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: 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: Polish Journal of Microbiology

Article Title: The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

doi: 10.21307/pjm-2018-022

Figure Lengend Snippet: Primer sets used in this study.

Article Snippet: Subsamples of either purified 16S rRNA (16S rDNA), gyr B ( gyr B was sequenced with UP-1S and UP-2Sr primers (Table )) or all ncc A-like amplicons from isolate were sequenced by GATC Biotech, Constance, Germany.

Techniques: Sequencing

Journal: Polish Journal of Microbiology

Article Title: The Heavy-Metal Resistance Determinant of Newly Isolated Bacterium from a Nickel-Contaminated Soil in Southwest Slovakia

doi: 10.21307/pjm-2018-022

Figure Lengend Snippet: Unrooted phylogenetic tree obtained by the maximum likelihood method with 100 bootstrap replications showing phylogeny of 16S rRNA (16S rDNA) gene sequences of MR-CH-I2 isolate (in bold) and members of the genera Ralstonia, Cupriavidus and Alcaligenes , respectively. Rhizobium sp. SCAU231 [HQ538623], Pseudomonas fluorescens strain MPF25 [AB621592], Streptomyces badius strain 3504 [JN180190], Olivibacter soli strain Gsoil 034 [NR_041503] and Brevibacillus parabrevis C8 [KX832687] were used as outgroup. Numbers in square brackets indicate the GenBank accession number and similarity to closest relative is shown after the clone designation. Sequences of about 1 500 bp in length were aligned with ClustalW.

Article Snippet: Subsamples of either purified 16S rRNA (16S rDNA), gyr B ( gyr B was sequenced with UP-1S and UP-2Sr primers (Table )) or all ncc A-like amplicons from isolate were sequenced by GATC Biotech, Constance, Germany.

Techniques:

Journal: Journal of Animal Science and Biotechnology

Article Title: Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

doi: 10.1186/s40104-021-00601-2

Figure Lengend Snippet: Dietary inclusion of FRS induced distinct shifts in the colon microbiota composition. Observed zOTUs and Shannon diversity based on rarefied zOTU table with Illumina sequencing on V3 region (Illumina V3) ( a ); Observed features and Shannon diversity based on species-level summarized table by Illumina V3 ( b ) and Oxford Nanopore sequencing on V1-V8 region (ONT V1-V8) ( c ). The mean value for each group is marked as a bold line respectively. PCoA plots of binary Jaccard and Bray Curtis distance metrics based on the rarefied ASV table of Illumina V3 ( d ), species-level summarized table of Illumina V3 ( e ) and species-level summarized table of ONT V1-V8 ( f ). The ellipses suggest the respective 80% confidential area following multivariate t-distribution. Respectively n = 9, 8, 10 for feeding regimens with 0%, 2.5% and 5% added lacto-fermented rapeseed-seaweed blend (FRS). For pairwise Wilcoxon rank-sum tests on alpha diversity metrics, the labels of *, ** represent P < 0.05, < 0.01 respectively. For PERMANOVA tests, P values below 0.05 are heighted in yellow

Article Snippet: Observed zOTUs and Shannon diversity based on rarefied zOTU table with Illumina sequencing on V3 region (Illumina V3) ( a ); Observed features and Shannon diversity based on species-level summarized table by Illumina V3 ( b ) and Oxford Nanopore sequencing on V1-V8 region (ONT V1-V8) ( c ).

Techniques: Illumina Sequencing, Nanopore Sequencing

Journal: Journal of Animal Science and Biotechnology

Article Title: Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

doi: 10.1186/s40104-021-00601-2

Figure Lengend Snippet: Dietary inclusion of 2.5% FRS increased the Prevotella stercorea and Mitsuokella abundance in colon. The Prevotella stercorea and Mitsuokella spp. abundances determined by Illumina sequencing on V3 region of 16S rRNA gene ( a ) and Oxford Nanopore sequencing on V1-V8 region of 16S rRNA gene ( b ). Data in the bar plot was presented as mean value and SEM error bar. Respectively n = 9, 8, 10 for feeding regimens with 0%, 2.5% and 5% added lacto-fermented rapeseed-seaweed blend (FRS). The labels of *, **, *** represent P < 0.05, < 0.01, < 0.005 respectively

Article Snippet: Observed zOTUs and Shannon diversity based on rarefied zOTU table with Illumina sequencing on V3 region (Illumina V3) ( a ); Observed features and Shannon diversity based on species-level summarized table by Illumina V3 ( b ) and Oxford Nanopore sequencing on V1-V8 region (ONT V1-V8) ( c ).

Techniques: Illumina Sequencing, Nanopore Sequencing

Journal: Limnology and Oceanography

Article Title: Aerobic and anaerobic methane oxidation in a seasonally anoxic basin

doi: 10.1002/lno.12074

Figure Lengend Snippet: Maximum likelihood phylogeny of near full length 16S rRNA gene sequences of gammaproteobacterial methanotrophs in Mariager Fjord. The scale bar denotes nucleotide substitutions. Bootstrap values > 80% (black circles) and > 50% (white circles) are shown (1000 maximum likelihood replicates). Strain sequences are adopted from Knief and MM2020 lake sequences are from Mayr et al. . The red line indicates the Deep Sea‐1 clade of the Methylococcales order.

Article Snippet: Long‐length bacterial 16S rRNA gene amplicons were synthesized from a subset of samples at the Next Generation Sequencing Facility of the Vienna Biocenter ( www.vbcf.ac.at ) using the bacteria‐specific primers 27F (5′‐AGRGTTYGATYMTGGCTCAG‐3′) and 1492R (5′‐RGYTACCTTGTTACGACTT‐3′).

Techniques: