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Unit II Classification of Microbes

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

Provides a reference for identifying organisms.


Taxonomy uses taxonomic units known as taxa (singular taxon). Taxonomic scheme is a particular classification, arranged in a hierarchical structure. For many species, there are often regional differences in their common names EX: Buzzard in the UK refers to a hawk, Buzzard in the US refers to a vulture. To eliminate such confusion, scientists agreed to use a single name for each species

Three Interrelated Parts of Taxonomy


Classification Arrangement into groups Nomenclature Assignment of Names Identification Determining Identity

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

Phenetic Classification System:


Groups do not necessarily reflect genetic similarity or evolutionary relatedness. Instead, groups are based on convenient, observable characteristics.

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

Taxonomic Hierarchy Domain Kingdom Phylum

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

Useful Properties in Classification


Colony morphology Cell shape & arrangement Cell wall structure (Gram staining) Special cellular structures Biochemical characteristics

Goals of Classification
Taxonomist strive to make classifications that have the following two qualities: Stability Predictability

Classification of Organisms : Scientific Nomenclature


1.Scientific nomenclature: Binomial: a genus and a specific epithet, or species. 2. The International Committee on Systematic Bacteriology assigns names to bacteria 3. The International Code of Botanical Nomenclature publishes rules for naming fungi and algae. 4. the International Code of Zoological Nomenclature publishes rules for naming protozoa.

General Methods of Classification


The arrangement of living things into categories is called classification. Living organisms have been classified as follows:

1.Two-Kingdom Classification - Plantae and animalia


2.Three-Kingdom Classification/Haeckels Kingdom protista- Third Kingdom protista 3.Coplands Four kingdom classification Monera,Protista,Plantae and Animalia 4.Five kingdom Classification/Whittakers Five-Kingdom ConceptMonera,Protista,fungi,plantae and animalia.

Level Above Kingdom: The Three-Domain System


Carl Woese 1978

Eubacteria Archaea Eukarya

4 main kingdoms:
Protista Fungi Plantae Animalia

Evolution -living things change gradually over millions of years


Changes favoring survival are retained and less beneficial changes are lost All new species originate from preexisting species Closely related organism have similar features because they evolved from common ancestral forms Evolution usually progresses toward greater complexity

Species and Subspecies


Species collection of bacterial cells which share an overall similar pattern of traits in contrast to other bacteria whose pattern differs significantly Strain or variety culture derived from a single parent that differs in structure or metabolism from other cultures of that species (biovars, morphovars) Type subspecies that can show differences in antigenic makeup (serotype or serovar), susceptibility to bacterial viruses (phage type) and in pathogenicity (pathotype)

General Methods of Classifying Bacteria


Intuitive Method Numerical taxonomy Genetic Relatedness DNA Homology Experiments Ribosomal RNA homology experiments and RNA oligonucleotide cataloging. Nomenclature

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.

Classifying Bacteria by Shape


Bacteria cells vary in shape: Cocci spherical Bacilli rods, or cylindrical Spirillum spiral, or helical Filamentous complex forms, like jellybeans in a straw'

4 Main Shapes of Bacteria

Examples of Bacteria Classified by Shape

Cocci: Streptococcus Staphylococcus Bacilli: Bacillus anthracis Clostridium Spirillum: Treponema pallidum Filamentous: Leptothrix, Crenothrix

Groups Based On wall Composition

Classifying Bacteria by Cell Wall Structure: The Gram Stain

Gram stain of Gram positive Staphylococcus

Gram stain of Gram negative E. coli cell

Distinctive Cell Walls: Peptidoglycan

Gram Positives and Gram Negatives: Key Differences

Gram Positives and Gram Negatives

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

Classifying Bacteria by Cellular Respiration


Aerobic bacteria, or strict aerobes - require oxygen Anaerobic bacteria, or strict anaerobes - cannot tolerate oxygen Facultative anaerobes are generally aerobes, but have the capacity to grow in the absence of oxygen Examples of Bacteria Classified by Cellular Respiration: Aerobic: Bacillus cereus Anaerobic: Clostridium spp. ( botulism, tetanus) Facultative anaerobes: Staphylococcus spp.

