1. Taxonomic profiling with MetaPhlAn2
Curtis Huttenhower
Galeb Abu-Ali
Ali Rahnavard
STAMPS 2017

2. Typical shotgun metagenome and metatranscriptome analyses
Taxonomic
Profiling
Assembly
Functional
Profiling
Samples
Microbes
Relative abundances
Samples
Genes or Pathways
Relative abundances
9/22/2018

3. Two big questions in meta’omics…
Who is there?
(taxonomic profiling)
What are they doing?
(functional profiling)
9/22/2018

4. A typical set of taxonomic profiles
9/22/2018

5. MetaPhlAn2: Taxonomic profiling using unique marker genes
X is a unique marker gene for clade Y
Gene X
~1M most representative markers used for identification
184±45 markers per species (target 200)
~7,100 species (excludes incomplete annotations, spp., etc.)
False positive/False negative rates of ~1 in 106
Profiles all domains of life: bacteria, viruses, euks, archaea
Strain level profiling using marker barcodes and SNPs
Quasi-markers used to resolve ambiguity in postprocessing
Nicola Segata
9/22/2018

6. Evaluating taxonomic profilers using synthetic metagenomes
200-organism synthetic communities
9/22/2018

7. 9/22/2018

8. MetaPhlAn2 (and GraPhlAn) tutorial
9/22/2018

10. The PhlAn tools: using genomes to understand metagenomesII
III IV V I II
III IV V
~1M most representative markers used for identification
184±45 markers per species (target 200)
~7,100 species (excludes incomplete annotations, spp., etc.)
False positive/False negative rates of ~1 in 106
Profiles all domains of life: bacteria, viruses, euks, archaea
Strain level profiling using marker barcodes and SNPs
Quasi-markers used to resolve ambiguity in postprocessing II
III II
Species 1 I IV I I II
III II
Species 2 V IV V V
Species pan-genomes
7,677
containing
18.6 million
gene clusters
Core
genes
Marker
genes
NCBI isolate
genomes
Archaea
300
Bacteria
12,926
Viruses
3,565
Eukaryota
112
Protein coding genes
49.0 million
total genes
RepoPhlAn
ChocoPhlAn (
9/22/2018

11. MetaPhlAn2: Trans-kingdom profiling
9/22/2018