Review
Immunology
Laura Avellaneda-Franco, Sofia Dahlman, Jeremy J. J. Barr
Summary: Alterations in the gut virome have an impact on human health, particularly due to the dominance of bacteriophages. These phages can be virulent or temperate, and while virulent phages solely replicate within and destroy bacterial cells, temperate phages can switch between an integrated state and a free virion state. This review summarizes current knowledge of the gut virome, discusses the variation in the proportion of induced temperate phages among individuals, age, and disease states, and emphasizes the importance of further research to better understand temperate phages for potential therapeutic use.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Microbiology
Daniel A. Schwartz, Josue A. Rodriguez-Ramos, Michael Shaffer, Rory M. Flynn, Rebecca A. Daly, Kelly C. Wrighton, Jay T. Lennon
Summary: Spore-forming bacteria are common in mammalian guts and affect host health and nutrition. Dormant spore production plays a crucial role in the colonization, persistence, and transmission of these bacteria. Recent studies have shown that phages can counteract dormancy-mediated defense mechanisms and alter the transitions between active and inactive states through the expression of phage-carried sporulation genes during infection. Identification of sporulation genes preferentially carried by phages that infect spore-forming bacteria can help in understanding the complex genetic network responsible for spore development.
Review
Gastroenterology & Hepatology
Han Shuwen, Ding Kefeng
Summary: This review presents the interactions between phages and bacteria in the human intestinal tract, as well as their roles in disease pathogenesis and treatment.
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)
Review
Microbiology
Marek Straka, Martina Dubinova, Adriana Liptakova
Summary: The treatment of bacterial infections has become more complicated due to the rise of antibiotic-resistant strains. Bacteriophage therapy, which uses natural predators of bacteria, shows great potential as an alternative. Although the discovery of antibiotics initially hampered the development of phage therapy, Western countries are now reintroducing it as a tool to combat drug-resistant bacteria.
Article
Gastroenterology & Hepatology
Shiqi Luo, Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Anna Ralser, Raquel Mejias Luque, Markus Gerhard, Li Deng
Summary: This study reveals the relationship between chronic Helicobacter pylori infection and colorectal cancer (CRC), and highlights the role of viral communities in the development of CRC. Using mouse models, the researchers found an expansion of temperate phages in early-stage carcinogenesis. Some of these phages were predicted to infect bacteria associated with CRC. Additionally, strong associations between viral and bacterial communities were observed in infected mice before the onset of carcinogenesis.
Review
Biochemistry & Molecular Biology
Benoit J. Pons, Stineke van Houte, Edze R. Westra, Anne Chevallereau
Summary: CRISPR-Cas is a defense system in prokaryotes that protects against invasion by mobile genetic elements, such as bacteriophages. Bacteriophages can overcome CRISPR-Cas defenses by encoding anti-CRISPR proteins, which inhibit the CRISPR-Cas machinery and promote phage replication. This review summarizes the current understanding of the distribution of anti-CRISPR genes in mobile genetic elements, the ecology of phages encoding anti-CRISPR proteins, and their coevolution with bacterial defense mechanisms. The need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in mobile genetic element-host interactions is highlighted.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
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
Biology
Manuel Menor-Flores, Miguel A. Vega-Rodriguez, Felipe Molina
Summary: This study introduces two innovative computational methods for designing phage cocktails to combat infections caused by multidrug-resistant bacteria. These methods focus on generating the best mixture and maintaining a short runtime, and have been integrated into a Cytoscape application available for all users.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Cell Biology
Beatriz Beamud, Neris Garcia-Gonzalez, Mar Gomez-Ortega, Fernando Gonzalez-Candelas, Pilar Domingo-Calap, Rafael Sanjuan
Summary: Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. In this study, 46 phages were isolated and tested against 138 clinical isolates of Klebsiella pneumoniae, revealing a narrow host range for most phages. Bacterial capsule diversity was found to be the main factor limiting phage host range, while phage-encoded depolymerases and their sequence types were associated with the ability to infect specific capsular types.
