Allow Myself to Introduce … Myself

1. Allow Myself to Introduce … Myself The Human Microbiomein 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, Bergey’s 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)

6. 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 Healy et al 2008 Otolaryngol Head Neck Surg Grice 2008 Genome Res.

10. 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.

11. 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)

21. Systemic Disease • Obesity • Vascular disease • Autoimmune diseases • Fevers Loscalzo et al 2006 The Scientist 1999

22. 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

23. 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

26. ‘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

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

28. 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