Module 2: Classification and Identification of Bacteria, Fungi, and Viruses

Question 1

The science that involves classification, identification, and nomenclature of microorganisms.

Answer 1

Taxonomy

Question 2

What are the 3 important terms that are commonly encountered in the study of bacterial classification?

Answer 2

Classification
Identification
Nomenclature

Question 3

It involves the orderly arrangement of microorganisms into groups. This involves arranging together or distinguishing microorganisms that are different from each other as a means of bringing order to a variety of organisms.

Answer 3

Classification

Question 4

True or False

There is no unified basis of classification, different groups of scientists and experts have the capacity to classify even the same organisms differently.

Answer 4

True

Question 5

True or False

Some microbiologists can classify organisms based on serotype,
antimicrobial resistance pattern, toxins and invasiveness factors in one pathogen while others may be interested in genes which are concerned with mutations and plasmids.

Answer 5

True

Question 6

Basic taxon

Answer 6

Species

Question 7

A group of microorganisms that possess characteristics analogous to other species within the genus.

Answer 7

Genus

Question 8

A group of microorganisms that possess characteristics analogous to
other genera within the family.

Answer 8

Family

Question 9

A group of microorganisms possess characteristics analogous to other
families within the order.

Answer 9

Order

Question 10

It includes groups of microorganisms that possess characteristics
analogous to other orders within the class.

Answer 10

Class

Question 11

Composes of a group of microorganisms that possess characteristics analogous to other classes.

Answer 11

Division

Question 12

It constitutes a group of microorganisms that possess characteristics analogous to other members of a division.

Answer 12

Kingdom

Question 13

It involves the practical use of classification criteria to distinguish certain organisms from others, to verify the authentic nature of a strain and to isolate and identify the organism that causes an infection.

Answer 13

Identification

Question 14

It involves the giving of an official name to a species of microorganism by which the characteristics of that species are defined and communicated among members of the scientific community. The designated names are often derived from names of persons, shapes or forms of microbes.

Answer 14

Nomenclature

Question 15

True or False

Names are always written in binomials (2 words).

Answer 15

True

Question 16

True or False

Binomials are italicized or underlined.

Answer 16

True

Question 17

What are the three-domain or large groups in the classification system of microorganisms which was introduced by Carl Woese and his colleague in 1990?

Answer 17

Archaea
Bacteria
Eukarya

Question 18

Domains _______ and _______ are made up of prokaryotic cells.

Answer 18

Bacteria
Archaea

Question 19

Domain _______ is made up of eukaryotic cells.

Answer 19

Eukarya

Question 20

This domain includes microorganisms that are associated with human or animal diseases. Most bacterial species do not cause disease but many of them reportedly play beneficial roles by producing antibiotics and food. The soil inhabited by free-living bacteria that perform many essential functions in
the biosphere (nitrogen fixation). The human body is covered with bacteria that make up the normal flora.

Answer 20

Bacterial domain

Question 21

This domain includes methanogens (methane-maker), extreme halophiles (salt lovers) and extreme thermophiles (heat/cold lovers). The
methanogens reportedly live in swamps, marshes, gut of cattle, termites, and other living substrates.

Answer 21

Archaen domain

Question 22

A domain that covers the protista, fungi, plants and animals. The protists include the single celled eukaryotes like euglena, amoeba, paramecium and protozoa.

Answer 22

Eukarya domain

Question 23

Cell shape, color, nature of cellular aggregates, motility-related organelles and formation of spores are important criteria in bacterial classification. Morphological features such as shape and color of colonies are purported to be not always constant and can be influenced by environmental conditions.

Answer 23

Morphological-based classification

Question 24

Gram staining and the application of other stains for bacteria are important methods in evaluating bacterial morphology. Of all the
different classification systems, the Gram stain has reportedly withstood the test of time.It allows a large proportion of clinically important bacteria to be classified as either
Gram-positive or Gram-negative based on their morphology and different staining properties. Slides are sequentially stained with crystal violet, iodine, then decolorized with alcohol and counter-stained with safranin. Gram-positive bacteria stain blue-purple and Gram-negative bacteria stain red.

Answer 24

Staining reactions

Question 25

Important in the classification of bacteria is the conduct of biochemical tests including the determination of the kinds of nutrients a bacterium can use, the products of its metabolism, the response to specific chemicals, and the presence of particular characteristic enzymes.

