Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
132
datasets available to search
ShareScore release 0.9.0
Dataset results
132 results for “Broiler”
Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
<p>Overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg (SH), a model food pathogen, to test if chicks raised antibiotic-free harbor transferable AR. We challenged chicks with an antibiotic susceptible SH strain using various routes of inoculation and determined if SH isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole genome sequencing (WGS) to show that chicks grown without antibiotics harbored antimicrobial resistant SH population 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing we found that SH infection perturbed the microbiota of broiler chicks and used metagenomics and WGS to confirm commensal Escherichia coli population as the main reservoir of IncI1 plasmid acquired by SH. The carriage of this IncI1 plasmid posed no fitness cost to SH but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of SH and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella.</p>
Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species
<p>Coccidiosis caused by the <em>Eimeria</em> species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of <em>Eimeria</em>-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of <em>Eimeria</em> infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after <em>Eimeria</em> infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and <em>Eimeria</em>. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.</p>
Demographics for all four breeds of broiler chickens
<p><span>In 2018, over nine billion chickens were slaughtered in the United States. As the demand for chickens increases, so too have concerns regarding the welfare of the chickens in these systems and the damage such practices cause to the surrounding ecosystems. To address welfare concerns, there is large-scale interest in raising chickens on pasture and switching to slower-growing, higher-welfare breeds as soon as 2024. We created a box model of US chicken demographics to characterize aggregate broiler chicken welfare and land use consequences at the country scale for US shifts to slower-growing chickens, housing with outdoor access, and pasture management. The US produces roughly 20 million metric tons of chicken meat annually. Maintaining this level of consumption entirely with a slower-growing breed would require a 44.6%–86.8% larger population of chickens and a 19.2% – 27.2% higher annual slaughter rate, relative to the current demographics of primarily "Ross 308" chickens that are slaughtered at a rate of 9.25 billion per year. Generating this quantity of slower-growing breeds in conventional concentrated animal feeding operations (CAFO) would require 90,582-98,687 km2, an increase of 19.9-30.6% over the 75,577 km2 of land used for current production of Ross 308. Housing slower-growing breeds on pasture, the more individually welfare-friendly option, would require </span><span>108,642-121,019 km2, a 43.8-60.1% increase over current land use. Allowing slower-growing breeds occasional outdoor access is an intermediate approach that would require 90,691-98,811 km2, an increase of 20-30.7% of the current land use, a very minor increase of land relative to managing slower-growing breeds in CAFOs. In sum, without a drastic reduction in consumption, switching to alternative breeds will lead to a substantial increase in the number of individuals killed each year, an untenable increase in land use, and a possible decrease in aggregate chicken welfare at the country-level scale. Pasture-based management requires substantial additional land use. These results demonstrate constraints and trade-offs in animal welfare, environmental conservation, and food animal consumption, while highlighting opportunities for policies to mitigate impacts in an integrated manner using a One Health approach.</span></p>
Dataset for broiler chicken trial_BW_FPD
<p>Dataset for broiler chicken trial - related to Deliverable 4.3 Report on the effect of feeding alternative proteins on productive traits, physiological indicators, gut health and product quality and safety in chickens and turkeys</p>
The behaviour of commercial broilers in response to a mobile robot - Behavioural dataset
<p>The data files associated with the paper titled 'The behaviour of commercial broilers in response to a mobile robot'.</p> <p> </p>
Supplementary_Gene ontology defines pre-post- hatch energy dynamics in the complexus muscle of broiler chickens
Open the record for dataset details and reuse information.
Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Chinese indigenous chickens constitute world-renowned genetic resources due to their excellent traits, including early puberty, good meat quality, and strong resistance to disease. Unfortunately, the introduction of a large number of commercial chickens in the past two decades has had an adverse effect on Chinese indigenous chickens. Using the chicken 60K single-nucleotide polymorphism (SNP) chip, we assessed the genetic diversity and population structure of 1,187 chickens, representing eight Chinese indigenous chicken breeds, two hybrid chicken breeds, two ancestral chicken breeds, two commercial populations, and additional red jungle fowl. By investigating haplotype similarity, we found extensive gene introgression from commercial broiler to almost all Chinese indigenous chickens. Approximately 15% of the genome, on average, of Chinese indigenous chickens was introgressed, ranging from 0.64% for Tibetan chicken to 21.52% for Huiyang Bearded chicken. Further analysis revealed signals consistent with positive selection in the introgression loci. For the first time, we systematically mapped and quantified introgression from commercial broiler to Chinese indigenous chickens at the whole genome level. Our data provided a usable resource for chicken genetic diversity, and our findings indicated a dire need for protecting the genetic resources of Chinese indigenous chickens.
