Journal: Applied and Environmental Microbiology

Article Title: Contrasting Microbiome Dynamics of Putative Denitrifying Bacteria in Two Octocoral Species Exposed to Dissolved Organic Carbon (DOC) and Warming

doi: 10.1128/AEM.01886-21

Figure Lengend Snippet: Community compositions and relative abundances of putative denitrifiers in corals X. umbellata and P. flava over the course of the experiment. (a) Relative proportions of denitrifier genera of corals X. umbellata and P. flava inferred by nirS in-silico PCR in relation to the total bacterial community from 16S rRNA gene sequencing. (b) Relative fold changes in copy numbers of nirS gene referenced to 16S rRNA gene and in relation to the day 0 control samples ( n = 3) of corals X. umbellata and P. flava . Values are means ± SD, and the asterisk indicates statistically significant differences (* P < 0.05).

Article Snippet: The 16S rRNA gene amplicon sequencing was conducted at LGC genomics (Berlin, Germany).

Techniques: In Silico, Sequencing

Journal: SpringerPlus

Article Title: Keratinolytic activities of alkaliphilic Bacillus sp. MBRL 575 from a novel habitat, limestone deposit site in Manipur, India

doi: 10.1186/s40064-016-2239-9

Figure Lengend Snippet: Neighbour-joining tree based on 16S rRNA gene sequences, showing the relationships between strain MBRL 575 and other type strains of Bacillus species. Escherichia coli strain SM 25(KF768068.1) was used as the outgroup. Numbers at nodes are levels of bootstrap support (%) for branch points (1000 resamplings). Bar 0.02 substitutions per nucleotide position

Article Snippet: The amplified 16S rRNA gene product was outsourced for sequencing at Xcelris Labs Ltd, India.

Techniques:

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