Lecture 2: Components of Taxonomy and Classification Systems Flashcards
- Discuss the components of taxonomy and the classification systems
The word taxonomy came from the word combination of Greek words ________ which means arrangement or order
and “nomos”, means law or “nomein” which means _______________.
“taxis” ; to distribute or govern
The science of classifying organisms. It provides universal names of organisms – humanity is composed of many nations with diverse
languages but with taxonomy the organism will have only one scientific identity. Moreover, it provides reference
for identifying organisms since in this science, technologies, strategies, and guidelines were developed to identity
and name (nomenclature) the organism.
Taxonomy
Component of Taxonomy which involves arrangement of organisms into groups or taxa based on mutual similarity or evolutionary relatedness
Classification
Component/branch of Taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules
Nomenclature
Component of Taxonomy which involves the process of determining that a particular isolate belongs to a recognized taxon
Identification
Study of the evolutionary history of organisms, with ultimate objective of characterizing and arranging them in an orderly manner
Systematics or phylogeny
True or False: Any study of the nature of organisms, when the knowledge gained is used in taxonomy, is part of systematics
True
A name given by the scientist who first discovered and/or described and published and
accepted in an appropriate scientific journal/article
Scientific Name
As a “name”, it has distinguishing features, it is written in a __________ following the binomial nomenclature crafted by ______________
Binomial or binomen manner ; Carolus Linnaeus
Another distinguishing features of a scientific name is that it is written in _________ and ___________
therefore by using it the meaning of the words chosen for a species will not change through time.
Italic and in Latinized form (Latin is dead language)
The naming of bacteria or bacterial nomenclature (through a lengthy method of identification methods) is regulated by the__________________.
International Code of Nomenclature of Prokaryotes (shortly the Prokaryotic Code)
The scientific name of a microorganism is composed of two words:
generic (genus) name and specific epithet
This microorganism is a thermophilic marine
archaeon that grows optimally between 100 and 103 °C. Its specific name is derived from the Latinized form of
Woese, named in honor of Dr. Carl Woese.
Pyrococcus woesei
Scientific names are created based on four sources.
1. _________ who provided a significant contribution in bacterial taxonomy. Provide an example.
Scientist’s name. (Klebsiella pneumoniae, honors
Edwin Klebs) pneumoniae denotes the disease (pneumonia an infection to one or both lungs
Scientific names are created based on four sources.
2. Descriptive based on the__________. Provide an example
Observable characteristics of the organism. (Streptococcus pyogenes, “strepto” which
means chains of cells and “coccus”, the shape of the cells. “pyo” –forms pus
Scientific names are created based on four sources.
3. ___________the area or location where the organism originated.
Geographic place
Scientific names are created based on four sources.
4. _________________–___________ was discovered after an outbreak in 1976 among people who went to a Philadelphia convention of the American Legion.
Organizations; Legionella
The taxonomic hierarchy or rank is composed of ____ groups namely: _____________________________.
8; Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species.
True of False. In the taxonomic hierarchy of Domain Bacteria, there is an assigned Kingdom.
False
An ________________ is that one strain or a set of strains showing the same or similar properties, and treated as a taxonomic group.
Infrasubspecific taxon
Give the Preferred Name, Synonym and Example of a Intrasubspecific rank under Special biochemical or physiological properties
Biovar, Biotype; Brucella microti Biovar 5 causes murine brucellosis isolated from voles and wild rodents.
Give the Preferred Name, Synonym and Example of a Intrasubspecific rank under Distinctive antigenic properties
Serovar, Serotype; Ureaplasma urealyticum serovar 4 predominant commensal bacterium in women’s urine.
Give the Preferred Name, Synonym and Example of a Intrasubspecific rank under Pathogenic properties for certain hosts.
Pathovar, Pathotype; Erwinia caratovora pv. atroseptica causes blackleg in potatoes
Give the Preferred Name, Synonym and Example of a Intrasubspecific rank under Ability to be lyzed by certain bacteriophages.
Phagovar, Phagotype; Staphylococcus aureus phagovar 81
Give the Preferred Name, Synonym and Example of a Intrasubspecific rank under Special morphological features.
Morphovar, Morphotype: Burkhoideria pseudomallei morphovar vgh 16W soil-borne
In the given example, Escherichia coli DSM 30083T, the superscript T denotes that __________.
this strain is a type strain (a copy of the original strain).
A group of closely related organisms that breed among themselves.
Eukaryotic species (higher organisms)
Prokaryotic species
A population of cells with similar characteristics. Collection of strains that share many stable properties and differ significantly from other groups of strains
A population that descends from a single organism/pure culture
Strain. (e.g. Type Strain)
of viruses with similar characteristics that occupies a par
Viral species
Major reference in identifying a strain of bacterium, based on morphology, differential staining, biochemical tests
Bergey’s Manual of Determinative Bacteriology (ID schemes for bacteria and archaea)
Major reference in identifying a strain of bacterium, based on rRNA sequencing
Bergey’s Manual of Systematic Bacteriology; Bergey’s Manual of Systematics of Archaea and Bacteria (BMSAB) - phylogenetic information on bacteria and archaea
Major reference in identifying a strain of bacterium, based on published articles (International Journal of Systematic and Evolutionary Microbiology USEM- previously Int. Journal of Systematic Bacteriology
Approved Lists of Bacterial Names (lists species of known prokaryotes)
Forms of classification systems
artificial and natural classification
Classification of organisms based on relatively few and trivial characteristics. This
method classifies organisms using easily recognizable characteristics, but the classifications do not always show the true ancestral relationships between organisms (evolutionary relationships).
