microbiome

2. The Human
Microbiome
With great thanks to
Dr. Jess Maher for
making a lot of these
community slides

3. Objectives 11/27/12
1. Describe the factors and processes that
influence community assembly and
composition
2. Describe how community composition
impacts function
3. Compare species diversity in different
communities
4. Apply ecological concepts to a new system

4. A microbe’s view of us
Skin Bacterial cells
outnumber your body
cells 10:1 and comprise
up to 4-6 lbs of your
body mass

5. Sites that harbor a normal flora:
Skin and mucous membranes
Upper respiratory tract
Gastrointestinal tract
Outer opening of urethra
External genitalia
Vagina
External ear canal
External eye (lids, conjunctiva)

6. 1. Synthesize and excrete vitamins
Vitamin K and Vitamin B12
2. Prevent colonization by pathogens
competing for attachment sites or for essential nutrients
3. May antagonize other bacteria
the production of substances which inhibit or kill non-indigenous
species(nonspecific fatty acids, peroxides, bacteriocins).
4. Stimulate the development of certain tissues
i.e., intestines, certain lymphatic tissues, capillary density
5. Stimulate the production of cross-reactive antibodies.
Low levels of antibodies produced against components of the normal
flora are known to cross react with certain related pathogens, and
thereby prevent infection or invasion.
Benefits of the normal flora

7. (Hooper et al. 2001 Science)
A healthy microbial community is essential
Mice raised in a germ-free environment display:
Decreased nutrient absorption
Less developed intestines
Vitamin deficiency
Underdeveloped immune system
Heighted sensitivity to pathogens

8. (Fierer et al 2012)

9. Dethlefsen, McFall-Ngai and Relman 2007

10. http://www.genome.gov

11. A belly button microbial 'portrait'
http://www.wildlifeofyourbody.org/

12. What factors determine the species composition of
normal flora in the human body?

13. What abiotic conditions might differ between
areas of the human body that are normally
colonized by microbes?

14. What biotic factors might differ between areas of
the human body that are normally colonized by
microbes?

15. Skin regions are like geographic regions of Earth

16. Individuals have different microbial
communities. Why?

17. abiotic biotic
dispersal
Although multiple scenarios are likely to apply to any real-world
setting, one may dominate. For example, differences between
body habitats may be best explained by environmental selection
(abiotic), differences between siblings for the same habitat may be
best explained by historical contingency (biotic), differences
between monozygotic twins prior to weaning highlight the role of
stochasticity (random), and differences between neonates born by
cesarean section versus vaginal delivery are likely to be explained
by dispersal limitation (dispersal).

18. Let’s focus on the microbial community in the gut:
How is the community assembled?
How does community composition affect function?

19. Families have more similar microbiomes

20. Families have more similar microbiomes
Think-Pair-Share: Why?
(remember that the uterus is a
sterile environment, so babies
are not born with their bacteria)

21. Community Assembly:
How do we acquire our resident flora?
Dispersal
1. From delivery: The gut flora of vaginally-
delivered babies differs from babies delivered by C-
section
The vaginal microbial community of pregnant women
contains bacteria involved in digesting milk (Lactobacillus)
2. From feeding: The nature of the flora
colonizing the intestines changes depending on
whether the baby is bottle- or breast-fed
(The skin, gastrointestinal tract, respiratory, and urogenital system all
continue to be colonized as contact with other humans continues)

22. Disturbance and succession: As the gut environment
changes, so does the microbial community
Why?
Switch to
solid foods

23. How does community composition
impact function?
Hypothesis: Gut microbial communities can
impact risk for obesity

24. Different gut microbial community
structure in obese mice
Firmicutes
Bacteroidetes
%
Sequences
Ley et al., PNAS 102: 11070-5 (2006)

25. Effects of dieting
Ley et al. Nature 444: 1022 (2006)

26. Microbiota fecal transplantation
ob
wt
Conventionally
raised donors
Germ-free
Wild type
recipients
wt wt
Donor
Turnbaugh et al., Nature 444: 1027-1031

27. Conventionalized mice (CONV-D) are formerly germ-free
(GF) recipients of a gut microbiota transplant from
conventionally-raised (CONV-R) donors
Mice that receive a fecal transplant from obese donors
not only become obese, but do so while eating less food…