Inclusion of Black Soldier Fly larvae in broiler chicken diet has a minor effect on caeca microbiota raw data
<p>Raw data to be published. </p>
Survival of Salmonella enterica serovar Heidelberg in pine shavings used as broiler litter
<p>Wood shavings is the most common bedding material used around the world to raise broiler. Therefore, wood shavings can be a vehicle for the transmission of pathogens to live birds. In this study, we performed an in-depth genomic characterization of three <em>Salmonella enterica </em>serovar Heidelberg (<em>S</em>. Heidelberg) strains recovered after their inoculation into fresh pine shaving. The three strains used for the microcosm study were previously isolated from broiler feces (SH-AAFC), broiler carcass (SH-ARS) and chicken thigh (SH-FSIS) and differed one from another by 46 - 94 single nucleotide variants. The SH-AAFC strain harbored an antimicrobial resistant gene (ARG) (<em>bla</em><sub>CMY-2</sub>) on an IncI1 plasmid while the SH-FSIS strain harbored multiple ARGs (<em>floR, cmlA1, tet(A), bla</em><sub>TEM-1B</sub><em>, ant(2'')-Ia, aph(6)-Id, aph(3'')-Ib </em>and<em> sul2</em>) on an IncC plasmid. The SH-ARS isolate was pan susceptible to several antibiotics evaluated. We determined the abundance of <em>Salmonella </em>at days 0, 1, 7, 14 and 21 and performed antibiotic susceptibility testing and whole genome sequencing (on 77 randomly selected <em>S</em>. Heidelberg isolates. After 21 days of incubation, <em>Salmonella </em>abundance decreased by 4.4 logs. <em>Salmonella</em> with high minimum inhibitory concentrations (MICs) against ampicillin showed a significantly higher abundance and survival rate compared to <em>Salmonella</em> with high MIC against gentamicin (<em>P</em>< 0.05). Clonal SH-AAFC was the most prevalent strain in the microcosms (48/77), followed by the strain SH-ARS (25/77). Only 4/77 isolates were determined to be clones of SH-FSIS. We identified recombination events and plasmid copy number changes that were associated with the fitness of <em>S</em>. Heidelberg strain carrying IncI1 and Col plasmids. Lastly, we found that litter physicochemical variables including water activity could explain up to 85% of the variability in our data.</p>
Database fro papers entitled Disease and viruses as negative factor prohibiting the growth of broiler chicken embryo as research topic trend: a bibliometric review
<p>This database of documents used for analysis using bibliometric review were downloaded from Scopus website. The data was used for a published paper in F1000 Research journal with intended title. This data can be downloaded and reproduced for research purpose </p>
Database for publication Costs and benefits of innovations able to reduce the use of Antimicrobials on Pig and Broiler Farms
<p>Database for publication Costs and Benefits of Innovations able to Reduce the Use of Antimicrobials on Pig and Broiler Farms HSOA Journal of Animal Research and Veterinary Science 2023 7:052</p>
Data underlying the publication Development and implementation of a risk assessment tool for broiler farm biosecurity and a health intervention plan in the Netherlands, Greece, and Cyprus
<p>Introduction</p> <p>Preventing pathogens from entering and spreading on farms is the first step in reducing health problems.<br> For this study a BiosEcurity Assessment Tool was developed to identify strengths and weaknesses in biosecurity on broiler farms,<br> which was used as a starting point to formulate tailor-made health plans to improve broiler health and reduce antimicrobial use.</p> <p>Measurements and data collection</p> <p>Farms were divided into 3 separate areas according to associated biosecurity risk; high disease risk external areas (red zone), medium risk service areas (orange zone),<br> and the clean and highly secure access-restricted green zone. In the Netherlands, Cyprus, and Greece, 13, 15, and 7 broiler houses were monitored for 4 production cycles (2 preintervention and 2 postintervention cycles).<br> At the start of the study the BiosEcurity Assessment Tool assessment was performed and a health plan was made in consultation with the veterinarian.<br> After the second cycle a start was made with the implementation of the health plan.</p>
Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
Open the record for dataset details and reuse information.
Data from: Widespread introgression in Chinese indigenous chicken breeds from commercial broiler
Open the record for dataset details and reuse information.
Demographics for all four breeds of broiler chickens
Open the record for dataset details and reuse information.
Data from: Uninhibited chickens: ranging behavior impacts motor self-regulation in free-range broiler chickens (Gallus gallus domesticus)
Open the record for dataset details and reuse information.
Earthworms to modulate broiler gut microbiota
Open the record for dataset details and reuse information.
Effect of different diet dilutions on body weight uniformity and its subsequent effect on peak production of broiler breeders
<p>This was research data </p>
Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth
GEO Series GSE65217. Gallus gallus. 23 samples. Type: Expression profiling by high throughput sequencing.
Metformin alters liver metabolism to sustain egg production in the reproductively aging broiler breeder hen
GEO Series GSE286522. Gallus gallus. 15 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.