scalable metabolic reconstruction for metagenomic data and the human microbiome
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Scalable metabolic reconstruction for metagenomic data and the human microbiome. Sahar Abubucker , Nicola Segata , - PowerPoint PPT PresentationTRANSCRIPT
Scalable metabolic reconstructionfor metagenomic data
and the human microbiomeSahar Abubucker, Nicola Segata,
Johannes Goll, Alyxandria M. Schubert, Jacques Izard,Brandi L. Cantarel, Beltran Rodriguez-Mueller, Jeremy Zucker,
Mathangi Thiagarajan, Bernard Henrissat, Owen White,Scott T. Kelley, Barbara Methé, Patrick D. Schloss,
Dirk Gevers, Makedonka Mitreva,Curtis Huttenhower
07-16-11Harvard School of Public HealthDepartment of Biostatistics
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What’s metagenomics?Total collection of microorganisms
within a community
Also microbial community or microbiota
Total genomic potential of a microbial community
Total biomolecular repertoire of a microbial community
Study of uncultured microorganisms from the environment, which can include
humans or other living hosts
Valm et al, PNAS 2011
What to do with your metagenome?
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Diagnostic or prognostic
biomarker for host disease
Public health tool monitoring
population health and interactions
Comprehensive snapshot of
microbial ecology and evolution
Reservoir of gene and protein
functional informationWho’s there?
What are they doing?
Who’s there varies: your microbiota is plastic and personalized.
What they’re doing is adapting totheir environment:
you, your body, and your environment.
The Human Microbiome Project for a normal population
300 People/15(18) Body
Sites
Multifaceted analyses
2 clin. centers, 4 seq. centers, data generation,technology development, computational tools,
ethics…
Multifaceted data
Human population
Microbial population
Novel organisms
BiotypesVirusesMetabolism
>6,000 samples>50M 16S seqs.4Tbp unique
metagenomicsequence
>1,900 referencegenomes
Full clinicalmetadata
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GeneexpressionSNPgenotypes
Metabolic/Functional Reconstruction: The Goal
Healthy/IBDBMIDiet
Taxon abundancesEnzyme family abundancesPathway abundances
http://huttenhower.sph.harvard.edu/lefse
LEfSe:LDA Effect Size
Metagenomic biomarker discovery
Nicola Segata
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HMP: Metabolic reconstruction
WGS reads
Pathways/modules
Genes(KOs)
Pathways(KEGGs)
Functional seq.KEGG + MetaCYC
CAZy, TCDB,VFDB, MEROPS…
BLAST → Genes
rra
a
raa
p
gap
ggc
)(
)(
1
)()1(
||1)(
Genes → PathwaysMinPath (Ye 2009)
SmoothingWitten-Bell
otherwiseTNNgcgcTNTVTN
gc)/()(
0)()/()/()(Gap filling
c(g) = max( c(g), median )
100 subjects1-3 visits/subject~7 body sites/visit
10-200M reads/sample100bp reads
BLAST
?Taxonomic limitation
Rem. paths in taxa < ave.
XipeDistinguish zero/low
(Rodriguez-Mueller in review)
HUMAnN:HMP UnifiedMetabolic AnalysisNetworkhttp://huttenhower.sph.harvard.edu/humann
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HUMAnN: Metabolic reconstruction
Pathway coverage Pathway abundance
← Samples →←
Pat
hway
s→
Vaginal Skin NaresGut Oral (SupP)Oral (BM) Oral (TD)
← P
athw
ays→
← Samples →
Vaginal Skin Nares GutOral (SupP) Oral (BM) Oral (TD)
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HUMAnN: Validating gene and pathwayabundances on synthetic data
Validated on individual gene families, module coverage, and abundance
• 4 synthetic communities:Low (20 org.) and high (100 org.) complexityEven and lognormal abundances
• Best-BLAST-hit overshoots false positives,
undershoot real pathways as a result• HUMAnN FNs: short genes (<100bp),
taxonomically rare pathways • HUMAnN FPs: large and multicopy
(not many in bacteria)
Individual gene families
ρ=0.91
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← R
elat
ive
abun
danc
e →
← Pathways →
A portrait of the healthy human microbiome:Who’s there vs. what they’re doing
Vaginal SkinNares Gut Oral (SupP)Oral (BM) Oral (TD)
← R
elat
ive
abun
danc
e →
← R
elat
ive
abun
danc
e →
← R
elat
ive
abun
danc
e →
← Phylotypes →
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Niche specialization in human microbiome function
Metabolic modules in theKEGG functional catalogenriched at one or more
body habitats
http://huttenhower.sph.harvard.edu/lefse Nicola Segata
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Proteoglycan degradationby the gut microbiota
AA coreGlycosaminoglycans(Polysaccharide chains)
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Proteoglycan degradation:From pathways to enzymes
10-310-8
Enzyme relative abundance
• Heparan sulfate degradation
missing due to the absence of
heparanase, a eukaryotic enzyme• Other pathways not
bottleneckedby individual
genes
• HUMAnN links microbiome-wide
pathway reconstructions →
site-specific pathways →individual gene families
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Patterns of variation in human microbiome function by niche
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Patterns of variation in human microbiome function by niche
• Three main axes of variation• Eukaryotic exterior• Low-diversity vaginal• Gut metabolism• Oral vs. tooth hard surface• Only broad patterns:
every human-associated habitat
is functionally distinct!
