The Role of the Skin

Microbiome in Eczema

Niranjan NagarajanAssociate Director and Group Leader

Computational & Systems Biology

Epidermal Hydration

Mechanical Barrier

Permeability Barrier

Waterproof Barrier

Anti-microbial Barrier

Anti-oxidant Barrier

Anti-UV Barrier

Initiation of inflammation

The human skin is an effective barrier

Slide credit: John Common

Infection transmission via skin

Conjuctivitis, Acne, Staph/Strep infections,

Herpes, Yeast infections, Ebola, RSV, Hand-

foot-mouth disease, Athlete’s foot, …

http://www.genome.gov/pressDisplay.cfm?photoID=20169

Microbial Communities on Skin

107 cells/cm2

Skin Microbiome

▪▪ Co-evolved with us

▪▪ Homeostatic and protective

function?

Gut Microbiome

▪▪ Nutrient Acquisition

▪▪ Drug Metabolism

▪▪ Development of Immune

System

Credit: Matej Bajzer & Randy J. Seeley. Nature 444, 1009-1010 (21 December 2006)

How do skin bacteria contribute to host health?

Disease Phenotype: Atopic Dermatitis (AD)

Dry and itchy skin

Broken skin barrier

Inflamed lesions that are

prone to bacterial infection

b

Slide credit: John Common

The Atopic EpidemicInternational study on Asthma and Allergies in childhood

Slide credit: John Common

What causes atopic dermatitis?

Complex interplay between

• Skin Barrier

• Immune system

• Environment

- Microbiome

Slide credit: John Common

Normals

no history of AD or allergy

SPT+

Allergy, no history ofAD

AD

Active AD patients

Sampling Area:

Antecubital fossa

High-throughput

DNASequencingRelative abundance

and statistical analysis

Coh

ort

sA

naly

sis

Microbiome-wide Association study forADOn visually normal, undamaged skin

Chng KR, Tay ASL, Li C, Ng AHQ, …, Lane EB, Chew FT, Common JEA#, Nagarajan N#"Whole

metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare"

Nature Microbiology 2016 1:16106 doi:10.1038/nmicrobiol.2016.106

Control-Case Case-Case

0.0

1.0

0.8

0.6

0.4

0.2

Yu

e-C

layto

nT

he

ta In

de

x

p-value = 2.4×10-6

Control (Normal)

Case (AD)

SPT+

Bacterial Diversity on Normal Skin

Enrichment of opportunistic pathogens in AD

0

2

4

6

8 Streptococcus

**

Re

lative

Ab

un

da

nce

(%

) Gemella

0.0

0.2

0.4

0.6

0.8

1.0

**

0.0

0.5

1.0

1.5

2.0 Haemophilus

*

Staphylococci produce

factors that promote the

growth of Haemophilus

Known to cause skin

and oral infections.

Changes specific to α-

hemolytic group

Can aggravate

symptoms in

Cystic Fibrosis

Control

Case

SPT+

Depletion of metabolically versatile bacteria

0.0

0.5

1.0

1.5

2.0

3.0

2.5

Dermacoccus

**

Re

lative

Abundance (

%)

0.0

0.1

0.2

0.3 *

0.0

0.2

0.4

0.6

0.8

0.4 1.0Deinococcus Methylobacterium

*

Actinomycetales are known for

producing secondary metabolites

with anti-inflammatory and anti-

microbial properties

Radiation tolerant and

metabolically versatile

Found commonly

on human feet

Control

Case

SPT+

Viruses & Eukaryotes

Re

lative

A

bun

da

nce

(%

)

0

2

4

6

8

10 Malasseziaceae

***▪▪ No association for Viruses

▪▪ Significant depletion of Malassezia

▪▪ Lipid dependent and adapted to skin

▪▪ Associated with Dandruff, Seborrhoeic

dermatitis, Tinea Versicolor

Malassezia Genome Database

Reference genome and annotation for all 14 species and 24 strains of the genus

RESEARCH ARTICLE

Genus-Wide Comparative Genomics of

Malassezia Delineates Its Phylogeny,

Physiology, and Niche Adaptation on Human

Skin

Guangxi Wu1, He Zhao2, Chenhao Li1, Menaka Priyadarsani Rajapakse1, Wing Cheong

Wong3, Jun Xu4, Charles W. Saunders4, Nancy L. Reeder4, Raymond A. Reilman4, Annika

Scheynius5, Sheng Sun6, Blake Robert Billmyre6, Wenjun Li7, Anna Floyd Averette6,

