Introduction to microbiology
• Microbiology includes the study of other things that are microbes. It includes the study of
bacteria, viruses, fungi, and eukaryotic parasites.
What is in a microbe?
• Microbes are microscopic. That is about the only definition for a microbe. You cannot see it,
unless you use a microscope. The size range is 10^-7 M to 10^-3 M, but at least 1-5 microns is
typical for a bacteria.
News from summer 2011
• The E. coli outbreak in Germany was the first time that we isolated the bacteria from sick
patients. Within 3-4 days, the entire genome of the bacteria was sequenced. We knew exactly
what we were dealing with in terms of what the bacteria was doing and in terms of the cause of
disease. We knew why it was a nasty bacteria. The speed at which we could analyze bacteria just
in the past two years has absolutely revolutionized. We will talk about bacterial genomics and
• A big problem that we will talk about towards the end of the course is that bacteria are
becoming increasingly resistant to antibiotics. Last summer, there was a Neisseria gonnorrhea
strain that is resistant to all known antibiotics.
Other recent outbreaks of bacterial disease
• Listeria is a soil bacteria. Most people do not get sick unless they are immunocompromised or
pregnant. The bad thing about it is that it can grow at 4°C, which means refrigeration on Listeria
does not control its growth. If you take some meat that is only mildly contaminated, put it in the
fridge, come back 3 weeks later and eat it, it will be much more contaminated. We will talk more
• The Bubonic plague wiped out between 1/3-1/2 of the population between Europe and Asia.
This is caused by a bacteria called Yersinia pestis. It is not that distantly related to E. coli or
salmonella. It was a real game changer in that it cause the fall of the Roman empire and
prolonged the length of the dark ages and the extent of death was unparalleled by any other
In the year 1900, infectious diseases were the biggest killers
• About 100 years ago, mortality rates were high due to infectious disease. Infectious disease up
to about 70 years ago were the number one killers. This is a graph showing in the year 1900, you
can see that heart disease, stroke, kidney disease, and cancer were all small in comparison to
influenza and pneumonia, caused by virus and bacteria, tuberculosis, gastroenteritis, infant
diseases and diphtheria. Of course, their ability to diagnose what they were dying from was
Leading causes of death in developed countries, 2004
• You can see that only one thing, lower respiratory infections, is in the top 10, and it is mostly in
elderly people. This is due to stunning improvements in public health within the past 100 years. GTA traffic fatalities
• We freak about 5-10 people dying of an outbreak of a disease when we have had huge plagues
with far more, far greater people dying. We also freak out about things like the E. coli outbreak
that killed 4 children. We don’t freak out about things like traffic fatalities. Did this get the same
attention as the Listeria outbreak going on about the same time? No. There is no government
inquiry publishing 400 pages on traffic fatality.
Discovery of microbes
• Microbes were discovered several hundred years before it was figured out that they could cause
disease. Robert Hooke developed a crude compound microscope and he was able to observe
small eukaryotes. Leeuwenhoek discovered bacteria. He would look at cloth and decide if it was
A grade or B grade. He had to develop these lenses to look at the fibers of the cloth to see if the
cloth was good for this type of work or this type of sale, and what kind of price you could get for
it. He found himself in a position where he made his own custom lenses. He started developing
more powerful lenses and finally developed a lens powerful enough to see bacteria in pond
water, saliva, and sweat. He saw tiny cells that swam and grew in different shapes. He was the
first one to publish about it.
Microbes are living organisms
• This means that microbes only come from another pre-existing microbe. If you took some soup,
sterilized it, closed it tightly, you could come back 100 years later and no bacteria would grow in
the soup. People always assumed that life could spontaneously generate. If you left some soup
out, then automatically, molecules from the soup would assemble and make a new bacteria.
The person who refuted this with a very classic experiment called the swan neck experiment
was Pasteur. He boiled some broth, killed off the microbes in it, had it in a flask that had a very
long, extended neck. Microbes could not get inside. If he broke the flask or made the neck
straight, then microbes could get inside, then the broth would be contaminated and the other
broth would not. Later on, Pasteur, with the work he was doing in looking silkworms, first
proposed the germ theory disease. The germ theory disease is that it is microbes that are
making us sick. This explains a lot of things that people had already observed. People already
had a sense that diseases were contagious, they thought it was bad ethers or fumes emanating
when they first didn’t know what it was. Pasteur said it was something living, which means it
was something that you could kill.
• He developed a set of criteria to decide whether a certain microbe could cause a certain disease.
They are called Koch’s postulates. If an organism satisfies Koch’s postulates, it is the causative
agent that you are looking at. If a microbe (viral or bacterial) satisfies Koch’s postulates, then
you have your disease causing agent. There are problems with Koch’s postulates. Some bacteria
can be carried in healthy carriers. There are people who carry certain types of bacteria that
cause harm in other people. Many people are asymptomatic carriers. The second thing is that
when you re-introduce the pure microbe into a healthy individual, that person has to be a
susceptible individual. Their immune system has to be in the right state, and not all animal
models will work. A bacteria that affects a person given to an animal cannot be expected to act
the same way. The animal will kill the microbe most of the time. You need to understand where
Koch’s postulates apply and where they don’t.
• I will ex