderophore repurposes a Pt anticancer agent into a targeted antibiotic that is recognized and transported by siderophore uptake machinery, providing a design strategy for drug repurposing by siderophore modification and heavy-metal "trojan-horse" antibiotics.

Evaluation of the genotoxic and mutagenic potentials of a living nosode compounded with Influenza A virus

Background: The influenza virus has been responsible for contagious respiratory diseases with high mortality rates [1]. Some drugs have been used to treat human influenza. However, these drugs cause many common side effects and induce the appearance of resistant viral strains [2]. The impact caused by the influenza virus has motivated the development of new approaches for the prevention and control of influenza [3]. Therefore, a new homeopathic medicine was developed using, as a starting point, the infectious influenza virus [4]. This belongs to a group called living nosodes [5]. However, its mutagenic and genotoxic potentials, especially when used in low dilutions, has not yet been evaluated and it is important because this biotherapic is prepared from living microorganisms. Different methods can be used to detect mutagenic and genotoxicic effects.
 
 Aims: This study aims to evaluate the genotoxic and mutagenic potentials of influenza A living nosode at different homeopathic potencies.
 
 Methodology: 1 ml of purified viral suspension was diluted in 9 ml of sterile distilled water. This sample was submitted to 100 mechanical succussions (approximately 3 Hz), using Autic® Brazilian machine, originating the first dilution, named decimal (1x). 1 ml of this solution was diluted in 9 ml of solvent and was submitted to 100 sucussions, generating biotherapic 2x. This procedure was successively repeated, according to Brazilian Homeopathic Pharmacopoeia, to obtain the biotherapic 30x [6]. By the same technique, water vehicle was prepared until 30x potency to be used as control. All samples were prepared in sterile and under aseptic conditions, using laminar flow cabinet, class II, and were stored in the refrigerator (8ºC). The samples 1x, 6x, 12x, 18x, 24x and 30x and water 30x (vehicle control) were analysed by: the Inductest, which assesses the ability of physical or chemical agents to promote lysogenic induction as a reflection of damage in DNA molecules in lysogenic bacteria, and the Ames test, which uses indicator strains of Salmonella typhimurium, sensitive to substances that can induce different types of mutation.
 
 Results: The Inductest showed no decrease in the survival fraction of the bacteria used, and no increase in the formation of lysogenic induction, in any tested potency. The same profile was obtained after the Ames test, with similar results to negative control.
 
 Conclusion: We can conclude that this living nosode compounded with Influenza A virus is not able to induce DNA damage in prokaryotic cells. This result permits us to conclude that patients who use this medicine have no side effects related to mutagenesis and genotoxicity.

Evaluation of the genotoxic and mutagenic potentials of phytotherapic and homeopathic solutions of Euphorbia tirucalli Lineu (Aveloz)

Introduction: Euphorbia tirucalli Lineu, commonly known as Aveloz, is a very common plant found in tropical regions [1]. The ingestion or contact with its latex causes symptoms such as vomiting and diarrhea, pallor, skin irritation, hepatotoxicity as well as carcinogenesis [2]. Moreover, the Aveloz latex is also responsible for a few important activities against some infectious and neoplastic diseases. Aveloz latex phytochemical composition may vary according to seasonal aspects and geographic location [3], and it is used either orally or topically in traditional medicine. Popularly known as an antitumoral agent (breast, prostate, lung, kidney), it is used not only in Brazil, but in several other countries. According to the literature, the latex could have a dual behaviour, activating or inhibiting tumoral events [3-6]. However, there are few reports discussing these mechanisms. Besides, the mutagenic and genotoxic potentials of phytochemical and homeopathic Aveloz have not yet been described. Several experimental methods have been used to evaluate the mutagenic and genotoxic effects, such as Inductest, the Ames test and the chromotest. Objective: This study aims to evaluate the genotoxic and mutagenic potentials of Aveloz latex and Aveloz phytotherapic and homeopathic solutions. Methodology: In this study, Aveloz 5 and 30cH are prepared according to Brazilian Homeopathic Pharmacopoeia [7], from Aveloz latex collected in the Center for Natural Products Research (NPPN) at the Universidade Federal do Rio de Janeiro [8]. The Aveloz phytochemical solution was prepared following the doses used in folk medicine: 2 drops diluted in 250ml of water and 2 drops diluted in 25 ml of water. All test solutions were submitted to the following methodologies: (a) Inductest: assesses the ability of physical or chemical agents to promote lysogenic induction as a response to DNA damage in lysogenic bacteria; (b) The Ames test: uses indicator strains of Salmonella typhimurium, which are sensitive to substances that can induce different types of mutation; (c) Chromotest: evaluates the genotoxicity of chemicals through the induction of the bacterial SOS system. Results: In the Inductest there was no decrease in bacterial survival fraction and no increase in lysogenic cycle. As measured by The Ames test and the chromotest no mutagenic or genotoxic potentials were detected. Discussion: The homeopathic and the phytochemical Aveloz solutions were unable to produce lysogenic induction or mutagenesis in bacterial cells and they were also unable to produce genotoxic effects, as measured by chromotest. Conclusion: Our results showed that no mutagenic or genotoxic damages were induced by all Aveloz preparations studied, thus we are led to believe that patients using Aveloz as a complementary therapy present no side effects in relation to mutagenesis and genotoxicity.