28. T-P-S: What might be functionally different about the gut
communities in the lean donor and the obese donor?
Donor

29. Energy extraction efficiency could be a
function of the gut community composition
Metagenomic analysis of obese/lean mouse gut microbiotas
Obese gut microbiome contains more genes predicted to harvest
energy from polysaccharides
Hypothesis: Differences in
gut microbial ecology among
humans affects the efficiency
of their energy
harvest/storage when
consuming a given diet
Turnbaugh et al., Nature 444: 1027-1031

30. Little-known fecal transplant cures
woman's bacterial infection
“After surviving a near-fatal car accident, Kaitlin Hunter found herself battling
a devastating bacterial infection in her colon that also threatened her life.
The persistent infection was beaten through a little-known technique
involving the transplant of fecal matter from Hunter's mother...
Following the July procedure, "I've been so happy," said Hunter, 20, of
Marietta, Georgia. "I'm cured."
Why did
this work?
What
happened
in Katie’s
colon?

31. Bacteriotherapy
Clostridium difficile-associated diarrhea (CDAD)
- usually results from prior antibiotic treatment
and persistant disruption of gut microbiota
- can be severe, even causing death
J Clin Gastroenterology (2010) 44:354-360

32. Patient:
61 year old woman
Chronic diarrhea
(8 mos, every 15 min)
Confined to wheelchair
Lost 60 lbs
Donor:
Husband
Patient
Day 0
Donor

33. T-P-S: Describe the
differences between the
gut communities from the
patient and the donor.
Patient
Day 0
Donor

34. Species Diversity
26
Species
21
Species
Richness = number of
species present
Evenness = relative
abundance of each species
Diversity measures both
richness and evenness

35. Fecal transplant =
assisted colonization
Patient:
Diarrhea subsided within
2 days
Gut flora similar to donor
within 14 days
Patient
Day 0
Donor Patient
Day 14

36. T-P-S: What might have been preventing the
women from having a “healthy” gut
community? (Think about the factors that can
influence species composition in a community)

37. How can you use the Human Microbiome in your
teaching about Ecology?

38. Evolution in the Human
Microbiome: Gonorrhea!
• Clap, Drip
• Sexually transmitted
infection caused by the
bacterium Neisseria
gonorrhoeae
• Can be detected by
microscopy, culturing,
or DNA testing
38

39. Who gets gonorrhea?
• Spread by sexual contact
• Those at highest risk are
young adults (women 15
– 19 and men 20 – 24)
• Can be passed from
mother to newborn
39

40. United States
Gonorrhea Infection Statistics
• Second most-frequently
reported STD
• ~700,000 Americans are
infected annually
• Treatment of gonorrhea
costs $1 billion/year
40

41. What are the symptoms?
• Most men who get gonorrhea experience
extremely painful urination and pus release
from the urethra
• Many women do not experience noticeable
symptoms
41

42. Why is proper detection and treatment of
gonorrhea important? This is serious!
• Co-infection can cause increased transmission of
other STDs including HIV
• If untreated, the bacteria can spread to other
sites in the body
– Pelvic Inflammatory Disease
– Ectopic pregnancy
– Infertility
– Meningitis
– Arthritis
– Blindness
– Death
42

43. What are some of the difficulties in treating the
disease?
• Some people do not know that they are
infected
• Can be a difficult topic for some to talk
about/embarrassment
• Many isolates of N. gonorrhoeae are resistant
to antibiotics commonly used to treat
gonorrhea
• The CDC announced in August 2012 we're
down to our last effective antibiotic
– injected ceftriaxone
43

44. Journalist Dan Avery argues "the AIDS epidemic
is what might help us prevent a catastrophe"
“Before AIDS, if you got a STD, your doctor gave you the
cure and told you to tell your partners (wink, wink). But
as AIDS cut a swath through society, learning how to
tracking disease vectors became a life-or-death issue.
... Before AIDS, medical professionals were not always
diligent about sterility—and nobody bothered putting
on gloves unless you were getting a prostate exam.
Now, the importance placed on antibacterial soap,
latex protection and other tools will help control the
spread of gonorrhea, which can transfer from a
patient’s genitals to a nurse’s hands to her eye.
That’s where some experts say we’re headed: working to
control the spread of gonorrhea instead of
administering a simple cure.“
44

