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

1. May the Microbes be Ever in Your Favor
Jonathan A. Eisen
@phylogenomics
University of California, Davis
Talk for CBS Cohort Program

2. Which Infection Would You Least Want to Get?
A. Rabies
B. Tapeworm
C. Filarial nematode (e.g., elephantiasis)
D. Cholera
E. Tuberculosis

3. Which of these will antibiotics help with?
A. Rabies
B. Tapeworm
C. Filarial nematode (e.g., elephantiasis)
D. Cholera
E. Tuberculosis

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. Which microbe product do you like most?
A. Beer/Wine
B. Bread
C. Yogurt
D. Chocolate
E. Kombucha

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. 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. Microbes 101

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. Diversity of Form

11. Diversity of Function
The Bad The Good The Unusual
The Consumable The Burnable The Planet

12. The Human Microbiome

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. Eisen Lab Study Subjects (Examples)

15. http://tinyurl/ucdavismicrobes

16.
The Human Microbiome

17. The Human Microbiome

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. Who Are We?
50

20. Microbes Can Make Mice Fat
Turnbaugh et al Nature. 2006 444(7122):1027-31.

21. Microbiome Involved in Many Functions
• Digestion
• Vitamin Production
• Protection from parasites / pathogens
• Metabolic rate
• Immune regulation
• Odor
• Behavior

22. Censored
Censored
The Human Microbiome: Variation

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. 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. The Human Microbiome: Disturbance
Antibiotics
Diet Changes
Hygiene
Hypothesis
C-sections

26. Restoring the Microbiome: Probiotics and Prebiotics

27. Intestinal Transplant
Hartman et al. PNAS 2009

28. Coprophagia

29. Transfaunation
• http://4.bp.blogspot.com/-
ojOdQeA56Fk/UDUTQsasvRI/
AAAAAAAAhtg/aWotjwTeT4c/s1600/
Untitled2.jpg

30. Fecal Transplants (FMT)

31. Openbiome: Stool Bank

32. DIY Fecal Transplant

33. DIY Fecal Transplant

34. DIY

35. Get Involved
Kitty Microbiome

36. CSI Microbiology

37. Great Plate Count Anomaly

38. Great Plate Count Anomaly

39. Culturing Microscopy
Great Plate Count Anomaly

40. Culturing Microscopy
CountCount
Great Plate Count Anomaly

41. <<<<
Culturing Microscopy
CountCount
Great Plate Count Anomaly

42. Culturing Microbes

43. <<<<
Culturing Microscopy
CountCount
Solution???
Great Plate Count Anomaly

44. <<<<
Culturing Microscopy
CountCount
DNA
ACTGAA
CCGAA
Great Plate Count Anomaly

45. Sequences vs. Bones

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