Unit II Classification of Microbes

ContentsTaxonomyGoals of ClassificationGeneral 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 Linné (1701-1778) • Identifying and classifying

organisms according to specific criteria

• Scientists classify organisms and assign each organism universally accepted name

TaxonomyTaxonomyThe 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 TaxonomyThree Interrelated Parts of Taxonomy

• ClassificationArrangement into groups

• NomenclatureAssignment of Names

• IdentificationDetermining 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 • Linnaeus’s 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

Class

Order

Family

Genus

Species

Binomal Nomenclature uses the Genus and Species name to identify each creature.

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/Haeckel’s Kingdom protista- Third Kingdom protista

3.Copland’s Four kingdom classification – Monera,Protista,Plantae and Animalia

4.Five kingdom Classification/Whittakers Five-Kingdom Concept- Monera,Protista,fungi,plantae and animalia.

Level Above Kingdom: The Three-Domain System

CarlWoese

1978

EubacteriaArchaeaEukarya

• 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 speciesClosely related organism have similar features because they

evolved from common ancestral formsEvolution 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.• Bergey’s 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 throatStaphylococcus aureus - causes skin infections and may be responsible for boils

Examples of Gram Negative Bacteria:Treponema pallidum - causes syphilisEscherichia 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 • Bergey’s 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).

Bergey’s ,Manual of Determination of Bacteriology (9th Volume)

Four Major groups1.Gram Negative Eubacteria that have cell walls2.Gram positive Eubacteria that have cell walls3.Cell Wall less Eubacteria4.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:ViralesThree 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(ØX174)

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

• Gibbs(1969):• 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

• Cajen’s and king’s Classification( 1975)• i)nucleic types ii) Symmetry iii) presence or absence of envelope

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.