A5009910958- Genomics and Phylogenetic Studies
- Probiotics and Fermented Foods
- Salmonella and Campylobacter epidemiology
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Legume Nitrogen Fixing Symbiosis
- Viral gastroenteritis research and epidemiology
- Vibrio bacteria research studies
- Identification and Quantification in Food
- Escherichia coli research studies
- Plant nutrient uptake and metabolism
- Listeria monocytogenes in Food Safety
- Plant-Microbe Interactions and Immunity
- Enterobacteriaceae and Cronobacter Research
- Enzyme Production and Characterization
- Genetic diversity and population structure
- Microbial Community Ecology and Physiology
- Antibiotic Resistance in Bacteria
- Infant Nutrition and Health
- Plant Pathogens and Resistance
- Trace Elements in Health
- Child Nutrition and Water Access
- Zoonotic diseases and public health
- Bacterial Identification and Susceptibility Testing
- Bartonella species infections research
University of California, Davis
2016-2024
Monsanto (United States)
2003
Many bacterial genomes are highly variable but nonetheless typically published as a single assembled genome. Experiments tracking genome evolution have not looked at the variation present given point in time. Here, we analyzed mouse-passaged
Complex glycans cover the gut epithelial surface to protect cell from environment. Invasive pathogens must breach glycan layer before initiating infection. While degradation is crucial for infection, this process inadequately understood. Salmonella contains 47 glycosyl hydrolases (GHs) that may degrade glycan. We hypothesized keystone genes entire GH complement of are required change This study determined GHs recognize terminal monosaccharides (N-acetylneuraminic acid (Neu5Ac), galactose,...
Campylobacter is the leading cause of human gastroenteritis worldwide. Wild birds, including American crows, are abundant in urban, suburban, and agricultural settings likely zoonotic vectors Their proximity to humans livestock increases potential spreading via crows between environment, livestock, humans. However, no studies have definitively demonstrated that a vector for pathogenic We used genomics evaluate from other animals with 184 isolates obtained chickens, cows, sheep, goats,...
Abstract Here we propose that using shotgun sequencing to examine food leads accurate authentication of ingredients and detection contaminants. To demonstrate this, developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed resolve the relative composition mixtures eukaryotic species RNA or DNA sequencing. Our comprehensive database includes >6000 plants animals may be present in food. accurately identified with 0.4% median absolute difference between...
In this work, we hypothesized that shifts in the food microbiome can be used as an indicator of unexpected contaminants or environmental changes. To test hypothesis, sequenced total RNA 31 high protein powder (HPP) samples poultry meal pet ingredients. We developed a analysis pipeline employing key eukaryotic matrix filtering step improved microbe detection specificity to >99.96% during silico validation. The identified 119 microbial genera per HPP sample on average with 65 present all...
A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from atmosphere and develops an extensive network mucilage-secreting aerial roots that harbors a diazotrophic (N2-fixing) microbiota. Targeting these diazotrophs, we selected nearly 600 microbes collection obtained mucilage confirmed their ability to incorporate heavy (15N2) metabolites vitro. Sequencing genomes...
Prebiotic oligosaccharides are used to modulate enteric pathogens and reduce pathogen shedding. The interactions with prebiotics that alter Listeria monocytogenes infection not yet clearly delineated. L. cellular invasion requires a concerted manipulation of host epithelial cell membrane receptors initiate internalization often via receptor glycosylation. Bacterial glycans intimately involved in modulating responses through signaling cascades at the intracellular compartments. Characterizing...
Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived the atmosphere via an undefined fixation mechanism. The diazotrophic microbiota associated with plant’s mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable biological (BNF) without containing any proposed essential genes for this trait (nifHDKENB). To determine in Lactococcus phenotype,...
The rising prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales is a significant threat to animal and human health. This study aims describe the clinical features, antimicrobial susceptibility patterns, genotypic features infections associated with ESBL-producing in dogs cats seen at tertiary referral veterinary teaching hospital. isolated from that underwent ESBL testing during period were identified using search hospital test software database. Medical records...
is the most common cause of seafood-borne illness reported in United States. The draft genomes 132 North American clinical and oyster
Campylobacter is a food-associated bacterium and leading cause of foodborne illness worldwide, being associated with poultry in the food supply. This initial public release 202 genome sequences as part 100K Pathogen Genome Project. These isolates represent global genomic diversity genus.
Sialidases, which are widely distributed in nature, cleave the α-ketosidic bond of terminal sialic acid residue. These emerging virulence factors degrade host glycan. We report here release seven sialidase and one transporter deletion Salmonella enterica serovar Typhimurium strain LT2, important cellular invasion during infection.
Salmonella is a common food-associated bacterium that has substantial impact on worldwide human health and the global economy. This public release of 1,183 draft genome sequences as part 100K Pathogen Genome Project. These isolates represent genomic diversity in genus.
ABSTRACT Campylobacter jejuni is an intestinal bacterium that can cause abortion in livestock. This publication announces the public release of 15 genome sequences from isolates linked to These are part 100K Pathogen Genome Project and clinical cases at University California (UC) Davis.
Hungatella hathewayi has been observed to be a member of the gut microbiome. Unfortunately, little is known about this organism in spite being associated with human fatalities; it important understand virulence mechanisms and epidemiological prospective cause disease. In study, patient chronic neurologic symptoms presented clinic subsequent isolation strain phenotypic characteristics suggestive Clostridium difficile. However, whole-genome sequence found H. hathewayi. Analysis including...
Rodents and bats are the most diverse mammal group that host Bartonella species. In Americas, they were described as harboring species; however, mostly characterized to genotypic level. We describe here isolates obtained from blood samples of one rodent (Peromyscus yucatanicus San José Pibtuch, Yucatan) two bat species (Desmodus rotundus Progreso, Pteronotus parnellii Chamela-Cuitzmala) Mexico. sequenced genomic features three strains performed phylogenomic pangenome analyses decipher their...
Food-producing animals such as dairy cattle are potential reservoirs of antimicrobial resistance (AMR), with multidrug-resistant (MDR) organisms
Abstract A geographically isolated maize landrace cultivated on nitrogen-depleted fields without synthetic fertilizer in the Sierra Mixe region of Oaxaca, Mexico utilizes nitrogen derived from atmosphere and develops an extensive network mucilage-secreting aerial roots that harbors a diazotrophic microbiota. Targeting these diazotrophs, we selected nearly 600 microbes collection plants confirmed their ability to incorporate heavy ( 15 N 2 ) metabolites vitro . Sequencing genomes conducting...
ABSTRACT Listeria monocytogenes is a food-associated bacterium that responsible for food-related illnesses worldwide. This the initial public release of 306 L. genome sequences as part 100K Pathogen Genome Project. These isolates represent global genomic diversity in .
Malnourishment is a risk factor for childhood mortality, jeopardizing the health of children by aggravating pneumonia/acute respiratory infections and diarrheal diseases. causes morphophysiological changes resulting in stunting wasting that have long-lasting consequences such as cognitive deficit metabolic dysfunction. Using pig model malnutrition, interplay between phenotypic data displayed malnourished animals, gene expression pattern along intestinal tract, microbiota composition...
ABSTRACT Campylobacter jejuni is an enteric bacterium that can cause abortion in livestock. This the release of a multidrug-resistant genome from isolate caused cow northern California. part 100K Pathogen Genome Project.