Journal: The ISME Journal

Article Title: The energy–diversity relationship of complex bacterial communities in Arctic deep-sea sediments

doi: 10.1038/ismej.2011.140

Figure Lengend Snippet: Changes in bacterial OTU richness, community structure and enzyme activity with pigment concentrations and correlation of changes in community structure with changes in enzyme activities for ARISA and 454 MPTS data. The plots in the left column of the figure ( a , d , b ) are based on the full ARISA dataset, the ones in the middle column ( b , e , h ) are based on a reduced ARISA dataset containing only samples used for 454 MPTS and plots in the right column ( c , f , i ) are based on 454 MPTS data. Linear regression R 2 values and Spearman's correlations as tested by Mantel tests with 999 permutations are indicated in the plots.

Article Snippet: When 454 MPTS (pyrosequencing of the variable V6 region of the 16S rRNA gene) was applied to a subset of samples to further explore the response of bacterial taxa to this range of energy availability, a similar linear relationship was found, appearing to level off at higher pigment concentrations (>3 μg cm −3 ; ).

Techniques: Activity Assay

Journal: PeerJ

Article Title: Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community

doi: 10.7717/peerj.7467

Figure Lengend Snippet: (A) Bacterial composition of OB and the IO biofilm cultures was determined by sequencing the V6–V7–V8 variable regions of the 16S rRNA gene by Illumina, whereas the other samples were determined by sequencing the V1–V2–V3 variable regions by pyrosequencing. (B) Principal component analysis of the bacterial profiles of the biofilm cultures and the OB listed in .

Article Snippet: The composition of the bacterial community of the OB and the IO biofilm cultures was derived from a different region of the 16S rRNA genes (V6–V8) than that used for the other biofilm cultures (V1–V3), and each region was sequenced by a different technology (Illumina and pyrosequencing, respectively).

Techniques: Sequencing

Journal: PeerJ

Article Title: Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community

doi: 10.7717/peerj.7467

Figure Lengend Snippet: Most probable affiliation of 16S rRNA gene sequences in the biofilm cultures and the original biofilm.

Article Snippet: The composition of the bacterial community of the OB and the IO biofilm cultures was derived from a different region of the 16S rRNA genes (V6–V8) than that used for the other biofilm cultures (V1–V3), and each region was sequenced by a different technology (Illumina and pyrosequencing, respectively).

Techniques:

Journal: PeerJ

Article Title: Dynamics of a methanol-fed marine denitrifying biofilm: 2—impact of environmental changes on the microbial community

doi: 10.7717/peerj.7467

Figure Lengend Snippet: 16S Operational Taxonomic Units (OTUs) affiliated to Hyphomicrobium spp. and Methylophaga spp. in the OB and the IO biofilm cultures.

Article Snippet: The composition of the bacterial community of the OB and the IO biofilm cultures was derived from a different region of the 16S rRNA genes (V6–V8) than that used for the other biofilm cultures (V1–V3), and each region was sequenced by a different technology (Illumina and pyrosequencing, respectively).

Techniques: Sequencing

Journal: Digestive diseases and sciences

Article Title: Microbiome Composition in Pediatric Populations from Birth to Adolescence: Impact of Diet and Prebiotic and Probiotic Interventions.

doi: 10.1007/s10620-020-06092-x

Figure Lengend Snippet: Characteristics of Studies Investigating Dietary Effects on Microbiome Composition in Infants and Children

Article Snippet: Italy and Burkina Faso 1-6 y N=29 , Cross-sectional , Italian parents completed a detailed medical, diet, and lifestyle survey Burkina Faso parents provided in-depth interview on children’s diet and a 3-d dietary questionnaire , V5-V6 16S rRNA by 454-pyrosequencing , Firmicutes-to-Bacteroidetes ratio (F:B ratio) was ~6-fold higher in Italian than Burkina Faso children 3 genera involved in utilization plant polysaccharides (Prevotella , Xylanibacter ( Bacteroidetes ), and Treponema ( Spirochaetes ) were higher in Burkina Faso children. , 28.

Techniques: Shotgun Sequencing, Starch, Microarray, Modification, Illumina Sequencing, Clinical Proteomics, Western Blot

Journal: Digestive diseases and sciences

Article Title: Microbiome Composition in Pediatric Populations from Birth to Adolescence: Impact of Diet and Prebiotic and Probiotic Interventions.

doi: 10.1007/s10620-020-06092-x

Figure Lengend Snippet: Characteristics of Studies Investigating Effects of Dietary Fibers and Prebiotics on the Fecal Microbiota of Healthy Children and Adolescents

Article Snippet: Italy and Burkina Faso 1-6 y N=29 , Cross-sectional , Italian parents completed a detailed medical, diet, and lifestyle survey Burkina Faso parents provided in-depth interview on children’s diet and a 3-d dietary questionnaire , V5-V6 16S rRNA by 454-pyrosequencing , Firmicutes-to-Bacteroidetes ratio (F:B ratio) was ~6-fold higher in Italian than Burkina Faso children 3 genera involved in utilization plant polysaccharides (Prevotella , Xylanibacter ( Bacteroidetes ), and Treponema ( Spirochaetes ) were higher in Burkina Faso children. , 28.

