Lecture 4: Bacterial taxonomy

Question 1

What are the 4 goals of the classification of microorganisms?

Answer 1

Stability, predictability, building larger hierarchical groups, and being able to learn about a whole group by studying an individual.

Question 2

Name the 7 levels of classification from broad to specific.

Answer 2

Kingdom/domain, phylum/division, class, order, family, genus, species

Question 3

What do the following names say about the appearance of a microorganism?
Staphyl, coccus, aureus, helico, campylo

Answer 3

Cluster, round, golden, spiral-shaped, curved

Question 4

What do the following names say about the habitat of microorganisms?
Jejuni, pylori

Answer 4

Gut, gatekeeper

Question 5

What is a species in bacteriology?

Answer 5

It is a collection of strains that share many stable properties and differ significantly from other groups of strains.

Question 6

What are 3 different ways of dividing up a species into strains?

Answer 6

Biovars (biochemical or physiological differences), morphovars (different morphology), serovars (different antigenic properties)

Question 7

What formula can be used to calculate the similarity between organisms?

Answer 7

Sj (Jacquard similarity constant) = # similarities shared/# similarities compared

Question 8

Explain how to interpret Sj scores.

Answer 8

Sj = 1 means the two organisms are totally identical for the characteristics being compared, while Sj = 0 means they share nothing in common. Using more similarities will lead to a more accurate comparison.

Question 9

What can Sj scores be used for?

Answer 9

They can be used to build dendograms.

Question 10

What is the difference between a dendogram and a phylogenetic tree?

Answer 10

A dendogram is based on visible characteristics, while a phylogenetic tree is based on genetic sequencing.

Question 11

Name 3 morphological features typically considered when distinguishing between microorganisms.

Answer 11

Shape (round, elongated, clusters, etc,), flagella (presence, location, number), gram-stain (gram-positive, gram-negative).

Question 12

Name 6 biochemical/physiological features typically considered when comparing microorganisms.

Answer 12

Aerobic or not, optimal temperature, optimal pH, salt concentration, carbon source (96 well plates), fermentation properties (produce acids or gases)

Question 13

What is phage typing?

Answer 13

It involves looking at whether bacteriophages can infect the microorganism you’re trying to classify, as bacteriophages have specific kinds of bacterium they can infect.

Question 14

Name two indirect methods and one direct method of using genomic characteristics to classify microoganisms.

Answer 14

Indirect: G+C content and DNA hybridization.
Direct: sequencing genes to uncover phylogenetic relationships

Question 15

Explain how G+C content can be used to classify microorganisms.

Answer 15

Since G-C base pairs have 3 H bonds, it takes more energy to break them. So the melting point of the genome will be higher with a greater % G+C. The density will also be higher proportional to GC content because GC base pairs are bigger.

Question 16

What are the two types of DNA hybridization?

Answer 16

Total genome hybridization and probe hybridization (targeting specific gene).

Question 17

Explain how complete genome hybridization works.

Answer 17

You need the genome of a control bug and of the one you’re trying to classify. You split open their genomes and take a single strand of each and mix them. If they don’t stay together at all, the two are very different. If they complete hybridize, they’re really similar. There can also be outcomes in between.

Question 18

Explain how specific gene hybridization works.

Answer 18

You take an unknown bacteria and once against separate the DNA into single strands. You can then synthesize the complement to a small part of a known genome (the gene in question). If it can hybridize with the unknown bacteria’s DNA, it tells us that the gene is present. If not, the gene is absent.

Question 19

What are dichotomous keys?

Answer 19

It is a series of yes or no questions that allow you to narrow down the type of bacteria an unknown specimen could be.

Question 20

How do procaryotes and eucaryotes differ in terms of cell organization?

Answer 20

Eucaryotic cells are complex and have organelles and compartments. The DNA is stored in the nucleus. In procaryotes, the DNA is free-floating in the cytoplasm and there are no organelles so that they can grow as fast as possible.

Question 21

How do eucaryotes and procaryotes differ in terms of cell wall?

Answer 21

Eucaryotes don’t have a cell wall, while bacterial cells specifically are surrounded by a cell wall of peptidoglycan (note archaea don’t have one either)

Question 22

How do eucaryotes and procaryotes differ in terms of size?

Answer 22

Eucaryotic cells are approximately 10 times larger.

Question 23

Name the 4 main shapes of cells and the proper term for them.

Answer 23

Spherical or ellipsoidal: cocci
Cylindrical or rodlike: bacilli
Helical or spiral: spirilla
Others: irregular, square, star, etc.

Question 24

What term describes:
A single coccus, two cocci, a chain of cocci, a group of 4, a group of 8, and a cluster?

Answer 24

Single, diplococci, streptococci, tetrad, sarcinae, staphylococci

Question 25

What term describes:
Two bacilli stuck together, a chain of bacilli

Answer 25

Diplobacillus, streptobacillus

Question 26

Explain why diplobacilli don’t arrange themselves one on top of the other.

Answer 26

Because it requires too much energy for them to divide along their large plane, so they divide along the smaller plane instead, forming chains.

Question 27

The science of taxonomy includes which 3 components?

Answer 27

Classification, nomenclature, and identification (based on visible characteristics)

Question 28

Who came up with the hiearchichal scheme of classification?

Answer 28

Carolus Linnaeus