Letteratura scientifica selezionata sul tema "Bactera/phage interactions"
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Articoli di riviste sul tema "Bactera/phage interactions"
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Zhang, Mingyue, Yanan Zhou, Xinyuan Cui e Lifeng Zhu. "The Potential of Co-Evolution and Interactions of Gut Bacteria–Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis". Microorganisms 12, n. 4 (31 marzo 2024): 713. http://dx.doi.org/10.3390/microorganisms12040713.
Testo completoAbstract (sommario):
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.
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Stone, Edel, Katrina Campbell, Irene Grant e Olivia McAuliffe. "Understanding and Exploiting Phage–Host Interactions". Viruses 11, n. 6 (18 giugno 2019): 567. http://dx.doi.org/10.3390/v11060567.
Testo completoAbstract (sommario):
Initially described a century ago by William Twort and Felix d’Herelle, bacteriophages are bacterial viruses found ubiquitously in nature, located wherever their host cells are present. Translated literally, bacteriophage (phage) means ‘bacteria eater’. Phages interact and infect specific bacteria while not affecting other bacteria or cell lines of other organisms. Due to the specificity of these phage–host interactions, the relationship between phages and their host cells has been the topic of much research. The advances in phage biology research have led to the exploitation of these phage–host interactions and the application of phages in the agricultural and food industry. Phages may provide an alternative to the use of antibiotics, as it is well known that the emergence of antibiotic-resistant bacterial infections has become an epidemic in clinical settings. In agriculture, pre-harvest and/or post-harvest application of phages to crops may prevent the colonisation of bacteria that are detrimental to plant or human health. In addition, the abundance of data generated from genome sequencing has allowed the development of phage-derived bacterial detection systems of foodborne pathogens. This review aims to outline the specific interactions between phages and their host and how these interactions may be exploited and applied in the food industry.
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Koskella, Britt, e Tiffany B. Taylor. "Multifaceted Impacts of Bacteriophages in the Plant Microbiome". Annual Review of Phytopathology 56, n. 1 (25 agosto 2018): 361–80. http://dx.doi.org/10.1146/annurev-phyto-080417-045858.
Testo completoAbstract (sommario):
Plant-associated bacteria face multiple selection pressures within their environments and have evolved countless adaptations that both depend on and shape bacterial phenotype and their interaction with plant hosts. Explaining bacterial adaptation and evolution therefore requires considering each of these forces independently as well as their interactions. In this review, we examine how bacteriophage viruses (phages) can alter the ecology and evolution of plant-associated bacterial populations and communities. This includes influencing a bacterial population's response to both abiotic and biotic selection pressures and altering ecological interactions within the microbiome and between the bacteria and host plant. We outline specific ways in which phages can alter bacterial phenotype and discuss when and how this might impact plant-microbe interactions, including for plant pathogens. Finally, we highlight key open questions in phage-bacteria-plant research and offer suggestions for future study.
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Dicks, Leon M. T., e Wian Vermeulen. "Bacteriophage–Host Interactions and the Therapeutic Potential of Bacteriophages". Viruses 16, n. 3 (20 marzo 2024): 478. http://dx.doi.org/10.3390/v16030478.
Testo completoAbstract (sommario):
Healthcare faces a major problem with the increased emergence of antimicrobial resistance due to over-prescribing antibiotics. Bacteriophages may provide a solution to the treatment of bacterial infections given their specificity. Enzymes such as endolysins, exolysins, endopeptidases, endosialidases, and depolymerases produced by phages interact with bacterial surfaces, cell wall components, and exopolysaccharides, and may even destroy biofilms. Enzymatic cleavage of the host cell envelope components exposes specific receptors required for phage adhesion. Gram-positive bacteria are susceptible to phage infiltration through their peptidoglycan, cell wall teichoic acid (WTA), lipoteichoic acids (LTAs), and flagella. In Gram-negative bacteria, lipopolysaccharides (LPSs), pili, and capsules serve as targets. Defense mechanisms used by bacteria differ and include physical barriers (e.g., capsules) or endogenous mechanisms such as clustered regularly interspaced palindromic repeat (CRISPR)-associated protein (Cas) systems. Phage proteins stimulate immune responses against specific pathogens and improve antibiotic susceptibility. This review discusses the attachment of phages to bacterial cells, the penetration of bacterial cells, the use of phages in the treatment of bacterial infections, and the limitations of phage therapy. The therapeutic potential of phage-derived proteins and the impact that genomically engineered phages may have in the treatment of infections are summarized.
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Loessner, Holger, Insea Schlattmeier, Marie Anders-Maurer, Isabelle Bekeredjian-Ding, Christine Rohde, Johannes Wittmann, Cornelia Pokalyuk, Oleg Krut e Christel Kamp. "Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy". Antibiotics 9, n. 7 (14 luglio 2020): 408. http://dx.doi.org/10.3390/antibiotics9070408.
Testo completoAbstract (sommario):
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage–host pair during the course of infection. We have elaborated such a kinetic fingerprint for a human urinary tract Klebsiella pneumoniae isolate and its phage vB_KpnP_Lessing by a modeling approach based on data from in vitro co-culture. We found a faster depletion of the initially sensitive bacterial population than expected from simple mass action kinetics. A possible explanation for the rapid decline of the bacterial population is a synergistic interaction of phages which can be a favorable feature for phage therapies. In addition to this interaction characteristic, analysis of the kinetic fingerprint of this bacteria and phage combination revealed several relevant aspects of their population dynamics: A reduction of the bacterial concentration can be achieved only at high multiplicity of infection whereas bacterial extinction is hardly accomplished. Furthermore the binding affinity of the phage to bacteria is identified as one of the most crucial parameters for the reduction of the bacterial population size. Thus, kinetic fingerprinting can be used to infer phage–host interactions and to explore emergent dynamics which facilitates a rational design of phage therapies.
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Karlsson, Fredrik, Carl A. K. Borrebaeck, Nina Nilsson e Ann-Christin Malmborg-Hager. "The Mechanism of Bacterial Infection by Filamentous Phages Involves Molecular Interactions between TolA and Phage Protein 3 Domains". Journal of Bacteriology 185, n. 8 (15 aprile 2003): 2628–34. http://dx.doi.org/10.1128/jb.185.8.2628-2634.2003.
Testo completoAbstract (sommario):
ABSTRACT The early events in filamentous bacteriophage infection of gram-negative bacteria are mediated by the gene 3 protein (g3p) of the virus. This protein has a sophisticated domain organization consisting of two N-terminal domains and one C-terminal domain, separated by flexible linkers. The molecular interactions between these domains and the known bacterial coreceptor protein (TolA) were studied using a biosensor technique, and we report here on interactions of the viral coat protein with TolA, as well as on interactions between the TolA molecules. We detected an interaction between the pilus binding second domain (N2) of protein 3 and the bacterial TolA. This novel interaction was found to depend on the periplasmatic domain of TolA (TolAII). Furthermore, extensive interaction was detected between TolA molecules, demonstrating that bacterial TolA has the ability to interact functionally with itself during phage infection. The kinetics of g3p binding to TolA is also different from that of bacteriocins, since both N-terminal domains of g3p were found to interact with TolA. The multiple roles for each of the separate g3p and TolA domains imply a delicate interaction network during the phage infection process and a model for the infection mechanism is hypothesized.
