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Taxonomy of Bacteria: Identification and Classification

December 3, 2019


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.

10 Comments

  • Reply Ayad Ali December 2, 2019 at 5:52 pm

    First!

  • Reply 👾BogerTheBully👾 December 2, 2019 at 5:52 pm

    Second

  • Reply Ayuen Kuol Guguei Biar December 2, 2019 at 5:53 pm

    Second

  • Reply The Joy of Reading December 2, 2019 at 6:01 pm

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  • Reply Zetsuke4 December 2, 2019 at 8:02 pm

    physiology videos please.

  • Reply Zetsuke4 December 2, 2019 at 8:03 pm

    can u make non-specific video covering lots of topic on clinical anatomy

  • Reply Briarn kech December 2, 2019 at 8:59 pm

    kk

  • Reply Cobweb Recordings December 2, 2019 at 10:49 pm

    Really loved ur video on Viruses, loving this one too. So facinating that there is an entire civilization inside all of us. Bacteria are cool too…… Well the good ones anyway 😉

  • Reply David Turner December 3, 2019 at 12:43 am

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  • Reply Valovetine December 3, 2019 at 2:03 pm

    I needed this SO much! Thank you!!!

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