Matthew C. Radey
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View article: The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome
The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome Open
Bacteria inhabiting the mammalian gut coexist in dense communities where contact-dependent antagonism mechanisms are widespread. The type VI secretion system (T6SS) is an interbacterial toxin delivery pathway prevalent among gut Bacteroida…
View article: Short tandem gene duplications as potential agents of genetic memory
Short tandem gene duplications as potential agents of genetic memory Open
Tandem gene duplications are spontaneous mutations that occur frequently but whose significance is often overlooked because they are genetically unstable and can be difficult to detect by sequencing. Here, we studied the spontaneous loss, …
View article: A conserved electron transport chain sensitizes Bacteroides to a pore-forming type VI secretion toxin
A conserved electron transport chain sensitizes Bacteroides to a pore-forming type VI secretion toxin Open
Data suggest that antagonism between bacteria is prevalent within the gut microbiome. Such antagonism could have profound consequences on the fitness of species; however, the susceptibility determinants to even the most pervasive antagonis…
View article: 58 Measuring origin-to-terminus ratios with droplet digital polymerase chain reaction to estimate bacterial growth rate in cystic fibrosis sputum
58 Measuring origin-to-terminus ratios with droplet digital polymerase chain reaction to estimate bacterial growth rate in cystic fibrosis sputum Open
View article: 84 Plasmids acquired during the course of cystic fibrosis infections cause extreme antibiotic resistance in Pseudomonas aeruginosa
84 Plasmids acquired during the course of cystic fibrosis infections cause extreme antibiotic resistance in Pseudomonas aeruginosa Open
View article: 57 Bronchoscopy sampling finds that intra-lung bacterial migration contributes to persistent Pseudomonas aeruginosa infection after elexacaftor-tezacaftor-ivacaftor
57 Bronchoscopy sampling finds that intra-lung bacterial migration contributes to persistent Pseudomonas aeruginosa infection after elexacaftor-tezacaftor-ivacaftor Open
View article: Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle Open
View article: Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species
Discovery of a glutathione utilization pathway in Francisella that shows functional divergence between environmental and pathogenic species Open
View article: WS13.06 Regional bronchoscopy sampling indicates that Pseudomonas aeruginosa infections persist throughout the lung after elexacaftor/tezacaftor/ivacaftor (ETI) due to intra-lung bacterial migration
WS13.06 Regional bronchoscopy sampling indicates that Pseudomonas aeruginosa infections persist throughout the lung after elexacaftor/tezacaftor/ivacaftor (ETI) due to intra-lung bacterial migration Open
View article: Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter
Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter Open
Summary The study of bacteria has yielded fundamental insights into cellular biology and physiology, biotechnological advances and many therapeutics. Yet due to a lack of suitable tools, the significant portion of bacterial diversity held …
View article: Discovery of a unique pathway for glutathione utilization in Francisella
Discovery of a unique pathway for glutathione utilization in Francisella Open
Glutathione (GSH) is an abundant metabolite that can act as a signal, a nutrient source, or serve in a redox capacity for intracellular pathogens. For Francisella, GSH is thought to be a critical in vivo source of cysteine; however, the ce…
View article: Genome Capture Sequencing Selectively Enriches Bacterial DNA and Enables Genome-Wide Measurement of Intrastrain Genetic Diversity in Human Infections
Genome Capture Sequencing Selectively Enriches Bacterial DNA and Enables Genome-Wide Measurement of Intrastrain Genetic Diversity in Human Infections Open
Genetic diversity evolves in bacterial strains during human infections and could affect disease manifestations and treatment resistance. However, the extent of diversity present in vivo and its changes over time are difficult to measure by…
View article: Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase
Genome-wide protein–DNA interaction site mapping in bacteria using a double-stranded DNA-specific cytosine deaminase Open
View article: Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism Open
Bacterial survival is fraught with antagonism, including that deriving from viruses and competing bacterial cells. It is now appreciated that bacteria mount complex antiviral responses; however, whether a coordinated defense against bacter…
View article: Author response: Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism
Author response: Discovery of coordinately regulated pathways that provide innate protection against interbacterial antagonism Open
View article: A population-level strain genotyping method to study pathogen strain dynamics in human infections
A population-level strain genotyping method to study pathogen strain dynamics in human infections Open
A hallmark of chronic bacterial infections is the long-term persistence of 1 or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually pres…
View article: Combining Ivacaftor and Intensive Antibiotics Achieves Limited Clearance of Cystic Fibrosis Infections
Combining Ivacaftor and Intensive Antibiotics Achieves Limited Clearance of Cystic Fibrosis Infections Open
Recent work shows that people with cystic fibrosis (CF) and chronic lung infections generally remain persistently infected after treatment with drugs that target the CF physiological defect (called CFTR modulators). However, changes produc…
View article: 429: Effects of elexacaftor/tezacaftor/ivacaftor on the CF sputum microbiome: Preliminary analysis from the Promise study
429: Effects of elexacaftor/tezacaftor/ivacaftor on the CF sputum microbiome: Preliminary analysis from the Promise study Open
View article: 517: Regional evolution of Pseudomonas aeruginosa in the human host
517: Regional evolution of Pseudomonas aeruginosa in the human host Open
View article: Coordinately regulated interbacterial antagonism defense pathways constitute a bacterial innate immune system
Coordinately regulated interbacterial antagonism defense pathways constitute a bacterial innate immune system Open
Bacterial survival is fraught with antagonism, including that deriving from viruses and competing bacterial cells 1–3 4 . It is now appreciated that bacteria mount complex antiviral responses; however, whether a coordinated defense against…
View article: Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase
Genome-wide protein-DNA interaction site mapping using a double strand DNA-specific cytosine deaminase Open
DNA–protein interactions (DPIs) are central to such fundamental cellular processes as transcription and chromosome maintenance and organization. The spatiotemporal dynamics of these interactions dictate their functional consequences; there…
View article: A Population-level Strain Genotyping Method to Study Pathogen Strain Dynamics in Human Infections
A Population-level Strain Genotyping Method to Study Pathogen Strain Dynamics in Human Infections Open
A hallmark of chronic bacterial infections is the long-term persistence of one or more pathogen species at the compromised site. Repeated detection of the same bacterial species can suggest that a single strain or lineage is continually pr…
View article: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here, we exami…
View article: Author response: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
Author response: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
View article: Cystic Fibrosis Lung Function Decline after Within-Host Evolution Increases Virulence of Infecting <i>Pseudomonas aeruginosa</i>
Cystic Fibrosis Lung Function Decline after Within-Host Evolution Increases Virulence of Infecting <i>Pseudomonas aeruginosa</i> Open
"Cystic Fibrosis Lung Function Decline after Within-Host Evolution Increases Virulence of Infecting Pseudomonas aeruginosa." American Journal of Respiratory and Critical Care Medicine, 203(5), pp. 637–640
View article: An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations
An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations Open
When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here we examin…
View article: A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing
A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial base editing Open
View article: Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells
Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells Open
View article: Human gut bacteria contain acquired interbacterial defence systems
Human gut bacteria contain acquired interbacterial defence systems Open
View article: Escherichia coli Clonobiome: Assessing the Strain Diversity in Feces and Urine by Deep Amplicon Sequencing
Escherichia coli Clonobiome: Assessing the Strain Diversity in Feces and Urine by Deep Amplicon Sequencing Open
Bacterial species in the microbiome are often represented by multiple genetically and phenotypically different strains, making insight into subspecies diversity critical to a full understanding of the microbiome, especially with respect to…