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Mohammed, Manal, e Beata Orzechowska. "Characterisation of Phage Susceptibility Variation in Salmonellaenterica Serovar Typhimurium DT104 and DT104b". Microorganisms 9, n. 4 (17 aprile 2021): 865. http://dx.doi.org/10.3390/microorganisms9040865.
Testo completoAbstract (sommario):
The surge in mortality and morbidity rates caused by multidrug-resistant (MDR) bacteria prompted a renewal of interest in bacteriophages (phages) as clinical therapeutics and natural biocontrol agents. Nevertheless, bacteria and phages are continually under the pressure of the evolutionary phage–host arms race for survival, which is mediated by co-evolving resistance mechanisms. In Anderson phage typing scheme of Salmonella Typhimurium, the epidemiologically related definitive phage types, DT104 and DT104b, display significantly different phage susceptibility profiles. This study aimed to characterise phage resistance mechanisms and genomic differences that may be responsible for the divergent phage reaction patterns in S. Typhimurium DT104 and DT104b using whole genome sequencing (WGS). The analysis of intact prophages, restriction–modification systems (RMS), plasmids and clustered regularly interspaced short palindromic repeats (CRISPRs), as well as CRISPR-associated proteins, revealed no unique genetic determinants that might explain the variation in phage susceptibility among the two phage types. Moreover, analysis of genes coding for potential phage receptors revealed no differences among DT104 and DT104b strains. However, the findings propose the need for experimental assessment of phage-specific receptors on the bacterial cell surface and analysis of bacterial transcriptome using RNA sequencing which will explain the differences in bacterial susceptibility to phages. Using Anderson phage typing scheme of Salmonella Typhimurium for the study of bacteria-phage interaction will help improving our understanding of host–phage interactions which will ultimately lead to the development of phage-based technologies, enabling effective infection control.
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Segundo-Arizmendi, Nallelyt, Dafne Arellano-Maciel, Abraham Rivera-Ramírez, Adán Manuel Piña-González, Gamaliel López-Leal e Efren Hernández-Baltazar. "Bacteriophages: A Challenge for Antimicrobial Therapy". Microorganisms 13, n. 1 (7 gennaio 2025): 100. https://doi.org/10.3390/microorganisms13010100.
Testo completoAbstract (sommario):
Phage therapy, which involves the use of bacteriophages (phages) to combat bacterial infections, is emerging as a promising approach to address the escalating threat posed by multidrug-resistant (MDR) bacteria. This brief review examines the historical background and recent advancements in phage research, focusing on their genomics, interactions with host bacteria, and progress in medical and biotechnological applications. Additionally, we expose key aspects of the mechanisms of action, and therapeutic uses of phage considerations in treating MDR bacterial infections are discussed, particularly in the context of infections related to virus–bacteria interactions.
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Beckett, Stephen J., e Hywel T. P. Williams. "Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks". Interface Focus 3, n. 6 (6 dicembre 2013): 20130033. http://dx.doi.org/10.1098/rsfs.2013.0033.
Testo completoAbstract (sommario):
Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins.
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Esteves, Nathaniel C., Danielle N. Bigham e Birgit E. Scharf. "Phages on filaments: A genetic screen elucidates the complex interactions between Salmonella enterica flagellin and bacteriophage Chi". PLOS Pathogens 19, n. 8 (3 agosto 2023): e1011537. http://dx.doi.org/10.1371/journal.ppat.1011537.
Testo completoAbstract (sommario):
The bacterial flagellum is a rotary motor organelle and important virulence factor that propels motile pathogenic bacteria, such as Salmonella enterica, through their surroundings. Bacteriophages, or phages, are viruses that solely infect bacteria. As such, phages have myriad applications in the healthcare field, including phage therapy against antibiotic-resistant bacterial pathogens. Bacteriophage χ (Chi) is a flagellum-dependent (flagellotropic) bacteriophage, which begins its infection cycle by attaching its long tail fiber to the S. enterica flagellar filament as its primary receptor. The interactions between phage and flagellum are poorly understood, as are the reasons that χ only kills certain Salmonella serotypes while others entirely evade phage infection. In this study, we used molecular cloning, targeted mutagenesis, heterologous flagellin expression, and phage-host interaction assays to determine which domains within the flagellar filament protein flagellin mediate this complex interaction. We identified the antigenic N- and C-terminal D2 domains as essential for phage χ binding, with the hypervariable central D3 domain playing a less crucial role. Here, we report that the primary structure of the Salmonella flagellin D2 domains is the major determinant of χ adhesion. The phage susceptibility of a strain is directly tied to these domains. We additionally uncovered important information about flagellar function. The central and most variable domain, D3, is not required for motility in S. Typhimurium 14028s, as it can be deleted or its sequence composition can be significantly altered with minimal impacts on motility. Further knowledge about the complex interactions between flagellotropic phage χ and its primary bacterial receptor may allow genetic engineering of its host range for use as targeted antimicrobial therapy against motile pathogens of the χ-host genera Salmonella, Escherichia, or Serratia.
Tesi sul tema "Bactera/phage interactions"
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Bou, habib Michèle. "Développement et analyse d'un modèle dynamique d'attaque de phages lors de l'acidification du lait pour la fabrication du fromage". Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASB061.
