Introduction to Metagenomics

Sünje Johanna Pamp

Associate Professor
Technical University of Denmark

sjpamp@food.dtu.dk
@SJPamp
Outline
• Surveillance of Pathogens & Antimicrobial resistance genes

• 4 Approaches in Microbial Genomics

• Metagenomics

• Current challenges

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Pathogen & Antimicrobial Resistance
Transmission

Where are the:

• Pathogens?
• Antibiotic resistance genes?

What are the transmission

patterns and routes?

How can we explain these?

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Pathogens & Antimicrobial Resistance
Pathogens are microorganisms that can cause disease in individuals.
They can harbour genes conferring resistance to antimicrobials.

bacteria fungi parasites viruses

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Metagenomics – One technology that takes all
DNA Sequence information
-Universal ”language”
-Standardized format
-Share across labs and disciplins
-Archive available for re-analysis

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 Metagenomics

Metagenomics

is defined as the sequencing-based analysis of genomes

contained with an environmental sample

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Handelsman et al., Chemistry & Biology (1998); Thomas et al., Microb Inform Exp (2012)
 Microbial Genomics

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 Microbial Genomics

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Metagenomics:
A tool to obtain actionable information on
Pathogens & Antimicrobial Resistance

bacteria
Taxonomic identity

fungi Phylogeny

DNA/RNA DNA Data Antibiotic resistance genes

Sequencing Analysis Virulence genes
parasites
Metabolic capacity

viruses

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Metagenomics projects - Outline

See lecture:
Considerations & Controls for
Metagenomic/Microbiome
Projects

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 Metagenomics: General laboratory steps

Reads

(RNA isolation -> cDNA) Illumina

PacBio
IonTorrent
454
Nanopore

Nanopore

See Module B

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Handelsman et al., Chemistry & Biology (1998); Thomas et al., Microb Inform Exp (2012)
 Metagenomics: Data analysis

Reads
Taxonomic identity
Phylogeny
Antibiotic resistance genes
Virulence genes
Metabolic capacity
…

Binning & Contigs/

Assembly Scaffolds
See Module C

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 Current Challenges

• Sequencing the tip of the iceberg (for highly complex samples)

• Background DNA sequences (e.g. host, environment)
• Lack of reference genomes (novel organisms)
• Low-quality reference genome (contaminant sequences -> false-positive)
• Quantification / Normalization
• Assembly: risk of chimera formation
• Function of most predicted proteins unknown
• Associations with covariates: Correlation ≠ Causation

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 Thank you!

Sünje Johanna Pamp

Associate Professor
Technical University of Denmark

sjpamp@food.dtu.dk
@SJPamp

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