Bart C Weimer

Bart C Weimer
University of California, Davis | UCD · Department of Population Health and Reproduction (VM)

Ph.D.

About

281
Publications
55,405
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Introduction
Dr. Bart C. Weimer is Professor and Chair in the Department of Population Health & Reproduction UC Davis. He holds degrees from the University of Arizona (BS) and Utah State University (PhD) with post-doctoral training at the University of Melbourne. His group studies food, health and the microbiome using bacterial population genomics, systems biology, population genomics and machine learning. He leads the 100K Pathogen Genome Sequencing Project enabling metagenomic solutions.
Additional affiliations
April 2020 - present
Taylor & Francis
Position
  • Editor
September 2008 - August 2020
University of California, Davis
Position
  • Chair
January 1999 - July 2000
University of Melbourne
Position
  • PostDoc Position

Publications

Publications (281)
Preprint
Less invasive rumen sampling methods such as oro-esophageal probes became widely popular to explore the rumen microbiome and metabolome. However, it remains unclear if such methods represent the rumen contents from fluid and particulate fractions well. Herein, we characterized the microbiome and metabolome in rumen content collected by an oro-esoph...
Article
Full-text available
Liquid dairy manure, which is produced in enormous quantities in flush dairy manure management systems, is commonly used as an alternative to chemical fertilizers. It provides nutrient benefits to crops and soils. While dairy waste is a well-accepted and widely used fertilizer, the presence of indicator organisms and human pathogens in manure may l...
Article
Full-text available
Fermentation of dietary nutrients in ruminants’ gastrointestinal (GI) tract is an essential mechanism utilized to meet daily energy requirements. Especially in lactating dairy cows, the GI microbiome plays a pivotal role in the breakdown of indigestible plant polysaccharides and supply most AAs, fatty acids, and gluconeogenic precursors for milk sy...
Article
Full-text available
Clostridioides difficile is a global public health problem, which is a primary cause of antibiotic-associated diarrhea in humans. The emergence of hypervirulent and antibiotic-resistant strains is associated with the increased incidence and severity of the disease. There are limited studies on genomic characterization of C. difficile in Latin Ameri...
Patent
For each unique pair of a complete set of data items, a computing device determines a distance between the data items of the unique pair. The computing device repeats the following until no data items remain in the complete set. For each data item remaining in the complete set, the computing device determines a similarity subset including each othe...
Article
Full-text available
Background Antibiotic resistance genes (ARGs) are considered to be emerging environmental contaminants of concern potentially posing risks to human and animal health, and this research studied the prevalence of antimicrobial resistance in dairy manure. Methods This study is focused on investigating prevalence of ARGs in California dairy farm manur...
Article
Full-text available
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 this hypothesis, we sequenced the total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic mat...
Article
Full-text available
Hungatella hathewayi has been observed to be a member of the gut microbiome. Unfortunately, little is known about this organism in spite of being associated with human fatalities; it is important to understand virulence mechanisms and epidemiological prospective to cause disease. In this study, a patient with chronic neurologic symptoms presented t...
Article
Full-text available
Microbial symbioses can mitigate drought stress in crops but harnessing these beneficial interactions will require an in-depth understanding of root microbiome responses to drought cycles. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during drought stress and recovery, we find that endosphere communities...
Article
Full-text available
Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for...
Article
Full-text available
Case description: In Latvia in 2014, acquired idiopathic megaesophagus (AIME) was observed in increased numbers of dogs that consumed varieties of 1 brand of dog food. Within 2 years, 253 dogs were affected. In Australia in November 2017, 6 working dogs that consumed 1 diet of another brand of dog food developed AIME. In total, 145 Australian dogs...
Article
Full-text available
The spread of SARS-CoV-2 created a pandemic crisis with > 150,000 cumulative cases in > 65 countries within a few months. The reproductive number (R) is a metric to estimate the transmission of a pathogen during an outbreak. Preliminary published estimates were based on the initial outbreak in China. Whole genome sequences (WGS) analysis found muta...
