BIS2C. Biodiversity and the Tree of Life. 2014. L12. Symbioses and the Human Microbiome

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014
Lecture 12
!
Lecture 12
!
Symbioses and The Human
Microbiome
!
!
BIS 002C
Biodiversity & the Tree of Life
Spring 2014
!
Prof. Jonathan Eisen
1

Where we are going and where we have been
• Previous Lecture:
!11: Symbioses and humans
• Current Lecture:
!12: Symbioses and humans
• Next Lecture:
!13: Fungi
2

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 3
Please arrive early bring the following to the exam:
1. A pen
2. A #2 pencil
3. Photo ID
BIS2C Midterm 1: B Sections 
April 21st 4:10pm – 5:00pm 
Freeborn Hall
Last Names: A - Sak
!
Chemistry 179
Last Names: San - Z

BIS2C Midterm 1 Review 
April 19th 11:00 am – 12:00 pm 
Rock Hall

Microbe Launch Today to ISS
5
see http://spacemicrobes.org
Follow live via
#SpaceMicrobes

Lecture 12 Outline
• Microbiome Continued
• Evolution
• Function
• Symbioses
• Pathogens
9

Microbiome Continued
10

DIY Fecal Transplant

!12
!
!
Lesson 2
!
The Importance of History
(i.e., Evolution)

Primate Evolution
13

History of an Ecosystem is Important
14

Vertebrate Microbiomes16SribosomalRNAsequences(%)
0
20
40
60
80
100
Bacteroidetes (red)
Firmicutes (blue)
Vertebrate gut
Termite gut
Salt-water surface
Salt water
Subsurface, anoxic or sediment
Other human
Non-saline cultured
Insects or earthworms
Soils or freshwater sediments
Mixed water
Figure 3 | Relative abundance of phyla in samples. Bargraphshowingtheproportionofsequencesfromeachsample
thatcouldbeclassifiedatthephylumlevel.ThecolourcodesforthedominantFirmicutesandBacteroidetesphylaareshown.15
Nat Rev Microbiol. 2008 October ; 6(10): 776–788. doi:10.1038/nrmicro1978.!

Evolution of the Human Microbiome
16

!21
!
!
Lesson 3:
!
Microbiome Roles

Microbiome Functions
• Digestion of food and metabolism of drugs
• Manages immune system
• Preventing infection by pathogens
• Heals wounds
• Contributes to metabolic rate/obesity
• Development of the immune system
• Vitamin production (e.g., B12 and K)
• Toxin degradation
• Appearance and odor
22

Who Are We?
23

Who is in Charge?
24

Overselling the Microbiome
• Correlation ≠ Causation
• Complexity is astonishing
! 1000s of taxa
! Each with intraspecific
variation
! Viruses, bacteria, archaea,
eukaryotes
• Massive risk for false positive
associations 
25

Crowdsourcing the Microbiome
26

Symbioses
27

Symbioses
• Symbiosis is an intimate association between at least
two different organisms in which at least one of them
benefits
!
• Endosymbiosis is a symbiosis (could be mutualism,
commensalism or parasitism) in which one of the
organisms live inside the cells of the other
28

Classes of symbiosis
Organism
Class of symbiosis A B
Mutualism + +
Commensalism + 0
Parasitism + -
29

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
30

Mutualistic Symbioses of Bacteria in Eukaryotes
• Digestive
! Ruminants
! Cellulolytic insects
• Defensive
• Behavioral
! Squid light organs
• Autotrophic
! Photosynthetic
! Chemosynthetic in deep sea
• Nutritional
! Aphids
! Nitrogen fixation in legumes
31

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
32

Organism
Mutualism + +
Commensalism + 0
Parasitism + -
33

Pathogens
Pathogens: infectious agents that cause a
disease.
34

Spirochetes
• Gram-negative
• Motile
• Chemoheterotrophic
• Unique rotating, axial
filaments (modified
flagella)
• Many are pathogens:
!Syphilis
!Lyme disease
• Others free-living
35

Chlamydias
• Gram-negative
• Cocci or rod-shaped
• Extremely small
• Live only as parasites
inside cells of
eukaryotes & cause
various diseases
!Trachoma
!Multiple sexually
transmitted
diseases
!Pneumonia
36
C. trachomatis

High-GC Gram Positives (Actinobacteria)
• High G+C/A+T ratio in DNA
• Elaborate branching
• Some reproduce by forming
chains of spores at tips of
filaments
• Most antibiotics are from this
group
• Causative agents of many
diseases such as
tuberculosis and leprosy
• Many originally misclassified
as fungi
37

