A5045034798- Antibiotic Resistance in Bacteria
- Legume Nitrogen Fixing Symbiosis
- Evolution and Genetic Dynamics
- Plant nutrient uptake and metabolism
- Vibrio bacteria research studies
- Bacterial Identification and Susceptibility Testing
- Bacteriophages and microbial interactions
- Antibiotic Use and Resistance
- Bacterial biofilms and quorum sensing
- Gut microbiota and health
- CRISPR and Genetic Engineering
- Diversity and Career in Medicine
- Nematode management and characterization studies
- scientometrics and bibliometrics research
- Escherichia coli research studies
- Health and Medical Research Impacts
- Agronomic Practices and Intercropping Systems
- Plant Virus Research Studies
- Microbial Fuel Cells and Bioremediation
- Cystic Fibrosis Research Advances
- Environmental and biological studies
- Mycobacterium research and diagnosis
- Microbial infections and disease research
- Soybean genetics and cultivation
- Energetic Materials and Combustion
Queen's University Belfast
2024-2025
Okinawa Institute of Science and Technology Graduate University
2025
University of Oxford
2016-2024
Mansfield University
2022
Institute for Advanced Study
2022
Significance Rhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes numerous rhizobia, but analysis gene function increasingly lags discovery. Mariner-based transposon insertion allowed us characterize fitness contribution bacterial genes determine those functionally important Rhizobium– legume symbiosis at...
Abstract CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by raises possibility these may constrain horizontal gene transfer. Here we test this hypothesis in opportunistic pathogen Pseudomonas aeruginosa, which has emerged as important model for understanding function. Across diversity P. active are associated smaller genomes higher GC content, suggesting inhibits acquisition Although...
Catabolism of dicarboxylates at low oxygen drives N 2 fixation and promotes ammonia secretion in rhizobium-legume symbioses.
Abstract It is well established that antibiotic treatment selects for resistance, but the dynamics of this process during infections are poorly understood. Here we map responses Pseudomonas aeruginosa to in high definition a lung infection single ICU patient. Host immunity and therapy with meropenem suppressed P. , second wave emerged due growth oprD wbpM resistant mutants evolved situ. Selection then led loss resistance by decreasing prevalence low fitness mutants, increasing frequency...
Abstract Bacteria have the potential to translocate between sites in human body, but dynamics and consequences of within-host bacterial migration remain poorly understood. Here we investigate link gut lung Pseudomonas aeruginosa populations an intensively sampled ICU patient using a combination genomics, isolate phenotyping, host immunity profiling, clinical data. Crucially, show that colonization was driven by translocation P. from gut. Meropenem treatment for suspected urinary tract...
Abstract Antibiotic resistance poses a global health threat, but the within-host drivers of remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and is thought emerge due selection for de novo variants. Here we show that mixed strain common in opportunistic pathogen P. aeruginosa . Crucially, evolves rapidly patients colonized by multiple strains through pre-existing resistant strains. In contrast, sporadically single novel mutations. However, strong...
Bacterial pathogens show high levels of chromosomal genetic diversity, but the influence this diversity on evolution antibiotic resistance by plasmid acquisition remains unclear. Here, we address problem in context colistin, a 'last line defence' antibiotic. Using experimental evolution, that carrying MCR-1 colistin gene dramatically increases ability Escherichia coli to evolve high-level acquiring mutations lpxC, an essential involved lipopolysaccharide biosynthesis. Crucially, lpxC...
Insertion sequencing (INSeq) analysis of Rhizobium leguminosarum bv. viciae 3841 (Rlv3841) grown on glucose or succinate at both 21% and 1% O2 was used to understand how concentration alters metabolism. Two transcriptional regulators were required for growth (pRL120207 [eryD] RL0547 [phoB]), five (pRL100388, RL1641, RL1642, RL3427, RL4524 [ecfL]), three (pRL110072, RL0545 [phoU], RL4042). A novel toxin-antitoxin system identified that could be important generation new plasmidless rhizobial...
Plasmids are a ubiquitous feature of bacterial genomes, but the evolutionary forces driving genes to become associated with plasmids poorly understood. To address this problem, we compared fitness effects chromosomal and plasmid in plant symbiont Rhizobium leguminosarum. Here show that depleted beneficial chromosome, effect is stronger for ancient recently acquired plasmids. These findings support hypothesis evolution drives localized resulting gradual decay ecological value question...
Abstract Parasites are foundational to ecosystem health both as indicator species of community productivity but also drivers diversity. In bacterial communities, bacteriophage viruses can play such a role they track the dynamic composition hosts, and in case lytic phages, confer growth advantage lower abundance bacteria while adapting more common ones. We set out test whether viromes be used signatures microbiome using previously published results across systems. By comparing observed phage...
Rhizobial attachment to host legume roots is the first physical interaction of bacteria and plants in symbiotic nitrogen fixation. The pH-dependent primary
Abstract The emergence and spread of antibiotic resistance in bacterial pathogens is a global health threat. One important unanswered question how influences the ability pathogen to invade host-associated microbiome. Here we investigate impacts bacteria from microbiome, using opportunistic Pseudomonas aeruginosa respiratory microbiome as our model system. We measure P. spontaneous antibiotic-resistant mutants pre-established cultures commensal microbes an assay that allows us link specific...
Abstract The host-associated microbiome is an important barrier to bacterial pathogen colonization and can mediate protection through a variety of mechanisms. We wanted investigate the potential consequences selection imposed by commensal competitors on invading pathogen. To do this, we tested ability opportunistic Pseudomonas aeruginosa invade pre-established communities abundant bacterium in human microbiome, Staphylococcus epidermidis . passaged ten independent lines P. daily invasion...
Abstract Primary attachment of rhizobia to host legume roots depends on pH and is the first physical interaction during nodulation. Genome-wide insertion sequencing, luminescence-based assays proteomic analysis demonstrate primary Rhizobium leguminosarum biovar viciae 3841 Pisum sativum (pea) more complex than previously thought. In total, 115 proteins are needed for initial under one or test conditions (acid, neutral alkaline pH), with 22 required all conditions. These include cell-surface...
Abstract Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which use plant-derived dicarboxylates as energy electron sources for reduction of atmospheric N 2 ammonia secretion to plants. Using heterogeneous genome-scale datasets, we reconstructed a model bacteroid metabolism investigate the effects varying dicarboxylate oxygen supply carbon nitrogen allocation. Modelling 13 C metabolic flux analysis in bacteroids indicate that microaerobiosis restricts...
Abstract Antibiotic resistance poses a global health threat, but the within-host drivers of remain poorly understood. Pathogen populations are often assumed to be clonal within hosts, and is thought emerge due selection for de novo variants. Here we show that pulmonary opportunistic pathogen P. aeruginosa polyclonal. Crucially, evolves rapidly in patients colonized by polyclonal through pre-existing resistant strains. In contrast, sporadically monoclonal novel mutations. However, strong...
Abstract By analyzing successive lifestyle stages of a model Rhizobium -legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N 2 -fixing bacteroids and release from legume (pea) nodules. While only 27 are annotated as nif fix in leguminosarum , show 603 genetic regions (593 genes, 5 tRNAs RNA features) competitive ability to nodulate pea . Of these, 146 common growth...
Abstract Bacteria have the potential to migrate between sites in human body, but dynamics and consequences of within-host translocation remain poorly understood. Here we investigate link gut lung Pseudomonas aeruginosa populations an intensively sampled ICU patient using a combination genomics, isolate phenotyping, host immunity profiling, clinical data. Crucially, show that colonization was driven by repeated bacterial clones from gut. Meropenem treatment for suspected urinary tract...