Microorganism Classification PDF

CLASSIFICATION OF MICROORGANISMS CLASSIFICATION: ATTEMPTS TO CATALOG ORGANISMS Taxonomy: Systematic arrangement of related microorganisms and other living organisms into logical categories. Taxonomy is generally divided into three parts: ▪ Classification ▪ Nomenclature ▪ Ident...

CLASSIFICATION OF MICROORGANISMS CLASSIFICATION: ATTEMPTS TO CATALOG ORGANISMS Taxonomy: Systematic arrangement of related microorganisms and other living organisms into logical categories. Taxonomy is generally divided into three parts: ▪ Classification ▪ Nomenclature ▪ Identification of an unknown organism DEVELOPMENT OF CLASSIFICATION OF LIVING ORGANISMS Adapted from: Fundamentals of microbiology DEVELOPMENT OF CLASSIFICATION OF LIVING ORGANISMS Modern taxonomy was devised by Carl von Linne or better known to history as Carolus Linnaeus in 1707- 1788 ▪ Linnaeus came up with the two-kingdom classification ✓ Vegetalia and animalia In 1866 Ernest Haeckel introduced a third kingdom Protista ▪ Protista, Plantae and Animalia In 1937 Edouard Chatton proposed two kingdom system ▪ Prokaryota and Eukaryota 1956 Herbert Copman proposed a four-kingdom system ▪ Protista, Monera, Plantae and Animalia In 1959 Robert H. Wittaker suggested a 5-kingdom system ▪ Monera, Protista, Fungi, Plantae and Animalia By 1990’s Carl Woese suggeste the three-kingdom system ▪ Bacteria, Archaea and Eukarya THE FIVE KINGDOM SYSTEM THE THREE KINGDOM SYSTEM  LINNAEUS TAXONOMIC GROUPS Adapted from: Alcamo's fundamentals of microbiology - page 79 NB: A basic principle of taxonomy is that members of higher-level groups share fewer common characteristics than those in lower-level groups HOW ARE ORGANISMS NAMED At species level organisms are named according to binomial nomenclature: ▪ a genus and species name. ▪ These are either underlined or italicized e.g. ▪ Bacillus subtilis or Bacillus subtilis ▪ Staphylococcus aureus or Staphylococcus aureus ▪ Escherichia coli or Escherichia coli ▪ The genus name starts with a capital letter and can be abbreviated e.g. B. subtilis BASES FOR IDENTIFICATION AND CLASSIFICATION Phenotypes based methods 1. Cultural (growth characteristics): Peculiar characteristics of microorganisms on solid and liquid media. ▪ Coloration ▪ Appearance on solid media ✓ margin, elevation, dry/mucoid/smooth ▪ Distribution in liquid media ✓ Homogeneous, pellicle, sediment. These attributes differ with different growth media Not reliable – can be similar for different organisms CULTURAL (GROWTH CHARACTERISTICS): Morphological characteristics of bacterial cultures CULTURAL (GROWTH CHARACTERISTICS): SHAPE MARGIN ELEVATION BASES FOR IDENTIFICATION AND CLASSIFICATION Phenotypes based methods 2. Morphological characteristics: Makes use of staining techniques: Gram stain, spore stain, acid-fast stain, etc. ▪ Gram staining ✓ differentiates between Gram (+) and Gram (-) bacteria ✓ Indicates different cell characteristics (shape, size, arrangement) ▪ Capsule staining ✓ Presence of a waxy layer around bacterial cell walls ▪ Spore staining ✓ Determines the presence of endospores, their position and shape BASES FOR IDENTIFICATION AND CLASSIFICATION 3. Classification based on shape a. Coccus (plural: cocci): Spherical. May have the following arrangements:  Diplococci: A pair of attached cocci. Remain attached after dividing.  Streptococci: Chainlike arrangement.  Tetrads: Groups of four. Divide in two planes.  Sarcinae: Groups of eight. Divide in three planes.  Staphylococci: Grapelike clusters. Divide in multiple planes. BASES FOR IDENTIFICATION AND CLASSIFICATION 3. Classification based on shape b. Bacillus (plural: bacilli): Rod- shaped. Most bacilli appear as single rods but may see:  Diplobacilli: A pair of attached bacilli. Remain attached after dividing.  Streptobacilli: Chainlike arrangement. c. Coccobacillus: Intermediate shape between coccus and bacillus. Oval rods. BASES FOR IDENTIFICATION AND CLASSIFICATION 3. Classification based on shape d. Spiral Bacteria: Have one or more twists:  Vibrio: A comma shaped cell. Look like curved rods.  Spirilla: Helical, corkscrew shaped bacteria with rigid bodies.  Use whiplike external flagella to move. e. Spirochetes: Helical bacteria with flexible bodies.  Use axial filaments (internal flagella) to move. BASES FOR IDENTIFICATION AND CLASSIFICATION 4. Metabolic characteristics: Types of substrates utilized; ▪ E.g. carbon and nitrogen sources utilized ▪ Types of metabolites Types of enzymes (oxidase, coagulase, catalase) Production of specific by-products or waste products Applying commercial kits ▪ e.g. API Strip BASES FOR IDENTIFICATION AND CLASSIFICATION 6. Growth requirements Oxygen requirement ▪ Anaerobic /aerobic/microaerophilic Temperature variations – optimum and range ▪ Psychrophiles (0ºC), Mesophiles(20 - 45ºC), thermophiles (55 - 70ºC) Salt tolerance ▪ Halophiles(10-20%), salt tolerance Tolerance to pressure; Barophiles Acid/alkali tolerance (pH) Acidophiles and alkaliphiles BASES FOR IDENTIFICATION AND CLASSIFICATION Molecular based methods Genetic material in living cells is either DNA or RNA – used to classify microorganisms BASES FOR IDENTIFICATION AND CLASSIFICATION a. Gene probe (hybridization) Measures degrees of genetic similarity between pools of DNA DNA from two organisms marked differently – fluorescent dye or radioactive material The double stranded DNA separated into a single strands by heating – denatured This breaks the hydrogen bonds between complementary base pairs Allowed to cool which enables complementary molecules to hybridize Genetic similarity read as follows ▪ Similar genetic makeup – complete hybridization ▪ Related – partial hybridization ▪ Unrelated – no hybridization BASES FOR IDENTIFICATION AND CLASSIFICATION c. Sequencing of 16S rRNA Ribosomes are cell structures responsible for proteins synthesis The component of ribosome responsible for linking amino acids components is known as rRNA 16S rRNA is the subunit of the rRNA mainly used for bacterial identification Why 16S rRNA ▪ Ubiquitous in almost prokaryotic life ▪ Highly conserved – its function hasn't changed over time ▪ The gene (1,500bp) is long enough for bioinformatics Shortcoming ▪ It has low phylogenetic power at species level in comparison to hybridisation BASES FOR IDENTIFICATION AND CLASSIFICATION d. Whole genome sequencing ▪ Shotgun sequencing REFERENCE BOOKS AND SYSTEMS USED IN CLASSIFICATION Text books Bergey's Manual of Systematic Bacteriology The Prokaryotes Applied Microbial Systematics Principles of fungal taxonomy Online resources Catalogue of Life PubMed Taxonomy UniProt Taxonomy Peer reviewed journals