A5042591265- Gut microbiota and health
- Plant Pathogenic Bacteria Studies
- Plant-Microbe Interactions and Immunity
- Infant Nutrition and Health
- Probiotics and Fermented Foods
- Breastfeeding Practices and Influences
- Cystic Fibrosis Research Advances
- Legume Nitrogen Fixing Symbiosis
- Gestational Diabetes Research and Management
- Plant Parasitism and Resistance
- Antibiotic Resistance in Bacteria
- Bacterial biofilms and quorum sensing
- Microbial Community Ecology and Physiology
- Bacteriophages and microbial interactions
- Acute Myeloid Leukemia Research
- Genomics and Phylogenetic Studies
- Plant pathogens and resistance mechanisms
- Plant Pathogens and Resistance
- Plant Pathogens and Fungal Diseases
- Evolution and Genetic Dynamics
- Chronic Myeloid Leukemia Treatments
- Clostridium difficile and Clostridium perfringens research
- Aquaculture disease management and microbiota
- Epigenetics and DNA Methylation
- Antifungal resistance and susceptibility
University of Toronto
2015-2024
Genetic Analysis (Norway)
2018
Pomona College
2014
University of Chicago
1997-2004
Cancer Research Center
1997-1999
Across plants and animals, host-associated microbial communities play fundamental roles in host nutrition, development, immunity. The factors that shape host–microbiome interactions are poorly understood, yet essential for understanding the evolution ecology of these symbioses. Plant roots assemble two distinct compartments from surrounding soil: rhizosphere (microbes roots) endosphere within roots). Root-associated microbes were key land underlie ecosystem processes. However, it is largely...
Abstract Understanding the significance of bacterial species that colonize and persist in cystic fibrosis (CF) airways requires a detailed examination community structure across broad range age disease stage. We used 16S ribosomal RNA sequencing to characterize lung microbiota 269 CF patients spanning 60 year range, including 76 pediatric samples from 4–17 cross-section status identify features their relationship stage age. The shows significant inter-individual variability structure,...
The leaf microbiome is influenced by both biotic and abiotic factors. Currently, we know little about the relative importance of these factors in determining microbiota composition dynamics. To explore this issue, collected weekly samples over a 98-day growing season from multiple cultivars common bean, soybean, canola planted at three locations Ontario, Canada, performed Illumina-based analysis. We find that beginning very strongly soil but, as progresses, it differentiates, becomes...
Next-generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed date require some prior genetic analysis, which can be very time-consuming even in genetically tractable organisms. Here we present a de novo method rapidly and robustly the physical location EMS by small pooled F₂ population. This method, called Next Generation Mapping (NGM), uses chastity...
The origins of crop diseases are linked to domestication plants. Most crops were domesticated centuries – even millennia ago, thus limiting opportunity understand the concomitant emergence disease. Kiwifruit (Actinidia spp.) is an exception: began in 1930s with outbreaks canker disease caused by P. syringae pv. actinidiae (Psa) first recorded 1980s. Based on SNP analyses two circularized and 34 draft genomes, we show that Psa comprised distinct clades exhibiting negligible within-clade...
ABSTRACT Individual strains of the plant pathogenic bacterium Pseudomonas syringae vary in their ability to produce toxins, nucleate ice, and resist antimicrobial compounds. These phenotypes enhance virulence, but it is not clear whether they play a dominant role specific pathogen-host interactions. To investigate evolution these virulence-associated phenotypes, we used functional assays survey for distribution among collection 95 P. strains. All were phylogenetically characterized via...
Significance Bacterial pathogens can use a syringe-like structure to inject virulence proteins (effectors) directly into host cells. The YopJ/HopZ superfamily of effectors found in animal and plant modify kinase suppress immunity. In the model Arabidopsis , HopZ1a is recognized by resistance protein ZAR1 induce robust immune response that blocks pathogen growth. Here, we show effector from Pseudomonas syringae targets nonfunctional pseudokinase ZED1 required for recognition ZAR1. We...
The eukaryotic cytoskeleton is essential for structural support and intracellular transport, therefore a common target of animal pathogens. However, no phytopathogenic effector has yet been demonstrated to specifically the plant cytoskeleton. Here we show that Pseudomonas syringae type III secreted HopZ1a interacts with tubulin polymerized microtubules. We demonstrate an acetyltransferase activated by co-factor phytic acid. Activated acetylates itself tubulin. conserved autoacetylation site...
ABSTRACT Pulmonary infections caused by Pseudomonas aeruginosa are a recalcitrant problem in cystic fibrosis (CF) patients. While the clinical implications and long-term evolutionary patterns of these well studied, we know little about short-term population dynamics that enable this pathogen to persist despite aggressive antimicrobial therapy. Here, describe genomic analysis 233 P. isolates collected from 12 sputum specimens obtained over 1-year period single patient. Whole-genome sequencing...
