The Human Microbiome in
Health and Disease
Curtis Huttenhower
Harvard School of Public Health
Department of Biostatistics
10-21-11
What’s metagenomics?
Total collection of microorganisms
within a community
Also microbial community or microbiota
Total genomic potential of
a microbial community
Study of uncultured microorganisms
from the environment, which can include
humans or other living hosts
Total biomolecular repertoire
of a microbial community
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Valm et al, PNAS 2011
What to do with your metagenome?
Reservoir of
gene and protein
functional
information
Who’s there?
What are they doing?
Comprehensive
snapshot of
microbial ecology
and evolution
Who’s there varies: your microbiota is
plastic and personalized.
What they’re doing is adapting to
their environment:
you, your body, and your environment.
Public health tool
monitoring
population health
and interactions
Who’s
Diagnostic
or there and what
prognostic
differ during disease and
biomarker for
host disease
they do
treatment.
4
Slides by Dirk Gevers
The NIH Human Microbiome Project (HMP):
A comprehensive microbial survey
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What is a “normal” human microbiome?
300 healthy human subjects
Multiple body sites
• 15 male, 18 female
Multiple visits
Clinical metadata
www.hmpdacc.org
A functional perspective on the
human microbiome
Healthy/IBD
BMI
Diet
100 subjects
1-3 visits/subject
~7 body sites/visit
10-200M reads/sample
100bp reads
BLAST
Functional seq.
KEGG + MetaCYC
Metagenomic
reads
CAZy, TCDB,
VFDB, MEROPS…
Taxon
Geneabundances
SNP
Enzyme
family abundances
expression
genotypes
Pathway abundances
?
Enzymes and
pathways
HUMAnN
HMP Unified Metabolic
Analysis Network
http://huttenhower.sph.harvard.edu/humann
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HUMAnN: Metabolic reconstruction
Oral (BM)
Oral (TD)
Gut
← Pathways→
Vaginal Skin Nares Oral (SupP)
← Samples →
Oral (BM)
Gut
Oral (SupP)
Oral (TD)
Skin Nares
← Pathways→
Vaginal
← Samples →
Pathway coverage
Pathway abundance
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A portrait of the healthy human microbiome:
Who’s there vs. what they’re doing
← Pathway abundance →
Nares
Oral (BM)
Vaginal Skin
Gut
Oral (SupP)
Oral (TD)
← Pathway abundance →
← Phylotype abundance →
← Phylotype abundance →
← Subjects →
← Subjects →
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Linking function to community composition
← Taxa and correlated metabolic pathways →
← 52 posterior fornix microbiomes →
Plus ubiquitous pathways: transcription, translation,
cell wall, portions of central carbon metabolism…
Lactobacillus crispatus
Phosphate and peptide
transport
Lactobacillus jensenii
Sugar transport
Lactobacillus gasseri
Embden-Meyerhof glycolysis,
phosphotransferases
Lactobacillus iners
F-type ATPase, THF
Gardnerella/Atopobium
AA and small molecule
biosynthesis
Candida/Bifidobacterium
Eukaryotic pathways
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Linking communities to host phenotype
Normalized relative abundance
Top correlates
with BMI in stool
Body Mass Index
Vaginal pH (posterior fornix)
Vaginal pH, community metabolism, and community
composition represent a strong, direct link between
phenotype and function in these data.
Vaginal pH (posterior fornix)
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So that’s normal – what about disease?
With Matthew Meyerson, Alex Kostic
LEfSe:
LDA Effect Size
Nicola Segata http://huttenhower.sph.harvard.edu/lefse
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So that’s normal – what about disease?
Total
Healthy
CD
UC
M
F
<18
18-65
>65
OSCCAR
116
8
61
47
68
48
23
84
9
PRISM
112
27
58
27
61
51
0
110
2
• Treatments:
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•
•
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• Location:
• Mucosal
(biopsy)
• Luminal (stool)
Antibiotics
Immunosup.
Mesalamine
Steroids
~1-4K 16S
reads/sample
• Genetics:
• ~200 loci,
IBD-targeted
Total
Healthy
CD
UC
M
F
Lean
Ov.
Ob.
Danish
86
86
0
0
42
44
35
14
37
Spanish
38
13
4
21
14
24
18
15
5
Qin 2010
~1-2Gbp 75bp
shotgun reads/sample
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Microbes and their environment:
What’s disease, what’s treatment, and what’s unrelated?
~200 OSCCAR+PRISM individuals
• Multiple Factor Analysis:
Form of Principal Components Analysis
• Separates individuals by similar
patterns of variation in the gut microbiota
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Microbes and their environment:
What’s disease, what’s treatment, and what’s unrelated?
