Taxonomy- It is the science of organism classification
· Classification is the assignment of organisms (species) into an organized scheme of naming
· These schemes are based on evolutionary relationships (i.e., the more similar the name, the closer the evolutionary relationship)
· Classification is concerned with the criteria for identifying organisms and assignment to groups (what belongs where)
Taxon (Singular- taxa)– It is a group or category of related organisms
· Members of lower level taxa (e.g., species) are more similar to each other than are members of higher level taxa (e.g., kingdoms or domain)
· Members of specific taxa are more similar to each other than any are to members of different specific taxa found at the same hierarchical level (e.g., humans are more similar to apes, i.e., comparison between species, than either is similar to, for example, Escherichia coli)
· The naming of organisms is called as binomial nomenclature (viruses are exceptions)
· Binomial nomenclature employs the names of the two lower level taxa, genus and species, to name a species
· Genus comes before species (e.g., Escherichia coli)
· Genus name is always capitalized (e.g., Escherichia)
· Species name is in small letter (e.g., coli)
· Both names are always either italicized or underlined (e.g., Escherichia coli)
· The genus name may be used alone, but not the species name (i.e., saying or writing "Escherichia," alone is legitimate while saying or writing "coli" is not)
Bacterial species- A bacterial species is defined by the similarities found among its members. Properties such as biochemical reactions, chemical composition, cellular structures, genetic characteristics, and immunological features are used in defining a bacterial species
I.The five-kingdom system – It was first proposed in 1969
The five kingdoms include:
1. Plantae (the plants)
2. Fungi (the fungi)
3. Animalia (the animals)
4. Protista (the unicellular eucaryotes)
5. Monera (the prokaryotes)
Kingdom Monera –Includes the eubacteria, the cyanobacteria, and the archaeobacteria
· The eubacteria are our common, every-day bacteria, some of which are disease-causing
· The cyanobacteria are photosynthetic eubacteria
· The archaeobacteria are distinctive in their adaptation to extreme environments (e.g., very hot, salty, or acidic) though not all archaeobacteria live in extreme environments
· Protista, like Monera, consists mostly of unicellular organisms
· Some members of protista are multicellular, however
· This group includes eukaryotic fungi
· They are nutrient absorbers plus have additional distinctive features
· Unicellular fungi are called as yeasts
Kingdom Plantae –Includes all plants
Kingdom animalia- includes all animals
II. The three-domain system- It was established by Carl Woese. The domain system contains three groups
1. Eukaryotes (domain Eukarya)
2. Eubacteria (domain Bacteria)
3. Archaebacteria (domain Archaea)
1. Archeabacteria: These are the bacteria living in extreme environmental conditions
· Methanogens live in anaerobic environments, breaking down organism molecules and giving rise to methane (i.e., swamp gas and cow farts)
· Halophiles live in highly saline environments such as inland seas as well as salt-preserved foods
· Thermoacidophiles live in geothermally heated waters (e.g., hot springs)
· Extremozymes- These are the highly heat-stabilized enzymes employed by extremely
thermophilic bacteria. Such enzymes can be employed industrially, or even in down to earth applications such as cleaning clothing in high temperature washes (i.e., washing machine on the hot cycle)
Numerical taxonomy- Numerical taxonomy is based on the idea that increasing the number of characteristics of organisms that we observe increases the accuracy with which we can detect similarities among them. If the characteristics are genetically determined, the more characteristics two organisms share, the closer their evolutionary relationship.
I. Phenotypic classification systems:
1.Gram stain : H.C. Gram in 1884 invented this technique. Bacteria are classified into Gram positive or negative based on their morphology and differential staining properties
Gram positive- Purple; Gram negative – Pink colour
2.Growth Requirements: Microorganisms can be grouped on the basis of their need for oxygen to
· Facultatively anaerobes- bacteria that grows in high oxygen or low oxygen content
· Strict anaerobes - bacteria that grows in the absence of oxygen environment . Ex bacteroides
· found in the large bowel
· Strict aerobes- Bacteria that grows only in the presence of oxygen. Ex. Pseudomonas aeruginosa,
· Microaerophiles- bacteria grows under conditions of reduced oxygen and sometimes also require increased levels of carbon dioxide. Ex; Neisseria
3.Biochemical reactions: Clinical microbiology laboratories typically will identify a pathogen in
a clinical sample, purify the microorganism by plating a single colony of the microorganism on a
separate plate, and then perform a series of biochemical studies that will identify the bacterial
· Selected antisera can be used to classify different bacterial species.
· This may be based on either carbohydrate or protein antigens from the bacterial cell wall or the
· (Group A streptococcal M proteins or O and H polysaccharide antigens of salmonella).
II. Genotypic classification system:
It is based in the Genetic homology- A homology is a similarity between two organisms that exists.
The similarity of the DNA (or RNA) of organisms may be determined by a number of means including determinations of base composition, nucleotide sequence, or DNA hybridization rates
Base composition-Chargaff's rule says that- adenines (A's) and thymines (T's) are always present in DNA in equal proportions, and that the same is true for cytosines (C's) and guanines (G's)
Distinguishing strains- Very closely related organisms, i.e., members of the same species, are typically sufficiently similar that there exist additional methods that are able to distinguish the small differences seen between them. These methods include:
· Protein profiling
· Ribosomal RNA (rRNA) sequence analysis
· Phage typing
· Molecular subtyping:
· Various techniques exist for isolating (separating) and then visualizing the proteins from cells
· By distinguishing proteins in terms of their sizes and/or charges one can construct reproducible patterns that are typical of a given organism
· More-similar organisms display more-similar protein patterns
· Typing of bacteria using bacteriophages are called as phage typing
· Different phages will have specific receptors for different bacteria
Ribosomal RNA (rRNA) sequence analysis:
· This has emerged as a major method for classification.
· It has been used to establish a phylogenetic tree.
· This may be done by examining the biochemical studies or the antibiotic susceptibility profile but a more reliable method is by molecular analysis.
· Pulsed Field Gel Electrophoresis (PFGE) is the most frequently used molecular technique
Bergey's Manual- Methods for distinguishing and identifying bacteria are assembled into Bergey's Manual of Determinative Bacteriology.
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