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
M. L. Domingo-Calap, M. Bernabeu-Gimeno, C. M. Aure, E. Marco-Noales, P. Domingo-Calap
Summary: Xanthomonas is a genus of plant-pathogenic bacteria that causes serious economic losses, and bacteriophages show promise as biocontrol tools to combat these pathogens.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Ahlam Alsaadi, Beatriz Beamud, Maheswaran Easwaran, Fatma Abdelrahman, Ayman El-Shibiny, Majed F. Alghoribi, Pilar Domingo-Calap
Summary: Misuse of antibiotics is leading to the emergence of multidrug-resistant bacteria, posing a major global threat. Alternatives like phage therapy have been proposed as promising tools to combat this issue, but further research and investment are essential to ensure safety protocols and develop appropriate regulations.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Li Ping, Li Zhuoya, Jia Pei, Chen Jingchao, Li Yi, Liu Guosheng, Wang Hailei
Summary: This study used native phages as a microbial editing tool to investigate the functions of a specific bacterium by reducing its abundance in the mouse gut. The impact of phage treatment on the microbial community structure of the mouse gut was not significant.
MICROBIOLOGY SPECTRUM
(2022)
Article
Engineering, Environmental
Alejandro Palomo, Arnaud Dechesne, Barth F. Smets, Yan Zheng
Summary: Biofiltration is widely used for water treatment, and bacteriophages play a significant role in regulating bacterial populations within biofilters through interactions with key bacterial species. However, there is limited research on phages in biofiltration systems.
Article
Biochemistry & Molecular Biology
Lise Dauban, Remi Montagne, Agnes Thierry, Luciana Lazar-Stefanita, Nathalie Bastie, Olivier Gadal, Axel Cournac, Romain Koszul, Frederic Beckouet
Article
Biochemical Research Methods
Lyam Baudry, Gael A. Millot, Agnes Thierry, Romain Koszul, Vittore F. Scolari
Article
Multidisciplinary Sciences
Kati Boehm, Giacomo Giacomelli, Andreas Schmidt, Axel Imhof, Romain Koszul, Martial Marbouty, Marc Bramkamp
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Charlotte Cockram, Agnes Thierry, Aurore Gorlas, Roxane Lestini, Romain Koszul
Summary: This study developed a cost-effective Hi-C protocol for exploring chromosome conformations in prokaryotes and archaea. By validating and applying this method in different microorganisms, the research found that these euryarchaeota lack compartment-like structures and their genomes are mainly composed of self-interacting domains and chromatin loops.
Article
Multidisciplinary Sciences
Cyril Matthey-Doret, Lyam Baudry, Axel Breuer, Remi Montagne, Nadege Guiglielmoni, Vittore Scolari, Etienne Jean, Arnaud Campeas, Philippe Henri Chanut, Edgar Oriol, Adrien Meot, Laurent Politis, Antoine Vigouroux, Pierrick Moreau, Romain Koszul, Axel Cournac
NATURE COMMUNICATIONS
(2020)
Article
Biology
Jeremy Gauthier, Helene Boulain, Joke J. F. A. van Vugt, Lyam Baudry, Emma Persyn, Jean-Marc Aury, Benjamin Noel, Anthony Bretaudeau, Fabrice Legeai, Sven Warris, Mohamed A. Chebbi, Geraldine Dubreuil, Bernard Duvic, Natacha Kremer, Philippe Gayral, Karine Musset, Thibaut Josse, Diane Bigot, Christophe Bressac, Sebastien Moreau, Georges Periquet, Myriam Harry, Nicolas Montagne, Isabelle Boulogne, Mahnaz Sabeti-Azad, Martine Maibeche, Thomas Chertemps, Frederique Hilliou, David Siaussat, Joelle Amselem, Isabelle Luyten, Claire Capdevielle-Dulac, Karine Labadie, Bruna Lais Merlin, Valerie Barbe, Jetske G. de Boer, Martial Marbouty, Fernando Luis Consoli, Stephane Dupas, Aurelie Hua-Van, Gaelle Le Goff, Annie Bezier, Emmanuelle Jacquin-Joly, James B. Whitfield, Louise E. M. Vet, Hans M. Smid, Laure Kaiser, Romain Koszul, Elisabeth Huguet, Elisabeth A. Herniou, Jean-Michel Drezen
Summary: Endogenous viruses make up a significant portion of eukaryote genomes and provide new functions, although the evolution of large DNA viruses integrated into genomes that benefit their host remains unknown. A study on parasitoid wasps reveals that bracovirus genes have colonized all ten chromosomes, with these gene clusters being established over 53 million years ago and showing remarkable stability in genomic structures constrained by evolution. Transcriptional analysis shows temporal synchronization of viral gene expression without immune gene induction, suggesting a lack of conflict between ancient symbiotic partners.
