PowerPoint Presentation€¦ · · 2017-03-03Liu J et al. ISME J 2015. Tomida S. et al. mBio....
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3/3/2017 1 What’s bugging you? Relevance of the Human Microbiome in Health and Disease Heidi H. Kong, MD, MHSc, FAAD Dermatology Branch DISCLOSURE OF RELATIONSHIPS WITH INDUSTRY Heidi H Kong, MD, MHSc, FAAD U097: Relevance of the Human Microbiome in Health & Disease DISCLOSURES No relevant conflicts to disclose Human Microbiome Defining ‘microbiome’ Microbiome in health & disease Non-dermatologic Arthritis, Cardiometabolism, Cancer Skin Potential applications Clostridium difficile colitis Definition of Microbiome Collection of microbes including bacteria, viruses, and eukaryotes (fungi) and their collective genomes Kong. Trends Molec Med. 2011 Collect superficial skin sample Isolate DNA Amplify DNA with primers (bacteria = 16S rRNA gene) DNA sequencing/analysis Pipeline for skin microbiome studies
Transcript of PowerPoint Presentation€¦ · · 2017-03-03Liu J et al. ISME J 2015. Tomida S. et al. mBio....
3/3/2017
1
What’s bugging you?
Relevance of the Human Microbiome
in Health and DiseaseHeidi H. Kong, MD, MHSc, FAAD
Dermatology Branch
DISCLOSURE OF RELATIONSHIPS WITH INDUSTRY
Heidi H Kong, MD, MHSc, FAAD
U097: Relevance of the Human Microbiome in Health & Disease
DISCLOSURES
No relevant conflicts to disclose
Human Microbiome
Defining ‘microbiome’
Microbiome in health & disease
Non-dermatologic
Arthritis, Cardiometabolism, Cancer
Skin
Potential applications
Clostridium difficile colitis
Definition of Microbiome
Collection of microbes including bacteria,
viruses, and eukaryotes (fungi) and
their collective genomes
Kong. Trends Molec Med. 2011
Collect superficial skin sample
Isolate DNA
Amplify DNA with primers
(bacteria = 16S rRNA gene)
DNA sequencing/analysis
Pipeline for skin microbiome studies
3/3/2017
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Direct sequencing vs.
culture-based methods
Diversity from culture
Diversity from direct
sequencing
NIH Common Fund:
Human Microbiome Project
Longitudinally assess
microbial diversity of 250
healthy subjects at 5 major
body sites
HMP Consortium. Nature 2012
Science 2009
Defining the Human Microbiome
Collection of microbes including bacteria, viruses, and
eukaryotes (fungi) and their collective genomes
Human microbes more diverse that observed with
traditional culturing
Integrating genomics into microbial investigations is
advancing our knowledge about our microbes
Different body sites contain distinctive microbial
communities
Obesity-associated fecal
transfer results in obese
phenotype
Obesity-associated fecal bacteria
Indigestible dietary complex
carbohydrates
Efficiently harvest energy
Facilitate absorption of short-
chain fatty acids
Turnbaugh P at al. Nature 2006.
Aron-Wishewsky A, Clement K. Nature Rev Nephrol 2016. Aron-Wishewsky A, Clement K. Nature Rev Nephrol 2016.
debated
observations
Linking diet, microbiota & cardiovascular/kidney disease
Meat, fish,
eggs
TMAO =
trimethylamine
N-oxide
MACE = major
adverse cardiac
events
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Bravo-Blas et al. Curr Opin Rheumatol 2016.
Arthritis & Microbiome
Bravo-Blas et al. Curr Opin Rheumatol 2016.
