Classification of Microorganisms

Scientific classification of microorganisms

1. Classification of Microorganisms By SAMIRA FATTAH HAMID Ph.D. Medical Bacteriology College of Health Sciences Hawler Medical University

2. Taxonomy Is the science of classification of living organisms into groups the grouping of organisms according to their mutual similarities (i.e., establishing relationships between one group of organisms and another; to differentiate one group of organisms from another). Provides universal names for organisms. – Aids in categorizing organisms not yet studied in detail – Aids in identifying already classified organisms – Provides common frame of reference when organisms are discussed

3. Components of taxonomy a) Classification • Ordering organisms with like characteristics into groups or taxa (singular - taxon) • Based on established procedures and rules • Describes groups of organisms, their interrelationships and boundaries between groups. b) Nomenclature • concerns the naming of those organisms • Use a binomial systems of nomenclature c ) Identification • Application of classification & nomenclature to assign proper name to unknown organism and place it in its proper position within classification system. Taxonomy consist of three components:-

4. Ancient Greeks classified all living organisms into two groups - Kingdom Plantae - Kingdom Animalia In 1850s bacteria and fungi were incorrectly placed in the Plant Kingdom. In 1860s Kingdom Protista was proposed to include bacteria, fungi, algae, and protozoa, but many scientists still classified bacteria and fungi as plants. Intense disagreement over classification of bacteria and fungi persisted over 100 years.

5. In 1930s electron microscopy made it clear that bacterial cells lacked a nucleus. The term prokaryote was introduced in 1937. In 1959 Kingdom Fungi was established. In 1961 the current definition of the term prokaryote was established. In 1968 the Kingdom Prokaryota was accepted by biologists. In 1969 Robert Whittaker proposed a five-kingdom system of biological classification for all living organisms.

6. Five-Kingdom System of Biological Classification Kingdom Prokaryotes (Monera) 2. Kingdom Protista 3. Kingdom Fungi 4. Kingdom Plantae 5. Kingdom Animalia

7. The Prokaryotes (Kingdom Monera) are: The eubacteria (so called “true” bacteria . Some of the eubacteria cause human disease, and this is why the eubacteria are those bacteria that are of main interest to medical microbiologists. 2) The cyanobacteria (so called and improperly referred to as blue-green algae) - common photosynthesizing bacteria often noted as the green scum on ponds in summer months. 3) The purple photosynthetic bacteria , these perform photosynthesis but they do not use chlorophyll, they use special purple pigments instead, they are found in brine ponds. 4) The Archaebacteria , a group of evolutionarily ancient bacteria which are adapted to living in extreme environments such as high salt, intense cold, high temperature, high acidity etc.

8. The Kingdom Protista . These are a diverse set of organisms Algae - fresh and saltwater, single cells to simple multicellular photosynthesizing organisms. Autotrophs, most have cell walls. Slime molds - they are NOT fungi, look like fungi but can also be animal or even plant-like in morphology. Heterotrophs. Protozoa - a diverse group of single celled creatures that look and act like animals often, but are not, includes amoeba, paramecia etc , they are heterotrophs.

9. The Kingdom Fungi Non photosynthesizing single celled to multicellular organisms most of which have cell walls. Heterotrophs. Includes yeasts (which are unicellular) and mycelial (filamentous) organisms such as bread mold and the mushroom forming fungi. Some fungi cause human disease, some are important in food preparation.

10. The Kingdom Plantae Autotrophs, m ulticellular photosynthesizing organisms with cell walls. -Trees Shrubs grasses moss ferns

11. The Kingdom Animalia Heterotrophs, c omplex multicellular organisms of diverse types, no cell walls. Some cause human disease (parasitic infections or act as vectors for other disease causing organisms).

12. The Three Domain System Domain: In 1978 Carl Woese proposed this level of classification above kingdom . There are three domains based on the following distinguishing criteria: Cell wall composition Membrane lipids RNA sequence Protein synthesis Antibiotic sensitivity Domain Eubacteria : “True bacteria”. II. Domain Archaebacteria: “Ancient bacteria” III. Domain Eukarya: All eukaryotes: Protista, Fungi, Plantae , and Animalia.

13. Viruses -Viruses are not classified by using the Binomial naming system and do not belong to any of the five kingdoms. -Viruses are not cellular and are dependent on host cells for their replication. -Viruses are classified in two different ways: according to their structure - genetic (DNA or RNA) and physical (shape ), this scheme is favored by scientists doing fundamental work. 2) according to the type of disease they cause, this scheme is favored by medical workers who need to correlate given viruses with given diseases.

