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Contents
Taxonomy Goals of Classification General Methods of classification of bacteria, Fungi and Viruses
Taxonomy
Organizing, classifying and naming living things Taxonomy- originated from Greek word taxis-Order/arrangement nomos- law/science Formal system originated by Carl von Linn (1701-1778) Identifying and classifying organisms according to specific criteria Scientists classify organisms and assign each organism universally accepted name
Taxonomy
The science of biological classification, by grouping organisms with similar characteristics.
Taxonomy
The science of classifying organisms Provides universal names for organisms
Taxonomy
Identification is "the practical side of taxonomy, the process of determining that a particular (organism) belongs to a recognized taxon. Classification is "the arrangement of organisms into groups or taxa. Nomenclature is "the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules.
Note that ideally names have taxonomic meaning, i.e., they give clues to phylogenetic relationships.
Classification Systems
Phylogenetic Classification System:
Groups reflect genetic similarity and evolutionary relatedness
Taxonomy
Binomial Nomenclature: Scientists assign each kind of organism a universally accepted name in the system Two word system using the Genus and Species Words are always written in italics First word (Genus) is capitalized and second word (Species) is lowercase Second word is a Latinized description of a particular trait Developed by an 18thC. Swedish botanist named Carolus Linnaeus
Taxonomy
Linnaeuss System of Classification: Based on Taxonomy naming system Taxonomy: a group at any level of an organization is referred to as a taxon Is hierarchical and consists of 7 taxonomic categories From largest to smallest: Kingdom = Made up of phylum Phylum = Made up of several different classes Class = Made up of several different orders Order = Made up of several different families Family = Made up of several different genus Genus = Made up of several different species Species Know classification order above
Class
Order Family Genus Species
Taxonomic Hierarchy Domain Kingdom Phylum Binomal Nomenclature uses the Genus and Species name to identify each creature.
Class
Order Family Genus Species
Definition of Species
The basic unit of taxonomy, representing a specific, recognized type of organism
Definition of Species
Definition of species in microbiology:
Classic definition: A collection of microbial strains that share many properties and differ significantly from other groups of strains Species are identified by comparison with known type strains: well-characterized pure cultures; references for the identification of unknowns There are several collections of type strains, including the American Type Culture Collection (ATCC)
Definition of Species
Definition of species in microbiology (cont.):
Strain:
A population of microbes descended from a single individual or pure culture Different strains represent genetic variability within a species Biovars: Strains that differ in biochemical or physiological differences Morphovars: Strains that vary in morphology Serovars: Stains that vary in their antigenic properties
Definition
Genus Collection of similar Species Family A group of similar Genera Order A group of Similar Families Class A group of similar Orders Division A group of similar classes Kingdom A group of similar divisions
Nomenclature
Scientific name (Systematic Name) Binomial System of Nomenclature
Genus name + species name
Italicized or underlined Genus name is capitalized and may be abbreviated Species name is never abbreviated A genus name may be used alone to indicate a genus group; a species name is never used alone eg: Bacillus subtilis B. subtilis
Nomenclature
Common or descriptive names (trivial names)
Names for organisms that may be in common usage, but are not taxonomic names
eg: tubercle bacillus (Mycobacterium tuberculosis)
Example
Goals of Classification
Taxonomist strive to make classifications that have the following two qualities: Stability Predictability
4 main kingdoms:
Protista Fungi Plantae Animalia
Classification of Bacteria
Scientific Nomenclature Bacterial species: Population of cells with similar characteristics. Bacterial strain: A subgroup of a bacterial species that has distinguishing characteristics. Identified by numbers, letters, or names that follow the scientific name. Escherichia coli O157:H7: Strain that causes bloody diarrhea. Bergeys Manual: Provides a reference for identifying and classifying bacteria. Classification initially based on cell morphology, staining, metabolism, biochemistry, serology, etc. More recently, DNA, RNA, and protein sequence analysis are being used to study evolutionary relationships.
Cocci: Streptococcus Staphylococcus Bacilli: Bacillus anthracis Clostridium Spirillum: Treponema pallidum Filamentous: Leptothrix, Crenothrix
Examples of Gram positive Bacteria: Streptococcus pyogenes - causes strep throat Staphylococcus aureus - causes skin infections and may be responsible for boils Examples of Gram Negative Bacteria: Treponema pallidum - causes syphilis Escherichia coli - may cause severe gastrointestinal problems
Classification of bacteria
Lysenko 1959- Gram Positive and Gram Negative Bergeys Mannual of determination of Bacteriology: 19 parts Revised between 1984 and 1989- 4 volumes -33 sections based on morphological and biochemical characteristics. Bacteria Groups divided into four volumes: 1.Gram negative 1984 general, medical industrial importance 2.Gram Positive -1986 other than actinomycetes 3.Gram negative 1989 with distinctive properties, cyanobacteria, and archaeobacteria and 4.Actinomycetes 1989 as Gram-positive filamentous bacteria.
Kingdom Prokaryotae
Division I:Gracilicutes(thin Skin) Prokaryotes with a complex characteristic of Gram negative bacteria (e.g. non-photosynthetic Bacteria). Division II:Firmicutes (Strong Skin) Prokaryotes a cell wall structure chacteristic of Gram positive bacteria (e.g.rods,cocci,actinomycetes). Division III: Tenericutes(soft/tender Skin) Prokaryotes lack a cell wall(e.g. mycoplasma). Division IV:Mendosicutes(Skin with faults ) Prokaryotes with unusual cell walls (e.g. archaeobacteria).
Classification of bacteria
Binomial System
Classification of Fungi
Division I : Myxomycota Class I Acrasiomycetes -Assimilative phase is free living amoebae which
unite as a pseudoplasmodium before reproduction.