Low-GC Gram Positives (Firmicutes)
• Low G+C/A+T ratio in DNA
• Some produce endospores
which are resistant “seeds”
that germinate when
conditions are good
• Many agents of diseases
(e.g., anthrax, MRSA,
Streptococcus, botulism,
tetanus)
• Many of agricultural and
industrial use (e.g., Lactic
acid bacteria)
• Some (Mycoplasmas) have
no cell wall and are
extremely small
38
Mycoplasmas

Proteobacteria
• Gram-negative
• Escherichia coli: model
organism and human
gut commensal and
pathogen
• Mitochondria evolved
from this group
• Includes many human
and animal
pathogens: plague,
cholera, typhoid
39

Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip
—the apical complex that help the
parasite enter the host’s cells.
40
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children

Alveolates: Ciliates
41
Movement in a ciliate from the gut of a termite
• All have numerous cilia, the structure
is identical to flagella.
• Most are heterotrophic; very diverse
group.
• Have complex body forms and two
types of nuclei.
• Some pathogens (e.g., Ick)

Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic.
• Are absorptive heterotrophs
• Once were classed as fungi, but
are unrelated.
42
Sudden Oak Death

Excavates: Diplomonads and Parabisalids
• Unicellular
• Lack mitochondria and most are
anaerobic. This is a derived condition
• Giardia lamblia - a diplomonad - is a
human parasite
• Trichomonas vaginalis - parabasalid - STD
43

Excavates: Kinetoplastids
• Unicellular parasites with two flagella and a
single mitochondrion.
• Mitochondrion contains a kinetoplast -
structure with multiple, circular DNA
molecules
• Includes trypanosomes and agents of
chagas, sleeping sickness, Leishmaniasis
Trypanosoma sp.!
mixed with blood cells
44

Excavates: Heteroloboseans
• Amoeboid body form.
• Naegleria can enter humans and
cause a fatal nervous system
disease - “brain eating”
• Some can transform between
amoeboid and flagellated stages.
45

• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
46
Amoebozoans: Loboseans

Pathogens
Pathogens: infectious agents that cause a
disease.
A small percentage of bacteria and
eukaryotes are pathogens.
No archaea are known to be pathogens.
47

Pathogens
Robert Koch set down rules to establish that
a particular organism causes a particular
disease—Koch’s postulates.
48

Figure 26.22 Satisfying Koch’s Postulates (Part 1)
49

50
Helicobacter pylori 1.5 µm

Proteobacteria
• Gram-negative
• Escherichia coli: model
organism and human
gut commensal and
pathogen
• Mitochondria evolved
from this group
• Includes many human
and animal
pathogens: plague,
cholera, typhoid
51

52

53

54
Test 1
Test 2
Test 3
Test 4
The microorganism must be present in every case of the disease.
The microorganism must be cultured from a sick host.
The isolated and cultured bacteria must be able to induce the disease.
The bacteria must be recoverable from newly infected individuals.

55
Marshall and Warren set out to satisfy Koch’s postulates:
Test 1
Test 2
Test 3
Test 4
Conclusion
The microorganism must be present in every case of the disease.
Results: Biopsies from the stomachs of many patients revealed that the bacterium was always present if
the stomach was inflamed or ulcerated.
The microorganism must be cultured from a sick host.
Results: The bacterium was isolated from biopsy material and eventually grown in culture media in the
laboratory.
The isolated and cultured bacteria must be able to induce the disease.
Results: Marshall was examined and found to be free of bacteria and inflammation in his stomach. After
drinking a pure culture of the bacterium, he developed stomach inflammation (gastritis).
The bacteria must be recoverable from newly infected individuals.
Results: Biopsy of Marshall’s stomach 2 weeks after he ingested the bacteria revealed the presence of
the bacterium, now christened Helicobacter pylori, in the inflamed tissue.
Antibiotic treatment eliminated the bacteria and the inflammation in Marshall’s stomach. The experiment
was repeated on healthy volunteers, and many patients with gastric ulcers were cured with antibiotics.
Thus Marshall and Warren demonstrated that the stomach inflammation leading to ulcers is caused by
H. pylori infections in the stomach.

Case Study: Anthrax
56

Bacillus anthracis
• A member of the Firmicutes
(low GC Gram positive)
phylum
• Sporulates
• Animal and human pathogen
• Highly invasive
• “Weoponized” by multiple
countries
57

"59
September 18, 2001: Anthrax = caused by Bacillus anthracis

Anthrax forensics
• Question - How do you figure out where the
Anthrax in the letters came from?
"60

Anthrax forensics
• Question - How do you figure out where the
Anthrax in the letters came from?
!
• Answer came from phylogenetics
"61

Anthrax Diversity
Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships
among 1,033 B. anthracis isolates.
doi:10.1371/journal.pone.0000461.g002
"62

DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrixPhylogenetic tree
PCR
rRNA1
Yeast
Makes lots
of copies of
the rRNA
genes in
sample
rRNA
5’ ...ACACACATAG
GTGGAGCTAGCGA
TCGATCGA... 3’
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
Anthrax1
E. coli Humans
Yeast
Phylogenetic analysis in the lab
"63
PCR = Polymerase Chain Reaction

DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrix
PCR
Anthrax2
Yeast
Makes lots
of copies of
the rRNA
genes in
sample
rRNA
5’ ...ACACACATAG
GTGGAGCTAGCGA
TCGATCGA... 3’
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
"64
Anthrax1 A C A C A C

DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrix
PCR
Anthrax3
Yeast
Makes lots
of copies of
the rRNA
genes in
sample
rRNA
5’ ...ACACACATAG
GTGGAGCTAGCGA
TCGATCGA... 3’
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
"65

DNA
extraction
PCR
Sequence
rRNA genes
Sequence alignment = Data matrixPhylogenetic tree
PCR
Anthrax3
Yeast
Makes lots
of copies of
the rRNA
genes in
sample
rRNA
5’ ...ACACACATAG
GTGGAGCTAGCGA
TCGATCGA... 3’
E. coli
Humans
A
T
T
A
G
A
A
C
A
T
C
A
C
A
A
C
A
G
G
A
G
T
T
C
1
E. coli Humans
Yeast
"66
Anthrax1 A C A C A C23

VNTRs
• rRNA evolves too slowly to distinguish different strains of
B. anthracis from each other
• Fortunately, some regions of the genome evolve much
more rapidly
• Known as VNTR (Variable Number of Tandem Repeats)
regions
• Mutation rate
! VNTR >>>> Coding Region Transition > Coding
Regions Transversion > rRNA
• Surveyed 50+ VNTRs
"67

Anthrax Diversity
Figure 3. Worldwide distribution of B. anthracis clonal lineages:Phylogenetic and geographic relationships
among 1,033 B. anthracis isolates.
doi:10.1371/journal.pone.0000461.g002
"68

VNTR Tree by Paul Keim et al
Figure 2. UPGMA dendrogram of VNTR data from worldwide B. anthracis isolates: Fifteen VNTR loci and
UPGMA cluster analysis were used to establish genetic relationships among the 1,033 B. anthracis isolates."69

• The “AMES”
strain of
anthrax
• Used in labs
throughout
world

• 50 VNTRs used evolve too slowly for distinguishing
AMES strains from each other
• Solution - sequence entire genomes of each strain
• Build tree from whole genome
"72

Where do viruses sit on the tree of life?
• Viruses are obligate parasites of other organisms and
cannot live on their own
• Three main theories about viruses and where they sit on
the tree of life
• 1. Viruses are relics from a pre-cellular world
• 2. Viruses are escaped portions of cellular organisms
• 3. Viruses are extremely derived and reduced cellular
organisms
74

Viruses on the Tree of Life?
75

Viruses on the Tree of Life?
75
- --

Virus Evolution Models

Bacteria Archaea Eukaryotes
Virus Evolution Model 1: The Fourth Domain
Viruses

Bacteria Archaea Eukaryotes
Virus Evolution Model 2: Separate Origin
Viruses

Bacteria Archaea EukaryotesViruses Viruses
Virus Evolution Model 3: From Within Other Groups

Probably a Little of Each
80

Case Study: Influenza Virus
81

Influenza Virus
• “Influenza” – term dates
from 15th century Italy when
epidemics were attributed to
the influence of the stars
• Negative strand RNA
viruses
• 8 single strand
chromosomes
• Two key proteins for
antigenicity
! H = Hemagglutanin
! N = Neuraminadase
82

Flu Phylogeny
PLoS Currents Influenza.
2009 Sep 3:RRN1031. 83
As with anthrax one
needs the sequence
of the entire genome
to accurately track flu
evolution
Most important result:
different segments of
the flu genome can
have very different
histories

Flu Recombination
84

Virus Evolution Models

DNA Viruses
• Some DNA viruses may be highly reduced
parasitic organisms that have lost their
cellular structure and ability to survive as
free-living species.
• The mimiviruses have genomes similar in
size to some parasitic bacteria.
• Phylogenetic analyses suggest that they
have evolved repeatedly from cellular
organisms.
86

Figure 26.25 Mimiviruses Have Genomes Similar in
87

Retroviruses
Retroviruses insert their genomes into the
host genome.
They may become nonfunctional and no
longer expressed and thus may provide a
record of ancient viral infections.
Humans have about 100,000 fragments of
endogenous retroviruses.
88

Phage
Bacteriophage viruses have been used to
fight bacterial infections in humans.
Called phage therapy, it was developed
during WWI, but was replaced by
antibiotics in the 1930s and 1940s.
As bacteria evolve resistance to antibiotics,
research in phage therapy has resumed.
89

BIS2C. Biodiversity and the Tree of Life. 2014. L12. Symbioses and the Human Microbiome

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