Article
Full-text available
A Correction to this paper has been published: https://doi.org/10.1038/s41587-021-00898-4.
Article
Ascorbic acid (AA) and uric acid (UA) are known as two of the major antioxidants in biological fluids. We report a novel liquid chromatography–mass spectrometry with time-of-flight (LC-MS-TOF) method for the simultaneous quantification of ascorbic and uric acids using MPA, antioxidant solution and acetonitrile as a protein precipitating agent. Both...
Chapter
LAB contain multiple systems to handle stress conditions in dairy processing. As more genome sequences are produced, additional systems and their regulation are being uncovered. Overlapping stress responses provide protection for multiple stresses. Common regulatory elements lead to broad phenotypic and genotypic changes. The large number of mobile...
Presentation
https://theconversation.com/where-coronavirus-variants-emerge-surges-follow-new-research-suggests-how-genomic-surveillance-can-be-an-early-warning-system-158733
Article
Full-text available
Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant's mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we fou...
Article
Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. Draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest...
Article
Poultry litter is used as soil amendment or organic fertilizer. While poultry litter is enriched with organic matter suitable for land, the presence of pathogens such as Salmonella in poultry litter is a concern. To investigate the effect of gaseous ozone on pathogen reductions in poultry litter, this study conducted a series of experiments that in...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Preprint
Full-text available
As extreme droughts become more frequent, dissecting the responses of root-associated microbiomes to drying-wetting events is essential to understand their influence on plant performance. Here, we show that rhizosphere and endosphere communities associated with drought-stressed rice plants display compartment-specific recovery trends. Rhizosphere m...
Article
Full-text available
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 the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic (N2-fixing) microbiota. Targeting these diazotrophs, w...
Article
Full-text available
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic (N 2-fixing) bacteria isolated...
Preprint
Full-text available
Antibiotic resistance genes (ARGs) are emerging environmental contaminants of concern to both human and animal health. Dairy manure is considered reservoir of ARGs. This study is focused on investigating prevalence of ARGs in California dairy farm manure under current common manure management. A total of 33 manure samples were collected from multip...
Preprint
Full-text available
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 this hypothesis, we sequenced total RNA of 31 high protein powder (HPP) samples of poultry meal pet food ingredients. We developed a microbiome analysis pipeline employing a key eukaryotic matrix...
Preprint
Full-text available
Sierra Mixe maize is a geographically remote landrace variety grown on nitrogen-deficient fields in Oaxaca, Mexico that meets its nutritional requirements without synthetic fertilizer by associating with free-living diazotrophs comprising the microbiota of its aerial root mucilage. We selected nearly 500 diazotrophic bacteria isolated from Sierra M...
Chapter
Full-text available
Genome methylation in bacteria is an area of intense interest because it has broad implications for bacteriophage resistance, replication, genomic diversity via replication fidelity, response to stress, gene expression regulation, and virulence. Increasing interest in bacterial DNA modification is coming about with investigation of host/microbe int...
Preprint
Full-text available
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 the atmosphere and develops an extensive network of mucilage-secreting aerial roots that harbors a diazotrophic microbiota. Targeting these diazotrophs, we selected n...
Article
Full-text available
Animal proteins are essential elements of human and animal feed chain and improving the safety of human and animal feed requires understanding and controlling of the transmission of infectious agents in food chain. Many pathogenic infectious agents, such as prion protein is known to damage the central nervous system in the cattle. Bovine spongiform...
Article
Full-text available
Highly dimensional data generated from bacterial whole-genome sequencing is providing an unprecedented scale of information that requires an appropriate statistical analysis framework to infer biological function from populations of genomes. The application of genome-wide association study (GWAS) methods is an appropriate framework for bacterial po...
Preprint
Full-text available
Background: Global spread of COVID-19 created an unprecedented infectious disease crisis that progressed to a pandemic with >180,000 cases in >100 countries. Reproductive number (R) is an outbreak metric estimating the transmission of a pathogen. Initial R values were published based on the early outbreak in China with limited number of cases with...
