Results: Taxonomy Analysis
Zymo Research Corporation
1 Composition Barplots
Composition barplots illustrate the microbial composition at different taxonomy levels from phylum to strain. The interactive figure below shows the microbial composition at the strain level. Additional composition barplots and abundance tables can be accessed by clicking on the link below the figure.
2 Taxonomy Heatmaps
The taxonomy abundance heatmap with sample clustering is a quick way to help identify patterns of microbial distribution among samples. Heatmaps at different taxonomic levels and with or without sample clustering can be found by clicking the links below the figure.
The following heatmap shows the microbial composition of the samples at the strain level with the top 50 strains identified. Each row represents the abundance for each taxon, with the taxonomy ID shown on the right. Each column represents the abundance for each sample, with the sample ID shown at the bottom. If available, group information is indicated by the colored bar located on the top of each column. Hierarchical clustering was performed on samples based on Bray-Curtis dissimilarity. Hierarchical clustering was also performed on the taxa so that taxa with similar distributions are grouped together.
Heatmaps with Sample Clustering:
Category1 1.Phylum 2.Genus 3.Species 4.Subspecies 5.Serotype 6.Strain
Heatmaps without Sample Clustering:
Category1 1.Phylum 2.Genus 3.Species 4.Subspecies 5.Serotype 6.Strain
3 Alpha Diversity
Alpha diversity is a measurement of the microbial diversity of each sample. The plot below shows the number of observed strains in the samples. For analyses without group comparison, a histogram of observed species in each sample is shown. For analyses with group comparison, a box-and-whisker plot of observed species in each group is shown. Alpha diversity graphs generated by other matrices can be found by clicking the last link
Normally, with deeper sequencing depth, the alpha diversity increases as more taxa at lower abundance are identified. Alpha diversity rarefraction graphs generated by other matrices can be found by clicking the link given below the figure.
Alpha Diversity Results: 1.Superkingdom 2.Phylum 3.Genus 4.Species 5.Subspecies 6.Serotype 7.Strain
4 Beta Diversity
Beta diversity is a measurement of microbial diversity differences between samples. The figure below is the 3-dimensional principle coordinate analysis (PCoA) plot created using the matrix of paired-wise distance between samples calculated by the Bray-Curtis dissimilarity at strain level. Interactive 3-dimensional plots of beta-diversity with different matrices can be accessed by clicking the links given below the figures.
Each dot on the beta diversity plot represents the whole microbial composition profile. Samples with similar microbial composition profiles are closer to each other, while samples with different profiles are farther away from each other.
Beta Diversity 3D Emperor Plot View: 1.Genus 2.Species 3.Strain
5 LEfSe Analysis
LEfSe analysis helps to identify taxa whose distributions are significantly and statistically different among pre-defined groups.
LEfSe uses statistical analysis to identify taxa whose distributions among pre-defined groups is significantly different. It also utilizes the concept of effect size to allow researchers to focus on the taxa of dramatic differences. By default, LEfSe identifies taxa whose distributions among different groups are statistically different with p-value <0.05 and the effect size (LDA score) higher than 2. LEfSe analysis is only possible if group information is given. It can conveniently help researchers identify biomarkers among/between groups (e.g. control group vs. disease group). Major outputs from LEfSe analysis includes the following:
1. Interactive Biomarkers Plot: This plot shows the distribution of the abundance of identified biomarkers among all samples. Click on the bars of biomarkers on the Interactive Biomarkers Plot to access the abundance distribution profile among groups.
2. Biomarkers Plot: This plot lists biomarkers by group definition and effect size.
3. Cladogram Plot: This plot illustrates identified biomarkers (colored based on groups) in a context of phylogenetic tree.
4. LEfSe Statistics Table(Output): This excel file stores the raw data of effect size (4th column/ column D) and P-values (5th column/ column E) from statistical analysis. The group in which the taxa was more abundant is in the 3rd column/column C.
Interactive Biomarkers Plot: Category1
Biomarkers Plot (PDF): Category1
Cladogram Plot (PDF): Category1
LEfSe Statistics Table (Output File): Category1