Testo completoAbstract (sommario):
Avec l'augmentation de la demande pour les produits fromagers, l'optimisation des procédés de production est devenue essentielle. L'une des premières étapes de la fabrication du fromage est l'acidification du lait, qui influence fortement les propriétés organoleptiques, la texture et la sécurité du produit final. Elle consiste à convertir le lactose, sucre du lait, en acide lactique par des bactéries lactiques. Cependant, ces bactéries sont sensibles aux attaques de virus appelés bactériophages. Ces attaques peuvent entraîner la lyse bactérienne, retardant ou arrêtant l'acidification, ce qui engendre des pertes économiques dues au rejet du lait et à la nécessité de nettoyer les installations. Cela souligne l'importance d'une meilleure compréhension des interactions phages-bactéries en fromagerie.Une approche novatrice pour étudier ces interactions est la modélisation mécaniste dynamique. Cette étude vise donc à contribuer à une meilleure compréhension des interactions phages-bactéries dans les processus de fermentation du lait en établissant un modèle dynamique.Pour ce faire, nous avons utilisé une méthode de mesure à haut débit du pH pour générer des données sur l'acidification dans différentes conditions initiales de bactéries et de phages. Cette approche nous a permis de distinguer trois résultats distincts en fonction de ces conditions : pour certaines conditions, l'acidification a été une réussite ; pour d'autres, elle a échoué ; et pour le reste, le résultat n'a été ni un échec complet ni une réussite complète.Le modèle mécaniste développé comprend cinq équations différentielles ordinaires (EDO) et prend en compte divers phénomènes, tels que l'inhibition par le produit, le temps de latence, l'adsorption des phages et la lyse cellulaire. Le modèle a donné des résultats satisfaisants, prédisant avec précision les données expérimentales et identifiant correctement le résultat de l'acidification. Nous avons également comparé différentes structures de modèle et effectué une analyse de sensibilité pour révéler les phénomènes dominants, ce qui a aussi aidé à concevoir de nouvelles expériences informatives.Une analyse théorique du modèle a révélé trois phases temporelles de l'attaque : d'abord, la phase de contamination, un court laps de temps où les phages s'adsorbent aux bactéries ; puis la phase de propagation, dominée par la propagation des phages et l'infection des bactéries sensibles ; et enfin, la phase de décharge, caractérisée par la lyse bactérienne et la libération de nouveaux phages. Le temps de transition entre les deux dernières phases, noté t*, a été relié aux conditions initiales. Nous avons également identifié une composante dynamique rapide qui peut être séparée des dynamiques lentes. En utilisant l'approximation de l'état quasi-stationnaire, nous avons établi une relation analytique entre les conditions initiales des bactéries et des phages et le pH final. Cela montre que l'acidification ne dépend pas uniquement du rapport des conditions initiales. Cette approximation a permis de réduire le modèle, économisant 83 % du temps de simulation.Enfin, nous avons développé un outil pour prédire le nombre d'acidifications réussies possibles avant qu'un nettoyage ne soit nécessaire. Les résultats sont basés sur des données faciles à obtenir, comme la quantité de bactéries utilisée et les résultats d'une acidification précédente. Cela représente une première étape vers la conception d'un outil d'aide à la décision pour les fromagers.Cette étude améliore notre compréhension des dynamiques d'attaque des phages lors de l'acidification du lait et permet des prédictions précises grâce à un système d'EDO et un modèle réduitAs the demand for diverse cheeses increases, there is a growing interest in optimizing production processes. One of the earliest steps in cheese-making is milk acidification, which highly influences the final product's organoleptic properties, texture, and safety. Milk acidification involves the conversion of lactose, the sugar in milk, into lactic acid by lactic acid bacteria. However, these bacteria are susceptible to attack by viruses known as bacteriophages. This attack can lead to bacterial lysis, resulting in delayed or halted acidification, which incurs significant economic losses as milk is discarded and production facilities require extensive cleaning. This highlights the need for a deeper understanding of phage-bacteria interactions in cheese-making. Research efforts in the dairy industry have primarily focused on characterizing the phages involved and finding new strategies to mitigate phage attacks.One novel approach to studying these interactions is through dynamic mechanistic modeling. Previous models have been developed but have never been applied to the dairy industry. This study aims to fill this gap by contributing to the broader understanding of phage-bacteria interactions in milk fermentation through the establishment of a dynamic model.To achieve this, we first employed a high-throughput pH measurement method to generate acidification data under different initial conditions of bacteria and phages. This methodology proved useful in distinguishing various dynamic behaviors depending on these conditions. It allowed us to delineate three distinct outcomes depending on these conditions: for some conditions the acidification was a success; for some others, it was a failure; and for the rest, the result was neither a complete failure nor a complete success.The mechanistic model we developed consists of five ordinary differential equations (ODEs) and accounts for various phenomena, including product inhibition, lag time, phage adsorption, and cell lysis. The model yielded satisfactory results, accurately predicting experimental data and correctly identifying the acidification outcome. We further investigated the model's structure by comparing various candidate structures and performing a sensitivity analysis to reveal the dominant phenomena throughout the process. The sensitivity analysis also contributed to the design of new informative experimental setups.A theoretical analysis of the model provided insights into the intrinsic dynamics of the system, revealing three time frames of the attack. First, the contamination phase, a short initial time where phages adsorb to the bacteria. Next, the spread phase, where the dominant dynamics involve the spread of phages and the infection of susceptible bacteria. Finally, the discharge phase, where the dominant dynamics are the lysis of bacteria and the release of new phages. The switch time between the last two phases was defined as t∗ and its dependency on the initial conditions was characterized.We also identified a faster dynamic component of the system that can be separated from slower ones. Utilizing the quasi-steady state approximation, we established an analytical relationship between the initial conditions of bacteria and phages and the resulting pH. This relationship indicates that the final outcome of acidification does not solely depend on the ratio of initial conditions but is more complex. The approximation resulted in a reduced model that saved 83% of the simulation time.Finally, we developed a tool to predict the number of potential successful acidifications that can be run before cleaning is required. The results are based on easily obtainable inputs. This represents a first step toward designing a decision aid tool to help cheese makers in their production.This study enhances our understanding of the dynamics of phage attack in milk acidification and facilitates accurate predictions of these dynamics through an ODE system and a reduced model
2
Bankier, Claire. "Coevolutionary interactions between bacteria and phage in natural environments". Thesis, Imperial College London, 2016. http://hdl.handle.net/10044/1/44556.
Testo completoAbstract (sommario):
Bacteria and their viruses (bacteriophage, phage) are the most abundant and diverse taxonomic groups, but ecological and evolutionary research on bacteria-phage interactions has largely focused on studies of simplified communities using a few model organisms. The goal of the thesis is to understand how bacteria and phage interact within natural environments, and how these interactions impact the patterns of phage infectivity and bacterial resistance. Here I investigate the effects of natural environments on the coevolutionary patterns of bacteria (Pseudomonas fluorescens) and phage (SBW25Φ2). In chapter 3 I investigate the effects of nineteen different communities on the coevolutionary interactions of SBW25 and phage, and the degree to which the infectivity of phage to its host, SBW25, changes depending on their local microbial community. Chapter 4 aimed to understand the effects of varying diversities of communities on coevolutionary interactions. In Chapter 5, I looked at how coevolutionary interactions were affected by different communities in different abiotic conditions (pH, temperature and nutrient concentration) and the effect communities had on the ability of SBW25 to adapt to the abiotic conditions. Understanding how biological and physical factors affect coevolutionary interactions in natural environments allows predictions of how phage and bacteria coevolve in natural and unnatural settings.
3
Marcinkiewicz, Ashley. "Bacterial and phage interactions influencing Vibrio parahaemolyticus ecology". Thesis, University of New Hampshire, 2016. http://pqdtopen.proquest.com/#viewpdf?dispub=10127507.
Testo completoAbstract (sommario):
Vibrio parahaemolyticus, a human pathogenic bacterium, is a naturally occurring member of the microbiome of the Eastern oyster. As the nature of this symbiosis in unknown, the oyster presents the opportunity to investigate how microbial communities interact with a host as part of the ecology of an emergent pathogen of importance. To define how members of the oyster bacterial microbiome correlate with V. parahaemolyticus, I performed marker-based metagenetic sequencing analyses to identify and quantify the bacterial community in individual oysters after culturally-quantifying V. parahaemolyticus abundance. I concluded that despite shared environmental exposures, individual oysters from the same collection site varied both in microbiome community and V. parahaemolyticus abundance, and there may be an interaction with V. parahaemolyticus and Bacillus species. In addition, to elucidate the ecological origins of pathogenic New England ST36 populations, I performed whole genome sequencing and phylogenetic analyses. I concluded ST36 strains formed distinct subpopulations that correlated both with geographic region and unique phage content that can be used as a biomarker for more refined strain traceback. Furthermore, these subpopulations indicated there may have been multiple invasions of this non-native pathogen into the Atlantic coast.
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Gonzalez, Floricel. "Investigation of flagellotropic phage interactions with their motile host bacteria". Diss., Virginia Tech, 2021. http://hdl.handle.net/10919/103940.
Testo completoAbstract (sommario):
Bacteriophages cohabit with their bacterial hosts and shape microbial communities. To initiate infection, phages use bacterial components as receptors to recognize and attach to hosts. Flagellotropic phages utilize bacterial flagella as receptors. Studies focused on uncovering mechanistic details of flagellotropic phage infection are lacking. As the number of phage-based applications grows, it is important to understand these details to predict the potential outcomes of phage therapy. To this end, we studied two flagellotropic phages: Agrobacterium phage 7-7-1 and bacteriophage χ. Phage 7-7-1 infects Agrobacterium spp., while bacteriophage χ infects Salmonella and Escherichia coli.