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How do microbes and function varywithin each body site across the population?
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How do body sites compare between individuals across the population?
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HMP: Prevalence of species (OTUs)across the population
Cumulative prevalence
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HMP: Prevalence of pathwaysacross the population
• 16 (of 251) modules strongly “core” at 90%+ coverage in 90%+ individuals at 7 body sites
• 24 modules at 33%+ coverage• 71 modules (28%) weakly “core” at 33%+ coverage in 66%+ individuals at
6+ body sites• Contrast zero phylotypes or OTUs meeting this threshold!• Only 24 modules (<10%) differentially covered by body site• Compare with 168 modules (>66%) differentially abundant by body site
Cumulative prevalence
Linking function to community composition
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← T
axa
and
corr
elat
ed m
etab
olic
pat
hway
s →
← 52 posterior fornix microbiomes →
F-type ATPase, THF
Sugar transport
Phosphate and peptide transport
AA and small molecule biosynthesis
Embden-Meyerhof glycolysis, phosphotransferases
Eukaryotic pathways
Plus ubiquitous pathways: transcription, translation, cell wall, portions of central carbon metabolism…
Lactobacillus crispatus
Lactobacillus jensenii
Lactobacillus gasseri
Lactobacillus iners
Gardnerella/Atopobium
Candida/Bifidobacterium
Linking communities to host phenotype
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Nor
mal
ized
rela
tive
abun
danc
e
Vaginal pH (posterior fornix)
Body Mass Index
Top correlates with BMI in stool
Vaginal pH, community metabolism, and community composition represent a strong, direct link between
phenotype and function in these data.
Vaginal pH (posterior fornix)
Microbial biomolecular function and metabolism in the human microbiome: the story so far?
• HUMAnN– Accurate metagenomic metabolic reconstruction– Sequences → genes → pathways → phenotypes– Validated on 4x synthetic communities
• Who’s there varies even in health– What they’re doing doesn’t (as much)
• There are patterns in this variation– Communities in related environments adapt using related functions– Function correlates with membership and phenotype
• ~1/3 to 2/3 of human metagenome characterized– Job security! 22
Ask both what you can do for your microbiomeand what your microbiome can do for you
Thanks!
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Jacques IzardAlyx SchubertPat Schloss
Nicola Segata Levi Waldron
FahSathira
Interested? We’re recruitingstudents and postdocs!
Human Microbiome Project
HMP Metabolic Reconstruction
George WeinstockOwen WhiteRob KnightMakedonka MitrevaErica SodergrenMihai PopVivien Bonazzi Jane PetersonLita Proctor
Johannes GollYuzhen Ye
Beltran Rodriguez-MuellerJeremy Zucker
Mathangi ThiagarajanBrandi CantarelQiandong Zeng
Maria RiveraBarbara Methe
Bill KlimkeDaniel Haft
Dirk Gevers
Bruce Birren Ramnik XavierDoyle Ward Eric AlmAshlee Earl Lisa Cosimi
http://huttenhower.sph.harvard.eduhttp://huttenhower.sph.harvard.edu/humann
http://huttenhower.sph.harvard.edu/lefse
BenGanzfried
Sahar Abubucker
LarisaMiropolsky
VagheeshNarasimhan
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HMP: Prevalence of genera (phylotypes)across the population
Cumulative prevalence