45. How have the gonorrhea populations
of the world developed resistance to
most of our antibiotics?
45

46. Antibiotics disrupt essential cell processes
• Antibiotics help cure infections by decreasing the
bacterial population to a level that the human
immune system can handle
• Gonorrhea is treated with antibiotics
Antibiotic
treatment
46

47. Cell processes of Gonorrhea
Transcription
Translation
Replication
RNA
Protein
DNA
• Enzymes
• Cell structure
• Signaling
47

48. What is the target of one specific
antibiotic, Ciprofloxacin?
• Ciprofloxacin binds to the DNA/enzyme
complex that forms during DNA replication
• This forms a physical barrier that prevents
movement of the replication fork and
replicating enzymes down the DNA strand
• The result: no DNA replication
48

49. Cell processes of Gonorrhea
Transcription
Translation
Replication
RNA
Protein
DNA
• Enzymes
• Cell structure
• Signaling
49

50. Mechanisms of Ciprofloxacin Resistance in N.
gonorrhoeae
• Deactivation of drug by a bacterial enzyme
digesting it
• Less drug enters the bacterium
– Changes to pore proteins in bacterial cell walls
• Concentration of drug within a bacterium is
lowered
– Protein pumps that pump out drugs
• Molecular target of drug is changed
50

51. Molecular target of antibiotic (DNA replication
enzymes) is changed
Enzyme active site
antibiotic
Wild type bacterial
DNA replication
protein
Mutant bacterial
DNA replication
protein
51

52. antibiotic
Wild type bacterial
DNA replication
protein
Mutant bacterial
DNA replication
protein
antibiotic
Enzyme active site Enzyme active site
52
Molecular target of antibiotic (DNA replication
enzymes) is changed

53. DNA mutations can alter protein structure
Wild type allele of gyrA gene Mutant allele of gyrA gene
RNA
Protein
DNA
53
Wild type gyrase protein Mutant gyrase protein

54. An Organism’s genotype codes for specific
proteins which cause a certain phenotype
RNA
Protein
DNA Genotype
Phenotype
Antibiotic
Sensitivity
antibiotic
(Wild type gyrA allele)
54

55. RNA
Protein
DNA Genotype
Phenotype
Antibiotic
Resistance
antibiotic
(Mutant gyrA allele)
55
An Organism’s genotype codes for specific
proteins which cause a certain phenotype

56. The following statements describe how a change in genotype can
perturb phenotype. Number them in the best sequential order
(1=earliest event, 4=latest event):
__ Mutant gyrA RNA is translated.
__ The gyrA gene of Neisseria gonorrhoeae acquires a mutation
because of a replication error.
__ Mutant gyrase enzyme is altered, allowing for DNA synthesis to
occur even in the presence of ciprofloxacin.
__ Mutant gyrA DNA is transcribed.
Changes to genotypes can change phenotypes
56

57. Mutations
When do mutations occur?
Do mutations occur in response to a selection
pressure (like humans using antibiotics on
bacteria)?
57

58. How have the gonorrhea populations
of the world developed resistance to
most of our antibiotics?
58

59. Some last Gonorrhea thoughts
“A lot of this is occurring not because of treatment
for gonorrhea but overuse for other infections,
such as urinary tract infections, upper respiratory
tract infections and so forth,” researcher
Jonathan Zenilman told NPR.
“There’s now essentially one drug left that
scientists feel is an effective treatment:
ceftriaxone. And its’ only a matter of time before
it ceases to work, too. Cases of untreatable
gonorrhea have already been found in Europe
and Asia.”
59

60. Evolutionary Trade-offs
Evolutionary trade-offs occur where pros and
cons exist for an allele or specific trait.

61. HIV—the virus that causes AIDS
The Ultimate Evolver!
http://evolution.berkeley.edu/evolibrary/article/medicine_04

62. So, what do we do? “Drug Cocktails”!
Why do they work?

63. THINK PAIR SHARE: What do you think might
happen to this person’s viral load if he stops
taking Drug A? Why?

64. Evolutionary Trade-off
Pro: drug resistance; con: slower growth rate

65. Interpret this figure: Think-Pair-Share
1) The CCR5 allele confers a resistance to HIV infection. What is the figure
telling you about the distribution of the CCR5 allele?
2) Can you hypothesize why the distribution of the CCR5 allele is the way it is?

66. In this example, past evolutionary
history affects the present

67. How can you use the Human Microbiome in your
teaching about Evolution?