MODULE 1 (Unit 3) Flashcards
a branch of biology that is concerned with the classification of all living organisms in ordered system that indicates a natural relationship
Taxonomy
- arrangement
- name
- taxis
- nomos
this approach is employed in which organisms are characterized, named, and classified according to defined criteria
systematic approach
In bacterial taxonomy, bacteria are grouped into [1], or [2] with precise names, to show degrees of similarities among them hence enabling microbiologists to communicate with each other in an efficient manner.
categories or taxa/taxon
Example, [1] which is a member of the normal intestinal flora of man belongs in the same family as the pathogenic [2].
- Escherichia coli
- Klebsiella pneumoniae
is the categorization of organisms into related group or taxon
Classification
The arrangement of organisms into groups are primarily based on [1], [2] or [3].
- similar characteristics
- evolutionary similarity
- common ancestry
refers to the naming of an organism by international rules according to its characteristics.
Nomenclature
- name
- to call
- nomen (L.)
- clare (L.)
involves the process of discovering and recording the traits of organisms so that they may be confirmed as belonging to a previously established taxon
Identification
In a clinical laboratory setting, it is the practical use of a [1] to isolate and identify the causative agent of a disease.
classification scheme
are needed to organize all of life into a system that everyone recognizes, to show evolutionary or other relationships between organisms
Classification systems
Similar with the field of microbiology, the classification of bacteria also have a long history which originated in the
1700’s
a Swedish botanist, was the first to classify organisms based on early descriptions of organisms as either animals (Kingdom Animalia) or plants (Kingdom Plantae). It is for this reason that he is know as the “Father of Taxonomy”.
Carl von Linné (Linnaeus; 1707 - 1778)
In Linneaus’ honor, the first classification system was referred to as the
Linnean taxonomy
he was the first to create a natural kingdom for microscopic organisms which have been discovered nearly 2 centuries before by Leeuwenhoek (1667) thereby introducing the so-called three-kingdom classification
Ernst Haeckel (1866)
The third group to which these microorganisms were grouped under was called
Kingdom Protista
The development of the [1] in the 1950s revealed a fundamental dichotomy among the microscopic Protista.
electron microscope
That is, some of these organisms possess [1] but are lacking of [2].
- membrane bound nucleus
- membrane-bound organelles
an ecologist working at Cornell University refined the existing three-kingdom classification of organisms into five kingdoms
Robert H. Whittaker (1969)
Whittaker’s five-kingdom classification include
- Animalia
- Plantae
- Protista (protozoans and single-celled algae)
- Fungi (Mycetae)
- Monera (Prokaryotae)
There were 3 major criteria used to classify organisms into each kingdom:
- Cell Type
- Cellular Organization
- Nutritional Type
Cell Type
possess a membrane-bound nucleus | Animals, plants, algae, protozoa, and fungi
Eukaryotic
Cell Type
lack nuclear membrane and other membrane-bound organelles
Prokaryotic
All bacteria are classified as
prokaryotes
kingdom Monera is also known as Kingdom
Prokaryotae
Cellular Organization
organism live in a colony such as in the case of bacteria
colonial
Cellular Organization
alone, similar with the protozoa
solitary
Cellular Organization
single cell like bacterium
unicellular
Cellular Organization
several cells such as plants and animals
multicellular
Nutritional Type - Food procurement
Some microbes obtain food either by way of mouth or a similar apparatus.
ingestion
Nutritional Type - Food procurement - Ingestion
A few protozoans for example possess a specialized “cell mouth” called [1] through which food passes.
cytostome
Nutritional Type - Food procurement - Ingestion
Another group of protozoans, the amoebas, are able to extend part of their cytoplasm and surround a nearby food particle thereby “[1]” it.
ingesting
Nutritional Type - Food procurement
Other microbes such as the fungi feed by [1] of readymade nutrients form their environment.
absorption
Nutritional Type - Energy source
obtains energy from sunlight by photosynthesis
phototroph
Nutritional Type - Energy source
obtains energy by oxidation of organic or inorganic chemical components
chemotroph
Nutritional Type - Carbon source
utilize the only inorganic carbon-containing compound, carbon dioxide as their sole carbon source. They are capable of synthesizing their own cellular materials from carbon dioxide, hence are known as “self-feeder”(auto = self; troph = feeding)
Autotrophs
Nutritional Type - Carbon source
require organic compounds as carbon source. Being unable to manufacture their own food, they rely on other sources of organic carbon for biosynthesis. For this reason, they are called “feeders on others” (hetero = other; troph = feeding).
Heterotrophs
Nutritional Type - Carbon source - Heterotrophs
feed on the living tissues or body fluids of their host
parasites
Nutritional Type - Carbon source - Heterotrophs
derive organic carbon from dead, decaying matter
saprobes or saprophytes
Nutritional Type - Energy source + Carbon source
- photoautotrophs
- photoheterotrophs
- chemoautotrophs
- chemoheterotrophs.
consists of multicellular, chemoheterotrophs that procure food mainly by ingestion
Animalia
include multicellular organisms that are absorptive and photoautotrophic
Plantae
are multicellular (except for yeast) organisms which are absorptive and are generally chemheterotrophs
Fungi
are organisms that have either a single cell or no distinct tissues and organs, such as protozoa and algae
Protista
are absorptive, photoautotrophic organisms
Algae
are ingestive chemoheterophic organisms
Protozoa
unicellular, absorptive organisms, which are diverse in terms of their carbon and energy source
Prokaryotes
examples of Prokaryotes
bacteria and archeae
Organisms are classified based on similarities of observable traits or characteristics | This system was widely used for bacterial classification.
