bacteriophages
Research ArticleCooperation between Different CRISPR-Cas Types Enables Adaptation in an RNA-Targeting SystemCRISPR-Cas systems are immune systems that protect bacteria and archaea against their viruses, bacteriophages. Immunity is achieved through the acquisition of short DNA fragments from the viral invader’s genome.
Research ArticleMycobacterium abscessus Strain Morphotype Determines Phage Susceptibility, the Repertoire of Therapeutically Useful Phages, and Phage ResistanceMycobacterium abscessus infections in cystic fibrosis patients are challenging to treat due to widespread antibiotic resistance. The therapeutic use of lytic bacteriophages presents a new potential strategy, but the great variation among clinical M. abscessus isolates demands determination of phage...
Research ArticleThe Prophage and Plasmid Mobilome as a Likely Driver of Mycobacterium abscessus Diversity...Mycobacterium abscessus is an important emerging pathogen that is challenging to treat with current antibiotic regimens. There is substantial genomic variation in M. abscessus clinical isolates, but little is known about how this influences pathogenicity and in vivo growth.
Research Article | Therapeutics and PreventionTargeting of Mammalian Glycans Enhances Phage Predation in the Gastrointestinal TractInvasive pathobionts or microbes capable of causing disease can reside deep within the mucosal epithelium of our gastrointestinal tract. Targeted effective antibacterial therapies are needed to combat these disease-causing organisms, many of which may be multidrug resistant.
Research Article | Ecological and Evolutionary ScienceSelection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer AgentsKin selection and group selection remain controversial topics in evolutionary biology. We argue that these types of selection are likely to operate in bacterial populations by showing that bacterial gene transfer agents (GTAs), but not related viruses, evolve under conditions of positive selection for the reduction of the energy cost of GTA particle production. We hypothesize that GTAs are dedicated devices mediating the survival of...
Editor's Pick Research Article | Host-Microbe BiologyProbiotic Properties of Escherichia coli Nissle in Human Intestinal OrganoidsProbiotic, or beneficial, bacteria, such as E. coli Nissle, hold promise for the treatment of human disease. More study is needed to fully realize the potential of probiotics. Safety and efficacy studies are critically important; however, mice are poor models for many human intestinal diseases. We used stem cell-derived human intestinal organoid tissues to evaluate...
Research Article | Therapeutics and PreventionTargeting Hidden Pathogens: Cell-Penetrating Enzybiotics Eradicate Intracellular Drug-Resistant Staphylococcus aureusThe increasing prevalence of antibiotic-resistant bacteria is one of the most urgent problems of our time. Staphylococcus aureus is an important human pathogen that has acquired several mechanisms to evade antibiotic treatment. In addition, S. aureus is able to invade and persist within human cells...
Research Article | Molecular Biology and PhysiologyProtein-Mediated and RNA-Based Origins of Replication of Extrachromosomal Mycobacterial ProphagesBacteriophages are the most abundant biological entities in the biosphere and are a source of uncharacterized biological mechanisms and genetic tools. Here, we identify segments of phage genomes that are used for stable extrachromosomal replication in the prophage state. Autonomous replication of some of these phages requires a RepA-like protein, although most lack repA and use RNA-based systems for replication initiation. We...
Research Article | Molecular Biology and PhysiologyParallel Genomics Uncover Novel Enterococcal-Bacteriophage InteractionsWe lack fundamental understanding of how phage infection influences bacterial gene expression and, consequently, how bacterial responses to phage infection affect the assembly of polymicrobial communities. Using parallel genomic approaches, we have discovered novel transcriptional regulators and metabolic genes that influence phage infection. The integration of whole-genome transcriptomic profiling during phage infection has revealed...
Research Article | Host-Microbe BiologyCharacteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil CrustThis work forms part of an overarching research theme studying the effects of a changing climate on biological soil crust (biocrust) in the Southwestern United States. To our knowledge, this study was the first to characterize bacteriophages in biocrust and offers a view into the ecology of phages in response to a laboratory wetting experiment. The phages identified here represent lineages of Caudovirales, and we found that the...