A5063983490- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Microbial Community Ecology and Physiology
- Cancer Immunotherapy and Biomarkers
- Clostridium difficile and Clostridium perfringens research
- Legume Nitrogen Fixing Symbiosis
- Immune Cell Function and Interaction
- Tryptophan and brain disorders
- Cervical Cancer and HPV Research
- Liver Disease Diagnosis and Treatment
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
- Liver physiology and pathology
- Immune cells in cancer
- Nematode management and characterization studies
- Soybean genetics and cultivation
- Diet and metabolism studies
- Immunotherapy and Immune Responses
- Hops Chemistry and Applications
- Bioenergy crop production and management
- Drug Transport and Resistance Mechanisms
- Dietary Effects on Health
- CAR-T cell therapy research
- Gene Regulatory Network Analysis
- Plant-Microbe Interactions and Immunity
Oregon State University
2017-2024
National Cancer Institute
2021-2024
Center for Cancer Research
2021-2024
Frederick National Laboratory for Cancer Research
2021-2024
National Institutes of Health
2022-2024
Government of the United States of America
2024
Leidos Biomedical Research Inc. (United States)
2022
Leidos (United States)
2021-2022
National Cancer Institute
2022
Virginia Tech
2013-2019
Anti-programmed cell death protein 1 (PD-1) therapy provides long-term clinical benefits to patients with advanced melanoma. The composition of the gut microbiota correlates anti-PD-1 efficacy in preclinical models and cancer patients. To investigate whether resistance can be overcome by changing microbiota, this trial evaluated safety responder-derived fecal transplantation (FMT) together PD-1-refractory This combination was well tolerated, provided benefit 6 15 patients, induced rapid...
Gut bacteria modulate the response to immune checkpoint blockade (ICB) treatment in cancer, but effect of diet and supplements on this interaction is not well studied. We assessed fecal microbiota profiles, dietary habits, commercially available probiotic supplement use melanoma patients performed parallel preclinical studies. Higher fiber was associated with significantly improved progression-free survival 128 ICB, most pronounced benefit observed sufficient intake no use. Findings were...
Honey bees (Apis mellifera) are the primary pollinators of major horticultural crops. Over last few decades, a substantial decline in honey and their colonies have been reported. While plethora factors could contribute to putative decline, pathogens, pesticides common concerns that draw attention. In addition potential direct effects on bees, indirect pesticide include alteration essential gut microbial communities symbionts important bee health (e.g., immune system). The objective this...
Abstract Western diet (WD) is one of the major culprits metabolic disease including type 2 diabetes (T2D) with gut microbiota playing an important role in modulating effects diet. Herein, we use a data-driven approach (Transkingdom Network analysis) to model host-microbiome interactions under WD infer which members contribute altered host metabolism. Interrogation this network pointed taxa potential beneficial or harmful on host’s We then validate functional predicted bacteria regulating...
A role for vitamin D in immune modulation and cancer has been suggested. In this work, we report that mice with increased availability of display greater immune-dependent resistance to transplantable cancers augmented responses checkpoint blockade immunotherapies. Similarly, humans, D-induced genes correlate improved inhibitor treatment as well immunity overall survival. mice, is attributable the activity on intestinal epithelial cells, which alters microbiome composition favor
The gut microbiome plays an important role in health and disease. Antibiotics are known to alter microbiota, yet their effects on glucose tolerance lean, normoglycemic mice have not been widely investigated. In this study, we aimed explore mechanisms by which treatment of lean with antibiotics (ampicillin, metronidazole, neomycin, vancomycin, or cocktail) influences the metabolism. Specifically, sought to: (i) study body weight, fasting glucose, tolerance, insulin, (ii) examine changes...
Gut-resident CX3CR1 hi macrophages drive formation of tertiary lymphoid structures that initiate IgA responses to Salmonella infection.
The importance of plant-microbe associations for the invasion plant species have not been often tested under field conditions. research sought to determine patterns change in microbial communities associated with establishment invasive plants different taxonomic and phenetic traits. Three independent locations Virginia, USA were selected. One site was invaded by a grass (Microstegium vimineum), another shrub (Rhamnus davurica), third tree (Ailanthus altissima). native vegetation from these...