Classifying Bacteria by Growth Factors


Energy Source Chemotroph chemical compounds as an energy source (most pathogenic bacteria are chemotrophs.) Phototroph - light as energy source Nutrient Source Heterotroph derive carbon from preformed organic nutrients such as sugar (most pathogenic bacteria are heterotrophs.) Autotroph derive carbon from inorganic sources such as carbon dioxide

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).

Bergeys ,Manual of Determination of Bacteriology (9th Volume)


Four Major groups
1.Gram Negative Eubacteria that have cell walls 2.Gram positive Eubacteria that have cell walls 3.Cell Wall less Eubacteria 4.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

SubDivision II: Zygomycotina


Class I :Zygomycetes: Two orders Mucorales and entomophtorales Class II: Trichomycetes: Group of uncertain affinity and are mostly parasitic in the guts of athropods.
E.g. insect larvae,millipedes.

Classification of Fungi
SubDivision III Ascomycotina
Class I :Hemiascomycetes: Ascocarps and asogenous hyphae lacking; Thallus
yeast like/mycelia

Class II: Loculoascomycetes: Ascocarps and asogenous hyphae present, thallus


mycelia,asci bitunicate,ascocarp

Class III: Plectomycetes :Asci Unitunicate, if Bitunicate-ascocarp is


apothecium, Asci evanescent, scattered within ascocarp- clestothecium

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

LHT system of classification(1962)


The LHT System of Virus Classification is based on chemical and physical characters like nucleic acid (DNA or RNA), Symmetry (Helical or Icosahedral or Complex), presence of envelope, diameter of capsid, number of capsomers. This classification was approved by the Provisional Committee on Nomenclature of Virus (PNVC) of the International Association of Microbiological Societies (1962).

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)

Family : Microviridae 12 capsomers(X174)


Parvoviridae 32 capsomers (rat viruses Papiloviridae 72 capsomers (papova viruses) Adenoviridae 252 capsomers (adeno viruses) Iridoviridae - 812 capsomers (Insect viruses)

Order : Peplovirales(mantle viruses) Family :Herpes viridae 162 capsomers (herpes virus)

Class :Deoxy binala (VIRUS WITH HEAD AND TAIL)


Order : Urovirales Family : Phagoviridae (bacteriophages)

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

Suborder : Flexivirdales (plant viruses)


Family : leptoviridae 10-11 nm Mesoviridae 12 -13 nm Adroviridae 15 nm Order : Sagovirales Family: Myxoviridae 9 nm Paramyxoviridae 18 nm Stomato viridae

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):

Cajens and kings Classification( 1975)

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)

International committee on Taxonomy of Viruses(ICTV)


The virology division of the international Union Of Microbiological Societies (IUMS)
The official Objectives:
To develop internationally agreed taxonomy for viruses To develop internationally agreed names for virus taxa, including species and subviral agents To communicate taxonomic decisions to all users of virus names, in particular the international committee of virologists by publications via the internet. To maintain an index to virus names. To maintain an ICTV database on the net

International committee on Taxonomy of Viruses(ICTV)


Principles of Nomencalture:
Stability To avoid or reject the use of names which might cause error and confusion To avoid unnecessary creation of names

Naming and Changing taxa


Viral classification order: Virales Family: Viridae subfamily : Virinae Genus: Species:

Five orders By ICTV


Caudovirales:Contains tailed dsDNA Group I bacteriophages Herpesvirales: large Eukaryotic dsDNA viruses Mononegavirales Non-segmented (-) ssRNA group V plant and animal viruses. Nidovirales: (+) ssRNA Group Iv viruses with vertebrate hosts Picornavirales: (+) ssRNA viruses that infects a variety of plants ,insects and animal host.

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

Satellite nucleic acids Single-stranded satellite DNAs


Double-stranded satellite RNAs Single-stranded satellite RNAs
Sub group 1 : Large satellite RNAs Sub group 2 : Small linear satellite RNAs Sub group 3: Circular satellite RNAs(virusoids)

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.