My master thesis half way there

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Statusseminar presentation at Aalborg University of my master thesis work so far. Hand in date: early June 2017. Check out https://knaldhat.shinyapps.io/shinyampvis/

Sciences

Exploring Microbial
Communities Using
Ordination
Enterotyping Danish Wastewater Treatment
Plants and explaining their Microbial
Compositions
Statusseminar January 2017
Kasper Skytte Andersen
Supervisor: Mads Albertsen
CENTER FOR MICROBIAL COMMUNITIES

Agenda
• Background
• Aims
• Introduction to ordination
• Using ordination to explore differences in microbial communities
• Easy data analysis with a custom made web app
• What’s next?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Agenda Background Aims Ordination Web app What's next?

CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Aalborg West - Wastewater Treatment Plant
Sewer
system
Bacteria clean our wastewater!
Agenda Background Aims Ordination Web app What's next?

Aims
To explore and explain patterns in the microbial community
composition of Danish Wastewater Treatment Plants using various
ordination methods and multivariate statistics.
• Is there a unique fingerprint (enterotype) of microorganisms for each
WWTP?
• How are they different and…
• Why?
• Test known environmental factors or operational parameters
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Agenda Background Aims Ordination Web app What's next?

What is ‘ordination’?
• A branch of multivariate statistics
• The term was first introduced in 1954 by Goodall (it’s nothing new!)
• A way to ‘simplify’ complex, multidimensional data
• Generally divided into two groups:
• Exploratory analysis
• Explanatory (constrained) analysis
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Agenda Background Aims Ordination Web app What's next?

Why use it?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Samples (52)
Species(14.942)
…
…
Species abundance
Agenda Background Aims Ordination Web app What's next?

A simple overview is fine, but…
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Aalborg
West
Aalborg
East
Agenda Background Aims Ordination Web app What's next?

Principal Component Analysis
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Agenda Background Aims Ordination Web app What's next?

Steps in ordination
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Abundance table (Samples x Species) Distance Matrix
Distance Metric
Ordination
“Dimensional yoga”
1
2
3
4
5
Agenda Background Aims Ordination Web app What's next?

Simplest example: 2 dimensions transformed to 1
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
(99%)
(1%)
Agenda Background Aims Ordination Web app What's next?

Effect of various distance metrics
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Same raw data!
[Enterotypes of the human gut microbiome, Arumugam et al., Nature 2011]
Agenda Background Aims Ordination Web app What's next?

Many distance metrics, but few relevant
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY[Enterotypes of the human gut microbiome, Arumugam et al., Nature 2011]
Agenda Background Aims Ordination Web app What's next?

Numerous types of ordination
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
• Exploratory analysis:
Principal Component Analysis (PCA)
Principal Coordinates Analysis (PCoA/mMDS)
(Non-)metric Multi Dimensional Scaling (nMDS)
Correspondence Analysis (CA)
• Explanatory (constrained) analysis:
Redundancy Analysis (RDA)
Canonical Correspondence Analysis (CCA)
Correspondence analysis (CA) Canonical Correspondence Analysis (CCA)
Agenda Background Aims Ordination Web app What's next?

Data analysis made easy
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
www.knaldhat.shinyapps.io/shinyampvis
Agenda Background Aims Ordination Web app What's next?

What’s next?
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
(Made with a shiny app )
Agenda Background Aims Ordination Web app What's next?
Half way!

Thank you
CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY
Environmental Biotechnology (EB-group)Supervisor: Mads Albertsen
http://github.com/knaldhat/ (Code stuff)
Follow me http://albertsenlab.org (Blog)OR

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1. Exploring Microbial Communities Using Ordination Enterotyping Danish Wastewater Treatment Plants and explaining their Microbial Compositions Statusseminar January 2017 Kasper Skytte Andersen Supervisor: Mads Albertsen CENTER FOR MICROBIAL COMMUNITIES

2. Agenda • Background • Aims • Introduction to ordination • Using ordination to explore differences in microbial communities • Easy data analysis with a custom made web app • What’s next? CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Agenda Background Aims Ordination Web app What's next?

3. CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Aalborg West - Wastewater Treatment Plant Sewer system Bacteria clean our wastewater! Agenda Background Aims Ordination Web app What's next?

4. Aims To explore and explain patterns in the microbial community composition of Danish Wastewater Treatment Plants using various ordination methods and multivariate statistics. • Is there a unique fingerprint (enterotype) of microorganisms for each WWTP? • How are they different and… • Why? • Test known environmental factors or operational parameters CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Agenda Background Aims Ordination Web app What's next?

5. What is ‘ordination’? • A branch of multivariate statistics • The term was first introduced in 1954 by Goodall (it’s nothing new!) • A way to ‘simplify’ complex, multidimensional data • Generally divided into two groups: • Exploratory analysis • Explanatory (constrained) analysis CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Agenda Background Aims Ordination Web app What's next?

6. Why use it? CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Samples (52) Species(14.942) … … Species abundance Agenda Background Aims Ordination Web app What's next?

7. A simple overview is fine, but… CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Aalborg West Aalborg East Agenda Background Aims Ordination Web app What's next?

8. Principal Component Analysis CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Agenda Background Aims Ordination Web app What's next?

9. Steps in ordination CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Abundance table (Samples x Species) Distance Matrix Distance Metric Ordination “Dimensional yoga” 1 2 3 4 5 Agenda Background Aims Ordination Web app What's next?

10. Simplest example: 2 dimensions transformed to 1 CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY (99%) (1%) Agenda Background Aims Ordination Web app What's next?

11. Effect of various distance metrics CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Same raw data! [Enterotypes of the human gut microbiome, Arumugam et al., Nature 2011] Agenda Background Aims Ordination Web app What's next?

12. Many distance metrics, but few relevant CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY[Enterotypes of the human gut microbiome, Arumugam et al., Nature 2011] Agenda Background Aims Ordination Web app What's next?

13. Numerous types of ordination CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY • Exploratory analysis: Principal Component Analysis (PCA) Principal Coordinates Analysis (PCoA/mMDS) (Non-)metric Multi Dimensional Scaling (nMDS) Correspondence Analysis (CA) • Explanatory (constrained) analysis: Redundancy Analysis (RDA) Canonical Correspondence Analysis (CCA) Correspondence analysis (CA) Canonical Correspondence Analysis (CCA) Agenda Background Aims Ordination Web app What's next?

14. Data analysis made easy CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY www.knaldhat.shinyapps.io/shinyampvis Agenda Background Aims Ordination Web app What's next?

15. What’s next? CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY (Made with a shiny app ) Agenda Background Aims Ordination Web app What's next? Half way!

16. Thank you CENTER FOR MICROBIAL COMMUNITIES | AALBORG UNIVERSITY Environmental Biotechnology (EB-group)Supervisor: Mads Albertsen http://github.com/knaldhat/ (Code stuff) Follow me http://albertsenlab.org (Blog)OR

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