Class II Hydromyxomycetes -plasmodium forming network. Class III Myxomycetes -plasmodium is saprobic and free living. Class IV Plasmodiophoromycetes -plasmodium is parasitic within
cell of the host plant .
Division II Eumycota
Subdivision 1: Mastigomycotina: Motile cells Zoospores present. Perfect stage is typically
Oospores
Subdivision 2: Zygomycotina :Perfect stage spores are Zygospores Subdivision 3 : Ascomycotina: Perfect stage spores are Ascospores
Classification of Fungi
Subdivision 4 : Basidiomycotina: Perfect stage spores are Basidiospores subdivision 5 : Deuteromycotina: Perfect stage is absent
SubDivision I Mastigomycotina
Class I :Chrtridiomycetes: Zoospores are posteriorly uniflagellate Class II: Hypochrtridiomycetes: Zoospores are anteriorly uniflagellate Class III: Oomycetes : Zoospores biflagellate ,cell wall consists of cellulose
Classification of Fungi
SubDivision III Ascomycotina
Class I :Hemiascomycetes: Ascocarps and asogenous hyphae lacking; Thallus
yeast like/mycelia
Class IV: Laboulbenomycetes : Asci regularly arranged in ascocarp -perithecium Class V: Plyrenomycetes :Not exoparasites of arthopods, ascocarp perithecium Class V: Discomycetes :Ascocarp Apothecium
Classification of Fungi
SubDivision IV: Basidiomycotina
Class I :Teliomycetes: No basicocarp- teliospores /chlamydospores- parasites on vascular plants Class II: Hymenomycetes: Basidiocarp -basidiospores Class III: Gasteromycetes:basidiocarp is angiocarpous-basidiospores
SubDivision V: Deuteromycotina
Class I :Blastomycetes: Budding-with/with pseudomycelium Class II: Hyphomycetes: Mycelium assimilative budding is absent-Sphorophores. Class III: Coelomycetes: Spores acervuli or pycnidia.
Virus Classification
Holmes classification LHT System Baltimore classification
Virus Classification
Holmes classification (1948)
Order:Virales Three sub-orders (i) Phaginae : Viruses attacking on bacteria (ii) Phytophagine :Viruses attacking on Plants (iii) Zoophaginae : Viruses attacking on animals
Phylum: Vira
Subphylum : Deoxyvira(DNA Viruses)
Class: Deoxy helica (helical symmetry) Order : Chitovirales (enveloped) Family : Pox Viridae (poxy viruses) Class : Deoxycubica (cubical symmetry) Order : Haplovirales (no envelope)
Order : Peplovirales(mantle viruses) Family :Herpes viridae 162 capsomers (herpes virus)
Subphylum: Ribovira
Class: Ribohelica (helical Symmetry) Order : Rahbdovirales (rodshaped viruses) Suborder : Rigidovirales (plant viruses) Family :Dolichoviridae 12-13 nm Deoxycubica - 15 nm Pachyviridae 20 nm
Class: Ribocubica (cubiodal symmetry) Order: Gymovirales 32 capsomers Family: Napoviridae(plant viruses, picrona viruses Reoviridae-92 capsomers(Reovirus) Order : Toga virales Family : Arboviridae(arboviruses) Encephaloviridae
Bellet Classification(1967):
i)Molecular weight ii)Percentage of Guanine + cytosine.serological and antigenic and phenotypic properties i) Shape of Capsid Ii) mode of transmission Iii) type of vector iV) Symptoms on host after infection V) nature of accessaory particles 135 viruses into 6 broad groups i)nucleic types ii) Symmetry iii) presence or absence of envelope
Gibbs(1969):
Baltimore classification
Baltimore classification (2008) ;Viral mRNA .Noble prize Biologist David Baltimore. Based on mRNA Production Viral genomes single stranded or double stranded RNA or DNA Mode of replication Mar or may not use reverse transcriptase ssRNA viruses may be either (+) sense or (-) antisense. Genome type 7 groups Group I : dsDNA viruses (Adenoviruses,Herpesviruses,Poxviruses) Group II : (+) Sense ssDNA viruses(e.g. Parvoviruses) Group III: dsRNA viruses (Reoviruses) Group IV: (+) sense ssRNA viruses (Picronaviruses, Tagoviruses) Group V : (-) sense ssRNA viruses (Orthomyxoviruses, Rhabdoviruses) Group VI: (+) sense ssRNA-Rt viruses RNA with DNA intermediate in life-cycle (Retroviruses) Group VII: dsDNA RT viruses (Hepandaviruses)
Sub-Viral agents
(i) Viroids Family Pospoviridae: Genus: Pospiviroid type Species : Potato spindle tuber viroid Genus : Hostuviriod Type species: Hop stunt viriod Genus : Cocadviriod type species : Coconut cadang-cadang viriod Genus : Apscaviriod type species : Apple scar skin viriod Genus : Coleviriod type species : Coleus blumei viroid I family : Asvunviroidae Genus: Asvunvirioid type species: Avocado sunblotch viriod Genus : Pelamoviriod ; type species : peach latent mosaic viriod
(II) Satellites
Satellite Viruses: Single-stranded RNA satellite viruses
Subgroups 1: Chronic bee-paralysis satellite virus Sub group 2: Tobacco necrosis satellite virus
References
Microbiology By Micheal J.Plecer, E.C.S.Chan and Noel R.Krieg. A Text Book on Microbiology by R.C. Dubey and D.K.Maheshwari Pharmaceutical Microbiology by Ashutosh Kar Pharmaceutical Microbiology principles and Applications by Dr. Chandrakant Kokare. Microbiology 6th Edition by Prescott Harley Klein.