Module 2: Classification and Identification of Bacteria, Fungi, and Viruses Flashcards
The science that involves classification, identification, and nomenclature of microorganisms.
Taxonomy
What are the 3 important terms that are commonly encountered in the study of bacterial classification?
Classification
Identification
Nomenclature
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.
Classification
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.
True
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.
True
Basic taxon
Species
A group of microorganisms that possess characteristics analogous to other species within the genus.
Genus
A group of microorganisms that possess characteristics analogous to
other genera within the family.
Family
A group of microorganisms possess characteristics analogous to other
families within the order.
Order
It includes groups of microorganisms that possess characteristics
analogous to other orders within the class.
Class
Composes of a group of microorganisms that possess characteristics analogous to other classes.
Division
It constitutes a group of microorganisms that possess characteristics analogous to other members of a division.
Kingdom
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.
Identification
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.
Nomenclature
True or False
Names are always written in binomials (2 words).
True
True or False
Binomials are italicized or underlined.
True
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?
Archaea
Bacteria
Eukarya
Domains _______ and _______ are made up of prokaryotic cells.
Bacteria
Archaea
Domain _______ is made up of eukaryotic cells.
Eukarya
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.
Bacterial domain
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.
Archaen domain
A domain that covers the protista, fungi, plants and animals. The protists include the single celled eukaryotes like euglena, amoeba, paramecium and protozoa.
Eukarya domain
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.
Morphological-based classification
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.
Staining reactions
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.
Biochemical features
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.
Growth requirements
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.
Antigenic composition, habitat and disease production
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.
Serologic systems
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.
Electron microscopy
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.
Genotypic and molecular analysis
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.
Genetic basis of classification
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.
Phylogeny based on nucleic homology
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.
Numerical taxonomy
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.
Bacteriophage typing
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.
Pathogenicity in animals
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.
Antibiotic sensitivity
What are the 3 traditional methods of bacterial identification rely on phenotypic identification of the causative organism?
Gram staining
Culture/ cultivation
Biochemical methods
Stains purple with Gram’s method, bacteria has a thick cell wall and no cell membrane.
Gram-positive
Stains red with Gram’s method, bacteria have a cell membrane outside a thin cell wall.
Gram-negative
Shaped like a sphere.
Coccus
Shaped like a rod.
Bacillus
Grows in the presence of oxygen.
Aerobic
Grows in the absence of oxygen.
Anaerobic
Able to grow in the presence or absence of oxygen.
Facultative Anaerobe
Grows in the presence of oxygen at lower concentrations than in air.
Microaerophilic
This method involves the application of a single stain solution to a fixed
bacterial smear.
Simple staining
This involves application of a dye or a stain that makes the differences
between cells and its ultra-structures visible.
Differential staining
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).
Gram staining
Stain method that differentiates acid fast from non-acid-fast bacteria.
Acid fast stain
Stain method that demonstrates shapes and location of spores in the cytoplasm structures.
Endospore stain
Stain method that differentiates bacteria in terms of the thickness of the cell structure.
Capsule stain
Stain method that demonstrates the presence, number and location of flagellae in bacteria.
Flagellar stain
Stain method that demonstrates intracellular deposits of starch and glycogen.
Cytoplasmic inclusion stain
Stain method for fungal spores and other structures.
Lactophenol cotton blue stains
Stain method recommended for rickettsial and protozoan specimens.
Giemsa stain
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.
True
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.
True
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.
True
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.
True
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.
Baltimore classification
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.
True
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.
True
Cocci in pairs
Diplococcus and Neisseria species
Cocci in chains
Streptococcus species
Cocci in clusters
Staphylococcus species
Coccoid bacteria in groups of 4
Sarcina species
True or False
Bacilli or rod-shaped bacteria come in different forms.
True
Short rods
Cocco-bacilli bacteria
Bacilli with round ends
Salmonella typhosa
Bacilli with tapering ends.
Fusobacterium necrophorum
Square-ended bacilli
B. anthracis
True or False
Some filamentous bacilli (these usually do not separate and to form “long threads”).
True
Club-shaped bacilli.
C. diphtheria
Rigid helical bacteria
Spirillum minus
Vibroid/ comma-shaped bacterium.
Vibrio cholera
Highly flexible helical Spirochetes.
Borrelia
Treponema
Leptospira
Pear-shaped bacteria.
Pasteuria species
Lobe-shaped bacteria
Sulfolobus species
Bacteria seen as discs and arranged like stacks of coins.
Caryophanon species