Chapter 1 consists of a literature review. Chapter 2 addresses factors underlying phage-bacteria coexistence. We document the emergence of a sector-shaped lysis pattern following co-inoculation of phage χ and one of its Salmonella hosts on swim plates. We propose that this pattern serves as a reporter for balanced phage-bacteria coexistence. Using a combined experimental and mathematical modelling approach, we discovered that variations to intrinsic factors (i.e., bacterial motility, phage adsorption) skews the pattern towards either bacterial or phage predominance. Thus, this computational model may be used to predict phage therapy application outcomes.
Chapter 3 details the identification of cell surface receptors essential for phage 7-7-1 infection using a transposon mutagenesis approach. We identified three Agrobacterium sp. H13-3 genes involved in phage 7-7-1 infection. Using mass spectrometry and other analyses, we determined that the LPS profiles of strains lacking these genes varied compared to the wild type. Thus, LPS is a secondary cell surface receptor for phage 7-7-1. Chapter 4 focuses on the discovery of phage encoded receptor binding proteins (RBPs) in Agrobacterium phage 7-7-1. Using an RBP screen, we discovered three candidate RBPs. We learned that our top candidate, Gp4, inhibits the growth of Agrobacterium sp. H13-3 cells in a motility and glycan dependent manner. Because of its bacteriostatic activities, this protein is a promising candidate for therapeutic use. Overall, the described works contribute to a deepened understanding of flagellotropic phage infection and the factors influencing their coexistence with motile bacteria. These works will contribute towards the development of phage therapies using whole phage or their components.Doctor of Philosophy
Bacteriophages, or phages for short, are the natural killers of bacteria. Like antibiotics, they can also be used as medicines to treat bacterial infections. Their attack on bacteria begins by recognizing specific parts of the bacterial cell and attaching to them. These parts are called receptors. To use phages as medicines it is important to understand how they recognize and kill bacteria. This information is helpful when deciding which phage should be given to treat a bacterial infection and to predict the outcomes of these treatments. In this work, we focused on two phages to answer different questions. Both phages use long helical thread-like structures, called flagella, as receptors. Flagella help the bacteria to move through the environment and reach new areas with more nutrients. One of these flagella-dependent phages, called phage 7-7-1, infects plant pathogens that cause tumor-like growth in plants. We found that this phage uses two very different host cell components during infection and identified one of the phage proteins that interacts with these receptors. This protein prevents the growth of the plant pathogen, which makes it a promising candidate for therapeutic use. We also investigated how another bacterial virus, bacteriophage χ, is spread throughout the environment and co-exists with its motile bacterial host. We built a computational model that can predict how altering different variables affects phage-bacteria coexistence. With additional research, this model will be a useful tool for predicting the outcomes following phage treatment.
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Räisänen, L. (Liisa). "Phage-host interactions in Lactobacillus delbrueckii: host recognition and transcription of early phage genes". Doctoral thesis, University of Oulu, 2007. http://urn.fi/urn:isbn:9789514284250.
Testo completoAbstract (sommario):
Abstract
The scope of this study includes aspects of phage evolution and antagonistic/mutualistic coevolution between a phage and its host. As a basic study it may provide tools for developing phage resistant starters and offer regulatory elements and factors for biotechnological applications.
The LL-H anti-receptor was characterized by isolation of spontaneous LL-H host range mutants and subsequent sequencing of candidate genes. All LL-H host range mutants carried a single point mutation at the 3' end of a minor tail protein encoding gene g71. The genomic location of g71 is congruent with the other verified anti-receptor genes found in the λ supergroup. The C-terminus of Gp71 determines the adsorption specificity of phage LL-H similarly for the number of phages infecting Gram-positive and Gram-negative bacteria. A Gp71 homolog of phage JCL1032 showed 62% identity to LL-H Gp71 within the last 300 amino acids at the C-terminus.
Lactobacillus delbrueckii phage receptors were investigated by the purification of different cell surface structures. Certain Lb. delbrueckii phages from homology groups a and c including LL-H, LL-H host range mutants and JCL1032, were specifically inactivated by the LTAs. In structural analyses LTAs showed differences in the degree of α-glucosyl and ᴅ-alanyl substitution. α-glucose is necessary for LL-H adsorption. A high level of ᴅ-alanine esters in LTA backbones inhibited Lb. delbrueckii phage inactivation in general. Lysogenization of strain ATCC 15808 with the temperate phage JCL1032 revealed a rarely described coexistence of phage adsorption resistance and phage immunity, which could not be explained by lysogenic conversion. In this case the role of spontaneously induced JCL1032 may be significant.
The LL-H early gene region was localized between the dysfunctional lysogeny module and the terminase encoding genes. The function of five ORFs could be connected to phage DNA replication and/or homologous recombination. Transcription of LL-H genes could be divided into two, possibly three, phases in which large gene clusters were sequentially transcribed. The intensity of the late transcripts exceeded the intensity of the early transcripts by several times. Two candidate genes for transcription regulators were found. One of the two candidates is the first ORF in the LL-H early gene region.
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McLean, Hector Alexander. "Application of phage display to the study of toxin-receptor interactions". Thesis, University of Glasgow, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301779.
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Flores, Garcia César O. "Phage--Bacteria Infection networks: from nestedness to modularity and back again". Diss., Georgia Institute of Technology, 2014. http://hdl.handle.net/1853/53007.
Testo completoAbstract (sommario):
Bacteriophages (viruses that infect bacteria) are the most abundant biological life-forms on Earth. However, very little is known regarding the structure of phage-bacteria infections. In a recent study we showed that phage-bacteria infection assay datasets are statistically nested in small scale communities while modularity is not statistically present. We predicted that at large macroevolutionary scales, phage-bacteria infection assay datasets should be typified by a modular structure, even if there is nested structure at smaller scales. We evaluate and confirm this hypothesis using the largest study of the kind to date.
The study in question represents a phage-bacteria infection assay dataset in the Atlantic Ocean region between the European continental shelf and the Sargasso Sea. We present here a digitized version of this study that consist of a bipartite network with 286 bacteria and 215 phages including 1332 positive interactions, together with an exhaustive structural analysis of this network. We evaluated the modularity and nestedness of the network and its communities using a variety of algorithms including BRIM (Bipartite, Recursively Induced Modules), NTC (Nestedness Temperature Calculator) and NODF (Nestedness Metric based on Overlap and Decreasing Filling). We also developed extensions of these standard methods to identify multi-scale structure in large phage-bacteria interaction datasets. In addition, we performed an analysis of the degree of geographical diversity and specialization among all the hosts and phages.
We find that the largest-scale ocean dataset study, as anticipated by Flores et al. 2013, is highly modular and not significantly nested (computed in comparison to null models). More importantly is the fact that some of the communities extracted from Moebus and Nattkemper dataset were found to be nested. We examine the role of geography in driving these modular patterns and find evidence that phage-bacteria interactions can exhibit strong similarity despite large distances between sites. We discuss how models can help determine how coevolutionary dynamics between strains, within a site and across sites, drives the emergence of nested, modular and other complex phage-bacteria interaction networks.
