Allow Myself to Introduce … Myself The Human Microbiome in Health and Disease CPT BC Kirkup, Ph.D

Allow Myself to Introduce … Myself

The Human Microbiome in Health and Disease

CPT BC Kirkup, Ph.D.

BLUF

• Humans are partly bacterial• There is a ‘normal flora’• Flora can ‘mis-provide’ functions– dysbiosis*

• Flora have a role in trauma and healing

* Sartor RB; and Sokol et al 2008 PNAS 105 Grice et al 2009 Science

Dicksved 2008

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

Culture Independence

• Culture independent methods– Detection– Quantification– Identification

• Microscopy• Molecular methods (protein and nucleic acid)• Do not rely on ‘isolates,’

CFUs, Bergey’sRogers GB et al 2009, J. Med. Microbiol 58 Anderson et al 2004 J. Clin. Microbiol 42’Klouche and Schroder 2008 Clin. Chem. And Lab. MedWoo et al 2008. Clin. Microbiol. Inf. 14Fenollar and Raoult D 2007. Int J. Antimicrob Agents 30Frank and Pace 2008 Curr. Opin. Gastroenterol.

Current Failures• Current Molecular Methods flawed• Detecting the known• Biases• Uninterpretable results– Higher taxonomic orders – Annotation problems

• Lack of mechanism

Roratto et al 2008 Genet Mol Biol 31(1)

Ashelford et al AEM 2005

Cost

ello

et a

l 200

9 Sc

ienc

e

Diversity: At One Site

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

• Palm• Forearm

Fierer et al 2008 PNAS

Yang et al 2009

Camp et al 2009 Costello et al 2009 Science

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

The Skin

Costello et al 2009 Science

Spatial Microdiversity

• Small Niches• Microcolonies• Biofilms

Grice 2008 Genome Res.

Poulsen et al 1994 Inf and Imm

Healy et al 2008 Otolaryngol Head Neck Surg

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(?)

Miragaia et al 2007 J. Bact.

Tang et al. 2009 PLoS Comp. Bio.

Diversity: Similar Hosts

• Individual Variation• Typically considered

priority/founder or family effects

Dicksved 2008

Diversity: Local Culture

Nadsidze et al 2009 Genome ResearchSalivary FloraPCA

Diversity: Across Species

• 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

Friswell et al PLOS One 2010

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

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…

Wid

ely

dist

ribut

ed im

age

Ley

et a

l Nat

ure

2006

Costello et al 2009 Science

Diversity: Over Millennia

• Evolution of symbionts and pathogens

Ley RE et al. 2008 Science

Local Function

• Integrated Physiology• Mucosal Immunity:

Subversion or cooperation?• Communication• Competitive

exclusion

Medical Microbiology, UT 1996

Hooper 2009

Systemic Function

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

Martin et al 2008

Functional Genomics

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

Jones et al 2009 PNASBile Salt Hydrolases in different gut microbiomes

Adams et al 2008 Nature Education 1

Local Disease

• Heart Valve Infections• Cariogenesis• Acne• Asthma• Cystic Fibrosis• Chronic UTIsBreitkopf et al 2005 Circulation 111Voldstedlund M et al 2008 APMIS 116

Peterson et al 2008 Cell Host and Microbe 3(6)

BBC

Systemic Disease

• Obesity• Vascular disease• Autoimmune diseases• Fevers

The Scientist 1999Loscalzo et al 2006

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

Mistreatment

• Broad spectrum, systemic therapies– Changes the flora– Does the flora reappear?

• Inappropriate nutritional inputs

Dethlefsen et al 2008

Khafipour et al 2009

Wounds

• Initial contamination • Colonization and

Critical Colonization• Spreading Infection, Sepsis• Non-healing wounds

Johnson & Johnson Wound Management

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

Univ. of Glamorgen

DoD

‘Chronic Wound’ Ecology

• Polymicrobial infections

Dowd et al 2008 BMC MicrobiologyDowd et al 2008 PLoS One

Wolcott et al 2009 BMC Microbiology

Venous Leg

Diabetic

Wound Care

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

• Logistics

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