Skin Microbiome (clean) - GitHub Pages microbiome.pdf · HOST-MICROBIOME INTERACTIONS Cause vs...

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 Skin107 cells/cm2

Skin Microbiome§  Co-evolved with us§  Homeostatic and protective

function?

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

Gut Microbiome§  Nutrient Acquisition§  Drug Metabolism§  Development of Immune

System

How do skin bacteria contribute to host health?

http://www.google.com.sg/url?sa=i&source=images&cd=&docid=79U3NUALWEbBrM&tbnid=3aSgFcIo_0tB0M&ved=0CAg

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EVpCoCdESIs-vcHubK_w&ust=1411654838367396

Disease Phenotype: Atopic Dermatitis (AD)

Dry and itchy skinBroken skin barrier

Inflamed lesions that are prone to bacterial infection

b






The Atopic Epidemic International study on Asthma and Allergies in childhood






What causes atopic dermatitis?

Complex interplay between

•  Skin Barrier

•  Immune system •  Environment -  Microbiome


On visually normal, undamaged skin

Normals no history of AD or allergy

SPT+Allergy, no history of AD

ADActive AD patients

Sampling Area:Antecubital fossa

High-throughput DNA Sequencing

Relative abundance and statistical analysis

Coh

orts

Ana

lysis

Microbiome-wide Association study for AD

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

0.2

0.4

0.6

0.8

1.0

Yue-

Cla

yton

The

ta In

dex

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

**

Rel

ativ

e A

bund

ance

(%) 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

**

Rel

ativ

e A

bund

ance

(%)

0.0

0.1

0.2

0.3

0.4 Deinococcus

*

0.0

0.2

0.4

0.6

0.8

1.0 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

Rel

ativ

e A

bund

ance

(%) Malasseziaceae

0

2

4

6

8

10

*** §  No association for Viruses§  Significant depletion of Malassezia

§  Lipid dependent and adapted to skin§  Associated with Dandruff, Seborrhoeic

dermatitis, Tinea Versicolor

Reference genome and annotation for all 14 species and 24 strains of the genusMalassezia Genome Database

RESEARCH ARTICLE

Genus-Wide Comparative Genomics ofMalassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on HumanSkinGuangxi Wu1, He Zhao2, Chenhao Li1, Menaka Priyadarsani Rajapakse1, WingCheongWong3, Jun Xu4, CharlesW. Saunders4, Nancy L. Reeder4, Raymond A. Reilman4,Annika Scheynius5, Sheng Sun6, Blake Robert Billmyre6, Wenjun Li7, AnnaFloyd Averette6, Piotr Mieczkowski8, Joseph Heitman6, Bart Theelen9, MarkusS. Schröder10, Paola Florez De Sessions1, Geraldine Butler10, Sebastian Maurer-Stroh3,11,Teun Boekhout9, Niranjan Nagarajan1*, Thomas L. Dawson, Jr.12*

1 Computational and Systems Biology, Genome Institute of Singapore, A*STAR, Singapore, 2 Procter &Gamble Singapore Innovation Center, Singapore, 3 Bioinformatics Institute, A*STAR, Singapore, 4 Procter& Gamble Mason Business Center, Mason, Ohio, United States of America, 5 Translational Immunology Unit,Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden, 6 DukeUniversity Medical Center, Durham, North Carolina, United States of America, 7 National Center forBiotechnology Information, Bethesda, Maryland, United States of America, 8 University of North Carolina atChapel Hill, Chapel Hill, North Carolina, United States of America, 9 Fungal Biodiversity Centre, CBS-KNAW,Utrecht, The Netherlands, 10 University College Dublin, Dublin, Ireland, 11 School of Biological Sciences,Nanyang Technological University (NTU), Singapore, 12 Institute of Medical Biology, A*STAR, Singapore

* [email protected] (NN); [email protected] (TLD)

AbstractMalassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina,(Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens.Malassezia are typically isolated from warm-blooded animals, are dominant members of thehuman skin mycobiome and are associated with common skin disorders. To characterizethe genetic basis of the unique phenotypes ofMalassezia spp., we sequenced the genomesof all 14 accepted species and used comparative genomics against a broad panel of fungalgenomes to comprehensively identify distinct features that define theMalassezia gene rep-ertoire: gene gain and loss; selection signatures; and lineage-specific gene family expan-sions. Our analysis revealed key gene gain events (64) with a single gene conservedacross allMalassezia but absent in all other sequenced Basidiomycota. These likely hori-zontally transferred genes provide intriguing gain-of-function events and prime candidatesto explain the emergence ofMalassezia. A larger set of genes (741) were lost, with enrich-ment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation toskin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turn-over and underlined the importance of secretory lipases, phospholipases, aspartyl prote-ases, and other peptidases. Combining genomic analysis with a re-evaluation of culturecharacteristics, we establish the likely lipid-dependence of allMalassezia. Our phylogeneticanalysis sheds new light on the relationship betweenMalassezia and other members of

