Classification L5

What is bacterial classification

Classification provides characteristics and a way to compare bacteria to help identify an organism.

Why is it sometimes important to classify an unknown bacterium

An unknown bacterium may cause disease or have useful industrial applications.

What methods can be used to classify bacteria

Visual methods, biochemical tests, serological tests, and DNA tests.

What is bacterial identification

Using characteristics of an unknown bacterium to determine its identity.

What criteria does bacterial identification use

It uses the same criteria used to classify bacteria.

What are databases such as Bergey’s used for

They are used to help identify unknown bacteria by comparing their characteristics.

What is the main goal of bacterial identification

To determine the identity of an unknown bacterium by comparing its characteristics.

What are the main categories of techniques used to identify bacteria

Visual, biochemical, serological, and genomic methods.

What does a positive identification require in this course

100% of the identification criteria must match.

What is the purpose of using multiple identification methods

Different characteristics and test results can be combined to identify an unknown bacterium.

What is visual identification of bacteria

Visual identification uses visible characteristics of bacteria to help identify them, such as cell morphology, flagella, endospores, colony morphology, and Gram staining.

What features of cell morphology can be used to identify bacteria

Cell size, cell shape, and cell arrangement can be used to help identify bacteria.

What are the three common bacterial cell shapes

Cocci are spherical, bacilli are rod-shaped, and spirilla are spiral-shaped.

What are cocci

Cocci are spherical or round bacterial cells.

What are bacilli

Bacilli are rod-shaped bacterial cells.

What are spirilla

Spirilla are spiral-shaped bacterial cells.

What is cell arrangement

Cell arrangement describes how bacterial cells are positioned relative to one another after cell division.

What are some common arrangements of cocci

Common arrangements include diplococci (pairs), streptococci (chains), tetrads (groups of four), sarcinae (cubical groups), and staphylococci (irregular clusters).

What are some common arrangements of bacilli

Common arrangements include diplobacilli (pairs) and streptobacilli (chains).

What are vibrio, spirillum, and spirochete

They are different spiral-shaped bacterial forms: vibrio is curved like a comma, spirillum has a rigid spiral shape, and spirochete has a flexible, tightly coiled shape.

What are the 5 common bacterial flagella arrangements

Peritrichous = flagella all over
Monotrichous = one flagellum
Lophotrichous = tuft of flagella on one side
Amphitrichous = flagella on both sides

How can flagella help identify bacteria

The number and arrangement of flagella can help identify bacteria.

What are endospores

Endospores are structures produced by some bacteria that can be identified by their presence, size, and position.

What is colony morphology

Colony morphology is the physical appearance of a bacterial colony.

What is a bacterial colony

A visible mass of microbial cells that comes from one cell of the same microbe.

What can affect the appearance of a bacterial colony

The growth medium can affect the appearance of a colony.

What is Gram staining

A differential stain used to distinguish Gram-positive and Gram-negative bacteria.

What colour are Gram-positive bacteria after Gram staining

Purple

What colour are Gram-negative bacteria after Gram staining

Pink

What is Gram staining based on

Differences in the chemical composition of bacterial cell walls.

Why are biochemical tests used to identify bacteria

Bacteria have different metabolic pathways and abilities to use resources.

What do biochemical tests usually test for

The presence or absence of a specific component or function.

What do positive and negative biochemical test results mean

Positive = the organism can perform the function.
Negative = the organism cannot perform the function.

Why are multiple biochemical tests used to identify bacteria

The results are combined to identify the organism, usually using a dichotomous key.

What is oxygen tolerance

The ability of bacteria to survive and grow in the presence or absence of oxygen.

What are obligate aerobes

Bacteria that require a high concentration of oxygen to grow.

What are obligate anaerobes

Bacteria that cannot tolerate oxygen.

What are facultative anaerobes

Bacteria that grow with or without oxygen, but grow faster with oxygen.

What are microaerophiles

Bacteria that grow best at low oxygen concentrations.

What are aerotolerant anaerobes

Bacteria that grow equally well with or without oxygen. But uses fermentation. It can live in oxygen environments but doesn’t use oxygen

What enzymes help bacteria tolerate oxygen

Superoxide dismutase (SOD) and catalase.

What do SOD and catalase do

They remove toxic oxygen products that can damage cells.

What does the catalase test detect

It detects the enzyme catalase.

What does catalase do

Catalase breaks down hydrogen peroxide, which is commonly found in bacteria able to grow in presence of oxygen

How is the catalase test performed

Bacteria are placed on a slide and hydrogen peroxide is added.

What is a positive catalase test

Bubbles form when hydrogen peroxide is added.

What does a positive catalase test mean

The bacteria contain catalase and can deal with oxygen.

What is a negative catalase test

No bubbles form when hydrogen peroxide is added.