Answer 25

Biochemical features

Question 26

Microorganisms can be grouped on the basis of their need for oxygen to grow. Facultatively anaerobic bacteria can grow in high oxygen or low oxygen content and are among the more adaptable bacteria. In contrast, strictly anaerobic bacteria grow only in conditions where there is minimal or no oxygen present in the environment.

Answer 26

Growth requirements

Question 27

Bacterial antigens include surface proteins, lipopolysaccharides and peptidoglycan structures that help bacteria invade host cells by gaining access between epithelial cells. Studies on surface structures are important in recognizing the ability of bacteria to infect hosts while this also helps in the recognition and classification of potential pathogens.

Answer 27

Antigenic composition, habitat and disease production

Question 28

Selected antisera are reportedly used to classify different bacterial species. This may be based on either carbohydrate or protein antigens from the bacterial cell wall or the capsular polysaccharide.

Answer 28

Serologic systems

Question 29

Microorganisms can also be classified based on the ultrastructure of the bacteria revealed under the electron microscope. This utilizes samples which are processed as thin sections and subjected to negative staining before electron microscopic evaluation.

Answer 29

Electron microscopy

Question 30

The classification of the 3 domains for all living organisms– bacteria, archaea and eucarya were reportedly based on the comparison of 16s ribosomal RNA sequences. These sequences are highly conserved and undergo change at a slow, gradual and consistent rate which makes comparisons among the different living organisms easier.

Answer 30

Genotypic and molecular analysis

Question 31

This classifies microorganisms-based gene-controlled metabolic patterns, production of cell polymers and organ structures. It embraces studies on DNA homology and composition, DNA sequences which evaluate surface polymers (Ex: capsules, teichoic acids and O-antigens) and used as references for comparison of bacterial relatedness.

Answer 31

Genetic basis of classification

Question 32

Phylogeny estimates and analyzes genetic relationships between different organisms. The approach compares nucleic acid or protein sequences from different organisms using computer programs and estimate the relationships based on the degree of homology between the sequences.

Answer 32

Phylogeny based on nucleic homology

Question 33

This is a classification system in which deals with the grouping by numerical methods of taxonomic units based on their character states. It aims to create a taxonomy using numeric algorithms like cluster analysis rather than using subjective evaluation of their properties. The concept was first developed by Robert Sokal and Peter Sneath in 1963.

Answer 33

Numerical taxonomy

Question 34

This differentiates serologically identical species of bacteria in terms of their susceptibility or resistance to the lytic effects of species-specific bacterial viruses known as phages.

Answer 34

Bacteriophage typing

Question 35

This differentiates certain organisms in terms of their lethal effects on laboratory animals (Example: test that differentiates between pathogenic from non-pathogenic strains of Mycobacterium tuberculosis that uses guinea pigs.

Answer 35

Pathogenicity in animals

Question 36

The test differentiates bacteria in terms of their sensitivity or resistance to the effect of antibiotics. The differences of bacterial responses that may be related to various concentrations applied may also be evaluated with the antibiotic sensitivity test.

Answer 36

Antibiotic sensitivity

Question 37

What are the 3 traditional methods of bacterial identification rely on phenotypic identification of the causative organism?

Answer 37

Gram staining Culture/ cultivation Biochemical methods

Question 38

Stains purple with Gram's method, bacteria has a thick cell wall and no cell membrane.

Answer 38

Gram-positive

Question 39

Stains red with Gram's method, bacteria have a cell membrane outside a thin cell wall.

Answer 39

Gram-negative

Question 40

Shaped like a sphere.

Answer 40

Coccus

Question 41

Shaped like a rod.

Answer 41

Bacillus

Question 42

Grows in the presence of oxygen.

Answer 42

Aerobic

Question 43

Grows in the absence of oxygen.

Answer 43

Anaerobic

Question 44

Able to grow in the presence or absence of oxygen.

Answer 44

Facultative Anaerobe

Question 45

Grows in the presence of oxygen at lower concentrations than in air.

Answer 45

Microaerophilic

Question 46

This method involves the application of a single stain solution to a fixed bacterial smear.

Answer 46

Simple staining

Question 47

This involves application of a dye or a stain that makes the differences between cells and its ultra-structures visible.

Answer 47

Differential staining

Question 48

This is a staining procedure that classifies microbes into Gram-positive and Gram-negative groups. It uses crystal violet (primary stain), iodine (mordant), acetone alcohol (decolorizer) and safranin (counterstain).