Phenetic System of Classification
Bacteria were grouped according to their
- similarities in morphology (cell shapes, grouping)
- staining property
- physiologic requirements (temperature, oxygen, pH)
- metabolism
- ecology
is based on the concept of evolutionary relationships among types of organisms
Phylogenetic Classification System
provide a method for comparing cells since they are present in all cells
Ribosomes
studied and compared the rRNA (ribosomal ribonucleic acid) sequences (16S) in different cell types and found that there are three distinctly different cell groups: the eukaryotes, and two different types of prokaryotes — the bacteria and archaea
Carl Woese (1978)
Carl Woese proposed elevating the three cell types to a level above kingdom, called
domain
three-domain system for classifying organisms includes the
- Domain Bacteria
- Domain Archaea
- Domain Eukarya
is a relatively new level in the classification hierarchy. It was erected mainly to preserve the kingdoms as we know them
The Domain
the former kingdom [1], which included all prokaryotes (lacking a nucleus), was recently split into two domains
Monera
Domain [1], which includes the true bacteria
Bacteria
Domain [1], a group of organisms completely unlike the bacteria, except for the lack of a nucleus.
Archaea
A taxonomy has an overlapping hierarchy that forms [1] or [2] similar to an organization chart.
levels of rank or category
Each rank contains microorganisms that have
similar characteristics
A rank can also have [1] that contain microorganisms
other ranks
Microorganisms that belong to a lower rank have characteristics that are associated with a [1] to which the lower rank belongs.
higher rank
However, characteristics of microorganisms of a lower rank are not found in microorganisms that belong to the same higher rank as the [1] microorganism.
lower-rank
In the taxonomy of prokaryotes, the most commonly used rank (in order from most general to most specific) is:
- Domain
- Kingdom
- Phyla (sing. Phylum)
- Class
- Order
- Family
- Genus (pl. Genera)
- Species
The basic taxonomic group in microbial taxonomy is the
species
Species in higher organisms is defined as a group of
interbreeding or potentially interbreeding natural population
Species among bacteria, however, is defined as a group of bacterial cells with shared characteristics, or a [1], a group of bacterial cells that descend from a single parent cell, and differs slightly from other cells within the same species
collection of strains
can also be further differentiated as to their physiology, morphology, pathology, and on the basis of their surface antigens
bacterial strains
Bacterial strains
is strain that differs physiologically or biochemically from other strains
biovar
Bacterial strains
are those strains that differ morphologically
morphovar
Bacterial strains
are those strains that have antigenic properties that differ from other strains
Serovars
Bacterial strains
is a bacterial strain or set of strains that differ from other strains on the basis of distinctive pathogenicity
pathovar
[1] is the assignment of names to taxonomic groups. Bacteria are named according to rules established by [2]
- Nomenclature
- International Code of Nomenclature
A standard reference is used for bacterial taxonomy which is the
Bergey’s Manual of Systematic Bacteriology
It is considered as the authority on bacterial taxonomy, with the [1], and [2] of all bacteria which is also a practical aid for bacterial identification.
- published classification
- approved names
Each taxon is given [1] names with suffixes to indicate a particular taxonomic group
latinized
These are the [1] that are used for various taxonomic levels.
endings
At present, the trend is to place emphasis on the Genus and species, aka [1], whereby each group of organism is given 2 names, the [2a] name and the [2b], which comprise the scientific name
- Binomial System of Nomenclature
- genus name and species epithet
The first letter of the Genus/generic name is ALWAYS [1]. The first letter of the species epithet is NEVER a [2].
- capitalized
- capital letter
When appearing in print, scientific names MUST BE [1] or [2].
italicized or underlined
Scientific names are often shortened by abbreviating the [1] with a single capital letter
genus name
Some bacteria are given common name/s – trivial names which may be:
a. descriptive of the organism’s…
b. honorary of the organism’s…
A. morphology, habitat or attribute
B. discoverer
is the process of observing and classifying organisms into a standard group that is recognized throughout the biological community
Identification
In the aspect of Clinical Bacteriology, pathogenic bacteria in patient specimens are identified by growing them in [1] in clinical laboratories.
pure cultures
A standard reference to aid in the identification of unknown bacteria, the [1] was published by the Committee on Characterization and Classification of the Society of American Bacteriologists.
Bergey’s Manual of Determinative Bacteriology
Bergey’s Manual of Determinative Bacteriology
The book consists of a systematic guide on the [1] of bacterial isolates
phenotypic characterization
Bergey’s Manual of Determinative Bacteriology
The outline of process includes:
- inoculation
- incubation
- isolation
- inspection
- identification of specific species