Evaluation of the genotoxic and mutagenic potentials of homeopathic Candida albicans solutions

Background: Candida spp is naturally found in humans’ flora of skin, gastrointestinal and genitourinary tracts and, in general, up to 75% of the population does not have any symptom [1]. However, oral candidiasis is very common among HIV patients and patients undergoing chemotherapy. The treatment of oral candidiasis is necessary once the disease causes discomfort and dysphagia, resulting in poor nutrition, slow recovery, and prolonged hospital stay [2,3]. Preliminary results obtained by our group with a new biotherapic prepared from Candida albicans (Candida 30x) showed a great potential to reduce the candida yeast adhesion rate when the epithelial cells were pre-treated. This study is currently being developed with the evaluation of mutagenic and genotoxic potentials of several homeopathic solutions.
 
 Aims: The goal of this study was to assess the genotoxic and mutagenic potentials of different homeopathic potencies of C. albicans.
 
 Methodology: One part of C. albicans yeast obtained from Brazilian patient’s blood [4] was diluted in 9 parts of sterile water. This sample was submitted to 100 mechanical succussions (approximately 3 Hz), using Autic® Brazilian machine, originating the first dilution (1x). Then, 1 ml of this solution was diluted in 9 ml of solvent, submitted to 100 succussions, obtaining 2x potency. This procedure was successively repeated to obtain 30x potency, according to Brazilian Homeopathic Pharmacopoeia [5]. By the same technique, water vehicle was prepared until 30x to be used as control. All samples were prepared in sterile and aseptic conditions, using laminar flow cabinet, class II and were stored in the refrigerator (8ºC). The samples 1x, 6x, 12x, 18x, 24x and 30x of C. albicans and water 30x (vehicle control) were analysed by: the Inductest, which assesses the ability of physical or chemical agents to promote lysogenic induction as a reflection of damage in DNA molecules in lysogenic bacteria, and the Ames test, which uses indicator strains of Salmonella typhimurium, sensitive to substances that can induce different types of mutation.
 
 Results: In the Inductest no decrease in survival fraction of bacteria and no increase in the formation of lysogenic induction were detected independently of the homeopathic potency employed. The same profile was obtained after the Ames test, with similar results to negative control.
 
 Conclusion: Afterwards, we can conclude that these samples are not able to induce DNA damage in the cells tested. So, the use of this medicine does not present any side effects related to mutagenesis and genotoxicity.

Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps.

Prophages affect bacterial fitness on multiple levels. These include bacterial infectivity, toxin secretion, virulence regulation, surface modification, immune stimulation and evasion and microbiome competition. Lysogenic conversion arms bacteria with novel accessory functions thereby increasing bacterial fitness, host adaptation and persistence, and antibiotic resistance. These properties allow the bacteria to occupy a niche long term and can contribute to chronic infections and inflammation such as chronic rhinosinusitis (CRS). In this study, we aimed to identify and characterize prophages present in Staphylococcus aureus from patients suffering from CRS in relation to CRS disease phenotype and severity. Prophage regions were identified using PHASTER. Various in silico tools like ResFinder and VF Analyzer were used to detect virulence genes and antibiotic resistance genes respectively. Progressive MAUVE and maximum likelihood were used for multiple sequence alignment and phylogenetics of prophages respectively. Disease severity of CRS patients was measured using computed tomography Lund–Mackay scores. Fifty-eight S. aureus clinical isolates (CIs) were obtained from 28 CRS patients without nasal polyp (CRSsNP) and 30 CRS patients with nasal polyp (CRSwNP). All CIs carried at least one prophage (average=3.6) and prophages contributed up to 7.7 % of the bacterial genome. Phage integrase genes were found in 55/58 (~95 %) S. aureus strains and 97/211 (~46 %) prophages. Prophages belonging to Sa3int integrase group (phiNM3, JS01, phiN315) (39/97, 40%) and Sa2int (phi2958PVL) (14/97, 14%) were the most prevalent prophages and harboured multiple virulence genes such as sak, scn, chp, lukE/D, sea. Intact prophages were more frequently identified in CRSwNP than in CRSsNP (P=0.0021). Intact prophages belonging to the Sa3int group were more frequent in CRSwNP than in CRSsNP (P=0.0008) and intact phiNM3 were exclusively found in CRSwNP patients (P=0.007). Our results expand the knowledge of prophages in S. aureus isolated from CRS patients and their possible role in disease development. These findings provide a platform for future investigations into potential tripartite associations between bacteria-prophage-human immune system, S. aureus evolution and CRS disease pathophysiology.

