The Human Microbiome inHealth and Disease
Curtis Huttenhower
10-21-11Harvard School of Public HealthDepartment of Biostatistics
2
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?
4
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.
Who’s there and what they dodiffer during disease and treatment.
The NIH Human Microbiome Project (HMP):A comprehensive microbial survey
• What is a “normal” human microbiome?• 300 healthy human subjects• Multiple body sites
• 15 male, 18 female• Multiple visits• Clinical metadata
www.hmpdacc.org
Slides by Dirk Gevers
GeneexpressionSNPgenotypes
A functional perspective on thehuman microbiome
6
Healthy/IBDBMIDiet
Taxon abundancesEnzyme family abundancesPathway abundances
Functional seq.KEGG + MetaCYC
CAZy, TCDB,VFDB, MEROPS…
100 subjects1-3 visits/subject~7 body sites/visit
10-200M reads/sample100bp reads
Metagenomic reads
Enzymes and pathways
?
HUMAnNHMP Unified Metabolic
Analysis Networkhttp://huttenhower.sph.harvard.edu/humann
BLAST
7
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)
8← Subjects →
← P
athw
ay a
bund
ance
→←
Phy
loty
pe a
bund
ance
→
A portrait of the healthy human microbiome:Who’s there vs. what they’re doing
Vaginal SkinNares Gut Oral (SupP)Oral (BM) Oral (TD)
← P
hylo
type
abu
ndan
ce →
← Subjects →
← P
athw
ay a
bund
ance
→
Linking function to community composition
9
← 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
10
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)
So that’s normal – what about disease?
11
With Matthew Meyerson, Alex Kostic
Nicola Segata http://huttenhower.sph.harvard.edu/lefse
LEfSe:LDA Effect Size
So that’s normal – what about disease?
12
Total Healthy CD UC M F Lean Ov. Ob.Danish 86 86 0 0 42 44 35 14 37Spanish 38 13 4 21 14 24 18 15 5
Qin 2010
~1-2Gbp 75bp shotgun reads/sample
Total Healthy CD UC M F <18 18-65 >65OSCCAR 116 8 61 47 68 48 23 84 9PRISM 112 27 58 27 61 51 0 110 2
~1-4K 16S reads/sample
•Treatments:•
Antibiotics•
Immunosup.•
Mesalamine•
Steroids
•Location:•
Mucosal
(biopsy)•
Luminal (stool)
•Genetics:•
~200 loci,
IBD-targeted
Microbes and their environment:What’s disease, what’s treatment, and what’s unrelated?
13
~200 OSCCAR+PRISM individuals• Multiple Factor Analysis:
Form of Principal Components Analysis• Separates individuals by similar
patterns of variation in the gut microbiota
Microbes and their environment:What’s disease, what’s treatment, and what’s unrelated?
14
~200 OSCCAR+PRISM individuals
?
Microbes and their environment:What’s disease, what’s treatment, and what’s unrelated?
15
~200 OSCCAR+PRISM individuals
Proteobacteria(Enterobacteriaceae)
Firmicutes(Clostridia)
Bifidobacteria
Environment and disease:You are your microbes’ environment: age, sampling, and treatment
16
~200 OSCCAR+PRISM individuals
Firm
icut
es
Stool vs. biopsy
Bifi
doba
cter
ium
AgeAntibiotics
Dor
ea
Immunosuppresion
Esch
eric
hia
But what about IBD?
17
Ros
ebur
ia
Rum
inoc
occu
sEg
gert
hella
• In this cohort, main effects are a
superset of previous findings• Eggerthella in UC, weaker
eff. than CD
Willing 2010• Roseburia
(Lachnospiraceae) down
Frank 2007, Willing 2010• Ruminococcus down
Willing 2010, Joossens 2011
• Also correctly classify environment• Proteobacteria up
(immunosup.)
Frank 2007, Willing 2010• Faecalibacterium down
(ileal)
Willing 2010, Frank 2011, Joossens 2011
• And hey, what about…• Diet? Sample handling?
Assay?
Ileal involvement
Faec
alib
acte
rium
But what about functional detail?IBD in the MetaHIT cohort
18
UC
Up in CDDown in CD
DNA maintenanceCC + growth
Sugar utilizationSignaling + secretionIron + drug transport
MetaHIT seqs. → HUMAnN → pathway abundances
What about the host?A preview of host genetics
19
Genotyped microbiomes:98 women
(twin pairs + mothers)vaginal microbiomes +
HPV phenotypes
With GwangPyo Ko
All linked to the same family of Clostridiales
glycoprotein
glycoprotein
glycoprotein
glycoproteinglycoprotein
innate immune sensor
extracellular signal transduction
unch. TF
glycoprotein
Host genetics matter when not trumped
by additional environment
20
A model forhost genetics and the microbiome
A few genes exert strong control over
a few bugs.
Many genes exert strong distal control
over many bugs due to founder effects.
Many genes exert indirect control over many bugs due to polygenic immunity and
disease phenotypes.
Environment exerts strong proximal control
over many bugs.
A few bugs and many functions are strong proximal indicators or controllers of disease.
Ask both what you can do for your microbiomeand what your microbiome can do for you
Matthew MeyersonAlex Kostic
Ramnik XavierHarry Sokol
Thanks!
22
Nicola Segata Levi Waldron
Fah Sathira
Human Microbiome Project
HMP Metabolic Reconstruction
George WeinstockKaren NelsonJoe PetrosinoOwen WhiteMihai PopPat SchlossMakedonka MitrevaErica SodergrenVivien Bonazzi Jane PetersonLita Proctor
Sahar AbubuckerYuzhen Ye
Beltran Rodriguez-MuellerJeremy ZuckerQiandong Zeng
Mathangi ThiagarajanBrandi Cantarel
Maria RiveraBarbara Methe
Bill KlimkeDaniel Haft
Dirk Gevers
Bruce Birren Mark DalyDoyle Ward Eric AlmAshlee Earl Lisa Cosimi
http://huttenhower.sph.harvard.edu
Joseph Moon
VagheeshNarasimhan
Tim Tickle
Xochi Morgan
Josh Reyes
Jeroen RaesKaroline Faust
Jacques Izard
Shuji OginoCharlie Fuchs
Wendy GarrettMichelle Rooks
Interested? We’re recruiting graduate and
rotation students!
24
Proteoglycan degradationby the gut microbiota
AA coreGlycosaminoglycans(Polysaccharide chains)
25
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
26
← P
athw
ay a
bund
ance
→
← ~700 HMP communities→
Niche specialization in human microbiome function
Metabolic modules in theKEGG functional catalogenriched at one or more
body habitats
• 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
27
Patterns of variation in human microbiome function by niche
28
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!
29
LEfSe: the TRUC murine colitis microbiotaWith Wendy Garrett
30
But what about functional detail?IBD in the MetaHIT cohort
UC
Bifi
doba
cter
ium
Age
Up in CDDown in CD