A5066967353- Gut microbiota and health
- Clostridium difficile and Clostridium perfringens research
- Diet and metabolism studies
- Inflammatory Bowel Disease
- Microscopic Colitis
- Gastrointestinal motility and disorders
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Helicobacter pylori-related gastroenterology studies
- Immune Cell Function and Interaction
- Infant Nutrition and Health
- IL-33, ST2, and ILC Pathways
- Mycobacterium research and diagnosis
- Oral microbiology and periodontitis research
- Genomics and Phylogenetic Studies
- Metabolomics and Mass Spectrometry Studies
- Respiratory Support and Mechanisms
- Pediatric health and respiratory diseases
- Viral gastroenteritis research and epidemiology
- Diverticular Disease and Complications
- Tryptophan and brain disorders
- Eosinophilic Esophagitis
- Soybean genetics and cultivation
- Advanced Chemical Physics Studies
- Dermatology and Skin Diseases
University of Pennsylvania
2016-2025
Children's Hospital of Philadelphia
2017-2025
California University of Pennsylvania
2019-2024
Rush University
2023
Intercept Pharmaceuticals (United States)
2023
The Wistar Institute
2023
Cornell University
2023
Rush University Medical Center
2023
Philadelphia University
2019-2020
Biology of Infection
2019
Diet strongly affects human health, partly by modulating gut microbiome composition. We used diet inventories and 16S rDNA sequencing to characterize fecal samples from 98 individuals. Fecal communities clustered into enterotypes distinguished primarily levels of Bacteroides Prevotella. Enterotypes were associated with long-term diets, particularly protein animal fat (Bacteroides) versus carbohydrates (Prevotella). A controlled-feeding study 10 subjects showed that composition changed...
Abstract Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of original implementation, it has not been as widely adopted possible. Python (PyNAST) a complete reimplementation NAST, which includes three convenient interfaces: Mac OS X GUI, command-line interface and simple application programming (API). Results: availability PyNAST will make popular NAST algorithm more...
Data from 16S ribosomal RNA (rRNA) amplicon sequencing present challenges to ecological and statistical interpretation. In particular, library sizes often vary over several ranges of magnitude, the data contains many zeros. Although we are typically interested in comparing relative abundance taxa ecosystem two or more groups, can only measure taxon specimens obtained ecosystems. Because comparison specimen is not equivalent ecosystems, this presents a special challenge. Second, because (as...
Defining the biogeography of bacterial populations in human body habitats is a high priority for understanding microbial-host relationships health and disease. The healthy lung was traditionally considered sterile, but this notion has been challenged by emerging molecular approaches that enable comprehensive examination microbial communities. However, studies are challenging due to difficulties working with low biomass samples.Our goal use methods define microbiota present lungs individuals...
Abstract Motivation: The human microbiome plays an important role in disease and health. Identification of factors that affect the composition can provide insights into mechanism as well suggest ways to modulate for therapeutical purposes. Distance-based statistical tests have been applied test association with environmental or biological covariates. unweighted weighted UniFrac distances are most widely used distance measures. However, these two measures assign too much weight either rare...
<h3>Importance</h3> Establishment of the infant microbiome has lifelong implications on health and immunity. Gut microbiota breastfed compared with nonbreastfed individuals differ during infancy as well into adulthood. Breast milk contains a diverse population bacteria, but little is known about vertical transfer bacteria from mother to by breastfeeding. <h3>Objective</h3> To determine association between maternal breast areolar skin gut bacterial communities. <h3>Design, Setting,...
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the research ecosystem, from scientists and engineers clinicians policy makers. 2 provides new features that will drive next generation of research. These include interactive spatial temporal analysis visualization tools, support for metabolomics shotgun metagenomics analysis, automated provenance tracking ensure reproducible, transparent science.
Recent studies have suggested that bacteria associated with the placenta—a "placental microbiome"—may be important in reproductive health and disease. However, a challenge working specimens low bacterial biomass, such as placental samples, is some or all of DNA may derive from contamination dust commercial reagents. To investigate this, we compared samples healthy deliveries to matched set controls, well oral vaginal same women. We quantified total 16S rRNA gene copies using quantitative PCR...
<h3>Objective</h3> The consumption of an agrarian diet is associated with a reduced risk for many diseases 'Westernised' lifestyle. Studies suggest that affects the gut microbiota, which subsequently influences metabolome, thereby connecting diet, microbiota and health. However, degree to composition controversial. Murine models studies comparing in humans residing versus Western societies influence large. To separate global environmental from dietary influences, we characterised host...
Cigarette smokers have an increased risk of infectious diseases involving the respiratory tract. Some effects smoking on specific tract bacteria been described, but consequences for global airway microbial community composition not determined. Here, we used culture-independent high-density sequencing to analyze microbiota from right and left nasopharynx oropharynx 29 33 nonsmoking healthy asymptomatic adults assess cigarette smoking. Bacterial communities were profiled using 454...
Intense interest centers on the role of human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study surveying bacterial communities feces using 454/Roche pyrosequencing 16S rRNA gene tags. We analyzed fecal samples from 10 individuals compared storage, DNA purification sequence acquisition. To assess reproducibility, one cm apart single stool specimen each individual. analyze storage methods, 1) immediate freezing at...
Abstract Motivation: The variation in community composition between microbiome samples, termed beta diversity, can be measured by pairwise distance based on either presence–absence or quantitative species abundance data. PERMANOVA, a permutation-based extension of multivariate analysis variance to matrix distances, partitions within-group and between-group distances permit assessment the effect an exposure intervention (grouping factor) upon sampled microbiome. Within-group...
Rationale: Long-term survival after lung transplantation is limited by infectious complications and bronchiolitis obliterans syndrome (BOS), a form of chronic rejection linked in part to microbial triggers.Objectives: To define populations the respiratory tract transplant patients comprehensively using unbiased high-density sequencing.Methods: Lung was sampled bronchoalveolar lavage (BAL) upper oropharyngeal wash (OW). Bacterial 16S rDNA fungal internal transcribed spacer sequencing used...
The mammalian intestine is colonized by beneficial commensal bacteria and a site of infection pathogens, including helminth parasites. Helminths induce potent immunomodulatory effects, but whether these effects are mediated direct regulation host immunity or indirectly through eliciting changes in the microbiota unknown. We tested this context virus-helminth coinfection. Helminth coinfection resulted impaired antiviral was associated with STAT6-dependent helminth-induced alternative...
Historically, the human womb has been thought to be sterile in healthy pregnancies, but this idea challenged by recent studies using DNA sequence-based methods, which have suggested that is colonized with bacteria. For example, analysis of from placenta samples yielded small proportions microbial sequences were proposed represent normal bacterial colonization. However, an our group showed no distinction between background negative controls and samples. Also supporting observation germ-free...