Professor Dave here, let’s classify some bacteria.
As we discussed in the previous tutorial, pretty much everything you can see or feel
is teeming with bacteria.
The air we breathe, the food we eat, the surfaces we touch, and especially all the natural wonders
around us.
If you were to scoop up about a tablespoon of soil or a small cup of ocean water, scientists
predict that you’d be holding as many as one million bacterial species in your hand.
Many of these bacterial species might contain critical answers to some of our biggest questions
in medicine, energy, and engineering, but there’s a catch.
We’re unable to grow the vast majority of bacterial species in the lab in order to study
them more closely.
But more on that later, first let’s cover the basics.
Of all these bacterial species, thousands cover the human body, some transiently stopping
by, others taking up permanent residence.
However, just a fraction, a few hundred or so, can cause disease in humans.
With so many different types of bacteria out there, how in the world do we keep them straight?
When we encounter an unknown species, perhaps during an outbreak, how do we identify it?
How do we know what it’s capable of?
How can we learn how to protect ourselves against it?
First, let’s back up and talk about how bacteria are named.
The science of classifying living beings is called taxonomy, and we’ve been doing it
ever since Swedish botanist Carl von Linné, also called Linnaeus, established a system
for classification using taxonomic categories in the 1700s.
He wanted to minimize chaos as new species were discovered, and provide a structure for
defining and recognizing any newly discovered species.
In the case of bacteria, we use a binomial, or two-name, system of nomenclature.
The scientific name for any bacteria is always the name of the genus first, which is capitalized,
followed by the species name, which begins with a lowercase letter.
Both should be italicized.
The names of the genus and species have a wide variety of origins.
Sometimes they were named after the microbiologist that discovered them.
In other cases, the name might be related to how the microbe looks, or the disease it
causes.
Now that we’ve covered the names, let’s talk about how bacteria got sorted into their
respective categories in the first place.
When it comes to classifying bacteria, it may seem a daunting or even impossible task.
However, scientists have developed a system to observe, test, and then categorize bacteria
into logical relationships.
There are three main types of classification: phenotypic, analytic, and genotypic.
Let’s talk about what each of these entails, and then discuss some categories that bacteria
are typically sorted into.
First, let’s talk about phenotypic characterization, meaning the set of observable characteristics
of bacteria.
Those are size, shape, and staining characteristics.
Before we had the advanced technology we have now, scientists relied on observing microscopic
and macroscopic morphologies of bacteria.
For example, using Gram staining, a method developed by Hans Christian Gram in 1884,
we can determine if bacteria are Gram-positive or Gram-negative, and thus how much peptidoglycan
their cell wall contains.
Gram-positive organisms have a thick peptidoglycan wall, retaining lots of crystal violet stain
when using this method, and thus appearing a vivid blue under a microscope.
Gram-negative organisms have a much thinner peptidoglycan layer which does not hold the
blue dye.
Even just separating bacteria into Gram-positive versus Gram-negative can tell us a lot about
how they might behave.
Certain microbes have unique staining characteristics, such as the genus Mycobacterium, which can
be detected by an acid-fast stain.
Another example involves identifying the shape of individual organisms under a microscope,
which will be either rods, cocci, curved, or spiral.
Zooming out a bit, scientists also look at how bacteria grow on agar in the lab.
They look at the colonies of bacteria that grow, taking note of the size, shape, color,
and even smell.
For instance, streptococci colonies tend to be smaller in relation to most other types
of bacteria, and Serratia marcescens typically appear red when grown at 22 degrees Celsius.
We can test for hemolytic properties on blood agar, identifying if the bacteria produce
toxic byproducts capable of destroying red blood cells.
For example, Streptococcus pyogenes, the causative agent of strep throat, is a gram-positive
bacterium that forms long cocci chains and grows as small, white, hemolytic colonies
on blood agar plates.
Since it is likely for multiple species to appear similar in these types of tests, these
phenotypic characterization methods serve only as a starting point for further investigation.