PLOS Genetics | DOI:10.1371/journal.pgen.1005614 November 5, 2015 1 / 26

a11111

OPEN ACCESS

Citation:Wu G, Zhao H, Li C, Rajapakse MP, WongWC, Xu J, et al. (2015) Genus-Wide ComparativeGenomics of Malassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on Human Skin.PLoS Genet 11(11): e1005614. doi:10.1371/journal.pgen.1005614

Editor: Gregory S. Barsh, Stanford University Schoolof Medicine, UNITED STATES

Received: August 30, 2015

Accepted: September 27, 2015

Published: November 5, 2015

Copyright: This is an open access article, free of allcopyright, and may be freely reproduced, distributed,transmitted, modified, built upon, or otherwise usedby anyone for any lawful purpose. The work is madeavailable under the Creative Commons CC0 publicdomain dedication.

Data Availability Statement: All relevant data arewithin the paper and its Supporting Information files.Genomic data has been submitted to genebankunder BioProject ID: PRJNA286710.

Funding: Studies in the JH lab were supported byNIH/NIAID R37 award AI39115-18 and R01 awardAI50113-11. AS is supported by the SwedishResearch Council. Studies in the NN lab weresupported by grants from the Agency for ScienceTechnology and Research (A!STAR), Singapore. Thefunders had no role in study design, data collection

RESEARCH ARTICLE

Genus-Wide Comparative Genomics ofMalassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on HumanSkinGuangxi Wu1, He Zhao2, Chenhao Li1, Menaka Priyadarsani Rajapakse1, WingCheongWong3, Jun Xu4, CharlesW. Saunders4, Nancy L. Reeder4, Raymond A. Reilman4,Annika Scheynius5, Sheng Sun6, Blake Robert Billmyre6, Wenjun Li7, AnnaFloyd Averette6, Piotr Mieczkowski8, Joseph Heitman6, Bart Theelen9, MarkusS. Schröder10, Paola Florez De Sessions1, Geraldine Butler10, Sebastian Maurer-Stroh3,11,Teun Boekhout9, Niranjan Nagarajan1*, Thomas L. Dawson, Jr.12*

1 Computational and Systems Biology, Genome Institute of Singapore, A*STAR, Singapore, 2 Procter &Gamble Singapore Innovation Center, Singapore, 3 Bioinformatics Institute, A*STAR, Singapore, 4 Procter& Gamble Mason Business Center, Mason, Ohio, United States of America, 5 Translational Immunology Unit,Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden, 6 DukeUniversity Medical Center, Durham, North Carolina, United States of America, 7 National Center forBiotechnology Information, Bethesda, Maryland, United States of America, 8 University of North Carolina atChapel Hill, Chapel Hill, North Carolina, United States of America, 9 Fungal Biodiversity Centre, CBS-KNAW,Utrecht, The Netherlands, 10 University College Dublin, Dublin, Ireland, 11 School of Biological Sciences,Nanyang Technological University (NTU), Singapore, 12 Institute of Medical Biology, A*STAR, Singapore

* [email protected] (NN); [email protected] (TLD)

AbstractMalassezia is a unique lipophilic genus in class Malasseziomycetes in Ustilaginomycotina,(Basidiomycota, fungi) that otherwise consists almost exclusively of plant pathogens.Malassezia are typically isolated from warm-blooded animals, are dominant members of thehuman skin mycobiome and are associated with common skin disorders. To characterizethe genetic basis of the unique phenotypes ofMalassezia spp., we sequenced the genomesof all 14 accepted species and used comparative genomics against a broad panel of fungalgenomes to comprehensively identify distinct features that define theMalassezia gene rep-ertoire: gene gain and loss; selection signatures; and lineage-specific gene family expan-sions. Our analysis revealed key gene gain events (64) with a single gene conservedacross allMalassezia but absent in all other sequenced Basidiomycota. These likely hori-zontally transferred genes provide intriguing gain-of-function events and prime candidatesto explain the emergence ofMalassezia. A larger set of genes (741) were lost, with enrich-ment for glycosyl hydrolases and carbohydrate metabolism, concordant with adaptation toskin’s carbohydrate-deficient environment. Gene family analysis revealed extensive turn-over and underlined the importance of secretory lipases, phospholipases, aspartyl prote-ases, and other peptidases. Combining genomic analysis with a re-evaluation of culturecharacteristics, we establish the likely lipid-dependence of allMalassezia. Our phylogeneticanalysis sheds new light on the relationship betweenMalassezia and other members of

