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Bacterial evolutionary genetics (MCB3023S) notes

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Comprehensive lecture notes for the Bacterial/Microbial evolutionary genetics module covered in MCB3023S. These notes cover all content taught in lectures as well as additional materials (powerpoints, textbooks) required to succeed. These notes were created by a student who achieved a distinction ...

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  • February 8, 2024
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  • 2022/2023
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MCB3023S

Microbial evolution

Introduction
What’s the point and how does it fit in




- 16F lineage is very different and when the genome was sequenced, was able to trace back to when this lineage was made
- introduced of an antibiotic exerted a selective pressure in the population structure that resulted in resistant strains being
selected through natural evolution
- environmental stressors and gene expression can use changes in bacterial populations
- in E, coli, using a fluorescence die, were able to trace their lineages back and found that E. coli could utilize citrate as a
carbon source, and this was a by chance observation

Microbes have evolved and diversified over billions of years
- prokaryotes have been around for billions of years
- these prokaryotes appeared before any detection of atmospheric
oxygen which tells us that these microbes were anaerobic as they
did not require oxygen
- this means that they had a long er time period to adapt before
oxygen because available




Bacteria: what you need to know
- they are living organisms
- the basis is that bacteria are ale to grow and divide (either
through symmetrical or asymmetrical binary fission)
- even within that, there can be diversification and changes that
can drive different lineages to homogenize
- in E. coli for example, there are different strains which have
different characteristics, within the same species, based on things
that they acquire overtime

- Mega plate: grow E. coli strains at 0 concentration of any antibiotic, the moment you increase the concentration, microbes
are able to sense this harsher environment
- microbes are metabolically active for example pneumococcus where it resides in mesopharynx which h has lots of
nutrients
- when it moves to the blood stream, there are different conditions such as pH changes, and the microbe can adapt and still
carry out its metabolic process
- for clostridium acetobutylicum: when the pH drops below 5, the bacteria uses a lot of ATP and changes the growth phase
(acetogenic to solventogenic) to produce solvents rather than acids in order to try equilibrate to the low pH and if it fails at
this, it can make pores in the membrane

Bacteria vs prokaryotes




- comparing them to eukaryotes
- they both contain a plasma membrane, cytoplasm and ribosomes

,Taxonomic Hierarchy: How realistic is “species” concept in bacteria
- different trees have been constructures based on how microbes behave
- as E. coli grow in different ecological niches, they can take up DNA which have an impact in their phenotype
- for example, urinary tract infection is a pathogenic E. coli strain

How many bacteria are there?
- very diverse, found in very large numbers and there are many different types of bacteria (over 500 different species in the
human mouth alone and different niches have different communities)
- While it is true that you will not find a surface without bacteria on it, the majority of bacteria that you’ll find are common,
non-dangerous species
- Studies have shown that of the bacteria found in indoor air, the most common four are: Micrococcus, Staphylococcus,
Bacillus, and Pseudomonas

Micrococcus
- is a sphere-shaped (coccus/cocci generally means spherical), relatively harmless bacterium. It is very common on skin,
and it can also be found in soil, water, and meat products. It is generally a saprophyte (meaning it feeds on dead and
decomposing materials), and can cause spoilage of fish.This organism can also be responsible for causing human sweat to
smell badly. In immunocompromised people, it can be an opportunistic pathogen. Some common species include M. luteus,
M. roseus, and M. varians. Micrococcus requires oxygen to grow and reproduce.

Staphylococcus
- is another sphere-shaped bacterium. It is much more well-known than Micrococcus, especially in the context of hospitals.
When the medical profession refers to MRSA, they mean a particularly drug-resistant strain of this bacterium.
However, Staphylococcus is found virtually everywhere, and usually does not result in infection. It is very common on skin,
and can also be found in the nasal passages, throats, and hair of 50% of healthy individuals. Food poisoning and skin
infections, as well as toxic shock syndrome, are among the illnesses caused by Staphylococcus. Unlike Micrococcus,
Staphylococcus is able to grow both with and without oxygen.

Bacillus
- is a rod-shaped bacterium (“bacillus” means “rod”). Bacillus is a very hardy bacterium, as it has the ability to produce
endospores – small, tough structures that can survive adverse conditions. For the most part, Bacillus is a harmless
saprophyte, and it can be found in soil, water, dust, and sometimes within the human digestive system.Some species of
Bacillus can cause food poisoning, and some can cause illness or infection. An interesting side-note about this genus is that
it contained the mystery organism isolated from a 250-million-year-old salt crystal, potentially the oldest living cell
discovered (the organism was later reclassified to Virgibacillus).

Pseudomonas
- is another rod-shaped bacterium. It can be found in soil and water, and on plants. It is an opportunistic pathogen, and
generally considered a nosocomial infection (gained while in the hospital), as the organism tends only to attack individuals
that are immunocompromised. Along with infection, it also has the ability to produce exotoxins. As a general rule, the
bacterium will not infect a healthy individual.

