Download Taxonomic profiling with MetaPhlAn2

Taxonomic profiling with MetaPhlAn2
Curtis Huttenhower
Galeb Abu-Ali
Eric Franzosa
Harvard T.H. Chan School of Public Health
Department of Biostatistics
08-12-16
The two big questions of microbial
community analysis...
Who is
there?
What
are they
doing?
2
Taxonomic profiling: who’s there
http://huttenhower.sph.harvard.edu/metaphlan2
3
Efficient assembly-free meta’omics by leveraging isolates
I
II
III
III
4
I
II
II
III
II
I
I
IV
II
II
IV
IV
V
V
I
IV
I
I
III
II
II
IV
II
II
V
IV
V
V
III
III
II
V
NCBI isolate
genomes
Archaea
300
Bacteria 12,926
Viruses
3,565
Eukaryota
112
V
II
Open reading
frames
49.0 million
total genes
RepoPhlAn
Species pangenomes
Core
genes
Marker
genes
7,677
containing
18.6 million
gene clusters
Nicola Segata
ChocoPhlAn
http://www.metaref.org
MetaPhlAn2: metagenomic
taxonomic profiling
http://huttenhower.sph.harvard.edu/metaphlan2
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
5
Coverage
Per-species abundance by
robust averaging
Multi-copy
genes
Plateau of genes from one metagenome’s strain
Absent genes
Abundance-sorted pan-gene families
6
Meta-analysis of metagenomic
taxonomic profiles
•
•
•
Waldron and Segata: meta-analysis of
>2,400 gut metagenomes.
Available as an R package.
Allows systematic tests of phenotypes across
datasets, or health vs. disease.
7