Nonmetric multidimensional scaling (NMDS) plots of fecal and biopsy sample-based Bray-Curtis distances computed from the relative abundances of the 258.

Slides:

Advertisements

Similar presentations

Nonmetric Multidimensional Scaling input data are ranks: most similar pair AB

Advertisements

Figure 1. The relationships of bacterial operational taxonomic unit richness (A) and phylogenetic diversity (B) with aridity index based on 97% sequence.

Nonmetric multidimensional scaling (NMDS) ordination of variation in bacterial community structure of tree phyllosphere along a gradient of urban intensity.

Multivariate community analysis

Volume 21, Issue 13, Pages (December 2017)

Boxplots displaying relative percent abundance of consistent abundance-based microbiome members present in the tissue, mucus, and holobiont (Holo) fractions.

Taxonomic composition of subway microbial communities.

Microbial community dissimilarity.

Heatmap displaying consistent similarity-based OTU results based on SIMPER intragroup similarity analyses for the tissue, mucus, holobiont, and seawater.

Relative abundances of the top 10 most abundant OTUs across all fish samples are shown along with the data from the probiotic B. pumilus RI06-95 (OTU 3673)

Nitrate-, nitrite-, and nitric oxide-reducing bacteria.

Heatmap summarizing the significant (P < 0

Microbial diversity was broadly compared across three unique built-environment study sites for 16S rRNA amplicon and shotgun metagenome sequencing. Microbial.

Volume 11, Issue 4, Pages (April 2015)

Volume 21, Issue 13, Pages (December 2017)

Conducting a Microbiome Study

Bacterial biomarkers associated with disease severity.

Gut microbial diversity of mice in voluntary and forced exercise groups. Gut microbial diversity of mice in voluntary and forced exercise groups. Weighted.

Microbial diversity of the 10 body locations sampled.

Fluoride affects stool-derived taxa found in the oral cavity.

Putative MBTA microbial community sources.

Plots of the number of sequences [log (x + 1) scale] from bacterial OTUs in both PCR replicates (PCR1 and PCR2) of the 348 wild rodents analyzed in the.

A small number of bacteria showed high levels of growth in the storage studies. A small number of bacteria showed high levels of growth in the storage.

(a) Correspondence analysis of 88 soil samples.

(A) Heat maps illustrate the percent abundances of the most abundant genera (all OTUs taxonomically classified to the same genus were collapsed into a.

The airway microbiome in patients with severe asthma: Associations with disease features and severity Yvonne J. Huang, MD, Snehal Nariya, BS, Jeffrey.

Distributions of pairwise correlation coefficients from cooccurrence models computed from temporal data (fecal) and spatial data (biopsy samples; means.

Comparison of distal gut metabolite profiles between Egyptian and U. S

The similar shifts of gut microbiota in IBD across cohorts.

Functional enrichment of differentially expressed genes.

Enterotypes of the distal gut microbial profiles.

ncRNAs are developmentally regulated as well as mRNAs.

Distribution of microbial functions in urban waterways.

Comparison of the original ITS primer pair and the new, modified ITS primer pair. Comparison of the original ITS primer pair and the new, modified ITS.

Comparison of the modified 515f/806rB V4 primer pair and the 515f (modified)/926r primer pair. Comparison of the modified 515f/806rB V4 primer pair and.

Stability of fecal microbiomes in different preservatives and under different temperature treatments. Stability of fecal microbiomes in different preservatives.

(a) Hierarchical clustering of closed-reference OTUs based on mean pH; (b) balance of low-pH-associated organisms (3.8 < mean pH < 6.7) and high-pH-associated.

Multilayered cooccurrence network analysis of OTUs that exhibited a significant positive Spearman’s correlation with oxalate consumption at the end of.

Experimental design. Experimental design. (a) Configuration of the sampling site in Flagstaff office 1. This configuration was similar to those set up.

Log- to stationary-phase growth results in differential acetyl abundance on specific proteins. Log- to stationary-phase growth results in differential.

Compositional PCA plot of samples (A) and OTU loadings (B) for the initial data set. Compositional PCA plot of samples (A) and OTU loadings (B) for the.

