Journal: Frontiers in Veterinary Science

Article Title: Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

doi: 10.3389/fvets.2020.547181

Figure Lengend Snippet: Difference of resistance gene targets between drug-free and conventional flocks for each farm at sampling time point one. Negative results indicate a decrease in gene target, and positive results indicate an increase in gene target in drug-free flocks. Data are presented as the mean (SEM) of 12 replicates. For the quantitative approach, each sample was run in triplicate ( n = 3). (A) Values are expressed on a ratio referenced to the total bacterial content of samples (16S rRNA). (B) Values are expressed on a weight basis (raw values). *Significant values are lower than the alpha level adjusted with the Benjamini–Hochberg method.

Article Snippet: For the 16S rRNA amplicon metagenomic sequencing analyses, the alpha and the beta diversity indices were calculated using Rstudio.

Techniques: Sampling

Journal: Frontiers in Veterinary Science

Article Title: Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

doi: 10.3389/fvets.2020.547181

Figure Lengend Snippet: Difference of resistance gene targets between flocks sampled from conventional barns at sampling time point one and the flock from the same barn at sampling time point two. At sampling time point one, conventional barns from farms C to F remained on a conventional rearing program after the 15-months study period, whereas barns from farms A and B moved to a program for judiciously using antibiotics. Negative results indicate a decrease in gene target, and positive results indicate an increase in gene target in the sampled flock at sampling time point two. Data are presented as the mean (SEM) of 12 replicates. For the quantitative approach, each sample was run in triplicate ( n = 3). (A) Values are expressed on a ratio referenced to the total bacterial content of samples (16S rRNA). (B) Values are expressed on a weight basis (raw values). *Significant values are lower than the alpha level adjusted with the Benjamini–Hochberg method.

Article Snippet: For the 16S rRNA amplicon metagenomic sequencing analyses, the alpha and the beta diversity indices were calculated using Rstudio.

Techniques: Sampling

Journal: Frontiers in Veterinary Science

Article Title: Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

doi: 10.3389/fvets.2020.547181

Figure Lengend Snippet: Difference of resistance gene targets between flocks sampled from drug-free barns at sampling time point one and the flock sampled from the same barn at sampling time point two. Drug-free barns from farms C to F went back to a conventional rearing protocol after the 15-months study period, whereas drug-free barns from farms A and B moved to a program for judiciously using antibiotics. Negative results indicate a decrease in gene target, and positive results indicate an increase in gene target in the sampled flock at sampling time point two. Data are presented as the mean (SEM) of 12 replicates. For the quantitative approach, each sample was run in triplicate ( n = 3). (A) Values are expressed on a ratio referenced to total bacterial content of samples (16S rRNA). (B) Values are expressed on a weight basis (raw values). *Significant values are lower than the alpha level adjusted with the Benjamini–Hochberg method.

Article Snippet: For the 16S rRNA amplicon metagenomic sequencing analyses, the alpha and the beta diversity indices were calculated using Rstudio.

Techniques: Sampling

Journal: Frontiers in Veterinary Science

Article Title: Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

doi: 10.3389/fvets.2020.547181

Figure Lengend Snippet: Difference of resistance gene targets at sampling time point two between flocks of the same participating farm that adopted either a conventional rearing program or a program for judiciously using antibiotics after the completion of the 15-months study period, considering the barn that was on a drug-free program during the 15-months study period as the comparison reference unit. Negative results indicate a decrease in gene target, and positive results indicate an increase in gene target in the flock sampled at sampling time point two used as a reference unit. Data are presented as the mean (SEM) of 12 replicates. For the quantitative approach, each sample was run in triplicate ( n = 3). (A) Values are expressed on a ratio referenced to total bacterial content of samples (16S rRNA). (B) Values are expressed on a weight basis (raw values). *Significant values are lower than the alpha level adjusted with the Benjamini–Hochberg method.

Article Snippet: For the 16S rRNA amplicon metagenomic sequencing analyses, the alpha and the beta diversity indices were calculated using Rstudio.

Techniques: Sampling, Comparison

Journal: Gut Microbes

Article Title: A bidirectional association between the gut microbiota and CNS disease in a biphasic murine model of multiple sclerosis

doi: 10.1080/19490976.2017.1353843

Figure Lengend Snippet: Composition of the microbiome at day 0, α diversity and species richness during disease. Stool samples were analyzed from No EAE control mice (n = 5), mice that developed mild disease (n = 5), and mice that developed severe EAE (n = 5). (A) Samples were collected from all 15 NOD mice. Clinical scores (mean +/− SEM) of mice at each time point of fecal collection (days 0, 14, 30 and 58 post-EAE induction) compared by two-way ANOVA. (B) To examine the compositional heterogeneity of the microbial communities found in the 3 groups, we used non-metric dimensional scaling (NMDS) in R to ordinate the microbial communities of samples based on the Bray-Curtis dissimilarity index using QIIME after the 16S rRNA (rRNA) gene sequencing analysis of stool samples, using the phyloseq package. Represented are the NMDS graph for the genus taxonomic level of OTUs identified in the analysis at day 0. The statistical comparison was performed using the permutational Multivariate Analysis of Variance Using Distance Matrices, ADONIS, in the vegan package. (C) Shannon index of α diversity and observed species measure in the 3 experimental groups compared by one-way ANOVA.

Article Snippet: Samples were sent to AKESOgen (Norcross, GA) for 16S rRNA analysis of the microbiome.

Techniques: Control, Sequencing, Comparison