PLOS Genetics | DOI:10.1371/journal.pgen.1005614 November 5, 2015 1 / 26

a11111

OPEN ACCESS

Citation:Wu G, Zhao H, Li C, Rajapakse MP, WongWC, Xu J, et al. (2015) Genus-Wide ComparativeGenomics of Malassezia Delineates Its Phylogeny,Physiology, and Niche Adaptation on Human Skin.PLoS Genet 11(11): e1005614. doi:10.1371/journal.pgen.1005614

Editor: Gregory S. Barsh, Stanford University Schoolof Medicine, UNITED STATES

Received: August 30, 2015

Accepted: September 27, 2015

Published: November 5, 2015

Copyright: This is an open access article, free of allcopyright, and may be freely reproduced, distributed,transmitted, modified, built upon, or otherwise usedby anyone for any lawful purpose. The work is madeavailable under the Creative Commons CC0 publicdomain dedication.

Data Availability Statement: All relevant data arewithin the paper and its Supporting Information files.Genomic data has been submitted to genebankunder BioProject ID: PRJNA286710.

Funding: Studies in the JH lab were supported byNIH/NIAID R37 award AI39115-18 and R01 awardAI50113-11. AS is supported by the SwedishResearch Council. Studies in the NN lab weresupported by grants from the Agency for ScienceTechnology and Research (A!STAR), Singapore. Thefunders had no role in study design, data collection

Control Case SPT+

Association with specific Malassezia species

Rel

ativ

e A

bund

ance

(%)

M. dermatis

0

2

4

6

8

Case Control SKP+

*

SKP+

M. restricta

0

20

40

60

80

100

Case Control

M. globosa

Case Control SKP+

**

0

10

20

30

40

50

60

M. sympodialis

Case Control SKP+

0

1

2

3

4

Rel

ativ

e A

bund

ance

(%)

Rel

ativ

e A

bund

ance

(%)

Rel

ativ

e A

bund

ance

(%)

SPT+ SPT+

SPT+ SPT+

HOST-MICROBIOME INTERACTIONSCause vs Effect in relation to AD

1.  Direct cell-to-cell interactionsMicrobe-human, microbe-microbe

2.  By altering the microenvironment

3.  Immune-system mediated

AD-associated microbiome inhibits S. aureus

Staphylococcus aureus

Dermacoccus MethylobacteriumA

ll Su

bjec

ts

Staphylococcus capitis

Streptococcus mitis

AD

Sub

ject

s

Bacterial Inhibition Assay – S. aureus culture

A – Streptococcus mitisB – Staphylococcus epidermidisC – 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

Log2 Conc.

DR

0.0

01%

DP

0.01

%

SE 0

.1%

SE

0.0

1%

SE 0

.001

%

SA 0

.1%

SA

0.0

1%

SA 0

.001

%

BF

0.1%

B

F 0.

01%

B

F 0.

001%

D

R 0

.1%

D

R 0

.01%

DP

0.1%

DP

0.00

1%

DN

0.1

%

DN

0.0

1%

DN

0.0

01%

MCP-3

IL-1a

VEGF

IL-1b IL-6

EGF Eotaxin

IL-10

TGF-a

MIP-1a

MDC MCP-1

IL-8

TNFa

PDGF-AA

TNFb

G-CSF IP-10

Flt-3L GRO FGF-2

PDGF-AB/BB

IFNa2

Fractalkine

IL-12p70

sCD40L

MIP-1b

IL-12p10

RANTES

IL-1RA

SE:StaphylococcusepidermidisSA:StaphylococcusaureusBF:Bacillusfirmus

DR:DeinococcusradioduransDN:DermacoccusnishinomiyaensisDP:Dermacoccusprofundi

Supernatants on Dendritic cells

Bacteria Human cells(NHEKs, MoDCs)

AD skin selects for S. aureus strains

DNA Sequence data

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.

Cases vs Controls in our study

Dry vs Moist sites in Oh et al, Nature 2014

Perturbed microbial metabolism on AD skin EC 3.5.3.6 Arginine Deaminase

Ammonia

Arginine

Citrulline

H2O

Ammonia

Carbamoyl-P Ornithine

Pi

(pH )

ATP + CO2

ADP

(pH )

EC 2.1.3.3 Ornithine Carbamoyltransferase

EC 2.7.2.2 Carbamate Kinase

Depleted in Cases

Enriched in Cases

Case Control Case Control Case Control

Rel

ativ

e A

bund

ance

(×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

****

*

Riskfactors

2.pHchange

NormalSkin

ADflareSkin

3.Increaseinpathobionts

ColonizaConbyopportunisCcpathogens

Immuneac3va3on,Inflamma3on

Summary

1.   Predisposingmicrobiome

Alteredmicroenvironment

Skin Microbiome (clean) - GitHub Pages microbiome.pdf · HOST-MICROBIOME INTERACTIONS Cause vs...

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