A5059180999- Gut microbiota and health
- Urinary Tract Infections Management
- Urinary Bladder and Prostate Research
- Pelvic floor disorders treatments
- Syphilis Diagnosis and Treatment
- Burn Injury Management and Outcomes
- Gastrointestinal motility and disorders
- Clostridium difficile and Clostridium perfringens research
- Metabolomics and Mass Spectrometry Studies
- Acne and Rosacea Treatments and Effects
- Autoimmune and Inflammatory Disorders
- Dermatology and Skin Diseases
- Genomics and Phylogenetic Studies
- Viral gastroenteritis research and epidemiology
- Energy and Environment Impacts
- Wound Healing and Treatments
- HIV/AIDS Research and Interventions
- Pneumocystis jirovecii pneumonia detection and treatment
- Reproductive tract infections research
- Advanced Statistical Modeling Techniques
- Rabies epidemiology and control
- Plant Disease Resistance and Genetics
- RNA and protein synthesis mechanisms
- Clinical Nutrition and Gastroenterology
- Transgenic Plants and Applications
University of Chicago
2024
Loyola University Chicago
2015-2021
Loyola University Medical Center
2021
University of California, San Diego
2021
Stanford University
2021
University of California, Los Angeles
2021
Kaohsiung Medical University
2014
Species-level classification for 16S rRNA gene sequences remains a serious challenge microbiome researchers, because existing taxonomic tools either do not provide species-level classification, or their results are unreliable. The unreliable due to the limitations in methods which lack solid probabilistic-based criteria evaluate confidence of assignments, use nucleotide k-mer frequency as proxy sequence similarity measurement.We have developed method that shows significantly improved over...
ABSTRACT The influence of the skin microbiota on host susceptibility to infectious agents is largely unexplored. harbors diverse bacterial species that may promote or antagonize growth an invading pathogen. We developed a human infection model for Haemophilus ducreyi in which volunteers are inoculated upper arm. After inoculation, papules form and either spontaneously resolve progress pustules. To examine role outcome H. infection, we analyzed microbiomes four dose-matched pairs “resolvers”...
Rationale: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that uninfected subjects. We hypothesized from more advanced disease would differ of an control population.Objectives: To measure HIV-infected population disease.Methods: 16s RNA gene sequencing performed on acellular bronchoalveolar lavage (BAL) fluid 30 (baseline mean CD4 count, 262 cells/mm3) before and up 3 years after starting highly active antiretroviral therapy (HAART) compared 22...
Domestic combustion of biomass fuels, such as wood, charcoal, crop residue and dung causes Household Air Pollution (HAP). These inhaled particulates affect more than half the world's population, causing respiratory problems infection inflammatory lung disease. We examined whether presence black carbon in alveolar macrophages was associated with alterations microbiome a Malawi population. Bronchoalveolar lavage samples from 44 healthy adults were sequenced using 16S rDNA amplification to...
The cutaneous microbiome maintains skin barrier function, regulates inflammation, and stimulates wound-healing responses. Burn injury promotes an excessive activation of the systemic immune response directed against commensal invading pathogens. Skin grafting is primary method reconstructing full-thickness burns, wound infection continues to be a significant complication.In this study, bacterial was evaluated subsequently compared patient outcomes. Three different specimens were assessed:...
The composition of the small intestinal microbiota has not yet been characterized thoroughly using culture-independent techniques. We compared microbial communities in patients with and without bacterial overgrowth (SIBO) culture-dependent identification approaches.Small bowel aspirate mucosal samples were collected from suspected SIBO. aspirates cultured to diagnose SIBO, defined as ≥10 colony-forming units/mL coliform or upper aerodigestive tract bacteria. Bacteria mucosa identified 16S...
Abstract Clostridioides difficile (C. difficile) strains belonging to the epidemic BI/NAP1/027 (RT027) group have been associated with increased transmissibility and disease severity. In addition major toxin A B virulence factors, RT027 also encode CDT binary toxin. Our lab previously identified a toxigenic isolate, ST1-75, that is avirulent in mice despite densely colonizing colon. Here, we show co-infecting ST1-75 virulent R20291 protects from colitis due rapid clearance of strain...
Exudative cutaneous ulcers (CU) in yaws-endemic areas are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD), but one-third of CU cases idiopathic (IU). Using mass drug administration (MDA) azithromycin, a yaws eradication campaign on Lihir Island Papua New Guinea reduced failed to eradicate yaws; IU rates remained constant throughout the campaign. To identify potential etiologies IU, we obtained swabs lesions (n = 279) skin asymptomatic controls (AC; n 233)...
Characterization of urinary bacterial microbiome and antimicrobial peptides after burn injury to identify potential mechanisms leading tract infections associated morbidities in patients.Retrospective cohort study using human urine from control subjects.University research laboratory.Burn patients.None.Urine samples catheterized patients were collected hourly for up 40 hours. Control was "healthy" volunteers. The peptide levels activity compared with patient outcomes. We observed a...
Dysbiosis of microbial communities is associated with various human diseases, raising the possibility using compositions as biomarkers for disease diagnosis. We have developed a Bayes classifier by modeling Dirichlet-multinomial distributions, which are widely used to model multicategorical count data extra variation. The parameters distributions estimated from training microbiome sets based on maximum likelihood. posterior probability sample belonging or healthy category calculated Bayes'...
Haemophilus ducreyi causes chancroid and is a major cause of cutaneous ulcers in children. Due to environmental reservoirs, both class I II H. strains persist ulcer regions endemicity following mass drug administration azithromycin, suggesting the need for vaccine. The hemoglobin receptor (HgbA) leading vaccine candidate, but its efficacy animal models specific. Controlled human infection can be used evaluate vaccines, only strain (35000HP) has been characterized this model. As prelude...
Abstract Objective To provide an open-source software package for determining temporal correlations between disease states using longitudinal electronic medical records (EMR). Materials and Methods We have developed R-based package, Disease Correlation Network (DCN), which builds retrospective matched cohorts from to assess significant diseases two independent methodologies: Cox proportional hazards regression random forest survival analysis. This optimizable has the potential control...