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Microbial diversity and virulence probing of five different body sites. Anu Rebbapragada, Pub. Health Ontario Central Lab. Canada Wei-Jen Lin, Cal State Polytech. Univ. Pomona, USA Thomas Keller, Oregon Health &Science Univ., USA Anna Edlund, JCVI, USA. Questions: - PowerPoint PPT Presentation
Citation preview
Microbial diversity and virulence probing of five different body sites
Anu Rebbapragada, Pub. Health Ontario Central Lab. Canada Wei-Jen Lin, Cal State Polytech. Univ. Pomona, USAThomas Keller, Oregon Health &Science Univ., USAAnna Edlund, JCVI, USA
Questions:
-What are the differences in taxonomic & functional diversity between and within body sites?
-Is there a difference in the diversity of virulence genes between body sites?
Sample selection in IMG/HMP- Downloaded 10 metagenomes - Selected 2 metagenomes per body site
Table for General Statistics•Compare Genomes•Genome Statistics•Breakdown by selected genomes, general statistics
Bar Graph for % GC•Created in Excel
Same person analyzed for skin and stool sample
Radial Tree by Class Radial Tree•Compare Genomes•Phylogenetic Distribution•Radial Tree of 5 selected metagenomes•Customize by Phyla, Class, Domain etc categories
Bacterial diversity at class level
14 2 411
5
Skin
Nose
Pie charts and tables created by clicking node on Radial Tree
Diversity of Archaea by Phyla and Class levels
Pie charts and tables created by clicking node on Radial Tree. Radial tree customized to display at either Phyla or Class level.
Bacterial diversity behind your ear
Left ear Right ear
Selected only 2 metagenomes (ear samples) to generate radial tree.Pie charts and tables created by clicking node on Radial Tree. Radial tree customized to display at either Phyla or Class level.
Functional diversity across the metagenomes
COG functions
Compare Genomes
Genome Clustering, Correlation Matrix
Select metagenomes of interest
Clustering method: Correlation Matrix
Function: COG
Display: r2 values by pairwise comparison across all metagenomes
PCA 2-D COG groups
Stool
Tongue
Skin
Nose Vagina
Compare Genomes
Genome Clustering, Correlation Matrix
Select metagenomes of interest
Clustering method: PCA Principle component analysis
Function: COG (clustering by COG pathways)
Display: 2D plot, mouse over redX to identify the metagenome identity
Created figure in powerpoint to show clustering of COGs across metagenomes
•Can also show Hierarchical clustering by Function (COG, Pfam etc) or Taxonomy (Genus, Family etc) or Function Categories (COG, KEGG, Pfam)
PCA COG pathways
Stool
Tongue
Skin
Nose
Vagina
Compare Genomes
Genome Clustering, Correlation Matrix
Select metagenomes of interest
Clustering method: PCA Principle component analysis
Function Category: COG pathway
Display: 2D plot, mouse over redX to identify the metagenome identity
Created figure in powerpoint to show clustering of COGs across metagenomesNow the Nose samples don’t cluster together suggesting
differences in pathways
Hierarchical Clustering across Metagenomes by COG
Compare Genomes
Genome Clustering, Correlation Matrix
Select metagenomes of interest
Clustering method: Hierarchical
Function: COG
Display: Phylogram showing distribution of metagenomes
Compare COG function between Metagenomes
Compare genomes•function comparison tool•abundance profile•function comparison•select query genome•Export table
Secretion PathwaysSelect Metagenomes of interestFind FunctionsSearch All pathways, Select KEGG pathways onlyType “secretion” as KeywordClick on Pathway OID for bacterial secretionView Map
Gene Products in Type III Secretion pathway
Select Metagenomes of interestFind Functions, Function Search
Keyword: “Secretion”, Gene Product name, Click GO
Text Filter: “Type III”, click ApplySelect MetaGenomes
View Profile
Output: Table of Function ID (gene product name) and abundance (gene counts) in each metagenome
Gene Products in Type Vb secretion (hemolysin) pathway
Select Metagenomes of interestFind Functions, Function Search
Keyword: “Secretion”, Gene Product name, Click GO
Text Filter: “ShlB”, click ApplySelect MetaGenomes
View Profile
Output: Table of Function ID (gene product name) and abundance (gene counts) in each metagenome
Gene Counts Across Metagenomes for Type VI Secretion Pathway
Distribution of antibiotic resistance genes by human body sites
Nose Ears Stool Tongue Vagina
Select Metagenomes of interestFind Functions, Function Search
Keyword: individual searches for each antibiotic resistance category under Gene Product name, Click GO
Output: Table of Function ID (gene product name) and abundance (gene counts) in each metagenome
Exported Table, Tally of totals in spreadsheet and created PieCharts in Excel
Antibiotic resistance in human body sitesNormalized to counts/10,000 genes
US Antibiotic Usage Data
Google search :)www.cddep.org/ResistanceMap
Study Limitations &
Future Analytical Directions