Article
Microbiology
Marta Lourenco, Lisa Osbelt, Virginie Passet, Francois Gravey, Daniela Megrian, Till Strowig, Carla Rodrigues, Sylvain Brisse
Summary: Klebsiella pneumoniae (Kp) is a major contributor to global antimicrobial resistance. This study presents a new strategy for isolating anti-Kp phages using capsule-deficient Kp mutants as hosts. This strategy offers promise for therapeutic development by circumventing the Kp capsule host restriction barrier.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Sam Ford, Sara Moeskjaer, Peter Young, Rosa I. Santamaria, Ellie Harrison
Summary: Temperate phages in rhizobia, including a novel group identified in this study, have the potential to impact the ecological dynamics of bacterial communities. Genome comparisons among these phages revealed a high degree of gene conservation with a region of hypervariability containing hypothetical genes. These phages exhibit a history of active mobilization within and between Rhizobium species, as indicated by phylogenetic discordance between prophage and host phylogenies.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Joshua M. Borin, Sarit Avrani, Jeffrey E. Barrick, Katherine L. Petrie, Justin R. Meyer
Summary: Training bacteriophages on target hosts before therapy can prolong suppression of antibiotic-resistant bacteria by delaying the evolution of resistance. Evolution of resistance to trained phages is more costly and requires multiple mutations, making them more effective in combating resistance. Transfer of genetic information from host genomes through recombination can enhance phage fitness and improve treatment outcomes, highlighting the potential of training in phage therapy development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Andrzej Zielezinski, Jakub Barylski, Wojciech M. Karlowski
Summary: Phirbo is a tool based on the extension of BLAST that improves the quality of phage host prediction, increasing precision and recall rates. It has high discriminatory power in identifying virus-host relationships compared to other tools.
Article
Microbiology
Kamil Albrycht, Adam A. Rynkiewicz, Michal Harasymczuk, Jakub Barylski, Andrzej Zielezinski
Summary: Understanding phage-host relationships is essential for studying virus biology and applying phages in biotechnology and medicine. However, information about the range of hosts for bacterial and archaeal viruses is scattered across various databases and is difficult to obtain. Therefore, PHD is introduced as a web application that provides a comprehensive and up-to-date catalog of known phage-host associations.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Microbiology
Cecile Philippe, Jeffrey K. Cornuault, Alessandra G. de Melo, Rachel Morin-Pelchat, Alice P. Jolicoeur, Sylvain Moineau
Summary: Over the past few decades, there has been a growing interest in lactic acid bacteria (LAB) due to their industrial use, health benefits, and ecological importance. However, phage infection poses a significant risk to LAB production and use. This review discusses the defense systems employed by LAB against phage infections and the strategies used by phages to overcome these defenses. It also explores the impact of phage-host interactions on their evolution and highlights the potential of novel defense systems discovered in other bacteria for phage research in LAB.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Yanze Mi, Yile He, Jinhui Mi, Yunfei Huang, Huahao Fan, Lihua Song, Xiaoping An, Shan Xu, Mengzhe Li, Yigang Tong
Summary: The emergence of phage-resistant bacterial strains poses challenges for phage therapy, but the resistant bacteria often come with adaptive trade-offs. This study investigates the impacts of phages targeting different bacterial receptors on the fitness of the bacterial population. The research findings suggest that phage-resistant bacteria may lose their resistance to antibiotics when countering with phages.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Kieran. A. Bates, Jai S. Bolton, Kayla C. King
Summary: The study revealed the differences of Leucobacter genus microbes in different geographical locations and host species, as well as the influence of Leucobacter community composition on host evolution. It discovered the protective effects of different Leucobacter species on hosts, as well as the competitive evolution process with parasitic species.
Article
Virology
Jupiter Myers, Joshua Davis II, Megan Lollo, Gabriella Hudec, Paul Hyman
Summary: The host range of bacteriophages is determined by their interactions with hosts. Broader host range phages are preferred for phage therapy to target a wide range of pathogen strains or related species. Using multiple hosts during phage isolation does not increase the likelihood of isolating broader host range phages, as shown in a study on the Bacillus cereus group system. Both narrow and broader host range phages can be isolated regardless of the isolation procedure. Other methods, such as sequential host isolation, are more reliable for obtaining broader host range phages.
