A5072661846- Ruminant Nutrition and Digestive Physiology
- Gut microbiota and health
- Milk Quality and Mastitis in Dairy Cows
- Asthma and respiratory diseases
- Plant and fungal interactions
- Genetic and phenotypic traits in livestock
- Reproductive Physiology in Livestock
- Gene expression and cancer classification
- Microbial Metabolic Engineering and Bioproduction
- Effects of Environmental Stressors on Livestock
- Wheat and Barley Genetics and Pathology
- Anaerobic Digestion and Biogas Production
- Genetics, Bioinformatics, and Biomedical Research
- Clostridium difficile and Clostridium perfringens research
- Bioinformatics and Genomic Networks
- Cancer-related molecular mechanisms research
- French Urban and Social Studies
- Soil Carbon and Nitrogen Dynamics
- Crustacean biology and ecology
- Biofuel production and bioconversion
- Microbial Community Ecology and Physiology
- Single-cell and spatial transcriptomics
- Animal health and immunology
- Cancer Genomics and Diagnostics
- Infant Nutrition and Health
University of Washington
2022-2025
University of Wisconsin–Madison
2016-2024
Crop rotation, the successive cultivation of different crops on same field, has been practiced for centuries, and it is often associated with increased crop yields. Cover cropping a less ubiquitous farming practice that also increases plant biodiversity over time. are soil conservation tool; they grown between harvest planting main to protect enrich soil. Increasing diversity rotation cover may contribute shifts in bacterial communities. Our first objective was investigate communities...
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.
Early gut microbial colonization is important for postnatal metabolic and immune development. However, little known about the effects of different feeding modes (suckling versus bottle-feeding) or sources on this process in farm animals. We found that suckled bottle-fed newborn lambs had their own distinct microbiota. Results from 16S rRNA gene sequencing qPCR showed that, compared with suckling, bottle significantly increased abundances Escherichia/Shigella, Butyricicoccus, Clostridium...
Asthma has striking disparities across ancestral groups, but the molecular underpinning of these differences is poorly understood and minimally studied. A goal Consortium on among African-ancestry Populations in Americas (CAAPA) to understand multi-omic signatures asthma focusing populations African ancestry. RNASeq DNA methylation data are generated from nasal epithelium including cases (current asthma, N = 253) controls (never-asthma, 283) 7 different geographic sites identify...
Abstract Understanding the mechanisms of early clearance Mycobacterium tuberculosis (Mtb) may illuminate new therapeutic strategies for (TB). We previously found genetic, epigenetic, and transcriptomic signatures associated with resistance (resister, RSTR) to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion among highly exposed TB contacts. hypothesized that integration these datasets multi-omic latent factor methods would detect pathways differentiating RSTR...
A major goal for the dairy industry is to improve overall milk production efficiency (MPE). With advent of next-generation sequencing and advanced methods characterizing microbial communities, efforts are underway MPE by manipulating rumen microbiome. Our previous work demonstrated that a near-total exchange whole contents between pairs lactating Holstein cows disparate resulted in reversal status ∼10 days: historically high-efficiency decreased MPE, low-efficiency increased MPE....
Abstract In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported importance early gut inhabitants on host health. However, few attempts been undertaken to directly interrogate role gut/rumen GIT development or health in neonatal ruminants through artificial manipulation rumen microbiome. Thus, molecular changes associated with are largely unknown cattle. this study, we dosed young...
Analysis of the cow microbiome, as well host genetic influences on establishment and colonization rumen microbiota, is critical for development strategies to manipulate ruminal function toward more efficient environmentally friendly milk production. To this end, validation noninvasive methods sample microbiota at a large scale are required. In study, we further optimized analysis buccal swab samples proxy direct bacterial dairy cows. identify an optimal time sampling, collected six different...
The objectives of this study were to determine if milk production efficiency (MPE) could be altered by near-total exchange ruminal contents between high- and low-MPE cows characterize bacterial community composition (BCC) before over time post-exchange. Three pairs ruminally cannulated, third-lactation selected whose MPE (energy corrected per unit dry matter intake [ECM/DMI]) at similar levels ECM differed their first two lactations when fed the same total mixed ration. At 79–279 DIM, ∼95%...
Development of a properly functioning gastrointestinal tract (GIT) at an early age is critical for the wellbeing and lifetime productivity dairy cattle. The role microbial colonization on GIT development in neonatal cattle associated molecular changes remain largely unknown, particularly small intestine. In this study, we performed artificial dosing exogenous rumen fluid during life calf, starting birth through weaning transition 8 wk. Six calves were included study. At wk age, tissue from...
This study aimed to investigate the changes in abomasum transcriptome and associated microbial community structure young calves with artificially dosed, adult rumen contents. Eight bull were randomly dosed freshly extracted contents from an cow (high efficiency (HE), n = 4), or sterilized content (Con, 4). The dosing was administered within 3 days of birth, then at 2, 4, 6 weeks following initial dosing. Abomasum tissues collected immediately after sacrifice 8 age. Five genera (Tannerella,...
Using oral swabs to collect the remnants of stomach content regurgitation during rumination in dairy cows can replicate up 70% ruminal bacterial community, offering potential for broad-scale population-based studies on rumen microbiome. The collected from often vary widely with respect sample quality, likely due several factors such as time collection and cow behavior, which may limit ability a given swab accurately represent One factor is color swab, significantly across different cows....
Abstract Understanding the mechanisms of early clearance Mycobacterium tuberculosis (Mtb) may illuminate new therapeutic strategies for (TB). We previously found genetic, epigenetic, and transcriptomic signatures associated with resistance (resister, RSTR) to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion among highly exposed TB contacts. hypothesized that integration these datasets multi-omic latent factor methods would detect pathways differentiating RSTR...
Abstract A major goal in dairy research is to improve milk production efficiency (MPE). With the advent of next-generation sequencing, efforts are underway MPE by manipulating rumen microbiota. correlates ruminal bacterial community composition (BCC), but adult microbiota highly stable and returns a baseline BCC after heavy perturbation. We seek influence early intervention pre-weaning calves. Two cannulated Holstein donors disparate were selected. Three cohorts 6 bull calves established...
Abstract We introduce kimma (Kinship In Mixed Model Analysis), an open-source R package for flexible linear mixed effects modeling of RNA-seq including covariates, weights, random effects, covariance matrices, and fit metrics. simulated datasets, detects differentially expressed genes (DEGs) with similar specificity, sensitivity, computational time as limma unpaired dream paired models. Unlike other software, supports matrices well metrics like AIC. Utilizing genetic kinship covariance,...
The composition of the nasal microbiota in surgical patients context general anesthesia and povidone-iodine decolonization is unknown. purpose this quality improvement study was to determine: (i) if associated with changes surgery (ii) preoperative intranasal patients.One hundred fifty-one ambulatory presenting for were enrolled a by convenience sampling. Pre- post-surgery samples collected from no group (control group, n = 54). Pre-decolonization (povidone-iodine 97). Intranasal...