Metagenomics 101 Dr Michael Imelfort m.imelfort@uq.edu.au IMB - - PowerPoint PPT Presentation

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Metagenomics 101 Dr Michael Imelfort m.imelfort@uq.edu.au IMB Winter School in Bioinformatics July 1 st 2013 What is Metagenomics? typically involves microbes typically uses next gen is new* is an open problem is

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Metagenomics 101

Dr Michael Imelfort

m.imelfort@uq.edu.au

IMB Winter School in Bioinformatics

July 1st 2013

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What is Metagenomics?

→ typically involves microbes → typically uses next gen → is new* → is an open problem → is difficult to do well → is very interesting

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16S rRNA pyrotagging “deep” metagenomics

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Volume Resolution

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16S rRNA pyrotagging

Exploits conserved Vs unconserved regions in 16S subunit “Roll call” Semi-quantitative

Multiple copies of 16S
Multiple copies of chromosomes

Inexpensive (relatively) Approximate

97% identity → species / genus

Established (1970s)

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Deep Metagenomics

DNA extraction and sequencing Assembly (including QA) Binning Analysis

Natural environments
Contamination
Low amounts of DNA
Wildly different coverage levels
Strain heterogeneity
GroopM
Coverage
ESOM
Kmers
T

axonomic assignment / Genome trees

Annotation
Metabolomic reconstruction
Population / community dynamics

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Case study - ANME2D

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Case study - ANME2D

Nitrogen removal (de nitrification) addition of methanol → $$$ produces methane → greenhouse gas There is some evidence to show that certain microbial populations can couple methane

xidisation (AOM) to nitrate reduction

WHO? HOW?

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Enrichment

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16S rRNA + FISH

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Assembly and binning

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The evidence

Abundance data ( 16S rRNA ) + full methanogenesis pathway + metatranscriptomic data + process data + metrics + isotope labelling

The data

16S rRNA: 454 Metagenome: Illumina HiSeq (1 lane PE) IonT

rrent PGM (MP)

Metatranscriptome: Illumina MiSeq IonT

rrent PGM

What next..?

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Next...

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Microbes are awesome

Postdoc / Phd / Masters / Honours

Bioinformatics and metagenomics Soil, engineered, Human, agricultural and marine systems. Whole community analysis and single amplified genomes. Tree of life, assembly, binning, annotation, more... Contact: Professor Phil Hugenholtz: p.hugenholtz@uq.edu.au Dr Gene Tyson: g.tyson@uq.edu.au Dr Michael Imelfort: m.imelfort@uq.edu.au

www.ecogenomic.org

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