Piotr Mieczkowski8, Joseph Heitman6, Bart Theelen9, Markus

S. Schröder10, Paola Florez De Sessions1, Geraldine Butler10, Sebastian Maurer-Stroh3,11,

Teun Boekhout9, Niranjan Nagarajan1*, Thomas L. Dawson, Jr.12*

Control

Case

SPT+

Association with specific Malassezia species

Rela

tiv

eA

bu

nd

an

ce (

%)

M. dermatis

0

2

4

6

8

CaseControl SKP+

*

SKP+

M. restricta

0

20

40

60

80

100

CaseControl

M. globosa

CaseControl SKP+

**

0

10

20

30

40

50

60

M. sympodialis

CaseControl SKP+

0

1

2

3

4

Rela

tiv

eA

bu

nd

an

ce (

%)

Rela

tiv

eA

bu

nd

an

ce (

%)

Rela

tiv

eA

bu

nd

an

ce (

%)

SPT+ SPT+

SPT+ SPT+

HOST-MICROBIOME INTERACTIONS

Cause vs Effect in relation to AD

1. Direct cell-to-cell interactions

Microbe-human, microbe-microbe

2. By altering the microenvironment

3. Immune-system mediated

AD-associated microbiome inhibits S. aureus

Dermacoccus Methylobacterium

All

Su

bje

cts

Staphylococcus

capitis

Streptococcus

mitis

AD

Su

bje

cts

Staphylococcus

aureus

Bacterial Inhibition Assay – S. aureus culture

A – Streptococcus mitis

B – Staphylococcus epidermidis

C – BHI Media

AD associated bacteria elicit distinct immune responses

1. Flare associated bacteria (S.

epidermidis and S. aureus)

induce strong immune

response

– TNF-driven myeloid activating and

Th1 polarizing cytokine signature

2. Depleted bacteria (D.

nishinomiyaensis and D.

radiodurans) elicit minimal

response

0.0 18.0

Log2Conc.% %

0.1%

0.01%

0.001

%

%1 %1%10%10100100. .. ... 000000

SE SESE SASASABFBFBF

0.1%0.01%0.001%

0.1%0.01%0.001%

0.1% 0.01%0.001%

DRDRDR DPDPDP

DNDNDN

MDCMCP-1 MIP-1b IL-8 MIP-1a TNFa TGF-aPDGF-AA IL-10TNFb EGFEotaxin G-CSF IP-10IL-1b IL-6Flt-3LGRO FGF-2 MCP-3PDGF-AB/BB IL-12p70IL-12p10 IL-1aRANTES VEGF IFNa2 sCD40LFractalkine IL-1RA

SE: Staphylococcus epidermidisSA: Staphylococcus aureusBF: Bacillusfirmus

DR: Deinococcus radioduransDN: Dermacoccus nishinomiyaensisDP: Dermacoccus profundi

Supernatants on Dendritic cells

BacteriaHuman cells(NHEKs, MoDCs)

AD skin selects for S. aureus strains

AD susceptible skin = geh Arg 373

Normal skin = geh Thr 373

Dry skin sites = geh Arg 373

Moist skin sites = geh Thr 373

Moist Dry

Healthy skin AD-susceptible skin

geh gene - Lipase gene

(glycerol ester hydrolase) is

important for virulence.

DNA Sequence data

Cases vs Controls in our study

Dry vs Moist sites in Oh et al, Nature 2014

Perturbed microbial metabolism on AD skin

EC 3.5.3.6Arginine Deaminase

Arginine

Citrulline

H2O

Ornithine

Pi

Ammonia (pH )

ATP + CO2

Carbamoyl-PADP

Ammonia(pH )

EC 2.1.3.3Ornithine

Carbamoyltransferase

EC 2.7.2.2Carbamate Kinase

Depleted in Cases

Enriched in Cases

Case CaseControl Case

Re

lati

ve

Ab

un

da

nc

e (×

10

-4)

0

2

4

6

8

10 EC 3.5.3.6

EC 2.1.3.3

EC 2.7.2.2

Combined p-

value = 0.0029

*Control

***

*Control

Normal Skin

AD flare Skin

3. Increase in pathobionts

Colonization by opportunistic pathogens

Immune activation, Inflammation

Summary

Altered microenvironment

2. pH change

Risk factors

1. Predisposing microbiome

Presented at the 3rd Microbiome R&D and

Business Collaboration Congress: Asia.

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