Soybean (Glycine max) and other legumes are key crops grown around the world, providing protein nutrients to a growing population, in way that is more sustainable than most cropping systems. Diazotrophs inhabiting root nodules provide soybean with nitrogen required for growth. Despite knowledge of culturable Bradyrhizobium spp. how they can differ across cultivars, less known about overall bacterial community (bacteriome) diversity within nodules, situ. This variability could have large...
Microbiota contribute to the induction of type 2 diabetes by high-fat/high-sugar (HFHS) diet, but which organs/pathways are impacted microbiota remain unknown. Using multiorgan network and transkingdom analyses, we found that microbiota-dependent impairment OXPHOS/mitochondria in white adipose tissue (WAT) plays a primary role regulating systemic glucose metabolism. The follow-up analysis established Mmp12+ macrophages link inflammation OXPHOS damage WAT. Moreover, molecular signature WAT...
Intratumoral TLR9 agonists and anti-PD-1 produce clinical responses broad immune activation. We conducted a single-arm study of neoadjuvant agonist vidutolimod combined with nivolumab in high-risk resectable melanoma. In 31 evaluable patients, 55% major pathologic response (MPR) was observed, meeting primary endpoint. MPR associated necrosis, melanophagocytosis increased CD8
Two hydrogenated xanthohumol (XN) derivatives, α,β-dihydro-XN (DXN) and tetrahydro-XN (TXN), improved parameters of metabolic syndrome (MetS), a critical risk factor cardiovascular disease (CVD) type 2 diabetes, in diet-induced obese murine model. It is hypothesized that improvements obesity MetS are linked to changes composition the gut microbiota, bile acid metabolism, intestinal barrier function, inflammation.To test this hypothesis, 16S rRNA genes were sequenced acids measured fecal...
The design of in vitro models that mimic the stratified multicellular hepatic microenvironment continues to be challenging. Although several cultures have been shown exhibit liver functions, their physiological relevance is limited due significant deviation from vivo cellular composition. We report assembly a novel three-dimensional (3D) organotypic model incorporating three different cell types (hepatocytes, sinusoidal endothelial cells, and Kupffer cells) polymeric interface mimics Space...
Abstract Nitrogen (N) bioavailability is a primary limiting nutrient for crop and feedstock productivity. Associative nitrogen fixation ( ANF ) by diazotrophic bacteria in root‐zone soil microbial communities have been shown to provide significant amounts of N some tropical grasses, but this potential switchgrass, warm‐season, temperate, US native, perennial tallgrass has not widely studied. ‘Alamo’ ‘Dacotah’ are cultivars adapted the southern northern regions United States, respectively,...
Cervical cancer is the fourth most common in women worldwide with human papillomavirus (HPV) being main cause disease. Chromosomal amplifications have been identified as a source of upregulation for cervical driver genes but cannot fully explain increased expression immune invasive carcinoma. Insight into additional factors that may tip balance from tolerance HPV to elimination virus lead better diagnosis markers. We investigated whether microbiota affect molecular pathways carcinogenesis by...
Microbial diversity on earth is extraordinary, and soils alone harbor thousands of species per gram soil. Understanding how this sorted selected into habitat niches a major focus ecology biotechnology, but remains only vaguely understood. A systems-biology approach was used to mine information from databases show it can be answer questions related the core microbiome habitat-microbe relationships. By making use burgeoning growth databases, our tool “COREMIC” meets great need in search for...
Abstract Shotgun microbiome sequencing analysis presents several challenges to accurately and consistently depict sample composition functional potential. Here we present a two-part framework – JAMS (Just Microbiology System) whereby with raw fastq files metadata as input, meaningful within between can be performed ease for either shotgun or 16S sequences. is the first package provide seamless deconvolution of functions into their taxonomic contributors. We validated our on two human gut...
Top-down analyses in systems biology can automatically find correlations among genes and proteins large-scale datasets. However, it is often difficult to design experiments from these results. In contrast, bottom-up approaches painstakingly craft detailed models that be simulated computationally suggest wet lab experiments. developing the a manual process take many years. These have largely been developed independently. We present Linker, an efficient automated data-driven method analyze...