Microbial diversity and virulence probing of five different body sites

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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
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• 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?

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• Sample selection in IMG/HMP
• Downloaded 10 metagenomes
• Selected 2 metagenomes per body site

Same person analyzed for skin and stool sample

• Table for General Statistics
• Compare Genomes
• Genome Statistics
• Breakdown by selected genomes, general statistics
• Bar Graph for GC
• Created in Excel

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Radial Tree by Class

• Radial Tree
• Compare Genomes
• Phylogenetic Distribution
• Radial Tree of 5 selected metagenomes
• Customize by Phyla, Class, Domain etc categories

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Bacterial diversity at class level
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Nose
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Skin
Pie charts and tables created by clicking node on
Radial Tree
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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.
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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.
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Functional diversity across the metagenomes
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
COG functions
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PCA 2-D COG groups

• 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)

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PCA COG pathways
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 metagenomes
Nose
Tongue
Skin
Vagina
Stool
Now the Nose samples dont cluster together
suggesting differences in pathways
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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
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• Compare genomes
• function comparison tool
• abundance profile
• function comparison
• select query genome
• Export table

Compare COG function between Metagenomes
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Secretion Pathways
Select Metagenomes of interest Find
Functions Search All pathways, Select KEGG
pathways only Type secretion as Keyword Click
on Pathway OID for bacterial secretion View Map
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Gene Products in Type III Secretion pathway
Select Metagenomes of interest Find Functions,
Function Search Keyword Secretion, Gene
Product name, Click GO Text Filter Type III,
click Apply Select MetaGenomes View
Profile Output Table of Function ID (gene
product name) and abundance (gene counts) in each
metagenome
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Gene Products in Type Vb secretion (hemolysin)
pathway
Select Metagenomes of interest Find Functions,
Function Search Keyword Secretion, Gene
Product name, Click GO Text Filter ShlB,
click Apply Select MetaGenomes View
Profile Output Table of Function ID (gene
product name) and abundance (gene counts) in each
metagenome
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Gene Counts Across Metagenomes for Type VI
Secretion Pathway
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Distribution of antibiotic resistance genes by
human body sites
Nose Ears Stool Tongue Vagina
Select Metagenomes of interest Find 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
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Antibiotic resistance in human body
sitesNormalized to counts/10,000 genes
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US Antibiotic Usage Data
Google search ) www.cddep.org/ResistanceMap
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Study Limitations Future Analytical Directions