COMMUNICATIONS BIOLOGY
(2021)
Article
Cell Biology
Aurele Piazza, Helene Bordelet, Agnes Dumont, Agnes Thierry, Jerome Savocco, Fabien Girard, Romain Koszul
Summary: This study characterizes two layers of spatial chromatin reorganization following DSB formation in Saccharomyces cerevisiae, uncovering multiple ways in which cohesin regulates homology search during recombinational DNA repair.
NATURE CELL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Brenna Conin, Ingrid Billault-Chaumartin, Hafez El Sayyed, Nicole Quenech'Du, Charlotte Cockram, Romain Koszul, Olivier Espeli
Summary: In bacteria, the decatenation activity of topoisomerase IV plays a crucial role in chromosome replication and segregation. This study reveals that inactivation of topoisomerase IV leads to massive chromosome reorganization and increased contacts between nearby and distant loci. The roles of Topo III, MatP, and MukB in this process were also investigated.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Nathalie Bastie, Christophe Chapard, Lise Dauban, Olivier Gadal, Frederic Beckouet, Romain Koszul
Summary: This study investigates the roles of various cohesin regulators in tuning chromatin loop expansion in budding yeast, revealing that Scc2 plays a key role in both stimulating cohesin ATPase activity and driving cohesin translocation on DNA, while Smc3 acetylation during S phase counteracts this activity by stabilizing Pds5 to finely tune loop size and stability in G2.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biology
Jonay Garcia-Luis, Helene Bordelet, Agnes Thierry, Romain Koszul, Luis Aragon
Summary: This study reveals that degradation of cohesin during anaphase onset leads to aberrant chromatid segregation in yeast cells. Hi-C analysis of segregating chromatids shows that depletion of cohesin results in loss of intrachromatid organization. Surprisingly, cleavage of cohesin through specific methods does not significantly disrupt chromatid organization during anaphase, explaining successful bulk segregation.
Review
Biochemistry & Molecular Biology
Fares Osam Yanez-Cuna, Romain Koszul
Summary: Chromosomes in all domains of life have well-defined structures and hierarchical organization. The regulation of this organization and its interplay with gene expression and other chromosome processes are actively studied. Bacterial chromosomes are gene-dense and organized into a nucleoid, a membraneless compartment composed of DNA, RNA, and proteins. Recent advances in imaging and genomic methods have improved our understanding of bacterial chromosomal organization.
CURRENT OPINION IN STRUCTURAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Charlotte Cockram, Agnes Thierry, Romain Koszul
Summary: By comparing eukaryotic and prokaryotic Hi-C protocols, we have developed a cost and time-effective approach to generate high-resolution contact matrices of both bacteria and archaea genomes.
Article
Microbiology
Quentin Lamy-Besnier, Romain Koszul, Laurent Debarbieux, Martial Marbouty
Summary: Researchers used genomic chromosome conformation capture (Hi-C) data to reorganize, close, and improve the quality of the genomes of the 12 strains in the OMM12 model, addressing the issue of unclosed genomes post-sequencing.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2021)
Article
Biotechnology & Applied Microbiology
Lyam Baudry, Nadege Guiglielmoni, Herve Marie-Nelly, Alexandre Cormier, Martial Marbouty, Komlan Avia, Yann Loe Mie, Olivier Godfroy, Lieven Sterck, J. Mark Cock, Christophe Zimmer, Susana M. Coelhe, Romain Koszul