The Human Microbiome inHealth and Disease

Curtis Huttenhower

10-21-11Harvard 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.

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

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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

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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)

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

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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)

So that’s normal – what about disease?

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With Matthew Meyerson, Alex Kostic

Nicola Segata http://huttenhower.sph.harvard.edu/lefse

LEfSe:LDA Effect Size

So that’s normal – what about disease?

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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?

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~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?

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~200 OSCCAR+PRISM individuals

?

Microbes and their environment:What’s disease, what’s treatment, and what’s unrelated?

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~200 OSCCAR+PRISM individuals

Proteobacteria(Enterobacteriaceae)

Firmicutes(Clostridia)

Bifidobacteria

Environment and disease:You are your microbes’ environment: age, sampling, and treatment

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~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?

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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

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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

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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

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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!

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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!

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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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← 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

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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 microbiotaWith Wendy Garrett

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But what about functional detail?IBD in the MetaHIT cohort

UC

Bifi

doba

cter

ium

Age

Up in CDDown in CD