Review
Microbiology
Greater Kayode Oyejobi, Xiaoxu Zhang, Dongyan Xiong, Faith Ogolla, Heng Xue, Hongping Wei
Summary: Phage treatment shows potential for bacterial infections, but bacterial resistance to phage is a challenge. Research on phage resistance and coevolutionary dynamics between phage and bacteria is crucial for successful phage therapy.
CRITICAL REVIEWS IN MICROBIOLOGY
(2023)
Article
Microbiology
Abraham G. Moller, Robert A. Petit, Timothy D. Read
Summary: Phage therapy is a potential alternative treatment for Staphylococcus aureus infections. The study found that phage adsorption genes are highly conserved in the S. aureus species, but horizontal gene transfer may play an important role in the strain-specific evolution of host range patterns.
Article
Computer Science, Interdisciplinary Applications
Maria Victoria Diaz-Galian, Miguel A. Vega-Rodriguez, Felipe Molina
Summary: Phage therapy is a strategy used to lyse bacteria that cause harm to health. This article introduces an R package called PhageCocktail that automatically designs efficient phage cocktails.
COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE
(2022)
Article
Chemistry, Medicinal
Shazeeda Koonjan, Carlos Cardoso Palacios, Anders S. Nilsson
Summary: This study explored the population dynamics of a two phage-one host system, finding that different phage infections result in different phage progeny production. The sequential order of phage infections also affects growth rates. Additionally, phage-resistant bacteria exhibit different morphotypes, with specific morphotypes showing a higher frequency of developing resistance.
Editorial Material
Biochemistry & Molecular Biology
Kelly A. Speer
Summary: Parasitic and parasitoid organisms rely on chemical cues to locate a host. Recent research suggests that the microbiome can emit volatile organic compounds that attract or repel parasites. This innovative mechanism changes our understanding of host-parasite coevolution and highlights the role of the microbiome as a third actor in this interaction.
Article
Biochemical Research Methods
Jing Liang, Huibin Zhang, Yee Ling Tan, Huimin Zhao, Ee Lui Ang
Summary: Bacteriophages are a promising alternative to antibiotics in combating antimicrobial resistance. This study presents a strategy for generating large libraries of phage variants, allowing for engineering of phage specificity and improved qualities. The findings demonstrate the potential of directed evolution in enhancing phage therapy for therapeutic applications.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Zoology
Lewis J. Bartlett, Michael Boots, Berry J. Brosi, Jacobus C. de Roode, Keith S. Delaplane, Catherine A. Hernandez, Lena Wilfert
Summary: The study investigates the persistent impact of management history on honeybee disease epidemiology by comparing virus abundances in colonies from different management histories. Findings suggest that high-intensity management history leads to higher viral abundances across all viruses, while low-intensity management history results in lower viral abundances in honeybee colonies. This highlights the significant impact of management history on pollinator health and warrants further investigation.
JOURNAL OF INVERTEBRATE PATHOLOGY
(2021)
Article
Ecology
Emily A. Dewald-Wang, Nicole Parr, Katie Tiley, Alina Lee, Britt Koskella
Summary: Coevolution is difficult to study directly, but time-shift experiments are a powerful tool to measure coevolution by challenging individuals from different time points. The experiments revealed an asymmetry in host resistance and phage infectivity, suggesting a need to revise existing coevolutionary theory to account for differing models for hosts and parasites.
AMERICAN NATURALIST
(2021)
Review
Microbiology
Reena Debray, Robin A. Herbert, Alexander L. Jaffe, Alexander Crits-Christoph, Mary E. Power, Britt Koskella
Summary: The order and timing of microbial arrival can significantly impact microbiome composition and function, with studies highlighting the importance of priority effects in different environments. Detection methods and mechanisms of priority effects are discussed in this review.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Ecology
Kyle M. Meyer, Robert Porch, Isabella E. Muscettola, Ana Luisa S. Vasconcelos, Julia K. Sherman, C. Jessica E. Metcalf, Steven E. Lindow, Britt Koskella
Summary: The microbial communities on plant leaf surfaces are influenced by dispersal from neighboring plants, with local dispersal being a key factor in their assembly. Host species, source of microbiome, and neighbors' identity contribute to the variation in phyllosphere bacterial composition.
Correction
Microbiology
Reena Debray, Robin A. Herbert, Alexander L. Jaffe, Alexander Crits-Christoph, Mary E. Power, Britt Koskella
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Plant Sciences
Reena Debray, Yvonne Socolar, Griffin Kaulbach, Aidee Guzman, Catherine A. Hernandez, Rose Curley, Alexander Dhond, Timothy Bowles, Britt Koskella
Summary: Water stress and disruption of mycorrhizal associations resulted in reduced leaf bacterial richness, homogenized bacterial community composition among plants, and decreased the relative abundance of dominant fungal taxa in the tomato phyllosphere. Soil conditions and belowground interactions can shape aboveground microbial communities, with significant implications for plant health and sustainable agriculture.