Arthritis & Microbiome
Mouse model of arthritis• Segmented filamentous bacteria found
to trigger autoimmune arthritis in germ-
free K/BxN mice
Wu H-J et al. Cell 2010
• Patient studies searching for
microbiome differences have been
mixed/inconclusive
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Human Microbiome
Defining ‘microbiome’
Microbiome in health & disease
Non-dermatologic
Arthritis, Cardiometabolism, Cancer
Skin
Potential applications
Clostridium difficile colitis
3/3/2017
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The Skin Microbiome
Skin
Microbes
Host
Host factors influence
skin microbial
composition
Skin microbiota
influence host skin
Skin Bacterial Genomic Data
16S rRNA gene
• Universal
• Assess phylogeny
Grice, Kong, et al. Genome Research 2008
Grice, Kong…Segre. Science. 2009
Skin bacterial communities demonstrate topographical
diversity and site-specificityOily
Moist
Dry
• Bacterial skin communities are site-specific
• Skin microenvironments are associated with
differences in the relative abundances of
predominant bacteria
20 skin sites
Naik S et al. Science 2012
0
5
10
15
20
25
IFN
-g+
TC
Rb
+(%
)
0
10
20
30
ns
Ctrl
Antibiotics
IL-1
7A
+ C
D4
5+
(%
)
0
2
4
6
8
0
2
4
6
8
ns
SkinGut
SkinGut
0
10
20
30
40
50
60
70
80
90
100
0
10
20
30
40
50
60
70
80
90
100
Actinobacteria
Bacteriodetes
Proteobacteria
Firmicutes
Other
Unclassified
Ctrl Antibiotics Ctrl Antibiotics
Commensal niches in distinct epithelia demonstrate differential
responses after antibiotics in mice
Topical S. epidermidis association can increase IL-17A production
in the skin of germ-free mice
SPF – Specific Pathogen FreeGF – Germ FreeGF + S.epi – Germ Free associated with S. epidermidis
513
315
GFSPF
Gut
IL-1
7A
Skin
TCRb
14
2
GF + S.epi
Naik S et al. Science 2012
Skin commensals restore immunity to Leishmania major in
germ-free mice
0
250
500
750
Para
sites p
er
10
3cells
SPF GF S.epi
L. major SPF GF
Parasite Burden
Naik S et al. Science 2012
IFN
-g
CD4
20 9 50
GF+S. epidermidis
In mice, skin microbes can: • Tune level of activation & function of skin-resident T cells• Promote immunity to pathogens
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Atopic Dermatitis (AD)
• Bacterial and viral skin infections
• Common treatments:
– Topical/systemic antimicrobials and steroids
• Incidence doubled in last 3 decades in
industrialized countries
– Possible external factor
– Mice: skin exposure to antigens
mucosal sensitization
• Understanding triggers of AD may allow us to modify the development of AD/atopic diseases and develop therapeutic targets
Baseline
Flare
Post-flare
26.2
47.353.6
11.136.7
28.2
Atopic dermatitis skin microbiome
Objective SCORAD range: 0-83
• Pediatric patients with
moderate to severe
disease (N=12)
• Healthy age-matched
controls (N=11)
• Sampled
characteristically
affected areas
Kong, Oh…Segre. Genome Res 2012.
?
Children with atopic dermatitisAge-matched controls
Kong, Oh…Segre. Genome Res 2012.
Staphylococcus spp increase during AD flares Hypothesis integrating AD flare, increase in
Staphylococcus and decrease in microbial diversity
Kong, Oh…Segre. Genome Res 2012.
Itchy dermatitis in Adam17 deficient mice
Kobayashi…Nagao. Immunity 2015.
• ADAM17 (A disintegrin and metalloproteinase 17):
• Cell surface protein that cleaves other surface proteins (pro-TNF-a and
pro-EGFR)
• Adam17fl/flSox9-Cre
Patients with ADAM17 deletion exhibit AD-like
disease
• Eczema
• Pustules
• S. aureus
infections
Blobel et al. NEJM 2011.
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Adam17 deficient mice exhibit atopic dermatitis-like
disease and bacterial dysbiosis
Adam17fl/flSox9-Cre WT
Wk 3
Wk 8
Wk 14
Adam17fl/flSox9-Cre WT
Kobayashi et al. Immunity 2015
Antibiotics reverse dysbiosis in Adam17 deficient mice
No abx
+ abx
+ abx
No abx
Week 10 Week 13
IL-4 ↑ dermatitis ↑
Staphylococcus aureus exacerbates skin
disease in Adam17 deficient mice
Nakatsuji T et al. Sci Transl Med 2017
Commensal staphylococci can produce AMPs to
selectively kill S. aureus
Acne association with Propionibacterium acnes
Similar relative abundance of P. acne in healthy individuals
(n=52) vs. acne patients (n=49)
Many different P. acnes strains
Identified some genetic differences between health-
associated vs acne-associated
Possible therapeutic strategy?
Liu J et al. ISME J 2015.
Tomida S. et al. mBio. 2013.
Fitz-Gibbon S et al. J Invest Dermatol 2013. http://www.futuretimeline.net/blog/images/112.jpg
Human Microbiome
Defining ‘microbiome’
Microbiome in health & disease
Non-dermatologic
Arthritis, Cardiometabolism, Cancer
Skin
Potential applications
Clostridium difficile colitis
3/3/2017
7
C. difficile colitis can follow antibiotic treatment
This infectious diarrhea may be mild to severe, with 20% relapse rate
Fecal Microbiota Transplant
FMT = Transfer of stool/bacteria from healthy donor to another individual
First reported use: 4th century China
1950s – in US without significant regulation
Recent increase in use (C. difficile colitis) – 80% remission rate
Fecal bacterial composition after FMT
61 yo female
8 month h/o of diarrhea after course of antibiotics
Recalcitrant
Bowel movements q 15 minutes
Wheelchair bound
Husband was donor
Solid stool within 2 days
Khoruts et al . J Clin Gastroenterol 2012.
Clostridium spp.
Fecal Microbiota Transplant
FDA evaluating FMT as a drug
How to ensure safety?
Variability of stool composition
Screening donors
Stool preparation methods
Active components?
Need controlled studies
Other GI disorders
Human Microbiome
Defining ‘microbiome’
Microbiome in health & disease
Non-dermatologic
Arthritis, Cardiometabolism, Cancer
Skin
Potential applications
Clostridium difficile colitis
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