14. Taxonomic categories Domain Kingdom Phylum Class Order Family Genus Species Subspecies

15. - Subspecies Describes a specific clone of cells that differs from others within the same species • physiologically - biovar • morphologically - morphovar • antigenically - serovar • pathogenically – pathovar - Strain - a population of cells that descended from a single cell.

16. Species vs. Strain Species : A specific or defined type of organism, defined by similarity with known species. Strain : Genetic variation within a species

17. Scientific Nomenclature Scientific nomenclature : Universal system for naming and classifying living organisms. Initially developed in the 18th century by Carl Linnaeus. Binomial nomenclature : Each organism has a two part name. Names are either italicized or underlined. - Genus name : Always capitalized, always a noun. May use initial. - species name : Always lower case, usually an adjective. Names are usually derived from Latin (or Greek) or may have latinized endings. Examples: Homo sapiens (H. sapiens) : Human Penicillium notatum (P. notatum) : Mold that produces penicillin Canis familiaris (C. familiaris ) : Domestic dog

18. Rules of Nomenclature Use Binary Names - Binary names consisting of a generic name and a species epithet (e.g., Escherichia coli ), must be used for all microorganisms. Names of categories at or above the genus level may be used alone, but species and subspecies names may not. In other words…never use a species name alone. When to Capitalize – The genus name (and above) is always capitalized, the species name is never capitalized, e.g. Bacillus anthracis

19. When to Italicize - Names of all taxa (kingdoms, phyla, classes, orders, families, genera, species, and subspecies) are printed in italics and should be underlined if handwritten; strain designations and numbers are not. If all the surrounding text is italic, then the binary name would be non-italic (Roman typeface) or underlined (e.g. A common cause of diarrhea is E. coli 0157, a gram negative bacillus ). When to use Initials - A specific epithet must be preceded by a generic name, written out in full the first time it is used in a paper. Thereafter, the generic name should be abbreviated to the initial capital letter (e.g., E. coli ), provided there can be no confusion with other genera used in the paper. Rules of Nomenclature

20. Common Names - Vernacular (common) names should be in lowercase roman type, nonitalic (e.g., brucella). However when referring to the actual genus name (or above) always capitalize and italicize. Subspecies and Serovars - For Salmonella, genus, species, and subspecies names should be rendered in standard form: Salmonella enterica at first use, S. enterica thereafter; Salmonella enterica subsp. arizonae at first use, S. enterica subsp. arizonae thereafter. Names of serovars should be in roman type with the first letter capitalized: Salmonella enterica subsp. arizonae serovar Typhimurium ( S. enterica  subsp. enterica  ser. Typhimurium ). After the first use, the serovar may also be given without a species name: Salmonella serovar Typhimurium ( S . Typhimurium ). Rules of Nomenclature

21. Abbreviations for Species – use “sp.” for a particular species, “spp.” for several species (“ spp ” stands for “species plural”). These abbreviations are not italicized; e.g. Clostridium sp. or Clostridium spp. Plural Forms Plural of genus is genera Plural of fungus is fungi Plural of streptococcus is streptococci (staphylococcus - staphylococci; enterococcus enterococci, etc ) Plural of bacillus is bacilli Plural of bacterium is bacteria Plural of protozoan is protozoa Rules of Nomenclature

22. Microorganism names originate from four different sources: Descriptive – For example Staphylococcus aureus (grape-like cluster of spheres, golden in color), Streptococcus viridans (chains of spheres, green in colony color), Proteus vulgaris (first and common), Helicobacter pylori (spiral shaped rod at the entrance to the duodenum). Scientist’s names – e.g., Escherichia coli (Theodor Esherich ), Erlichia (Paul Erlich ), Nessieria (Albert Neisser ), Listeria (Joseph Lister), Pasturella (Louis Pasteur), Yersinia ( AlexandreYersin ), Bartonella (Alberto Barton), Morganella (H. de R. Morgan), Edwardsiella (P. R. Edwards)

23. Geographic places – e.g., Legionella longbeachiae (Long Beach, California), Pasturella tularensis (Tulare County, California), Pseudomonas fairmontensis (Fairmount Park, Pennsylvania), Mycobacterium genavense (Geneva, Switzerland), Blastomyces brasiliensis (Brazil), Providencia spp. (Brown University, Providence, Rhode Island, USA  ). Organizations – e.g., Legionella (American Legion), Afipia felis (Air Force Institute of Pathology), Cedecea spp. (Centers for Disease Control), Bilophila wadsworthia (VA Wadsworth Medical Center in Los Angeles)

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