~200 OSCCAR+PRISM individuals
?
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Microbes and their environment:
What’s disease, what’s treatment, and what’s unrelated?
~200 OSCCAR+PRISM individuals
Firmicutes
(Clostridia)
Bifidobacteria
Proteobacteria
(Enterobacteriaceae)
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Environment and disease:
You are your microbes’ environment: age, sampling, and treatment
Firmicutes
Escherichia
~200 OSCCAR+PRISM individuals
Stool vs. biopsy
Dorea
Bifidobacterium
Immunosuppresion
Antibiotics
Age
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• In this cohort, main effects are a
superset of previous findings
• Eggerthella in UC, weaker eff. than CD
Faecalibacterium
Roseburia
Ruminococcus
But what about IBD?
Willing 2010
Frank 2007, Willing 2010
• Ruminococcus down
Willing 2010, Joossens 2011
• Also correctly classify environment
• Proteobacteria up (immunosup.)
Eggerthella
• Roseburia (Lachnospiraceae) down
Ileal involvement
Frank 2007, Willing 2010
• Faecalibacterium down (ileal)
Willing 2010, Frank 2011, Joossens 2011
• And hey, what about…
• Diet? Sample handling? Assay?
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But what about functional detail?
IBD in the MetaHIT cohort
MetaHIT seqs. → HUMAnN → pathway abundances
Up in CD
Down in CD
DNA maintenance
CC + growth
Sugar utilization
Signaling + secretion
Iron + drug transport
UC
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What about the host?
A preview of host genetics
With GwangPyo Ko
All linked to the same family of Clostridiales
Host genetics matter
when not trumped
by additional
environment
glycoprotein
glycoprotein
glycoprotein
glycoprotein
Genotyped microbiomes:
98 women
(twin pairs + mothers)
vaginal microbiomes +
HPV phenotypes
innate immune sensor
extracellular signal transduction
unch. TF
glycoprotein
glycoprotein
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A model for
host genetics and the microbiome
Many genes exert indirect
control over many bugs due
to polygenic immunity and
disease phenotypes.
A few genes exert
strong control over
a few bugs.
A few bugs and many
functions are strong
proximal indicators or
controllers of disease.
Many genes exert
strong distal control
over many bugs due to
founder effects.
Environment exerts
strong proximal control
over many bugs.
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Ask both what you can do for your microbiome
and what your microbiome can do for you
Thanks!
Human Microbiome Project
Nicola Segata
Levi Waldron
Xochi Morgan
Dirk Gevers
George Weinstock
Karen Nelson
Joe Petrosino
Sahar Abubucker
Owen White
Yuzhen Ye
Mihai Pop
Beltran Rodriguez-Mueller
Pat Schloss
Jeremy Zucker
Makedonka Mitreva
Qiandong Zeng
Erica Sodergren
Mathangi Thiagarajan
Vivien Bonazzi
Brandi Cantarel
Jane Peterson
Maria Rivera
Lita Proctor
Barbara Methe
Bill Klimke
Daniel Haft
HMP Metabolic Reconstruction
Joseph Moon
Fah Sathira
Tim Tickle
Ramnik Xavier
Harry Sokol
Jacques Izard
Vagheesh
Narasimhan
Josh Reyes
Wendy Garrett
Michelle Rooks
Jeroen Raes
Karoline Faust
Shuji Ogino
Charlie Fuchs
Bruce Birren Mark Daly
Doyle Ward Eric Alm
Ashlee Earl Lisa Cosimi
Interested? We’re
recruiting graduate and
rotation students!
Matthew Meyerson
Alex Kostic
http://huttenhower.sph.harvard.edu
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Proteoglycan degradation
by the gut microbiota
Glycosaminoglycans
(Polysaccharide chains)
AA core
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Proteoglycan degradation:
From pathways to enzymes
Enzyme relative abundance
10-8
10-3
• Heparan sulfate degradation
missing due to the absence of
heparanase, a eukaryotic enzyme
• Other pathways not bottlenecked
by individual genes
• HUMAnN links microbiome-wide
pathway reconstructions →
site-specific pathways →
individual gene families
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Niche specialization in human
microbiome function
← Pathway abundance→
Metabolic modules in the
KEGG functional catalog
enriched at one or more
body habitats
← ~700 HMP communities→
• 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
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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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LEfSe: the TRUC murine colitis microbiota
With Wendy Garrett
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But what about functional detail?
IBD in the MetaHIT cohort
Bifidobacterium
Up in CD
Down in CD
Age
UC
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