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May the Microbes Be Ever in Your Favor

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Slides for talk on "The Human Microbiome" to UC Davis Freshman Cohort Class

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May the Microbes Be Ever in Your Favor

  1. 1. May the Microbes be Ever in Your Favor Jonathan A. Eisen @phylogenomics University of California, Davis Talk for CBS Cohort Program
  2. 2. Which Infection Would You Least Want to Get? A. Rabies B. Tapeworm C. Filarial nematode (e.g., elephantiasis) D. Cholera E. Tuberculosis
  3. 3. Which of these will antibiotics help with? A. Rabies B. Tapeworm C. Filarial nematode (e.g., elephantiasis) D. Cholera E. Tuberculosis
  4. 4. Which have you done most recently? A. Taken antibiotics B. Gotten a vaccine C. Taken probiotics D. Gotten a fecal transplant E. Made something with the help of microbes
  5. 5. Which microbe product do you like most? A. Beer/Wine B. Bread C. Yogurt D. Chocolate E. Kombucha
  6. 6. Which has more bacterial cells in it? A. A gram of soil B. A gram of human poop C. A gram of yogurt D. A gram of saliva E. A gram of ocean water
  7. 7. Most likely place to find dangerous microbes? A. Your phone B. A toilet / bathroom C. Your animal companion (cat/dog) D. The person sitting next to you E. A hospital
  8. 8. Microbes 101
  9. 9. The Microbe Challenge • Microbes are small • But diversity and numbers are very high • Appearance not a good indicator of type or function • Field observations of limited value
  10. 10. Diversity of Form
  11. 11. Diversity of Function The Bad The Good The Unusual The Consumable The Burnable The Planet
  12. 12. The Human Microbiome
  13. 13. 11 Things Everyone Should Know 1. Microbes are small, mostly 2. Microbes are not simple 3. No microbe alive today is ancient 4. There are no good or bad microbes 5. We know very little about microbial diversity 6.  Microbes can move (using their own power) 7. Trying to make world sterile a bad idea 8. Microbes are both underappreciated and oversold 9. Microbes evolve 10. Microbes are everywhere but no one microbe is 11. Microbes are critical to our past, present and future
  14. 14. Eisen Lab Study Subjects (Examples)
  15. 15. http://tinyurl/ucdavismicrobes
  16. 16. 
 The Human Microbiome
  17. 17. The Human Microbiome
  18. 18. Microbes are all over us http://commons.wikimedia.org/wiki/ File:Man_shadow_-_upper.png Thousands of different species on the skin alone Some thrive on dry patches of the elbow, others thrive in moist environment of armpit There are millions of microbes per square inch on your body It is estimated that there are more microbes in your intestine than there are human cells in your body!
  19. 19. Who Are We? 50
  20. 20. Microbes Can Make Mice Fat Turnbaugh et al Nature. 2006 444(7122):1027-31.
  21. 21. Microbiome Involved in Many Functions • Digestion • Vitamin Production • Protection from parasites / pathogens • Metabolic rate • Immune regulation • Odor • Behavior
  22. 22. Censored Censored The Human Microbiome: Variation
  23. 23. Glans penis Hair Labia minora Acinetobacter Actinomycetales Actinomycineae Alistipes Anaerococcus Bacteroidales Bacteroides Bifidobacteriales Branhamella Campylobacter Capnocytophaga Carnobacteriaceae1 Carnobacteriaceae2 Clostridiales Coriobacterineae Corynebacterineae Faecalibacterium Finegoldia Fusobacterium Gemella Lachnospiraceae Lachnospiraceae (inc. sed.) Lactobacillus Leptotrichia Micrococcineae Neisseria Oribacterium Parabacteroides Pasteurella Pasteurellaceae Peptoniphilus Prevotella Prevotellaceae Propionibacterineae Ruminococcaceae Staphylococcus Streptococcus Veillonella Other Axilla (L) Ext. auditory canal (L) Volar forearm (L) Palmar index finger (L) Popliteal fossa (L) Naris (L) Plantar foot (L) Oral cavity Umbilicus External nose Lat. pinna (L) Palm (L) Gut Plantar foot (R) Forehead Dorsal tongue Lat. pinna (R) Palm (R) Axilla (R) Ext. auditory canal (R) Volar forearm (R) Palmar index finger (R) Popliteal fossa (R) Naris (R) The Human Microbiome: Variation
  24. 24. Variation May Affect Health • Microbial community different in many disease states compared to healthy individuals • Unclear if this is cause or effect in most cases
  25. 25. The Human Microbiome: Disturbance Antibiotics Diet Changes Hygiene Hypothesis C-sections
  26. 26. Restoring the Microbiome: Probiotics and Prebiotics
  27. 27. Intestinal Transplant Hartman et al. PNAS 2009
  28. 28. Coprophagia
  29. 29. Transfaunation • http://4.bp.blogspot.com/- ojOdQeA56Fk/UDUTQsasvRI/ AAAAAAAAhtg/aWotjwTeT4c/s1600/ Untitled2.jpg
  30. 30. Fecal Transplants (FMT)
  31. 31. Openbiome: Stool Bank
  32. 32. DIY Fecal Transplant
  33. 33. DIY Fecal Transplant
  34. 34. DIY
  35. 35. Get Involved Kitty Microbiome
  36. 36. CSI Microbiology
  37. 37. Great Plate Count Anomaly
  38. 38. Great Plate Count Anomaly
  39. 39. Culturing Microscopy Great Plate Count Anomaly
  40. 40. Culturing Microscopy CountCount Great Plate Count Anomaly
  41. 41. <<<< Culturing Microscopy CountCount Great Plate Count Anomaly
  42. 42. Culturing Microbes
  43. 43. <<<< Culturing Microscopy CountCount Solution??? Great Plate Count Anomaly
  44. 44. <<<< Culturing Microscopy CountCount DNA
 CCGAA Great Plate Count Anomaly
  45. 45. Sequences vs. Bones
  46. 46. Some Findings .. • There may be > 1 billion species of microbes on the planet • This does not even include viruses for which there are likely many billions of kinds • There are more genes in the microbes on your body than in your genome • For 99.9999999999% of microbes, we know NOTHING about them - so much cool work to do