Finally, we releases a computational library (BiMAT)to help to help the ecology research community to perform bipartite network analysis of the same nature I did during my PhD.
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Mansos, Lourenço Marta. "Deciphering in vivo efficacy of virulent phages in the mammalian gut". Electronic Thesis or Diss., Sorbonne université, 2019. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2019SORUS260.pdf.
Testo completoAbstract (sommario):
L'intestin des mammifères est peuplé de nombreux et divers microbes comprenant des bactéries et leurs prédateurs viraux, des bactériophages (phages). Les interactions entre les phages et les bactéries intestinales sont encore mal comprises. Des expériences indépendantes ont montré que les phages virulents n’avaient aucun effet majeur sur l’abondance des bactéries intestinales ciblées, en dépit de leur amplification durable. Cela suggère que des facteurs encore inconnus de l'environnement intestinal modulent ces interactions. À l’aide d’une analyse transcriptomique comparative de la bactérie Escherichia coli cultivée in vitro et in vivo (dans l’intestin de mammifères), nous avons constaté que, dans l’intestin, les bactéries réduisent l’expression de gènes liés aux récepteurs du phage. Ceci permet d’expliquer l’absence de sélection des bactéries mutées devenues résistantes aux phages lors d'expériences in vivo. D’autre part, nous avons montré que l'acquisition d'un îlot de pathogénicité, souvent associé aux souches intestinales humaines d'E. coli, affecte la susceptibilité aux phages en régulant négativement un mécanisme de défense contre l'ADN étranger. Enfin, nous avons examiné la répartition des phages et des bactéries dans les parties mucosales et luminales de l’intestin et avons observé une distribution spatiale hétérogène de ces deux populations antagonistes, corroborant l'hypothèse d'une dynamique « source-sink ». Globalement, nos données démontrent que de multiples facteurs incluant la distribution spatiale, la physiologie bactérienne et les défenses contre l’ADN étranger modulent les interactions entre bactéries et phages dans l’intestin des mammifèresThe mammalian gut is a heterogeneous environment inhabited by a large and diverse microbial community, including bacteria and their viral predators, bacteriophages (phages). Dynamic interactions between virulent phages and bacteria in the gut are still poorly understood, which is also an obstacle for the design of successful therapeutic interventions based on phages. Independent experiments have shown that virulent phages were found to have no major effects on their targeted bacteria in the gut, in spite of sustainable phage amplification. This suggests that there are unknown factors in the gut environment that modulate these interactions. Using comparative transcriptomics analysis of E. coli grown in vitro and in vivo (within the mammalian gut) we found that in the gut, bacteria downregulate the expression of genes related to phage receptors, which provides an explanation for the lack of selection of phage-resistant bacteria during in vivo experiments. We also found that the acquisition of a pathogenicity island commonly found in human E. coli isolates affects phage susceptibility possibility by downregulating a defense mechanism against invading DNA. Finally, we examined the repartition of phages and bacteria through mucosal and luminal gut sections and observed a heterogeneous spatial distribution of these two antagonist populations, supporting the hypothesis of source-sink dynamics. Altogether our data demonstrates that multiple factors encompassing, spatial distribution, bacterial physiology and defenses against foreign DNA modulate the interactions between bacteria and phages within the gut
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Hosseinidoust, Zeinab. "An investigation of bacteriophage-bacteria interactions: development of phage resistance and associated variations in virulence and biofilm formation". Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=114443.
Testo completoAbstract (sommario):
The rise of antibiotic resistance has rekindled interest in the development of alternative antimicrobial agents. Bacteriophages, bacteria's obligate parasites, have drawn a lot of interest from the scientific community and from the industry due to their many advantages. However, there are various challenges hindering the use of bacteriophages as antimicrobial agents. In this dissertation, a number of these challenges have been addressed. After a brief introduction on the advantages and drawbacks of using phage in chapter one, the inherent limitation of using immobilized phage for antimicrobial surfaces is presented in chapter two. In the subsequent three chapters, one of the main issues of challenging bacterial communities with phage was addressed, namely emergence of phage-resistant bacteria variants. The effect of phage on biofilm formation was investigated and it was observed that in some cases they can lead to increase in biofilm formation. Furthermore the colonies of phage-resistant bacteria emerged in contact with phage were studied. It was reported that their phenotype, their virulence traits as well as their in vitro virulence towards mammalian cells had been significantly affected. This investigation highlights the importance of awareness of the effect of phage on bacterial communities for effective utilization of their potential.L'augmentation de la résistance aux antibiotiques a ravivé l'intérêt dans le développement d'agents antimicrobiens alternatifs. Les bactériophages, parasites bactériens obligatoires, ont suscité beaucoup d'intérêt de la part de la communauté scientifique et de l'industrie à cause de leurs nombreux avantages. Cependant, plusieurs défis restent à relever pour résoudre les problèmes qui empêchent l'utilisation des bactériophages comme agents antimicrobiens. Un certain nombre de ces défis sont adressés dans cette dissertation. Après une brève introduction sur les avantages et désavantages de l'utilisation des bactériophages dans le premier chapitre, nous présentons dans le second chapitre les limitations intrinsèques de l'utilisation de bactériophages immobilisés pour créer des surfaces antimicrobiennes. Dans les trois chapitres suivants, nous traitons de l'une des principales questions concernant l'infection de cultures bactériennes par les bactériophages, à savoir l'émergence de variants bactériens résistants. L'effet des bactériophages sur la formation de biofilms a été étudié et nous avons observé que dans certains cas, les bactériophages peuvent augmenter la formation de biofilms. En outre, nous avons étudié les colonies bactériennes résistantes qui émergent après l'infection par des bactériophages. Nous avons trouvé que leur phénotypes, leurs caractères de virulence ainsi que leurs virulences in vitro envers les cellules mammifères avaient été affectés de manière significative. Cette investigation souligne l'importance des effets des bactériophages sur les cultures bactériennes pour une utilisation efficace de leur potentiel antimicrobien.
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Feichtmayer, Judith [Verfasser], Christian [Akademischer Betreuer] Griebler, Wolfgang [Gutachter] Liebl e Christian [Gutachter] Griebler. "Bacteria-phage interactions: Insights into quorum sensing-induced anti-phage defense, phage therapy and the pulmonary human virome composition / Judith Feichtmayer ; Gutachter: Wolfgang Liebl, Christian Griebler ; Betreuer: Christian Griebler". München : Universitätsbibliothek der TU München, 2019. http://d-nb.info/1193650429/34.
Testo completoLibri sul tema "Bactera/phage interactions"
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Zürich, Eidgenössische Technische Hochschule, a cura di. Phage-host interaction in lactic acid bacteria: Insights from genomics and phage transcription analysis. 2003.
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Kirchman, David L. Introduction to geomicrobiology. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0013.
