Shift of Microbiota and Modulation of Resistome in the Ceca of Broiler Chicken Fed Berry Pomace Alone or in Combination of a Multienzyme Mixture.

Alternative feed additives are being investigated due to the restriction of antibiotics use to decrease antimicrobial resistance (AMR) in food-producing animals. This study investigated the effects of dietary American cranberry () and wild blueberry () pomaces on the cecal microbiota and resistome profiles as well as the short-chain fatty acid levels. Male broiler chickens Cobb500 were fed a basal diet with either 55 ppm bacitracin methylene disalicylate (BMD); 0.

Cecal microbiome in broiler chicken related to antimicrobial feeding and bird's sex.

This study investigated the cecal microbiome of broilers raised under specific antimicrobial feeding programs (AFPs). A total of 2304 day-old Ross-708 male (M,  = 1152) and female (F,  = 1152) chicks were distributed into 48 floor pens which were allocated to one of three AFPs: Conventional, raised without medically important antibiotics (RWMIA), and raised without antibiotics (RWA). At 28 (D28) and 41 (D41) days of age, cecal contents were collected for culture dependent and independent analyses.

Crossing the streams: improving data quality and integration across the One Health genomics continuum with data standards and implementation strategies.

The Canadian Genomics Research and Development Initiative for Antimicrobial Resistance (GRDI-AMR) uses a genomics-based approach to understand how health care, food production and the environment contribute to the development of antimicrobial resistance. Integrating genomics contextual data streams across the One Health continuum is challenging because of the diversity in data scope, content and structure. To better enable data harmonization for analyses, a contextual data standard was developed.

Organic cranberry pomace and its ethanolic extractives as feed supplement in broiler: impacts on serum Ig titers, liver and bursal immunity.

With the pressure to reduce antibiotics use in poultry production, cost-effective alternative products need to be developed to enhance the bird's immunity. The present study evaluated the efficacy of cranberry fruit by-products to modulate immunity in broiler chickens. Broiler Cobb 500 chicks were fed a control basal diet, basal diet supplemented with bacitracin (BACI, 55 ppm), cranberry pomace at 1% and 2% (CP2), or cranberry pomace ethanolic extract at 150 and 300 ppm (COH300) for 30 d.

Gut Microbiota, Blood Metabolites, and Spleen Immunity in Broiler Chickens Fed Berry Pomaces and Phenolic-Enriched Extractives.

This study evaluated the performance, gut microbiota, and blood metabolites in broiler chickens fed cranberry and blueberry products for 30 days. A total of 2,800 male day-old broiler Cobb-500 chicks were randomly distributed between 10 diets: control basal diet; basal diet with bacitracin (BACI); four basal diets with 1 and 2% of cranberry (CP1, CP2) and blueberry (BP1, BP2) pomaces; and four basal diets supplemented with ethanolic extracts of cranberry (COH150, COH300) or blueberry (BOH150, BOH300) pomaces. All groups were composed of seven replicates (40 birds per replicate).

Scavenger: A pipeline for recovery of unaligned reads utilising similarity with aligned reads.

Read alignment is an important step in RNA-seq analysis as the result of alignment forms the basis for downstream analyses. However, recent studies have shown that published alignment tools have variable mapping sensitivity and do not necessarily align all the reads which should have been aligned, a problem we termed as the false-negative non-alignment problem. Here we present Scavenger, a python-based bioinformatics pipeline for recovering unaligned reads using a novel mechanism in which a putative alignment location is discovered based on sequence similarity between aligned and unaligned reads.

Discovery of perturbation gene targets via free text metadata mining in Gene Expression Omnibus.

There exists over 2.5 million publicly available gene expression samples across 101,000 data series in NCBI's Gene Expression Omnibus (GEO) database. Due to the lack of the use of standardised ontology terms in GEO's free text metadata to annotate the experimental type and sample type, this database remains difficult to harness computationally without significant manual intervention.

Changes in Gene Transcription Induced by Hydrogen Peroxide Treatment of Verotoxin-Producing O157:H7 and Non-O157 Serotypes on Romaine Lettuce.

Disease outbreaks of verotoxin-producing (VTEC) O157:H7 and non-O157 serotypes associated with leafy green vegetables are becoming a growing concern. A better understanding of the behavior of VTEC, particularly non-O157 serotypes, on lettuce under stress conditions is necessary for designing more effective control strategies. Hydrogen peroxide (HO) can be used as a sanitizer to reduce the microbial load in leafy green vegetables, particularly in fresh produce destined for the organic market.

The effect of oxidative stress on gene expression of Shiga toxin-producing Escherichia coli (STEC) O157:H7 and non-O157 serotypes.

Understanding the survival mechanisms used by Shiga toxin-producing Escherichia coli (STEC), including O157:H7 and non-O157 serotypes, is important for minimizing contamination of fresh produce and occurrence of foodborne outbreaks. Recent outbreaks linked to leafy green vegetables and sprouted seeds have prompted researchers to focus on investigating decontamination strategies. Several studies showed that hydrogen peroxide (H2O2) treatment has been effective in reducing pathogens on fresh produce.