A5015540039- Gut microbiota and health
- Tuberculosis Research and Epidemiology
- Asthma and respiratory diseases
- Ruminant Nutrition and Digestive Physiology
- Clostridium difficile and Clostridium perfringens research
- IL-33, ST2, and ILC Pathways
- Mycobacterium research and diagnosis
- Immune Cell Function and Interaction
- Probiotics and Fermented Foods
- interferon and immune responses
- Immune responses and vaccinations
- Cytokine Signaling Pathways and Interactions
- Pediatric health and respiratory diseases
- Immune cells in cancer
- Neuroendocrine regulation and behavior
- Genetics, Bioinformatics, and Biomedical Research
- Diet and metabolism studies
- Bat Biology and Ecology Studies
- Nutritional Studies and Diet
- Chronic Obstructive Pulmonary Disease (COPD) Research
- Anaerobic Digestion and Biogas Production
- HIV Research and Treatment
- Immunodeficiency and Autoimmune Disorders
- Stress Responses and Cortisol
- Biomedical and Engineering Education
University of Washington
2020-2025
Seattle University
2025
University of Idaho
2024
ENT and Allergy
2023
University of British Columbia
2017-2021
University of Wisconsin–Madison
2013-2019
Alzheimer's disease (AD) is the most common form of dementia. However, etiopathogenesis this devastating not fully understood. Recent studies in rodents suggest that alterations gut microbiome may contribute to amyloid deposition, yet microbial communities associated with AD have been characterized humans. Towards end, we bacterial taxonomic composition fecal samples from participants and without a diagnosis dementia due AD. Our analyses revealed has decreased diversity compositionally...
Abstract Social relationships shape human health and mortality via behavioral, psychosocial, physiological mechanisms, including inflammatory immune responses. Though not tested in studies, recent primate studies indicate that the gut microbiome may also be a biological mechanism linking to health. Integrating microbiota data into 60-year-old Wisconsin Longitudinal Study, we found socialness with family friends is associated differences fecal microbiota. Analysis of spouse (N = 94) sibling...
Abstract Development of the dairy calf gastrointestinal tract (GIT) and its associated microbiota are essential for survival milk production, as this community is responsible converting plant-based feeds into accessible nutrients. However, little known regarding establishment microbes in GIT. Here, we measured fecal-associated bacterial, archaeal, fungal communities cows from 2 weeks to middle first lactation (>2 years) well rumen-associated weaning (8 weeks) lactation. These were then...
Microbial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about establishment microbial calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes bacterial rumen, jejunum, cecum, colon 26 crossbred at four developmental stages (7, 28, 49, 63 days old). Alpha diversity differed among regions with lowest evenness whereas no alpha...
The gut microbiota is essential for the survival of many organisms, including ruminants that rely on microorganisms nutrient acquisition from dietary inputs production products such as milk and meat. While alteration adult ruminant to improve possible, changes are often unstable fail persist. In contrast, early-life may be more amenable sustained modification. However, few studies have determined impact interventions downstream production. Here, we investigated agriculturally relevant calf...
At birth, calves display an underdeveloped rumen that eventually matures into a fully functional as result of solid food intake and microbial activity. However, little is known regarding the gradual impact pre-weaning diet on establishment microbiota. Here, we employed next-generation sequencing to investigate effects inclusion starter concentrate (M: milk-fed vs. MC: milk plus fed) archaeal, bacterial anaerobic fungal communities in rumens 45 crossbred dairy across development (7, 28, 49,...
Abstract The gut microbiota plays important roles in animal nutrition and health. This relationship is particularly dynamic hibernating mammals where fasting drives the community to rely on host‐derived nutrients instead of exogenous substrates. We used 16S rRNA pyrosequencing caecal tissue protein analysis investigate effects hibernation mucosa‐associated bacterial host responses 13‐lined ground squirrels. mucosal was less diverse winter hibernators than actively feeding spring summer...
Symbiotic microbial communities are critical to the function and survival of animals. This relationship is obligatory for herbivores that engage gut microorganisms conversion dietary plant materials into nutrients such as short-chain organic acids (SCOAs). The constraint on body size imposed by their arboreal lifestyle thought make this symbiosis especially important sloths. Here, we use next-generation sequencing identify bacteria present in fore distal guts wild two- three-toed sloths,...
The identification of differentially expressed genes (DEGs) from transcriptomic datasets is a major avenue research across diverse disciplines. However, current bioinformatic tools do not support covariance matrices in DEG modeling. Here, we introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling including covariates, weights, random effects, matrices, and fit metrics.