Testo completoAbstract (sommario):
Geomicrobiology, the marriage of geology and microbiology, is about the impact of microbes on Earth materials in terrestrial systems and sediments. Many geomicrobiological processes occur over long timescales. Even the slow growth and low activity of microbes, however, have big effects when added up over millennia. After reviewing the basics of bacteria–surface interactions, the chapter moves on to discussing biomineralization, which is the microbially mediated formation of solid minerals from soluble ions. The role of microbes can vary from merely providing passive surfaces for mineral formation, to active control of the entire precipitation process. The formation of carbonate-containing minerals by coccolithophorids and other marine organisms is especially important because of the role of these minerals in the carbon cycle. Iron minerals can be formed by chemolithoautotrophic bacteria, which gain a small amount of energy from iron oxidation. Similarly, manganese-rich minerals are formed during manganese oxidation, although how this reaction benefits microbes is unclear. These minerals and others give geologists and geomicrobiologists clues about early life on Earth. In addition to forming minerals, microbes help to dissolve them, a process called weathering. Microbes contribute to weathering and mineral dissolution through several mechanisms: production of protons (acidity) or hydroxides that dissolve minerals; production of ligands that chelate metals in minerals thereby breaking up the solid phase; and direct reduction of mineral-bound metals to more soluble forms. The chapter ends with some comments about the role of microbes in degrading oil and other fossil fuels.
Capitoli di libri sul tema "Bactera/phage interactions"
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Selvaraj, Chandrabose, e Sanjeev Kumar Singh. "Phage Protein Interactions in the Inhibition Mechanism of Bacterial Cell". In Biocommunication of Phages, 121–42. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-45885-0_6.
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Svircev, Antonet M., Susan M. Lehman, Peter Sholberg, Dwayne Roach e Alan J. Castle. "Phage Biopesticides and Soil Bacteria: Multilayered and Complex Interactions". In Soil Biology, 215–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-14512-4_8.
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Williamson, Kurt E. "Soil Phage Ecology: Abundance, Distribution, and Interactions with Bacterial Hosts". In Soil Biology, 113–36. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-14512-4_4.
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Salton, M. R. J. "Interaction of Phages with Bacterial Cell Walls and the Development of Phage in the Wall-Less Protoplast". In Ciba Foundation Symposium - The Nature of Viruses, 263–76. Chichester, UK: John Wiley & Sons, Ltd., 2008. http://dx.doi.org/10.1002/9780470715239.ch17.
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Loos, M., B. Euteneuer e F. Clas. "Interaction of Bacterial Endotoxin (LPS) with Fluid Phase and Macrophage Membrane Associated C1q, the FC-Recognizing Component of the Complement System". In Endotoxin, 301–17. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4757-5140-6_26.
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Choudhary, Manoj, Mathews Paret, Aleksa Obradović, Katarina Gašić e Jeffrey B. Jones. "Bacteriophages to control plant diseases". In Microbial bioprotectants for plant disease management, 473–506. Burleigh Dodds Science Publishing, 2021. http://dx.doi.org/10.19103/as.2021.0093.18.
Testo completoAbstract (sommario):
Crop yield loss due to bacterial plant pathogens need to be reduced to increase global food production demand. Currently available disease management strategies involving copper-based bactericides and antibiotics are losing efficacy due to development of resistance in bacteria. There is long familiar demand of environmentally friendly and sustainable strategies to control bacterial diseases. Bacteriophages are virus that kill target bacteria without affecting another microorganism and environment. Bacteriophage efficiency on phyllosphere is mainly affected by ultraviolet (UV) light. Use of combination of phage, mixture with phage carrier bacteria and optimizing time of application helps in persistence of bacteriophage. There are several bacteriophage products already available in the market to control destructive bacterial diseases. Unlike chemical based traditional control measure, bacteriophage mixture can be easily amended to reduce resistance development in bacteria. In this chapter, the authors discuss from phage isolation to interaction with bacteria and control mechanism of plant diseases.
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Reisoglu, Şuheda, e Sevcan Aydin. "Bacteriophage as Biotechnological Tools to Improve the Effectiveness of Anaerobic Digestion Process". In Anaerobic Digestion - Biotechnology for Reactor Performance and Environmental Sustainability [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.113904.
Testo completoAbstract (sommario):
Wastewater treatment plants (WWTPs) serve as habitats for diverse and densely populated bacterial communities, fostering intricate microbial interactions. Conventional treatment methods employed often fail to completely eliminate pathogens. Consequently, inadequate chemical treatments lead to the eventual release of waterborne bacterial pathogens into the environment through effluent water. Anaerobic digestion represents a biological treatment approach for organic waste and wastewater, providing cost-reduction benefits and enabling energy generation through biogas production from organic waste. However, the role of viruses-host interactions in anaerobic digestion and their effects on biological wastewater treatment (WWT) has been lacking and requires further research and attention. Bacteriophages (phages), viruses that target specific bacteria, are abundant within WWTPs and engage in diverse interactions with their host organisms. Also, there are reports indicating the presence of archaeal viruses capable of impacting crucial methanogenic organisms in anaerobic digestion, alongside phages. Despite their apparent lack of discernible metabolic functions, viral community have significant potential to influence WWT by shaping the structure of microbial communities, thereby impacting the efficiency of the processes. This chapter aims to explore the influence of reported viral communities, especially phages on shaping microbial communities; elucidate the dynamics and limitations of phage-host relationships; and evaluate their potential as biological tools for enhancing the anaerobic digestion process in WWT.
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Pandey, Neha. "BACTERIAL PATHOGENESIS". In Microbes of Medical Importance, 3–28. Iterative International Publishers, Selfypage Developers Pvt Ltd, 2024. http://dx.doi.org/10.58532/nbennurmmch1.
Testo completoAbstract (sommario):
Bacterial pathogenesis refers to the process by which bacteria cause disease in their hosts. It involves a series of interactions between the bacteria and the host organism, leading to tissue damage, dysfunction, and clinical manifestations of illness. Bacterial infections are a significant global health burden, contributing to morbidity and mortality worldwide. Bacterial pathogens can cause a wide range of illnesses, from mild infections to life-threatening conditions, highlighting the importance of studying their mechanisms of pathogenicity (Peterson, 1996). The significance of bacterial pathogenesis within the broader landscape of global health cannot be overstated. In recognizing the gravity of this health burden, an in depth comprehension of bacterial pathogenesis emerges as a linchpin in the development of effective strategies for the prevention, diagnosis, and treatment of infectious diseases. The nuanced exploration of the mechanisms underpinning bacterial pathogenicity is paramount, as bacterial pathogens wield the potential to instigate a spectrum of illnesses, ranging from seemingly benign infections to severe, life-threatening conditions. In this pursuit, unraveling the intricacies of bacterial pathogenesis not only broadens our understanding of microbial host interactions but also lays the groundwork for targeted interventions that address the diverse challenges posed by bacterial infections in contemporary healthcare (Casadevall & Pirofski, 2000; Peterson, 1996). In the complex interplay between pathogenic bacteria and their host organisms, the process of infection unfolds through distinct stages, each marked by intricate molecular interactions and dynamic strategies employed by both parties. The initial phase, colonization, signifies the establishment of bacteria on host tissues or mucosal surfaces through specific adhesive interactions mediated by microbial adhesins and host cell receptors. Subsequently, the invasion stage ensues as bacteria breach host barriers, such as epithelial cells and mucosal membranes, employing various mechanisms, both active and passive. Following successful invasion, bacteria enter a phase of active replication and multiplication within the host environment, utilizing host resources for growth while simultaneously producing virulence factors that contribute to tissue damage. The final stage, dissemination, marks the migration of bacteria from the initial site of infection to other tissues or organs within the host, either locally or systemically. This process may occur through the bloodstream, lymphatic vessels, or direct extension from adjacent sites of infection, ultimately contributing to the progression of infectious diseases. Understanding these sequential stages provides valuable insights into the intricate dynamics of bacterial infections and informs efforts to develop targeted therapeutic interventions (Casadevall & Pirofski, 2000; Peterson, 1996).