Article
Biotechnology & Applied Microbiology
Elijah C. Mehlferber, Kent F. McCue, Jon E. Ferrel, Britt Koskella, Rajnish Khanna
Summary: This study examined the effects of a volcanic ash deposit fertilizer on microbial communities in soil and plants, focusing on core taxa identified in the rhizosphere and root endosphere. The fertilizer had little overall effect on microbial composition but selectively influenced the core taxa, leading to changes in functional pathway enrichment associated with carbohydrate metabolism.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Elijah C. Mehlferber, Michael J. Song, Julianne Naomi Pelaez, Johan Jaenisch, Jeremy E. Coate, Britt Koskella, Carl J. Rothfels
Summary: The microbiome and ploidy level both play important roles in the host organism's response to disease. This study investigates the interaction between whole-genome duplication and the above-ground microbiome in Arabidopsis thaliana, and finds that polyploids have enhanced immunity to pathogens and reduced dependence on the microbiome for protection.
Article
Virology
Britt Koskella, Catherine A. Hemandez, Rachel M. Wheatley
Summary: Bacteriophages have significant effects on bacterial ecology and evolution, shaping microbial interactions, diversity, and nutrient cycling in ecosystems. They rapidly evolve in response to bacterial host dynamics and the study of their evolution in vitro can provide insights into natural bacteria-phage interactions. Recent advancements in metagenomics approaches have allowed for a better understanding of phage evolution and ecology in complex microbial communities.
ANNUAL REVIEW OF VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Reena Debray, Nina De Luna, Britt Koskella
Summary: Bacteria and lytic viruses (phages) have a coevolutionary relationship, and this study explores how phages shape the future evolutionary trajectories of their host populations. The researchers found that some bacteria populations re-evolved phage sensitivity over time, while others acquired compensatory mutations that reduced the costs of resistance. The genetic mechanisms of resistance and the initial evolution of resistance played a significant role in these outcomes. This study highlights the importance of phages in the ecological and evolutionary dynamics of their host communities and provides insights into the genetic architecture of historical contingency.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Evolutionary Biology
C. Jessica E. Metcalf, Burcu Tepekule, Marjolein Bruijning, Britt Koskella
Summary: The absence of microbial exposure early in life can lead to immune overreaction later in life. Understanding the critical windows during which the host's immune system can learn tolerance is crucial. Animal models suggest that multiple mechanisms have evolved to enable critical windows, indicating strong evolutionary selection. By exploring the evolutionary ecology of critical windows, we found that both direct and indirect effects of microbes determine the optimal length of the critical window. Various factors such as transmission magnitude, infection duration, reinfection rates, host demography, and seasonality can influence the timing and likelihood of encounters with microbes, affecting the optimal length of the critical window. Decline in microbial population abundance and diversity may result in increased immune dysfunction. Our research provides insights into the impact of host-microbiome/pathogen interactions, dispersal, and the current loss of microbial diversity and infectious diseases on critical windows.
Article
Biochemistry & Molecular Biology
Catherine A. A. Hernandez, Veronique A. Delesalle, Greg P. P. Krukonis, Jenna M. M. DeCurzio, Britt Koskella
Summary: The rate and trajectory of evolution in an obligate parasite is highly influenced by its host(s). This study investigates the impact of evolutionary history of bacterial hosts on the genotypic and phenotypic evolution of bacteriophages. By comparing coevolved phages and phages passaged on an ancestral strain, it is revealed that coevolution leads to more mutations in phage genomes, particularly in genes encoding phage tail-associated proteins. Coevolved phages exhibit more efficient reduction of population growth and have more predictable effects on infectivity range.
Article
Ecology
Reena Debray, Asa Conover, Xuening Zhang, Emily A. A. Dewald-Wang, Britt Koskella
Summary: In microbial community assembly, species that establish earlier often have an advantage. Experimental evolution selecting for host colonization alters priority effects among competitors in the tomato plant-associated microbiome. Understanding how in situ evolution alters priority effects is crucial for predicting the composition and function of ecological communities over time.
NATURE ECOLOGY & EVOLUTION
(2023)