Techniques: Bacteria, Control

Journal: Digestive diseases and sciences

Article Title: Microbiome Composition in Pediatric Populations from Birth to Adolescence: Impact of Diet and Prebiotic and Probiotic Interventions.

doi: 10.1007/s10620-020-06092-x

Figure Lengend Snippet: Characteristics of Studies Investigating Probiotic Administration during Pregnancy and after Delivery on Infant Fecal Microbiota

Article Snippet: Italy and Burkina Faso 1-6 y N=29 , Cross-sectional , Italian parents completed a detailed medical, diet, and lifestyle survey Burkina Faso parents provided in-depth interview on children’s diet and a 3-d dietary questionnaire , V5-V6 16S rRNA by 454-pyrosequencing , Firmicutes-to-Bacteroidetes ratio (F:B ratio) was ~6-fold higher in Italian than Burkina Faso children 3 genera involved in utilization plant polysaccharides (Prevotella , Xylanibacter ( Bacteroidetes ), and Treponema ( Spirochaetes ) were higher in Burkina Faso children. , 28.

Techniques: Capsules, Bacteria, Control, Sequencing

Journal: Digestive diseases and sciences

Article Title: Microbiome Composition in Pediatric Populations from Birth to Adolescence: Impact of Diet and Prebiotic and Probiotic Interventions.

doi: 10.1007/s10620-020-06092-x

Figure Lengend Snippet: Characteristics of Studies Investigating Probiotic Administration on the Fecal Microbiota of Healthy Children Under 18 Years-of-Age

Article Snippet: Italy and Burkina Faso 1-6 y N=29 , Cross-sectional , Italian parents completed a detailed medical, diet, and lifestyle survey Burkina Faso parents provided in-depth interview on children’s diet and a 3-d dietary questionnaire , V5-V6 16S rRNA by 454-pyrosequencing , Firmicutes-to-Bacteroidetes ratio (F:B ratio) was ~6-fold higher in Italian than Burkina Faso children 3 genera involved in utilization plant polysaccharides (Prevotella , Xylanibacter ( Bacteroidetes ), and Treponema ( Spirochaetes ) were higher in Burkina Faso children. , 28.

Techniques: Control, Microarray, Suspension

Journal: The ISME Journal

Article Title: Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem

doi: 10.1038/ismej.2011.12

Figure Lengend Snippet: Spatial distribution of bacterioplankton community types in the 2009 synoptic survey. Surface DNA samples are symbol/color coded according to five community types defined as 85% Bray–Curtis similarity group average (unweighted pair group method with arithmetic mean) clusters of 16S bacterial rRNA gene amplicon TRFLP fingerprints (a; vertical line demarks the 85% cluster threshold, triangles indicate samples without significant differences by SIMPROF bootstrapping). Samples are annotated in the dendrogram according to nominal sample habitats for clarity. The map (b) is loosely shaded according to depth and substrate type keyed at the upper right, with samples symbol-coded according to TRFLP cluster. The inset map in (b) shows community types found at the offshore sampling locations, which were within ∼6 km of Moorea in >200 m deep water. A color reproduction of this figure is available on the html full text version of the manuscript.

Article Snippet: The observed gradients in the relative abundance of specific bacterioplankton phylotypes among offshore, forereef, backreef and bay habitats ( , , , Supplementary Figure S3) were clear and consistent among years (2008 and 2009; and Supplementary Figure S3), seasons (austral summer and winter 2008; ( and Supplementary Figure S3), and methods (16S rRNA V6 amplicon pyrosequencing and TRFLP fingerprinting; , , Supplementary Figure S3).

Techniques: Amplification, Terminal Restriction Fragment Length Polymorphism, Sampling

Journal: The ISME Journal

Article Title: Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem

doi: 10.1038/ismej.2011.12

Figure Lengend Snippet: Spatial variability in relative abundance of bacterial classes derived from pyrosequencing of environmental 16S rRNA V6 amplicons sampled in the vicinity of Moorea 11–13 January 2008. Replicate samples are labeled (top) according to collection location (see Supplementary Table S1) and clustered (bottom) by relative abundance of sequences matching reference OTUs aggregated by class (cluster lines are colored the same when there is no significant difference in communities; SIMPROF P>0.05). Classes are clustered (left) according to relative variance across the spatial gradient, with green below average and red above average. Mean and ranges of relative abundance of each class across the dataset are given at right with color codes matching the heat map. Clustering and heatmaps were generated in the JMP v8 statistical package using group average clustering of samples according to class relative abundances between samples.

Article Snippet: The observed gradients in the relative abundance of specific bacterioplankton phylotypes among offshore, forereef, backreef and bay habitats ( , , , Supplementary Figure S3) were clear and consistent among years (2008 and 2009; and Supplementary Figure S3), seasons (austral summer and winter 2008; ( and Supplementary Figure S3), and methods (16S rRNA V6 amplicon pyrosequencing and TRFLP fingerprinting; , , Supplementary Figure S3).

Techniques: Derivative Assay, Labeling, Generated

Journal: Preventive Nutrition and Food Science

Article Title: The Efficacy of Probiotics Supplementation on the Quality of Life of Patients with Gastrointestinal Disease: A Systematic Review of Clinical Studies

doi: 10.3746/pnf.2024.29.3.237

Figure Lengend Snippet: Notable outcomes of selected RCT studies assessing the effects of probiotics on GI diseases

Article Snippet: , Japan , ·Purified DNA was used as a template for the following two-step polymerase chain reaction. ·Fecal microbiota was measured using fecal bacterial 16S rDNA V4-V6 region-targeted pyrosequencing. , CP2305 favorably changed the fecal characteristics compared with placebo among patients with IBS with either diarrhea or constipation subtypes.

Techniques: Probiotics, Bacteria, Derivative Assay, Sequencing, Extraction, Polymerase Chain Reaction, Amplification, Real-time Polymerase Chain Reaction, Purification