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: Microorganisms

Article Title: Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods

doi: 10.3390/microorganisms13010131

Figure Lengend Snippet: Workflow in the investigation of the aetiology of PLAs (microbiological culture and massive sequencing by Illumina platform) of patients with a diagnosis of HA seen at Hospital Juárez de México.

Article Snippet: Bello-López, Juan Manuel (2024), “Massive Sequencing of V3-V4 Hypervariable Region in Pyo-genic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods”, Mendeley Data, V1, doi: 10.17632/8gwdjdhbph.1.

Techniques: Sequencing, Biomarker Discovery

Journal: Microorganisms

Article Title: Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods

doi: 10.3390/microorganisms13010131

Figure Lengend Snippet: Analysis of sequence quality by base (Forward and Reverse) of the data obtained by massive sequencing of the 16s rRNA gene of the PLAs of the patients treated at Hospital Juárez de México . ( A1 , B1 ): PLA S178 reads, ( A2 , B2 ): PLA S179, and ( A3 , B3 ): PLA S180. Green: High-quality sequencing reads; red: low-quality sequencing reads.

Article Snippet: Bello-López, Juan Manuel (2024), “Massive Sequencing of V3-V4 Hypervariable Region in Pyo-genic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods”, Mendeley Data, V1, doi: 10.17632/8gwdjdhbph.1.

Techniques: Sequencing

Journal: Microorganisms

Article Title: Massive Sequencing of V3-V4 Hypervariable Region in Pyogenic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods

doi: 10.3390/microorganisms13010131

Figure Lengend Snippet: Analysis of the error rates for each possible nucleotide transition of the data obtained by massive sequencing of the 16s rRNA gene from the PLA of patients treated at Hospital Juárez de México. ( A ). Forward sequence and ( B ). Reverse sequence. Red line: Expected error rates under the nominal Q-score definition.

Article Snippet: Bello-López, Juan Manuel (2024), “Massive Sequencing of V3-V4 Hypervariable Region in Pyo-genic Liver Abscesses Reveals the Presence of Unusual Bacteria Not Detected by Classical Culture Methods”, Mendeley Data, V1, doi: 10.17632/8gwdjdhbph.1.

Techniques: Sequencing