Chapter
Lactic acid bacteria (LAB) generate a complex diversity of flavor compounds in dairy systems that deliver positive or negative attributes, depending on their absolute and relative levels in a product and the way in which they are released on consumption. This article provides an overview of the complexity, range, and potential of flavor compound pr...
Article
Full-text available
Here we propose that using shotgun sequencing to examine food leads to accurate authentication of ingredients and detection of contaminants. To demonstrate this, we developed a bioinformatic pipeline, FASER (Food Authentication from SEquencing Reads), designed to resolve the relative composition of mixtures of eukaryotic species using RNA or DNA se...
Preprint
Full-text available
The potential of mesenchymal stem cells (MSCs) for tissue repair and regeneration has garnered great attention. While MSC interaction with microbes at sites of tissue damage and inflammation is likely, especially in the gut, the consequences of bacterial association have yet to be elucidated. This study investigated the effect of Salmonella enteric...
Article
Full-text available
Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into questi...
Preprint
Full-text available
Highly dimensional data generated from bacterial whole genome sequencing is providing unprecedented scale of information that requires appropriate statistical frameworks of analysis to infer biological function from bacterial genomic populations. Application of genome wide association study (GWAS) methods is an emerging approach with bacterial popu...
Poster
Full-text available
RNA viruses are hypermutable. Using reovirus as model system for hypermutable virus evolution and reassortment. Avian reovirus (ARV) in meat type chickens manifests as a plethora of clinical signs ranging from runting and stunting to a severe disease characterized by viral tenosynovitis, pericarditis and myocarditis. The strategy to control the dis...
Poster
Full-text available
Non-jejuni Campylobacter species identification is quite challenging for a diagnostic microbiology laboratory due to suboptimal isolation protocols and lack of differentiating biochemical features. Here we applied whole genome sequencing in an outbreak investigation of a cryptic pathogen Campylobacter hyointestinalis subsp. hyointestinalis in great...
Poster
Full-text available
The goal of the project is to determine novel biomarkers of abortion in ruminants due to Campylobacter jejuni infection using predictive modeling of whole genome sequencing and machine learning. Determining the genomic basis for phenotypes is going to impact infectious disease surveillance, vaccine design and public health. Here we applied a novel...
Preprint
Full-text available
Taxonomic classification is an essential step in the analysis of microbiome data that depends on a reference database of whole genome sequences. Taxonomic classifiers are built on established reference species, such as the Human Microbiome Project database, that is growing rapidly. While constructing a population wide pangenome of the bacterium Hun...
Article
Full-text available
Bacillus velezensis CE2 produces potent antimicrobial compound(s). The draft genome sequence of the strain reported here is 4.1 Mb with a G+C content of 46.1%. Whole-genome sequencing revealed that the strain genetically encodes a novel multicomponent lantibiotic, velezensicidin.
Article
Full-text available
Ontologies are built in various domains such as biology, chemistry, and business. Ontologies as knowledge bases have great potential to serve as providers of context for analytics not only to yield more relevant results but also to provide meaning in explaining results. Simply put, analysis without context ignores the underlying meaning in data. In...
Article
Full-text available
Plants are associated with a complex microbiota that contributes to nutrient acquisition, plant growth, and plant defense. Nitrogen-fixing microbial associations are efficient and well characterized in legumes but are limited in cereals, including maize. We studied an indigenous landrace of maize grown in nitrogen-depleted soils in the Sierra Mixe...
Data
Taxonomic distribution at the family level of the 25 most abundant bacterial families in (A) rRNA gene libraries and (B) whole-genome shotgun libraries. (EPS)
Data
Proportion of nitrogen derived from biological N2 fixation (%Ndfa) in Sierra Mixe maize. Plants grown in Sierra Mixe during 2010 (light gray bars), 2011 (dark grey bars), and 2012 (black bars) were evaluated for %Ndfa; values were calculated using δ15N values in Table 1. Bar = standard error of the mean. %Ndfa, percent of nitrogen derived from the...