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Brüssow, Harald. "Prophage Genomics". In The Bacteriophages, 17–25. Oxford University PressNew York, NY, 2005. http://dx.doi.org/10.1093/oso/9780195148503.003.0003.
Testo completoAbstract (sommario):
Abstract At the time of this writing, the GenBank phage database comprises 200 complete phage genome sequences. An equivalent number of phage sequences were passively acquired as prophages in bacterial genome sequencing projects. The scientific value of these prophage sequences was only recently recognized (13, 14). It goes beyond their potential to double the content of the current phage database and to correct a bias of the database towards selected phage systems (coliphages, dairy phages, mycobacteriophages) (7, 9). These prophage sequences allowed a first insight into the evolution of phage^host genome interactions at a molecular level. This analysis turned out to be especially fruitful for bacterial pathogens (1, 5, 49).
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Brussow, Harald. "Prophage Genomics". In The Bacteriophages, 17–25. Oxford University PressNew York, NY, 2005. http://dx.doi.org/10.1093/oso/9780195168778.003.0003.
Testo completoAbstract (sommario):
Abstract At the time of this writing, the GenBank phage database comprises 200 complete phage genome sequences. An equivalent number of phage sequences were passively acquired as prophages in bacterial genome sequencing projects. The scientific value of these prophage sequences was only recently recognized (13, 14). It goes beyond their potential to double the content of the current phage database and to correct a bias of the database towards selected phage systems (coliphages, dairy phages, mycobacteriophages) (7, 9). These prophage sequences allowed a first insight into the evolution of phage^host genome interactions at a molecular level. This analysis turned out to be especially fruitful for bacterial pathogens (1, 5, 49).
Atti di convegni sul tema "Bactera/phage interactions"
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Breica Borozan, Aurica, Despina-Maria Bordean, Gabriel Bujanca, Delia Dumbrava e Sorina Popescu. "CONTROL OF PLANTS OF LOTUS CORNICULATUS L. ON AEROBIC AND ANAEROBIC FREE NITROGEN-FIXING BACTERIA". In GEOLINKS International Conference. SAIMA Consult Ltd, 2020. http://dx.doi.org/10.32008/geolinks2020/b1/v2/07.
Testo completoAbstract (sommario):
The free nitrogen fixing bacteria are able to mobilize important soil nutrients, transforming through biological processes the unusable molecular nitrogen into an active form and to improve soil fertility, influence many aspects of plant health and ensure their growth, showing interest for the scientific world and farmers. But, on the other hand, this bacterial segment may be influenced by the edaphic factors and the interconnection with the plants, the growth phase, the physiological state and the root system of the plant, by the root exudates, which demonstrates the importance of the bacterial community monitoring from the area of plants influence throughout the growing periods The aim of this study was to evaluate the influence of the age of the plants used as biofertilizer and soil moisture on the free nitrogen fixing bacterial communities (the genera Azotobacter and Clostridium) associated with the roots of the perennial plants of Lotus corniculatus L. There were two zones of interest, namely the area of influence of the roots of the plants (rhizosphere) but also the more distant area (edaphosphere). For the study of aerobic and anaerobic free nitrogen fixing bacteria soil samples were taken together with adjacent plants of Lotus corniculatus L. The experimental variants were located in the western part of Romania, the plants being cultivated on the same soil type, but on different plots, that were in the I-IV years of culture. The influence of Lotus corniculatus L. plants on the free nitrogen fixing bacteria has been reported in control experimental variants. Isolation and study of this bacterial group from the 8 experimental variants was performed on a specific mineral medium, favorable for the growth of the two bacterial genera. The results were evaluated after 5 and 10 days of incubation. Between the two assesments there were no noticeable differences in the nitrogen fixing bacterial community, except for the stimulatory effect observed in the control vatiant and rhizosphere of the first year culture. The plants influence on aerobic and anaerobic free nitrogen fixing bacteria was obvious in the II and IV years of the Lotus corniculatus L. culture, compared to the 76 control variants and varies substantially depending on the age of the plant. In most analyzed soil samples, both bacterial genera, Azotobacter and Clostridium were present, confirming the known ecological relation of unilateral advantage or passive stimulation of the aerobic bacteria compared to the anaerobic clostridia. Exceptions were the samples from the cultures of the first year (rhizosphere and control), but also the rhizosphere from the culture of the year II, where only anaerobic nitrogen fixing bacteria were detected. Our results suggested that plant-soil interactions exert control over the bacteria being studied.
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Ligocki, Tomasz. "Application of structural sums to study collective behavior of bacteria". In 38th ECMS International Conference on Modelling and Simulation. ECMS, 2024. http://dx.doi.org/10.7148/2024-0304.
Testo completoAbstract (sommario):
In the papers related to the subject of bacteria moving in the studied environments, it was established that the hydrodynamic interactions between the swimming bacteria can lead to collective motion, evidence of which has been confirmed by a reduction in effective viscosity. In the above-mentioned works, a new quantitative criterion for detecting such collective behavior is proposed. The presented criterion is based on the new computationally efficient theory of RVE (representative volume element) based on fundamental statistical moments (e-sums or generalized Eisenstein-Rayleigh sums) and this criterion can be applied to various two-phase media dispersed (e.g. biological systems, composites, etc.). Bacterial locations are modeled with short, narrow-width segments randomly embedded in the medium without overlapping. E-sums of simulated disordered harvests and observed experimental Bacillus subtilis locations will be calculated. The results obtained indicate a difference between the two sets that demonstrates the collective movement of the bacteria.
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Lopez, Juan Fernando, Jesus Alfonso Lopez Sotelo, Diogo Leite e Carlos Pena-Reyes. "Applying one-class learning algorithms to predict phage-bacteria interactions". In 2019 IEEE Latin American Conference on Computational Intelligence (LA-CCI). IEEE, 2019. http://dx.doi.org/10.1109/la-cci47412.2019.9037032.
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Tereshkina, K. B., E. V. Tereshkin, V. V. Kovalenko, Y. F. Krupyanskii e N. G. Loiko. "Supercomputer modeling in the problems of bacterial antibiotic resistance". In V ALL-RUSSIAN (NATIONAL) SCIENTIFIC CONFERENCE SCIENCE, TECHNOLOGY, SOCIETY: ENVIRONMENTAL ENGINEERING IN THE INTERESTS OF SUSTAINABLE DEVELOPMENT OF TERRITORIES, 14–21. Krasoyarsk Science & Technology City Hall, 2024. http://dx.doi.org/10.47813/nto.5.2024.1002.
Testo completoAbstract (sommario):
In this paper, the molecular mechanisms of interaction between the antibiotic ciprofloxacin and the main protein of the stationary phase of bacterial culture development (Dps, DNA-binding protein from starved cells) studied to solve problems of increasing antibiotic resistance. Unfavorable environmental conditions lead to inhibition of bacterial cell division and transfer cells to the states of internal resource conservation. The main task for the survival of bacteria in difficult external conditions is the preservation of DNA. DNA protection under a number of stresses (starvation, oxidative, etc.) is carried out by its condensation by the DNA-binding protein Dps. In the exponential phase, the content of Dps is 60, in the stationary phase ~200 molecules per cell. The paper considers the effect of the antibiotic ciprofloxacin on this protein. The methods of modern molecular modeling were used: docking, umbrella sampling, molecular dynamics. The energy characteristics of antibiotic binding to the protein were found. The spatial distribution of small molecules relative to the protein at 28oC and 55oC was shown. It was found that the antibiotic can migrate into the protein molecules.