Pseudomonas syringae is a highly diverse bacterial species complex capable of causing wide range serious diseases on numerous agronomically important crops. We examine the evolutionary relationships 391 agricultural and environmental strains using whole-genome sequencing genomic analyses.We describe phylogenetic distribution all 77,728 orthologous gene families in pan-genome, reconstruct core genome phylogeny 2410 genes, hierarchically cluster accessory genome, identify diversity type III...
Abstract Chronic airway infections caused by Pseudomonas aeruginosa contribute to the progression of pulmonary disease in individuals with cystic fibrosis (CF). In setting CF, within-patient adaptation a P. strain generates phenotypic diversity that can complicate microbiological analysis patient samples. We investigated within- and between- sample 34 phenotypes among 235 isolates cultured from sputum samples collected single CF over span one year assessed colony morphology as screening tool...
The ability to efficiently characterize microbial communities from host individuals can be limited by co-amplification of organellar sequences (mitochondrial and/or plastid), which share a common ancestor and thus sequence similarity with extant bacterial lineages. One promising approach is the use sequence-specific peptide nucleic acid (PNA) clamps, bind to, block amplification of, host-derived DNA. Universal PNA clamps have been proposed plant-derived mitochondrial (mPNA) plastid (pPNA) at...
Loss of a whole chromosome 5 or deletion the long arm, del(5q), is recurring abnormality in malignant myeloid diseases. In previous studies, we delineated commonly deleted segment ≈4 Mb within band 5q31 that was flanked by IL9 on proximal side and D5S166 distal side. We have generated physical map P1 (PAC), bacterial (BAC), yeast artificial (YAC) clones this interval. The contig consists 108 (78 PACs, 2 BACs, 28 YACs) to which 125 markers (5 genes, 11 expressed sequence tags, 12...
The microbiome shapes diverse facets of human biology and disease, with the importance fungi only beginning to be appreciated. Microbial communities infiltrate anatomical sites as respiratory tract healthy humans those diseases such cystic fibrosis, where chronic colonization infection lead clinical decline. Although are frequently recovered from fibrosis patient sputum samples have been associated deterioration lung function, understanding species population dynamics remains in its infancy....
Abstract Background Identification of protein-protein interactions is a fundamental aspect understanding protein function. A commonly used method for identifying the yeast two-hybrid system. Results Here we describe application next-generation sequencing to interaction screens and develop Quantitative Interactor Screen Sequencing (QIS-Seq). QIS-Seq provides quantitative measurement enrichment each interactor relative its frequency in library as well general stickiness (non-specific binding)....
The recognition of microbe-associated molecular patterns during infection is central to the mounting an effective immune response. In spite their importance, it remains difficult identify these molecules and host receptors required for perception, ultimately limiting our understanding role in evolution host-pathogen relationships. We employ a comparative genomics screen six new eliciting peptides from phytopathogenic bacterium Pseudomonas syringae. then perform reverse genetic Arabidopsis...
Abstract Over 90% of cystic fibrosis (CF) patients die due to chronic lung infections leading respiratory failure. The decline in CF function is greatly accelerated by intermittent and progressively severe acute pulmonary exacerbations (PEs). Despite their clinical impact, surprisingly few microbiological signals associated with PEs have been identified. Here we introduce an unsupervised, systems-oriented approach identify key members the microbiota. We used two sputum microbiome data sets...
IgA nephropathy (IgAN) is a leading cause of kidney failure, yet little known about the immunopathogenesis this disease. IgAN characterized by deposition in glomeruli, but source and stimulus for production are not known. Clinical experimental data suggest role aberrant immune responses to mucosal microbiota IgAN, some countries with high disease prevalence, tonsillectomy regarded as standard-of-care therapy. To evaluate relationship between responses, we tonsil patients versus nonrelated...
The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways which microbial affect ecosystem functioning human health. Here we describe Serial Illumina Sequencing (SI-Seq): a method for deep 16S rRNA gene next-generation technology. SI-Seq serially sequences portions V5, V6 V7 hypervariable regions from barcoded amplicons an short-read genome analyzer. obtains taxonomic resolution similar 454...
The emergence of antimicrobial resistance is a major threat to global health and has placed pressure on the livestock industry eliminate use antibiotic growth promotants (AGPs) as feed additives. To mitigate their removal, efficacious alternatives are required. AGPs thought operate through modulating gut microbiome limit opportunities for colonization by pathogens, increase nutrient utilization, reduce inflammation. However, little known concerning underlying mechanisms. Previous studies...