Transcript 2016_Huttenhower_Stamps09

Strain profiling with StrainPhlAn
Curtis Huttenhower
Galeb Abu-Ali
Eric Franzosa
Harvard T.H. Chan School of Public Health
Department of Biostatistics
08-12-16
Efficient assembly-free meta’omics by leveraging isolates
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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
PanPhlAn: the approach
http://bitbucket.org/CibioCM/panphlan
Gene coverage
Read
mapping
Metagenomic
sample
Microbial
pangenomes
Cluster to
Gene families
Coverage
Pan-gene family coverage
Multi-copy
genes
Plateau of genes from one metagenome’s strain
Absent genes
Abundance-sorted pan-gene families
PanPhlAn for “meta-epidemiology”
http://bitbucket.org/CibioCM/panphlan
Metagenomes from [Loman et al., 2013]
Strain-level tracking with other species
Prevotella copri
Synthetic and semi-synthetic validation
Coverage
Coverage
Coverage
Coverage
Coverage
StrainPhlAn: metagenomic
strain identification and tracking
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A tool for strain level population genomics
China
Denmark
Estonia
Finland
Peru’
Hungary
Italy
Norway
France
Spain
Sweden
USA
Germany
P. copri as an example species
Alignment length: 66k nt
Median SNPs: 830 [3.6%]
# pos. samples: 123
A tool for strain level population genomics
Alignment length: 62k nt
Median SNPs: 830 [1.3%]
# pos. samples: 123
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Strains in the HMP1-II
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Most bugs are dominated by one stable strain
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Most bugs are dominated by one stable strain
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There’s a lot of strain-level
variation left to discover
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There’s a lot of strain-level
variation left to discover
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Thanks!
http://huttenhower.sph.harvard.edu
Human Microbiome Project 2
Alex
Ayshwarya
Xochitl
Kostic Subramanian Morgan
Casey
DuLong
Daniela
Boernigen
Lauren
McIver
Ramnik Xavier
Lita Procter
Bruce Birren
Jon Braun
Chad Nusbaum
Dermot McGovern
Clary Clish
Subra Kugathasan
Joe Petrosino
Ted Denson
Thad Stappenbeck
Janet Jansson
Human Microbiome Project
George
Weingart
Emma
Schwager
Eric
Franzosa
Boyu
Ren
Tiffany
Hsu
Ali
Rahnavard
Joseph
Moon
Jim
Kaminski
Tommi
Vatanen
Koji
Yasuda
Siyuan
Ma
Galeb
Abu-Ali
Bahar
Sayoldin
Randall
Schwager
Melanie
Schirmer
Himel
Mallick
Moran
Yassour
Alexandra
Sirota-Madi
Hera Vlamakis
Dirk Gevers
Jane Peterson
Sarah Highlander
Barbara Methe
Nicola Segata
Clary Clish
Justin Scott
Karen Nelson
George Weinstock
Owen White
Levi
Waldron
Wendy Garrett