Answer 48

Gram staining

Question 49

Stain method that differentiates acid fast from non-acid-fast bacteria.

Answer 49

Acid fast stain

Question 50

Stain method that demonstrates shapes and location of spores in the cytoplasm structures.

Answer 50

Endospore stain

Question 51

Stain method that differentiates bacteria in terms of the thickness of the cell structure.

Answer 51

Capsule stain

Question 52

Stain method that demonstrates the presence, number and location of flagellae in bacteria.

Answer 52

Flagellar stain

Question 53

Stain method that demonstrates intracellular deposits of starch and glycogen.

Answer 53

Cytoplasmic inclusion stain

Question 54

Stain method for fungal spores and other structures.

Answer 54

Lactophenol cotton blue stains

Question 55

Stain method recommended for rickettsial and protozoan specimens.

Answer 55

Giemsa stain

Question 56

True or False DNA-DNA hybridization was developed in the 1980s and is used to determine the similarity of DNA sequences from different organisms. The degree of similarity is reflected in the degree to which a strand of DNA from the organism of interest passively hybridizes with (attaches to) a single strand of DNA from a known organism.

Answer 56

True

Question 57

True or False DNA fingerprinting methods for bacterial identification is centered on the use of the polymerase chain reaction (PCR). Repetitive element-PCR targets specific DNA segments that are repeated at random in the bacterial genome. The identification of repetitive elements is powerful and is capable of resolving bacteria at intraspecies levels.

Answer 57

True

Question 58

True or False DNA sequencing methods like whole genome sequencing and multi-locus sequence analysis (MLSA) have been proven to be useful in the identification of bacteria. MLSA which involves DNA sequencing of subsets of so-called housekeeping (or conserved) genes has been shown to provide resolution down to intraspecies levels.

Answer 58

True

Question 59

True or False Microarrays combine the potential of simultaneous bacterial identification and speciation. This method is versatile and makes it possible to detect and discriminate against different bacterial samples on a single slide. DNA microarray-based approach is used for the quick detection and identification of bacteria using species-specific oligonucleotide probes designed for specific regions of various targeted genes.

Answer 59

True

Question 60

It is a system that classifies viruses based on the manner by which messenger RNA (mRNA) is synthesized. By studying viruses based on the manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group.

Answer 60

Baltimore classification

Question 61

True or False The main source for determining the identity of prokaryotic organisms particularly bacterial species that uses characterizing parameters is the Bergey’s manual of systematic bacteriology. The Bergey’s manual was published subsequent to the Bergey's Manual of Determinative Bacteriology which is still reportedly published as a guide for identifying unknown bacteria. The author David Hendricks Bergey used to classify bacteria based on their structural and functional attributes by arranging them into specific familial orders.

Answer 61

True

Question 62

True or False The length of bacteria usually varies from 0.5 μm to 500 μm and the width also varies from 0.2 μm to 5 μm.

Answer 62

True

Question 63

Cocci in pairs

Answer 63

Diplococcus and Neisseria species

Question 64

Cocci in chains

Answer 64

Streptococcus species

Question 65

Cocci in clusters

Answer 65

Staphylococcus species

Question 66

Coccoid bacteria in groups of 4

Answer 66

Sarcina species

Question 67

True or False Bacilli or rod-shaped bacteria come in different forms.

Answer 67

True

Question 68

Short rods

Answer 68

Cocco-bacilli bacteria

Question 69

Bacilli with round ends

Answer 69

Salmonella typhosa

Question 70

Bacilli with tapering ends.

Answer 70

Fusobacterium necrophorum

Question 71

Square-ended bacilli

Answer 71

B. anthracis

Question 72

True or False Some filamentous bacilli (these usually do not separate and to form "long threads").

Answer 72

True

Question 73

Club-shaped bacilli.

Answer 73

C. diphtheria

Question 74

Rigid helical bacteria

Answer 74

Spirillum minus

Question 75

Vibroid/ comma-shaped bacterium.

Answer 75

Vibrio cholera

Question 76

Highly flexible helical Spirochetes.

Answer 76

Borrelia Treponema Leptospira

Question 77

Pear-shaped bacteria.

Answer 77

Pasteuria species

Question 78

Lobe-shaped bacteria

Answer 78

Sulfolobus species

Question 79

Bacteria seen as discs and arranged like stacks of coins.

Answer 79

Caryophanon species