Next, there are tests to determine what biochemical properties the bacteria have, like the ability
to ferment specific carbohydrates, what carbon sources they can use for growth, and the presence
or absence of different enzymes, like lipases, proteases, or nucleases.
All of these observations combined can identify with reasonable precision a species of bacteria.
These techniques have also been used to subdivide groups of organisms beyond the species level,
down to a specific strain.
Doing this by looking at the genetic makeup of the organism, especially in the case of
an outbreak, is called biotyping.
Many bacteria also possess antigens, which might be a toxin or other substance that triggers
an immune response in the body.
Grouping bacteria based on these antigens is called serotyping.
Using serotyping, scientists can work backwards using antibodies to detect which antigens
are present, thus allowing them to narrow down the bacterial possibilities.
Serotyping is a powerful tool for classification, especially for those species that are difficult
to grow, those that are difficult to test biochemically, or those that need to be identified
rapidly, such as during an outbreak.
Scientists can also look at which antibiotics bacteria are susceptible to, which is called
analyzing their antibiogram patterns.
Finally, using phage typing, scientists can assess which bacteriophages bacteria might
be susceptible to.
Now that we’ve covered phenotypic classification, let’s move onto analytic classification.
Analytic classification methods include whole cell lipid analysis, cell wall fatty-acid
analysis, whole cell protein analysis via mass spectroscopy, and the presence of cellular
enzymes via multilocus enzyme electrophoresis.
Analytic classification can be a bit labor-intensive, requiring expensive machines and specialized
training.
For these reasons, analytic classification is typically done in special laboratories.
Finally, the most precise method for classifying bacteria is through genotypic classification.
Put simply, this means using bacterial DNA to determine what species or family bacteria
might belong to.
In the early days, scientists used the ratio of guanine to cytosine to classify bacteria.
As technology has progressed, so has our ability to quickly and accurately identify bacteria
using DNA.
Using DNA-DNA hybridization, scientists measure the degree of genetic similarity among bacterial
isolates.
Taking this a step further, scientists can extract DNA from an organism and expose it
to species-specific molecular probes.
If the nucleic acid probe binds to the DNA, then you know you’ve properly identified
the organism.
We can also use nucleic acid sequence analysis to compare unknown bacteria with already known
sequences that are unique to a genus, species, or subspecies.
Additionally, some bacteria carry plasmids, which are small circular DNA strands that
replicate independently of the chromosome.
And, while the genetic makeup of bacteria can vary drastically between species, their
ribosomal genes are remarkably well conserved.
Scientists routinely use 16S ribosomal RNA sequences to establish taxonomic relationships
between prokaryotic strains.
That’s why in situations such as an outbreak or epidemiological investigation, scientists
can use plasmid analysis or ribotyping to quickly identify bacteria.
Now here’s the thing, bacterial classification into families, genera, and species changes
all the time, evolving as we learn more about these microscopic creatures.
Generally speaking, however, our classification system is a robust starting point.
Using all of these techniques we discussed, we can organize bacteria into categories and
predict their pathogenic capabilities.
Let’s look at some of these categories for medically important bacteria.
First, aerobic, gram-positive cocci, which can be further subdivided into catalase-positive
cocci, which includes the Staphylococcus group of bacteria, and catalase-negative cocci,
which includes the Enterococcus and Streptococcus groups.
Next, aerobic, gram-positive rods, which can be grouped into actinomycetes with cell wall
mycolic acids, actinomycetes with no cell wall mycolic acids, and miscellaneous gram-positive rods.
Then, aerobic gram-negative rods, cocci, and curved rods, which include a wide variety
of pathogenic organisms.
Additionally, there are anaerobic gram-positive and gram-negative bacteria, which are further
grouped by shape: cocci or rods.
Now that we’ve gotten classification out of the way, let’s talk about how these bacteria
are able to cause damage to the human body.