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INTRODUCTION OF MICROBIOLOGY :microscope: (TAXONOMIC METHODS (interpret a…
INTRODUCTION OF MICROBIOLOGY :microscope:
MICROBIAL EVOLUTION
microbiology
micro = small, bios = life
cannot be seen clearly by naked eyes
if multicellular = lack differentiated tissues
classes
bacteria
human microbiome
there are as many bacteria as cells in the body
consist of
bacteria
archaea
fungi
viruses
archaea
protozoa
algae
fungi
virus
everywhere
only small amount is pathogenic
infect all 3 domains of life
more viruses than bacteria
prions
unicellular
EVOLUTION
reason for diversity
positive selection
new advantageous mutations spread in population
able to improve fitness
SWEEP
MRSA is an example
genetic drift
evolutionary divergence
not selection
due to
random
events
bottleneck
diverse population at first
tragic accident happened, a few with certain trait survived
those traits propagate while other traits died out
founder effect
newly founded populations don't always represent the genetic diversity in their sources
a small group move to a different area and form their colonies
definition: change in allele frequency in a population over time
2 cases studies
MRSA
strong selective pressure:
positive selection
resistant to 3 antibiotics
after being treated with antibiotic
vancomycin
rifampin
ciprofloxacin
partly resistant to linezolid
methicillin-resistant staphylococcus aureus infection
condition for growing
aerobic
on blood agar plate
E. coli
long-term experiment
overview
every 24h, 1% of each population transferred to new medium
grow 6.7 generation/ day -
ancestral
12 populations in medium with limited glucose
frozen samples taken every 500 generations -
fossil
ancestral and evolved cells grown together in
liquid medium with glucose
both ancestral and evolved have white color
ancestral and evolved cells plated on
solid medium with arabinose
measure fitness: counting dots with color
ancestral ara+
evolved ara -
observation
fitness increase a lot at first
after initial peak, fitness change is gradual
mutation rate is constant over time
new observation
medium has citrate as pH buffer : cannot be used by E.coli
after 31,500 generations, one culture evolved to use citrate
citrate mutant low fitness at first, then gradually increase till reached plateau
Cit (-) continue to survive because the product of Cit (+) is the substrate for Cit (-)
KEY: THERE'S NO POSITIVE SELECTION
THE GENE JUST HAPPEN TO BE ADVANTAGEOUS
HORIZONTAL GENE TRANSFER
3 types in prokaryotes
TRANSFORMATION
dead bacterium
release DNA fragment
transfer of free DNA
GRIFFITH EXPERIMENT
smooth strain - viruluent
polysaccharide capsule
prevent host immune dection
rough strain - nonvirulent
lack protective capsule
is recognized and destroyed by host immune system
heat-killed smooth strain - mouse live
heat-killed smooth strain and rough strain - mouse dies
Avery
- DNA from heat killed smooth strain and rough strain - mouse die
random/ stochastic
CONJUGATION
come from alive baterium
plasmid transfer
targeted
TRANSDUCTION
viral delivery
random/ sotchastic
movement of DNA between prokaryotes of the same or different species
GROW BACTERIA IN A LAB
liquid media
solid media: agar
complex polysaccharide from marine red algae
not metabolized by microbes
liquefies at 100 C
solidify at 40 C
culture media
chemically defined media
known exact chemical composition
minimal media
complex media
most commonly used
extracts and digests of yeasts meat or plants
TAXONOMIC METHODS
PHYLOGENETIC ANALYSIS
overview: conserve sequences -
chronometer
/ a molecular clock
16s rRNA as chronometer
because
it is present in both bacteria and archaea,
well conserved
it mutates at a constant rate
GENOTYPIC ANALYSIS
the presence of an allele
interpret a tree
align the sequence of interest with sequences from other strains or species - the matrix
orthologous = homologous gene with same function across the species
homologous = common ancestor
cladistics
- make sense of molecular sequences
character-state methods for tree reconstruction
define phylogenetic relationships
examine changes in nucleotides at individual positions in the sequence
define monophyletic groups - use the phylogenetic relationships
common methodes
algorithms
programmed series of steps
unweighted pair group method with arithmetic mean
neighbor joining methods
optimality criteria
pick the best of many possible trees
parismony principle
simplest explanation is the most preferred
occam's razor - best explanation fits data with the fewest assumptions
maximum likelihood
bayesian analysis
bootstrap value at the node
assessing robustness of alignment
all trees are estimate
cannot know the ancestral sequence
estimate the reproducibility
not accuracy
definition: probability of a clade
set of descendants of a particular node
which share common ancestor
probability that members of a clade are always members of the same clade
node
terminal node = existing species
internal node = ancestor
branch
relationship between taxa in terms of descent and ancestry
intermediate sequences of same gene now extinct organisms
bipartition
only one branch connects any two adjacent nodes
length
scaled - represent the number of changes that have occurred in the branch a function of time
PHENOTYPIC ANALYSIS
what something "looks like"
morphology: Gram reaction, size, shapre
SCIENTIFIC TERMINOLOGY
phylogenetic tree give information regard
evolutionary relationship - VGT - parent to offsprings
evidence for HGT - from microbes to microbes
PREDICT HORIZONTAL GENE TRANSFER
criteria for xenologs
GC content
% of G + C in genome can be determined by measuring the melting temperature of DNA
vary wide range among prokaryotes (20% - 80%)
useful taxonomic tool
unusual codon usage
degenerate codons
meaning: >1 codons specifies a single aa are not used at equal frequency
Ex: 80% of Ile come from AUU, but 20% of Ile come from AUA <- different DNA sequence