What does a negative catalase test suggest

The bacteria lack catalase and are likely unable to tolerate oxygen.

What does the catalase test NOT prove

It does not prove that bacteria can use oxygen. But it proves that it can tolerate it

What does the oxidase test detect

It detects cytochrome c oxidase.

What does cytochrome c oxidase do

It is used by aerobic organisms that use oxygen as the terminal electron acceptor.

What is a positive oxidase test

The test area turns dark blue, maroon, and eventually almost black.

What is a negative oxidase test

There is no colour change within 30 seconds.

What does the oxidase test show

It shows that the bacteria can use oxygen.

What does the fermentation test determine

It tests whether bacteria can ferment a specific carbohydrate.

What is added to a fermentation test

A specific carbohydrate, pH indicator, and inverted Durham tube.

What does phenol red indicate in a fermentation test

Red = neutral
Yellow = acidic

What does the Durham tube detect

Gas produced during fermentation.

What does a yellow colour with no gas mean

Fermentation occurred and no gas was produced.

What does a positive fermentation test show

The bacteria can ferment the specific carbohydrate.

What does a yellow colour with gas mean

Fermentation occurred and gas was produced.

What does a negative fermentation test look like

The medium remains red and there is no gas.

What causes the colour change during fermentation

Acidic products are produced, causing the pH indicator to turn yellow.

What is Mannitol Salt Agar used for

It tests whether bacteria can grow in high salt and ferment mannitol.

What is the purpose of the salt in Mannitol Salt Agar

Salt is selective and allows salt-tolerant bacteria to grow.

What is the purpose of mannitol in Mannitol Salt Agar

Mannitol is differential and shows whether bacteria can ferment it.

What does yellow colour on Mannitol Salt Agar mean

The bacteria grew in salt and fermented mannitol.

What are selective tests

Tests that select for bacteria with a specific ability, such as growing in high salt.

What are differential tests

Tests that distinguish bacteria based on a specific characteristic, such as fermentation.

What is rapid identification

A method that uses pre-packaged test chemicals to identify bacteria more quickly.

What is the advantage of pre-packaged test chemicals

They decrease labour and the chance of contamination.

What is the advantage of doing several tests at once

Multiple biochemical tests can be completed at the same time instead of using several tubes or plates.

What is the RapID System used for

It is used to rapidly identify bacteria using several biochemical tests at once.

How are RapID System results used

The results of multiple tests are analyzed together to identify the bacterium.

Why is the RapID System faster than using separate tests

Several biochemical tests are performed at once instead of being done separately.

What is serology

The use of specific tests to identify bacterial species.

How are antibodies formed

Microbes in the body cause the immune system to make antibodies.

How can antibodies help identify bacteria

Antibodies can bind to specific bacterial antigens and indicate the presence of that bacterium.

What are antigens

Molecules on microbes that can be recognized by specific antibodies.

What happens when an antibody binds to its specific antigen

An antibody-antigen reaction occurs.

What does antibody-antigen binding indicate

The specific bacterium or antigen is present.

What does no antibody-antigen binding indicate

The specific bacterium or antigen is not present.

What are enzyme immunoassays (EIA)

Tests that use enzyme-linked antibodies to detect specific antigens or antibodies.

What happens when the enzyme in an EIA reacts with its substrate

A coloured product is produced.

What does a darker colour in an EIA indicate

A higher amount of the detected antigen or antibody.

What are the two types of EIA

Direct EIA and indirect EIA.

What does a direct EIA detect

It detects an antigen from the patient’s sample.

What is the basic setup of a direct EIA

Antibody → antigen → antibody

What does an indirect EIA detect

It detects antibodies from the patient’s serum.

What is the basic setup of an indirect EIA

Antigen → patient antibody → secondary antibody

What is the main difference between direct and indirect EIA

Direct EIA detects the patient’s antigen.
Indirect EIA detects the patient’s antibody.

What does the enzyme-linked antibody do in an EIA

It produces a coloured product when its substrate is added.

What does a positive EIA result show

A colour change shows that the target antigen or antibody was detected.

What can direct EIA be used to detect

Specific antigens, such as drugs in urine.

What can indirect EIA be used to detect

Specific antibodies in a patient’s serum or specific antigens in a patient sample.

What enzymes can be used in EIA

Peroxidase, alkaline phosphatase, and β-galactosidase.

What is molecular identification

Using DNA sequences to help identify and classify microorganisms.

What are the steps for doing sequencing target

1. Target the rRNA (16s For Prokaryotes, 18S for Eukaryotes)

2. Run a PCR

3. Run a Gel

4. do a Multiple Sequence Alignment (MSA)

5. BLAST

6. Phylogenic Tree

First Step: Targeting rRNA

In prokaryotes you target the 16S rRNA subunit.

In Eukaryotes you target the 18S rRNA subunit