What do bacteria look like?
- shows the shape and size of the microbes
- relationship between shape and size
- there are some exceptions as some are star shaped or rectangular or
triangular
- note: generally most bacteria are monomorphic (maintain a single
shape), however environmental conditions may alter that shape and
this makes identification difficult, while some bacteria are genetically
pleomorphic (can have many shapes)
- some exist as single cells while others may cluster together (biofilms)

,Bacteria: Size and cell wall architecture
- cell architecture will determine the cells shape
- for many cocci and gram positive, they have a thicker cell wall and
determines shape
- eukaryotic cells are larger than bacteria and prokaryotic cells
- depiction of cell wall of gram positive and negative bacteria
- this has implications of classification

Cell wall functions:
- prevent desiccation and serve to retain nutrients as well as acting as a
source of nutrients
- allow bacteria to bind and attach to surfaces
- protect the bacteria from phagocytosis


Bacterial cell wall: Differential (Gram stain)
- in a clinical setting, if a patient underwent a surgical procedure and all of a sudden goes into shock, a gram stain is a first
point of call for rapid treatment
- illustration of how you stain bacteria, the cell wall
- test classifies bacteria into two large groups: gram positive and gram negative, based on differences in cell wall
composition
- Why do some microbes retain the purple strain and others have it washed out by the decolorizing agent?




- E. coli are gram negative; streptococcus are gram positive
- indicated by the colour of the cell (able to retain the counter stain or not)
- from a diagnostic point of view, helps us to understand what kind of antibiotics can be prescribed
- for gram negative (STIs for example), need other antibiotics such as vimpamycin, compared to positive

Bacteria classification (by phenotype)




Bacteria: Genome size
- Species which occupy restricted ecological niches, (e.g. obligate intracellular parasites
and endosymbionts) tend to have smaller genomes (<1.5 Mb) than generalist bacteria
- Bacterial genomes usually consist of a single circular xsome, but species with more than
one xsome (eg. Deinococcus radiodurans), linear xsomes (eg. Bacillis subtilis) and
combinations of linear & circular xsomes (eg. Agrobacterium tumefaciens) also exist

, - dinococcus for example, has 2 chromosomes and 2 plasmids which is an evolutionary trait because of its use in
detoxifying reductive materials
- so, it can grow n radioactive environments and so need important properties in order to survive harsh conditions
- DNA repair mechanisms need be very good
- this is a good organism to study DNA repair mechanisms
- bacteria normally has 1 circular chromosome

- most microbes are less than 3MB
- There is a limit that certain hosts restrict on microbes
- Dinococcus being an exception as most microbes have linear/circular genomes whereas bacillus has a single linear DNA
but with Dinococcus, it has more than one chromosome

- how would you experimentally show that X, Y, Z is part of a core genome?
- introduce mutations and grow the auxotroph’s in minimal media, and is the bacteria is unable to grow, the mutation is in a
gene that is part of the core genome (is essential for survival and the mutation is lethal)
- the core genome is a set of conserved genes that is contained within a bacterial species
- to graphically show the relationship between strain A, B and C?
- chart shows this relationship, the core genome is shred across all the species (red)
- the accessory genome: may be shared between 2 species that are more similar
- strain specific genes are unique to a particular strain and these characteristics are only found in that strain (blue)
- alternative representation is the graph
- looking at microbes in the gut: variety of species of bacteria and all those make up the metagenome for example

Bacteria genomes: Composition
- The complete genome sequence of the radiation-resistant bacterium Deinococcus radiodurans R1 is composed of two
chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base
pairs), yielding a total genome of 3,284, 156 base pairs
- Multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of D. radiodurans to
survive under conditions of starvation, oxidative stress, and high amounts of DNA damage were identified.
- Deinococcus radiodurans represents an organism in which all systems for DNA repair, DNA damage export, desiccation
and starvation recovery, and genetic redundancy are present in one cell!!

- The Dinococcus genome is as a result of its adaptation over time
- People have huge resulted (and mega plasmids) which resulted from: recombination (homologous or non-homologous)
- prospect: bioremediation of radioactive metals and harvesting electricity from waste organic matter

Core genomes vs pangenomes
- Core genome: pool of conserved genes shared by all
members of a bacterial species and are critical for survival
- Accessory or dispensable genome: Niche-specific pool
of genes present in some but not all genomes within the
same bacterial species
- pan-genome: global gene repertoire of a bacterial
species, comprised of the core genome + accessory
genome
- metagenome: global gene repertoire of mixed microbial
population


Concept check:
a) with aid of an appropriate diagram, describe what constitutes the pan-genome? Briefly explain how can you
experimentally show that a given genome is part of the core genome.

ANS: A pan genome is made up of the core genome and accessory genomes and the strain specific genes. In a diagram,
draw what is on the slide (the red part). To experimentally show that a given gene is part of the core genome: By
introducing random mutations and tracking the ability of the mutants to survive. If a critical gene is disabled, the
microorganism will fail to survive under the culture conditions.

b) Although Meningococcus has an open pan-genome, Budroni et al. has shown that it is composed of 79% core, 21%
dispensable, <0.01% strain specific genes. What is the consequence of this observation on the bacteriums gene diversity?
i.e. What drives diversity in these microbes that have such a small % of strain specific genes?

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