Artificial classification
A system of classification that arranges organisms into groups whose members share many characeteristics and reflect the biological nature of organisms.
Natural Classification
Groups organisms together based on the mutual similarity of their phenotypic characteristics
Phenetic system
Is a natural classification that groups organisms based on evolutionary relationships rather than general resemblance.
Phylogenetic or phyletic resemblance
The evolutionary history of a group of genetically related species or group is called ___________. It is composed of
two Greek words ___________ and __________
phylogeny; phylon (tribe or race) and geny (generation or production).
According to Hideux (1978), Sneath & Sokal (1973) defined the term ________________ as “the grouping by numerical methods of taxonomic units on the basis of their character states”.
numerical taxonomy
True or False: Numerical Taxonomy is arrangement is based on quantification of the prsence and absence of characters among organisms and quantification approach was developed with the use of computers
True
True or False: In numerical taxonomy, the process starts with the determination of the presence or absence of selected
characters in the target group of microorganisms. Hence, that the character is defined as an attribute about which
a single statement can be made.
True
True or False: In numerical taxonomy, At least 10 characters is used but preferablytwenty of characters (morphological, biological, chemical and physiological data) for a robust and reliable classification.
False
In numerical taxonomy, after character analysis ____________ a function that measures the agreement between characters held by two organisms is calculated for each pair of organisms in the group (Prescott et al., 1993).
Association coefficient
In bacteriology, ____________ is the commonly utilized coefficient. It is the proportion of characteristics that match regardless of whether the attribute is present or absent. Mathematically it is defined as the number of present characteristics and number of absent characteristics over the total number of
characteristics.
simple matching coefficient
The ___________ ignores the calculation of characteristics that are absent for both strains.
Jaccard Coefficient
The ______________is the tree-like diagram as a summary result of numerical taxonomic analysis (Prescott, et al., 1993).
dendrogram (not dendogram)
True or False: In dendrogram, the result of a clustering is presented either as the distance or the similarity between the clustered rows or columns depending on the selected distance measure. An example, clustering is presented as percent similarity of the organisms being compared. Strains of a given species may cluster at a 90% similarity level, species within a given genus may cluster at the 70 percent level, and different genera in the same family may cluster at the 50 percent or lower level.
True
In a ______________ of identification, the pure culture will be subjected to colony and gram staining to know the morphological characteristics of the organism. Biochemical, antigenic properties and growth characteristics will follow to determine the physico-chemical characteristics of the organisms.
conventional method
True or False: In convetional method, molecular methods like
percent G+C, DNA homology, thermal stability of the DNA is used to determine the genetic characteristics. The data obtained will be analyzed and compared with the existing databases or data from references like Bergey’s Manual of Determinative Bacteriology, Bergey’s Manual of Systematic Bacteriology to identify the organism.
True
As technically defined by Gillis et al., (2015) _________________ refers to a consensus type of taxonomy and aims to utilize all the available data in delineating consensus groups, decisive for the final conclusions. In other words, it assembles and assimilates many levels of information from cultural, morphological, physiological and chemical, molecular to ecological data to identify the organism.
polyphasic taxonomy
In polyphasic approach, the isolate to be identified must be a _________________.
pure culture (prerequisite)
True or False: In polyphasic approach, the DNA of the pure culture is isolated for 18s rRNA gene amplification and followed by sequencing. The sequencing results will be trimmed, aligned and compared with existing database like in BLASTn search
False: 16s
True or False: In polyphasic approach, From the sequences obtained, a phylogenetic tree can be inferred to know the taxonomic position of the isolate and sequence similarities can be calculated. If for example the sequence similarity of the
isolate is 97% or below it is probable that it is a novel isolate.
True
In taxonomy there are hundreds of tests available to determine the characteristics of the organism. And, ALL these tests will be used. The gram reaction result will serve as a guide for suggested tests for the isolates.
For example, Gram negative will be subjected to analysis of sphingolipids and lipopolysaccharides and will be subjected to cell wall analysis because the variability of amino acid and cell wall sugars in Gram negative isolate is significant since its peptidoglycan (PG) layer is thin. Despite, the amount of PG is low isolation and purification will be tedious.
False: NOT All test will be used.
True or False: In polyphasic approach, After the chemical analyses, a set of biochemical, physiological/cultural tests will be performed. The choice of the test will be dependent of the possible identity of your isolates based on 16s RNA similarity. Once you collated all the results, a possible ID of the organism can be determined or proposed (if novel strains).
True
True or False: In polyphasic approach, After the chemical analyses, a set of biochemical, physiological/cultural tests will be performed. The choice of the test will be dependent of the possible identity of your isolates based on 16s RNA similarity. Once you collated all the results, a possible ID of the organism can be determined or proposed (if novel strains).
True
True or False: In polyphasic approach, For novel isolates to be recognized and accepted as new description of species, it must be published and accepted in the International Journal of Systematic and Evolutionary Microbiology (previously International Journal of Systematic Bacteriology). It is the journal of record for publication of novel microbial taxa and the official publication of the International Committee on Systematics of Prokaryotes and the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies.
True