Data
δN15 (‰) distribution in root and shoot samples. Data are from a single sampling date (May 2012) in Sierra Mixe maize, with 30 replicates analyzed for each sample reported. (DOCX)
Data
Shoot and root height and diameter measurements for field trials in Sierra Mixe in 2016 and 2017. Numbers followed by different letters are significantly different based on Least Significant difference at p = 0.05. (DOCX)
Data
Soil analyses for samples taken at 0–60 cm before planting for fields in Sierra Mixe, Mexico. (A) Macroelements and soil characteristics. (B) Microelements for fields in 2017. (DOCX)
Data
Heat map showing the hierarchal complete linkage clustering of samples. The heat map depicts the abundances of (A) 1,000 most abundant SVs and (B) 20 most abundant SVs in the dataset that were transformed using variance-stabilizing transformation in DESeq2. The libraries are Mucilage (Blue; OLMC00, OLMD00, OLMV00, OLMX00), Aerial Root (Gray; OLAR00...
Data
Nitrogenase (acetylene reduction) activity in different organs of Sierra Mixe maize. Significant nitrogenase activity was only found on aerial roots with mucilage. (EPS)
Data
Aerial root development in teosinte, Sierra Mixe maize, and a conventional variety, Hickory King grown in the field in Madison, USA. (A) Number of nodes with aerial roots and (B) number of aerial roots observed on teosinte, Sierra Mixe maize, and Hickory King after 14 weeks. Bar = standard error of the mean. Different letters indicate statistically...
Data
Effect of reconstituted mucilage on oxygen diffusion and acetylene reduction. (A) Oxygen measured at 3 depths in Fahraeus medium with (black bars) or without (gray bars) 0.2% agar. (B) Effect of the different sugars present in the mucilage on the ability of H. seropedicae, (C) A. brasilense, and (D) B. unamae to reduce acetylene. (EPS)
Data
Box plot indicating the alpha diversity as calculated by Phyloseq using (A) Simpson index and (B) Shannon index. (EPS)
Data
Reference plants sampled in the Fields 3 and 4 in Sierra Mixe in 2011 and 2012 and summarized in Table 2B. (DOCX)
Data
δ15N (‰) was determined in Sierra Mixe maize, and reference plants sampled from three 10 × 10 m locations were randomly selected from farmers’ fields in Sierra Mixe. From each location, 6 leaf samples were randomly sampled from Sierra Mixe maize plants and 6 leaf samples from each of 2 reference plants. The third emergent leaf of each maize plant w...
Data
Example of two 2D gels for non-reduced (A) and reduced (B) gels used to obtain protein spots for ID. Circled locations show areas that were a combination of bacterial and host proteins. Numbers indicate specific spots that were picked for ID. Comparing those locations between gel (A) and gel (B) indicated that those were cross-linked and released i...
Data
Phylogenetic tree of amino acid sequences alignments of CdpA and its homologs. Phylogenetic tree of amino acid sequence alignments of CdpA, Lba0222, and homologs. Asterisks indicate the proteins identified in cross-linking assay.
Data
Unique cdpA gene neighborhood structure and CdpA protein network analysis. (A) Functional protein network prediction of CdpA and LBA0222. Each unique protein network partner is indicated by a colored sphere. Blue lines joining each sphere indicate predicted partnership by text mining. Green lines joining each sphere indicate predicted partnership b...
Data
LBA0222 and CdpA (LBA0223) protein domain analysis. Dark and light purple arrows indicate operon membership. Domain analyses are listed in the tables below each gene.
Data
PCR primer sequences used in this study.
Article
Full-text available
Bacterial surface ligands mediate interactions with the host cell during association that determines the specific outcome for the host–microbe association. The association begins with receptors on the host cell binding ligands on the microbial cell to form a partnership that initiates responses in both cells. Methods to determine the specific cogna...