A5016538517- Nutritional Studies and Diet
- Gut microbiota and health
- Diet and metabolism studies
- Environmental DNA in Biodiversity Studies
- Bacterial Genetics and Biotechnology
- Respiratory viral infections research
- Microbial infections and disease research
- Bacteriophages and microbial interactions
- Genetic and Environmental Crop Studies
- Microbial Community Ecology and Physiology
- Pneumonia and Respiratory Infections
- Cancer-related molecular mechanisms research
- Enzyme Structure and Function
- Nutrition, Genetics, and Disease
- Molecular Biology Techniques and Applications
- Obesity, Physical Activity, Diet
- RNA modifications and cancer
- Botanical Research and Chemistry
- Plant Pathogens and Resistance
- Yersinia bacterium, plague, ectoparasites research
- Food Security and Health in Diverse Populations
- Salmonella and Campylobacter epidemiology
- Bacterial Infections and Vaccines
- CRISPR and Genetic Engineering
- Biosensors and Analytical Detection
Duke University
2019-2025
National Center for Immunization and Respiratory Diseases
2015
Centers for Disease Control and Prevention
2013
New York State Department of Health
2012-2013
Wadsworth Center
2013
Albany Research Institute
2013
Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead varying effects on SCFA production human studies, and microbial responses nutritional interventions vary by individual. It is therefore possible that prebiotic therapies will require customizing individuals.Here, we explored personalization conducting a three-way crossover study...
Recombineering is a widely-used approach to delete genes, introduce insertions and point mutations, epitope tags into bacterial chromosomes. Many recombineering methods have been described, for wide range of species. These are often limited by (i) low efficiency, and/or (ii) introduction "scar" DNA the chromosome. Here, we describe rapid, efficient, PCR-based method, FRUIT, that can be used scar-free deletions, tags, promoters genomes enteric bacteria. The efficiency FRUIT far higher than...
ABSTRACT Escherichia coli AraC is a well-described transcription activator of genes involved in arabinose metabolism. Using complementary genomic approaches, chromatin immunoprecipitation (ChIP)-chip, and profiling, we identify direct regulatory targets AraC, including five novel target genes: ytfQ , ydeN ydeM ygeA polB . Strikingly, only has an established connection to metabolism, suggesting that broader function than previously described. We demonstrate arabinose-dependent repression...
Eating a varied diet is central tenet of good nutrition. Here, we develop molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with the chloroplast trnL-P6 marker 1,029 fecal samples from 324 participants across two interventional feeding studies and three observational cohorts. The number taxa per sample (plant richness or pMR) correlated recorded intakes in diets indices calculated food frequency questionnaire typical (ρ = 0.40 0.63). In adolescents unable...
An outbreak at a university in Georgia was identified after 83 cases of probable pneumonia were reported among students. Respiratory specimens obtained from 21 students for the investigation. The TaqMan array card (TAC), quantitative PCR (qPCR)-based multipathogen detection technology, used to initially identify Mycoplasma pneumoniae as causative agent this outbreak. TAC demonstrated 100% diagnostic specificity and sensitivity compared those multiplex qPCR assay agent. All M. (n=12) isolates...
Salmonella enterica serovar Typhimurium (S. Typhimurium) pathogenicity island 1 (SPI-1) encodes a type III secretion system required for invasion of host gut epithelial cells. Expression SPI-1 virulence genes is controlled by complex hierarchy transcription factors encoded within and outside SPI-1. The master regulator SPI-1, HilA, itself regulated three homologous factors, HilD, HilC, RtsA. HilD activates hilA other target in response to environmental conditions associated with the...
Yersinia pestis, the etiologic agent of plague, is closely related to pseudotuberculosis evolutionarily but has a very different mode infection. The RNA-binding regulatory protein, Hfq, mediates regulation by small RNAs (sRNAs) and required for virulence both Y. pestis pseudotuberculosis. Moreover, Hfq growth not pseudotuberculosis, at 37°C. Together, these observations suggest that sRNAs play important roles in survival may account some differences between We have used deep sequencing...
Current methods for capturing human dietary patterns typically rely on individual recall and as such are subject to the limitations of memory. DNA sequencing-based approaches, frequently used profiling nonhuman diets, do not suffer from same limitations. Here, we metabarcoding broadly characterize plant portion diets first time. The majority sequences corresponded known foods, including all but one foodstuff included in an experimental plant-rich diet. Metabarcoding could distinguish between...
Mycoplasma pneumoniae is a leading cause of community-acquired pneumonia (CAP) across patient populations all ages. We have developed loop-mediated isothermal amplification (LAMP) assay that enables rapid, low-cost detection M. from nucleic acid extracts and directly various respiratory specimen types. The implements calcein to facilitate simple visual readout positive results in approximately 1 h, making it ideal for use primary care facilities resource-poor settings. analytical sensitivity...
Abstract Objective We assessed the impact of a food‐provisioning intervention on diet quality in children with obesity. Methods Participants ( n = 33, aged 6–11 years) were randomly assigned to either usual care (intensive health behavior and lifestyle treatment) or (usual + food provisioning; high‐fiber, low‐dairy diet) for 4 weeks. The primary outcome was change child at Week 4. Secondary outcomes changes weight, insecurity, gut microbiome composition (16S ribosomal RNA), dietary intake,...
Abstract Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected blood, urine, skin or hair, but detection consumed foods stool also been shown be possible via DNA sequencing. An additional macromolecule that harbors sequence information is protein. However, the use protein as an only explored very limited extent. Here, we evaluate and compare measurement residual food-derived potential intake....
In a pilot study of five individuals, we evaluated the concordance between conventional diet records and DNA- protein-based biomarkers food intake in their stool.
Macrolide-resistant Mycoplasma pneumoniae is an increasing problem worldwide but not well documented in the United States. We report a cluster of macrolide-resistant M. cases among mother and two daughters.
Abstract Background Short-chain fatty acids (SCFAs) derived from gut bacteria are associated with protective roles in diseases ranging obesity to colorectal cancers. Intake of microbially accessible dietary fibers (prebiotics) lead varying effects on SCFA production human studies, and microbial responses nutritional interventions vary by individual. It is therefore possible that prebiotic therapies will require customizing individuals. Results Here, we explored personalization conducting a...
Abstract Eating a varied diet is central tenet of good nutrition. Here, we develop the first molecular tool to quantify human dietary plant diversity by applying DNA metabarcoding with chloroplast trnL -P6 marker 1,001 fecal samples from 310 participants across four cohorts. The number taxa per sample (plant richness, or pMR) correlated recorded intakes in interventional diets (ρ=0.31) and indices calculated food-frequency questionnaire freely-chosen (ρ=0.40-0.63). In adolescents unable...