Moderate Seasonal Dynamics Indicate an Important Role for Lysogeny in the Red Sea.

Viruses are the most abundant microorganisms in marine environments and viral infections can be either lytic (virulent) or lysogenic (temperate phage) within the host cell. The aim of this study was to quantify viral dynamics (abundance and infection) in the coastal Red Sea, a narrow oligotrophic basin with high surface water temperatures (22–32 °C degrees), high salinity (37.5–41) and continuous high insolation, thus making it a stable and relatively unexplored environment. We quantified viral and environmental changes in the Red Sea (two years) and the occurrence of lysogenic bacteria (induced by mitomycin C) on the second year. Water temperatures ranged from 24.0 to 32.5 °C, and total viral and bacterial abundances ranged from 1.5 to 8.7 × 106 viruses mL−1 and 1.9 to 3.2 × 105 bacteria mL−1, respectively. On average, 12.24% ± 4.8 (SE) of the prophage bacteria could be induced by mitomycin C, with the highest percentage of 55.8% observed in January 2018 when bacterial abundances were low; whereas no induction was measurable in spring when bacterial abundances were highest. Thus, despite the fact that the Red Sea might be perceived as stable, warm and saline, relatively modest changes in seasonal conditions were associated with large swings in the prevalence of lysogeny.

On the role of viruses in nature and what this means for the COVID-19 pandemic.

On the role of viruses in nature and what this means for the COVID-19 pandemic.

Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut

Bacteria evolve by mutation accumulation in laboratory experiments, but tempo and mode of evolution in natural environments are largely unknown. Here, we study the ubiquitous natural process of host colonization by commensal bacteria. We show, by experimental evolution of Escherichia coli in the mouse intestine, that the ecology of the gut controls the pace and mode of evolution of a new invading bacterial strain. If a resident E. coli strain is present in the gut, the invading strain evolves by rapid horizontal gene transfer (HGT), which precedes and outweighs evolution by accumulation of mutations. HGT is driven by 2 bacteriophages carried by the resident strain, which cause an epidemic phage infection of the invader. These dynamics are followed by subsequent evolution by clonal interference of genetically diverse lineages of phage-carrying (lysogenic) bacteria. We show that the genes uptaken by HGT enhance the metabolism of specific gut carbon sources and provide a fitness advantage to lysogenic invader lineages. A minimal dynamical model explains the temporal pattern of phage epidemics and the complex evolutionary outcome of phage-mediated selection. We conclude that phage-driven HGT is a key eco-evolutionary driving force of gut colonization-it accelerates evolution and promotes genetic diversity of commensal bacteria.

Life cycles of coral-associated-viruses related to diffrent health states collected in Hang Rai - Ninh Thuan, Vietnam

In recent years, coral associated viruses could play primal role in protecting coral health, yet their ecological traits are poorly investigated. In this study, the abundance and life cycles (lysogeny and lytic) of viruses associated with contrasted coral health states (healthy and bleached) were studied and compared. In addition, the density of bacteria and Symbiodium were also be determined by epifluorescence microscopy. The results showed that viral abundance increased 1.2 times and bacterial abundance decreased 0.6 times in healthy corals compared to bleached ones. The number of Symbiodinium significantly reduced 5.6 times in bleached corals compared to healthy corals. One of the most important results in this study was the coexistence of the both lysogenic and lytic viruses in healthy coral. The fraction of lysogenic bacteria was 2 times higher in healthy corals than in bleached ones. Healthy corals carried 3.5-fold more viral production than the diseased ones. Overall, the results showed that, in healthy state, corals might be a favorable environment for viral infection, promoting the development of both temperate and virulent phages. This coexistence might be crucial for coral viability through the complex links with their coral-associated bacterial hosts.