Functional potential analyses.

(A) Box-and-whisker plots illustrate the median, maximum, minimum, and first and third quartiles of the distribution of the number of observed OTUs and.

Altered mycobiota and bacterial-fungal correlation in AS patients receiving different therapeutic regimens. Altered mycobiota and bacterial-fungal correlation.

A principal-coordinate analysis plot of UniFrac distances from de novo OTUs as visualized by Emperor. A principal-coordinate analysis plot of UniFrac distances.

Benchmarks of OTU picking tools on artificial communities.

Shifts in the microbial community compositions of the control and antibiotic groups. Shifts in the microbial community compositions of the control and.

(a) A band table where the y axis data represent individual OTUs and the x axis data represent samples. (a) A band table where the y axis data represent.

Relationship between relative abundance and transcription/abundance ratio (logarithmic scales) of OTUs (brown), ZOTUs (turquoise), and population genomes.

Nonmetric multidimensional scaling (NMDS) (A) and dendrogram and heat map (B) of the relative abundances of the data in the custom database across the.

Multivariate analysis of community structure data

A principal-coordinate analysis plot of UniFrac distances from Deblur as visualized by Emperor. A principal-coordinate analysis plot of UniFrac distances.

Differences in Verrucomicrobia genera across plant community types.

Association of specific phylotypes with walnut consumption and carcinogen exposure (Study 2). Association of specific phylotypes with walnut consumption.

Heatmap showing Spearman’s rho values for significant correlations between weed abundances and bacterial classes (i.e., OTU data pooled at the class level;

Above- and belowground community structure along cheatgrass, spotted knapweed, and leafy spurge invasion transects. Above- and belowground community structure.

PCoA plots of subgingival samples with disease classification overlaid

Fig. 1 The seven nasal CSTs and their respective bacterial densities shown in boxplots and composition shown in heatmap visualization and non-metric multidimensional.

Relative abundance of the predicted KEGG orthologous groups (KOs) in the fecal (A) and salivary (B) samples from the clindamycin group plotted against.

Shannon rarefaction analysis.

Hierarchically clustered heat map showing correlations between the relative abundances of microbial species and the levels of volatile compounds in kefir.

Acarbose reversibly changes the structure of the murine gut community.

Variations in beta and alpha diversity of gut microbiome bacterial communities in relation to presence of Blastocystis. Variations in beta and alpha diversity.

Variations in beta and alpha diversity of gut microbiome eukaryotic communities explained by presence of Blastocystis. Variations in beta and alpha diversity.

Comparison of distal gut microbiota composition between Egyptian and U

Northern shovelers may have unique microbiome differences with respect to IAV infection, relative to the other duck species. Northern shovelers may have.

Longitudinal dynamics of in vivo human oral microbiota.

Effect of bloom filtering on American Gut data.

Comparison of 16S sequencing and shallow shotgun recovery of species-level taxa. Comparison of 16S sequencing and shallow shotgun recovery of species-level.

Relative abundances of bacterial/archaeal groups in 16S rRNA data set.

Presentation transcript:

Nonmetric multidimensional scaling (NMDS) plots of fecal and biopsy sample-based Bray-Curtis distances computed from the relative abundances of the 258 most prevalent OTUs. (A) NMDS plot displaying fecal and biopsy samples from the main study individual. Nonmetric multidimensional scaling (NMDS) plots of fecal and biopsy sample-based Bray-Curtis distances computed from the relative abundances of the 258 most prevalent OTUs. (A) NMDS plot displaying fecal and biopsy samples from the main study individual. Colors represent the different sampling sites, and the distance between the circles represent similarity of the assemblage of OTUs comprising a sample. Clear separation was observed between the fecal samples and the biopsy samples (P << 0.001 by ANOSIM). Dim1, dimension 1. (B) NMDS plot of the biopsy samples obtained in triplicate from seven different locations along the GI tract. Significant structuring was observed between the anatomically distinct sampling sites (P << 0.001 by ANOSIM). Eric J. de Muinck et al. mSystems 2017; doi:10.1128/mSystems.00086-17