Although genetic factors contribute to tuberculosis (TB) risk, no cross-population causal variants have been identified by genome-wide association studies (GWAS). Here, we utilized low-pass whole genome sequencing (lpWGS) with imputation plus detailed epidemiologic risk and single-cell expression quantitative loci (sceQTL) address prior GWAS limitations. Using 947 pulmonary (PTB) cases 1807 close contact controls in the Regional Prospective Observational Research TB (RePORT) study Brazil,...
Perturbations in the gastrointestinal microbiome caused by antibiotics are a major risk factor for Clostridium difficile infection (CDI). Probiotics often recommended to mitigate CDI symptoms; however, there exists only limited evidence showing probiotic efficacy CDI. Here, we examined changes GI microbiota study population where treatment was associated with significantly reduced duration of diarrhea. Subjects being treated standard care primary episode were randomized or placebo 4 weeks....
Abstract Prolonged diffuse laryngeal inflammation from smoking and/or reflux is commonly diagnosed as chronic laryngitis and treated empirically with expensive drugs that have not proven effective. Shifts in microbiota been associated many inflammatory diseases, though little known about how resident microbes may contribute to laryngitis. We sought characterize the core of disease-free human tissue investigate shifts microbial community membership exposure cigarette smoke reflux. Using 454...
Dietary shifts can result in changes to the gastrointestinal tract (GIT) microbiota, leading negative outcomes for host, including inflammation. Giant pandas (Ailuropoda melanoleuca) are physiologically classified as carnivores; however, they consume an herbivorous diet with dramatic seasonal dietary and episodes of chronic GIT distress symptoms abdominal pain, loss appetite excretion mucous stools (mucoids). These adversely affect overall nutritional health status giant pandas. Here, we...
After heavy M. tuberculosis exposure, the events that determine why some individuals resist TST/IGRA conversion are poorly defined. Enrichment of TNF signaling gene set among RSTR monocytes from multiple distinct cohorts suggests an important role for monocyte response in determining this alternative immune outcome.
Heifers emit more enteric methane (CH4 ) than adult cows and these emissions tend to decrease per unit feed intake as they age. However, common mitigation strategies like expensive high-quality feeds are not economically feasible for pre-production animals. Given its direct role in CH4 production, altering the rumen microbiota is another potential avenue reducing production by ruminants. identify effective microbial targets, a better understanding of relationship across heifer development...
(Mtb) exposure leads to a range of outcomes including clearance, latent TB infection (LTBI), and pulmonary tuberculosis (TB). Some heavily exposed individuals resist tuberculin skin test (TST) interferon-gamma (IFNγ) release assay (IGRA) conversion (RSTR), which suggests that they employ IFNγ-independent mechanisms Mtb control. Here, we compare monocyte epigenetic profiles RSTR LTBI from Ugandan household contact cohort. Chromatin accessibility did not differ between uninfected monocytes. By...
Genome-wide association studies have identified SH2B3 as an important non-MHC gene for islet autoimmunity and type 1 diabetes (T1D). In this study, we found a single haplotype significantly associated with increased risk human T1D. Fine mapping has demonstrated the most credible causative variant is nucleotide rs3184504*T polymorphism in SH2B3. To better characterize role of T1D, used mouse modeling T cellintrinsic regulating peripheral tolerance. deficiency had minimal effect on TCR...
<p dir="ltr">Genome-wide association studies have identified <i>SH2B3 </i>as an important non-MHC gene for islet autoimmunity and type 1 diabetes (T1D). In this study, we found a single <i>SH2B3</i> haplotype significantly associated with increased risk human T1D. Fine mapping has demonstrated the most credible causative variant is nucleotide rs3184504*T polymorphism in <i>SH2B3</i><i>.</i> To better characterize role of SH2B3 T1D, used...
<p dir="ltr">Genome-wide association studies have identified <i>SH2B3 </i>as an important non-MHC gene for islet autoimmunity and type 1 diabetes (T1D). In this study, we found a single <i>SH2B3</i> haplotype significantly associated with increased risk human T1D. Fine mapping has demonstrated the most credible causative variant is nucleotide rs3184504*T polymorphism in <i>SH2B3</i><i>.</i> To better characterize role of SH2B3 T1D, used...
ABSTRACT Macrophages serve as important sites of bacterial replication and host immune response during Mycobacterium tuberculosis (Mtb) infection with distinct roles for alveolar macrophages (AMs) early in monocyte-derived (MDMs) later stages disease. Here, we leverage data from human mouse models to perform a cross-species analysis macrophage responses Mtb infection. Overall, find that both subsets murine mount strong interferon However, AM across species do not generate pro-inflammatory...