Allow Myself to Introduce … Myself

1
Allow Myself to Introduce Myself

• The Human Microbiome in Health and Disease
• CPT BC Kirkup, Ph.D.

2
BLUF

• Humans are partly bacterial
• There is a normal flora
• Flora can mis-provide functions
• dysbiosis
• Flora have a role in trauma and healing

Dicksved 2008
Grice et al 2009 Science
Sartor RB and Sokol et al 2008 PNAS 105
3
Prokaryotic Personality

• Humans are 90 bacterial
• Cell counts
• 99 by gene diversity
• Communication andcross-feeding
• Integrates with systems

Davis CP 1976 AEM 31
Willing and Finlay 2009 Current Biology
4
Culture Independence

• Culture independent methods
• Detection
• Quantification
• Identification
• Microscopy
• Molecular methods (protein and nucleic acid)
• Do not rely on isolates, CFUs, Bergeys

Rogers GB et al 2009, J. Med. Microbiol 58
Anderson et al 2004 J. Clin. Microbiol
42 Klouche and Schroder 2008 Clin. Chem. And
Lab. Med Woo et al 2008. Clin. Microbiol. Inf.
14 Fenollar and Raoult D 2007. Int J. Antimicrob
Agents 30 Frank and Pace 2008 Curr. Opin.
Gastroenterol.
5
Current Failures

• Current Molecular Methods flawed
• Detecting the known
• Biases
• Uninterpretable results
• Higher taxonomic orders
• Annotation problems
• Lack of mechanism

Ashelford et al AEM 2005
Costello et al 2009 Science
Roratto et al 2008 Genet Mol Biol 31(1)
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Diversity At One Site

• Stomach
• Very different by culture
• 100-250 OTUs or more
• Palm
• Forearm

Yang et al 2009
Fierer et al 2008 PNAS
Camp et al 2009
Costello et al 2009 Science
7
Diversity Number of Sites

• What is a site?
• Forearm vs. antecubital fossa
• Left hand vs. Right hand

Fierer et al 2008 PNAS
Costello et al 2009 Science
8
The Skin
Costello et al 2009 Science
9
Spatial Microdiversity

• Small Niches
• Microcolonies
• Biofilms

Poulsen et al 1994 Inf and Imm
Grice 2008 Genome Res.
Healy et al 2008 Otolaryngol Head Neck Surg
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Genetic Microdiversity

• Clonal expansions appear infrequent
• Observations from marine bacteria
• High diversity below the species level
• Gene content, allelic, SNP variation all high
• Selective sweeps
• Small scale or rare?
• Impact of phage?
• Not well explored for human microbiome
• Differs by genera, guild(?)

Tang et al. 2009 PLoS Comp. Bio.
Miragaia et al 2007 J. Bact.
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Diversity Similar Hosts

• Individual Variation
• Typically considered priority/founder or family
  effects

Dicksved 2008
12
Diversity Local Culture
Nadsidze et al 2009 Genome Research
Salivary Flora PCA
13
Diversity Across Species
Friswell et al PLOS One 2010

• Different animals have different flora
• Formerly study isolates
• Studies of enterics
• Allows for bigdiet differences

Ley RE et al. 2008 Nat. Rev. Micro.
Ley RE et al. 2008 Science
14
Diversity During the Day

• Diurnal cycles
• Hand washing
• Down Propionibacteria, Neisseriales,
  Burkholderiales, Pasteurallaceae
• Up Staphylococcus, Streptococcus,
  Lactobacillus
• Reduces gender differences
• Population reestablished quickly

Costello et al 2009 Science
15
Stability Months Years

• Strain turn over
• E. coli turns over 8 36 mo.
• Changes in abundance
• Occur during many life changes
• New methods and long term effects

Widely distributed image
Ley et al Nature 2006
Costello et al 2009 Science
16
Diversity Over Millennia

• Evolution of symbionts and pathogens

Ley RE et al. 2008 Science
17
Local Function

• Integrated Physiology
• Mucosal Immunity Subversion or cooperation?
• Communication
• Competitive exclusion

Hooper 2009
Medical Microbiology, UT 1996
18
Systemic Function

• Systemic Immunity
• Control inputs and process outputs
• Function as a secretory organ

Martin et al 2008
19
Functional Genomics

• Another way to study bacterial function
• Genes, not taxa

Jones et al 2009 PNAS Bile Salt Hydrolases in
different gut microbiomes
Adams et al 2008 Nature Education 1
20
Local Disease

• Heart Valve Infections
• Cariogenesis
• Acne
• Asthma
• Cystic Fibrosis
• Chronic UTIs

BBC
Breitkopf et al 2005 Circulation 111 Voldstedlund
M et al 2008 APMIS 116
Peterson et al 2008 Cell Host and Microbe 3(6)
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Systemic Disease

• Obesity
• Vascular disease
• Autoimmune diseases
• Fevers

Loscalzo et al 2006
The Scientist 1999
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Systemic and Local Treatments

• Local dysbiosis can yield systemic disease
• Local treatment can yield systemic cure
• Systemic treatment collateral damage
• Cure a local disease, cause other local dysbiosis
• Expose more strains to adverse selection

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Mistreatment

• Broad spectrum, systemic therapies
• Changes the flora
• Does the flora reappear?
• Inappropriate nutritional inputs

Khafipour et al 2009
Dethlefsen et al 2008
24
Wounds
Johnson Johnson Wound Management

• Initial contamination
• Colonization and Critical Colonization
• Spreading Infection, Sepsis
• Non-healing wounds

25
Wounds

• Chronic vs. Acute Wounds
• False dichotomy
• Wounds with Co-morbidities
• Diabetes, vascular insufficiency
• Traumatic wounds
• Healthy tissue injured by physical forces
• Burns
• Heat and chemical degradation

DoD
Univ. of Glamorgen
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Chronic Wound Ecology

• Polymicrobial infections

Venous Leg
Wolcott et al 2009 BMC Microbiology
Diabetic
Dowd et al 2008 PLoS One
Dowd et al 2008 BMC Microbiology
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Wound Care

• Full Spectrum Wound Care
• Decontamination
• Colonization management
• Decolonization
• Debridement of advanced infections
• Logistics

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Questions

• About the microbiome?
• About wound microbiology?
• About innovative wound care concepts?
• About Army microbiology?

The views expressed here are the author's alone
and do not necessarily represent those of the
Department of Army or the Department of Defense