Identification and characterization of an endolysin – Like from Bacillus subtilis

Drug-resistant Gram-positive pathogens have been a rising risk in hospitals and food industries from the last decades. Here in, the potential of endolysin production in Dasht Desert Bacterial Culture Collection (DDBCC), against indicator bacteria, was investigated. DDBCC was screened against autoclaved-indicator bacteria; Streptococcus faecalis, Streptococcus pyogenes, Bacillus sp, Bacillus subtilis and Staphylococcus aureus as the substrates for the endolysin enzymes. The endolysins were produced in BHI medium followed by ammonium sulfate purification. Peptidoglycan hydrolytic activity was tested by zymogram method. Lysogenic bacteria were induced by 0.1 μg/ml mitomycin C for bacteriophages extraction. The lysogenic bacteria inhibited S. pyogenes, S. faecalis, Bacillus sp. and B. subtilis. The strain DDBCC10 was selected for further experiments on its higher and specific activity against the cell wall of S. faecalis. The highest activity for the endolysin was obtained at 50–60% ammonium sulfate saturation as 8 U/ml. Lys10, a 22 kDa enzyme, digested the cell wall of S. faecalis in 15 min while the whole phage from DDBCC10 could form plaque on S. faecalis and S. pyogenes. In a Transmission Electron Microscopy assay (TEM), the phage was distinguished as a member of Siphoviridae. Here; Lys10 is introduced as a new biocontrol agent against S. faecalis for therapeutics, disinfection, and food preservatives purposes at a much lower expense than recombinant endolysins.

Lysogeny is prevalent and widely distributed in the murine gut microbiota.

Bacteriophages are central members and potential modulators of the gut microbiome; however, the ecological and evolutionary relationships of gut bacteria and phages are poorly understood. Here we investigated the abundance and diversity of lysogenic bacteria (lysogens) in the bacterial community of C57BL/6J mice by detecting integrated prophages in genomes reconstructed from the metagenome of commensal bacteria. For the activities of lysogens and prophages, we compared the prophage genomes with the metagenome of free phages. The majority of commensal bacteria in different taxa were identified as lysogens. More lysogens were found among Firmicutes and Proteobacteria, than among Bacteroidetes and Actinobacteria. The prophage genomes shared high sequence similarity with the metagenome of free phages, indicating that most lysogens appeared to be active, and that prophages are spontaneously induced as active phages; dietary interventions changed the composition of the induced prophages. By contrast, CRISPR-Cas systems were present in few commensal bacteria, and were rarely active against gut phages. The structure of the bacteria-phage infection networks was "nested-modular", with modularity emerging across taxonomic scales, indicating that temperate phage features have developed over a long phylogenetic timescale. We concluded that phage generalists contribute to the prevalence of lysogeny in the gut ecosystem.

New aspects of the environmental risks of quantum dots: prophage activation

CdTe QDs induce lysogenic bacteria into the lytic cycle by damaging the DNA.

Microbial players and processes involved in phytoplankton bloom utilization in the water column of a fast-flowing, river-dominated estuary.

Fueled by seasonal phytoplankton blooms, the Columbia River estuary is a natural bioreactor for organic matter transformations. Prior metagenome analyses indicated high abundances of diverse Bacteroidetes taxa in estuarine samples containing phytoplankton. To examine the hypothesis that Bacteroidetes taxa have important roles in phytoplankton turnover, we further analyzed metagenomes from water collected along a salinity gradient at 0, 5, 15, 25, and 33 PSU during bloom events. Size fractions were obtained by using a 3‐μm prefilter and 0.2‐μm collection filter. Although this approach targeted bacteria by removing comparatively large eukaryotic cells, the metagenome from the ES‐5 sample (5 PSU) nevertheless contained an abundance of diatom DNA. Biogeochemical measurements and prior studies indicated that this finding resulted from the leakage of cellular material due to freshwater diatom lysis at low salinity. Relative to the other metagenomes, the bacterial fraction of ES‐5 was dramatically depleted of genes annotated as Bacteroidetes and lysogenic bacteriophages, but was overrepresented in DNA of protists and Myxococcales bacterivores. We suggest the following equally plausible scenarios for the microbial response to phytoplankton lysis: (1) Bacteroidetes depletion in the free‐living fraction may at least in part be caused by their attachment to fluvial diatoms as the latter are lysed upon contact with low‐salinity estuarine waters; (2) diatom particle colonization is likely followed by rapid bacterial growth and lytic phage infection, resulting in depletion of lysogenic bacteriophages and host bacteria; and (3) the subsequent availability of labile organic matter attracted both grazers and predators to feed in this estuarine biogeochemical “hotspot,” which may have additionally depleted Bacteroidetes populations. These results represent the first detailed molecular analysis of the microbial response to phytoplankton lysis at the freshwater–brackish water interface in the fast‐flowing Columbia River estuary.