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Alimova, Alexandra, Karin Block, Elizabeth Rudolph, A. Katz, J. C. Steiner, P. Gottlieb e R. R. Alfano. "Bacteria-clay interactions investigated by light scattering and phase contrast microscopy". In Biomedical Optics 2006, a cura di Gerard L. Coté e Alexander V. Priezzhev. SPIE, 2006. http://dx.doi.org/10.1117/12.648042.
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Leite, Diogo Manuel Carvalho, Juan Fernando Lopez, Xavier Brochet, Miguel Barreto-Sanz, Yok-Ai Que, Gregory Resch e Carlos Pena-Reyes. "Exploration of multiclass and one-class learning methods for prediction of phage-bacteria interaction at strain level". In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2018. http://dx.doi.org/10.1109/bibm.2018.8621433.
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Shakeel, Mariam, Daniyar Yerniyazov, Madi Yesmukhambet, Amina Dauyltayeva, Laila Maratbekkyzy, Razida Kenes, Azamat Bukayev et al. "Screening, Design, and Application of Chemical EOR to Control High Water-Cut and Reduce Residual Oil in a Complex Sandstone Oilfield in Kazakhstan". In GOTECH. SPE, 2024. http://dx.doi.org/10.2118/219217-ms.
Testo completoAbstract (sommario):
Abstract This paper presents the results acquired during first laboratory-scale chemical flooding evaluation for a giant waterflooded oilfield in Kazakhstan. A carefully-designed chemical flood recipe involves the injection of a mixture of surfactant and alkali/nanoparticles followed by polymer to reduce oil-water interfacial tension (IFT) by surfactant, minimize surfactant and polymer adsorption by alkali or nanoparticles (NPs), and provide mobility control by polymer. Collectively, such an efficient design yields considerable improvement in residual oil mobilization and recovery. Field A in Kazakhstan, one of the oldest fields in the country, has been waterflooded for decades. Currently, the water cut of the field is more than 90%, with a high residual oil saturation. For the targeted reservoir conditions, four hydrolyzed polyacrylamide (HPAM) based polymers and around 10 different surfactant formulations were tested. Alkali and nanoparticles were then assessed for chemical adsorption control for the most optimum polymer and surfactant. The evaluation was done at reservoir temperature of 63 °C and Caspian seawater of 13000 ppm salinity was used as the makeup brine for all the formulations. The performance of the screened chemicals in the porous media was analyzed by a series of coreflood experiments on the reservoir cores. The critical parameters such as chemical adsorption, IFT, mobility ratio, resistance factor, and oil recovery were obtained and compared to select the best chemical enhanced oil recovery (CEOR) scheme. During screening phase of the study, one of the polymers, ASP3, displayed pronounced resistance against bacterial attack under reservoir conditions. Adsorption for the same polymer was also 13-14% less compared to its counterparts. Optimum surfactant was selected based on the generation of Winsor Type III microemulsion and a minimum IFT of 0.2 mN/m. The adsorption study indicated a 9-21% reduction in surfactant adsorption by alkali. In the case of polymer, NPs demonstrated better performance and caused an 18% decrease in polymer adsorption whereas alkali showed negligible effect. Corefloods were performed for various combinations of screened chemicals. In comparison with NPs-surfactant-polymer (NSP) design, surfactant-polymer (SP) and alkali-surfactant-polymer (ASP) schemes recovered more residual oil by effectively generating and producing microemulsion. However, ASP design outperformed the rest by recovering 96% of the remaining oil, which translated to 11% higher recovery compared to polymer flooding and 13% more oil compared to NSP flooding. This screening and design study demonstrates that the selection of chemicals for EOR strictly depends on the oil, formation and injection water, and reservoir rock interactions. Our study proved that appropriate design of chemical EOR constituents can yield favorable results in high salinity challenging formations that contain waxy oils with high paraffin content.
Rapporti di organizzazioni sul tema "Bactera/phage interactions"
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Lindow, Steven, Isaac Barash e Shulamit Manulis. Relationship of Genes Conferring Epiphytic Fitness and Internal Multiplication in Plants in Erwinia herbicola. United States Department of Agriculture, luglio 2000. http://dx.doi.org/10.32747/2000.7573065.bard.
Testo completoAbstract (sommario):
Most bacterial plant pathogens colonize the surface of healthy plants as epiphytes before colonizing internally and initiating disease. The epiphytic phase of these pathogens is thus an important aspect of their epidemiology and a stage at which chemical and biological control is aimed. However, little is known of the genes and phenotypes that contribute to the ability of bacteria to grow on leaves and survive the variable physical environment in this habitat. In addition, while genes such as hrp awr and others which confer pathogenicity and in planta growth ability have been described, their contribution to other aspects of bacterial epidemiology such as epiphytic fitness have not been addressed. We hypothesized that bacterial genes conferring virulence or pathogenicity to plants also contribute to the epiphytic fitness of these bacteria and that many of these genes are preferentially located on plasmids. We addressed these hypotheses by independently identifying genes that contribute to epiphytic fitness, in planta growth, virulence and pathogenicity in the phytopathogenic bacterium Erwinia herbicola pv gypsophilae which causes gall formation on gypsophila. This species is highly epiphytically fit and has acquired a plasmid (pPATH) that contains numerous pathogenicity and virulence determinants, which we have found to also contribute to epiphytic fitness. We performed saturation transposon mutagenesis on pPATH as well as of the chromosome of E.h. gypsophilae, and identified mutants with reduced ability to grow in plants and/or cause disease symptoms, and through a novel competition assay, identified mutants less able to grow or survive on leaves. The number and identity of plasmid-borne hrp genes required for virulence was determined from an analysis of pPATH mutants, and the functional role of these genes in virulence was demonstrated. Likewise, other pPATH-encoded genes involved in IAA and cytokinin biosynthesis were characterized and their pattern of transcriptional activity was determined in planta. In both cases these genes involved in virulence were found to be induced in plant apoplasts. About half of avirulent mutants in pPATH were also epiphytically unfit whereas only about 10% of chromosomal mutants that were avirulent also had reduced epiphytic fitness. About 18% of random mutants in pPATH were avirulent in contrast to only 2.5% of random chromosomal mutants. Importantly, as many as 28% of pPATH mutants had lower epiphytic fitness while only about 10% of random chromosomal mutants had lower epiphytic fitness. These results support both of our original hypotheses, and indicate that genes important in a variety of interactions with plant have been enriched on mobile plasmids such as pPATH. The results also suggest that the ability of bacteria to colonize the surface of plants and to initiate infections in the interior of plants involves many of the same traits. These traits also appear to be under strong regulatory control, being expressed in response to the plant environment in many cases. It may be possible to alter the pattern of expression of such genes by altering the chemical environment of plants either by genetic means or by additional or chemical antagonists of the plant signals. The many novel bacterial genes identified in this study that are involved in plant interactions should be useful in further understanding of bacterial plant interactions.