Chapter 10: Classification of microorganisms

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Taxonomy

-the science of classification
-provides universal names for organisms
-provides a reference for identifying organisms

Systematics/Phylogengy

-The study of the evolutionary history of organisms

Phylogenetics

-Each species retains some characteristics of its ancestor
-Grouping organisms according to common properties implies that a group of organisms evolved from a common ancestor
-Anatomy
-Fossils
-rRNA
-mtDNA

mtDNA

-mitochondrial DNA
-only passed through maternal lineage

Common names (scientific nomenclature)

-vary with languages
-vary with geography

Binomial nomenclature (scientific nomenclature)

-genus + specific epthiet
-used worldwide
-Escherichia coli
-Homo sapiens

Taxonomic hierarchy

-Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species (dear king phillip came over for great spaghetti)

The Taxonomic Hierarchy

-species: include both genus and species
-viruses start at family
-no kingdom associated with bacteria

Classification of Eukaryotes

-Animalia
-Plantae
-Fungi
-Protista

Animalia (classification of eukaryote)

-Multicellular
-no cell walls
-chemoheterotrophic

Plantae (classification of eukaryote)

-multicellular
-cellulose cell walls
-usually photoautotrophic

Fungi (classification of eukaryote)

-unicellular or multicellular
-cell walls of chitin
-chemoheterotrophic
-develop from spores or hyphal fragments

Protista (classification of eukaryote)

-a catchall kingdom for eukaryotic organisms that do not fit other kingdoms
-Grouped into clades based on rRNA
-Mostly unicellular
-nutritionally diverse

Clades

genetically related groups

Eukaryotic species (classification of eukaryotes)

-a group of closely related organisms that bree among themselves
-breed successfully (fertile offspring)

viral species (Classification of viruses)

-population of viruses with similar characteristics that occupies a partcular ecological niche

Characteristics of viral species (classification of viruses)

-type of nucleic acids
-shape
-replication strategy

Prokaryotic species (Classification of prokaryotes)

-a population of cells with similar characteristics
-culture
-clone
-strain
-ex: E. coli O157:H7 vs. E. coli K-12
-O157:H7= strain

Culture (classification of prokaryote)

-bacteria grown in laboratory medi

Clone (classification of prokaryote)

-population of cells derived from a single cell

Strain (classification of prokaryote)

-genetically different cells within a clone

Bergry's manual

-provide official taxonomic classification scheme for prokaryotes
-Divides prokaryotes into two domains:
-Archae
-Bacteria

Bergey's Manual of Determinative Bacteriology

-identification schemes
-biochemical, morphology, staining, cell wall, etc
-identification of unknown
-hospital labs

Bergey's Manual of Systematic Bacteriology

-phylogenetic information
-rRNA sequence
-classify things
-DNA sequencing takes a while

Classification

-placing organisms in groups of related species
-lists of characteristics of known organisms
-often uses genetic relatedness (rRNA)

Identification

-matching characteristics of an "unknown" organism to lists of known organisms
-clinical lab identification
-used for practical purposes

classification and identification

-identification techniques are not necessarily the same as those used for classification

Identification methods

-morphological characteristics
-differential staining
-boichemical tests
-serology

Morphological characteristics (identification methods)

-useful for identifying eukaryotes

Differential staining (identification methods)

-gram staining
-acid gast staining

Biochemical tests (identification methods)

-determines presence of bacterial enzymes

Serology (identification methods)

-uses specific antiserum to identify unknown organisms
-antibodies

Serology

-study of blood serum and antigen::antibody interactions in vitro
-Antigen (Ag)
-Antibody (Ab)
-Antigen-antibody complex
-combine known antiserum (Ab) plus unkown bacterium to identify bacterium

Antigen (Ag)

-any substance that causes antibody (Ab) formation and reacts only with its specific Ab

Antibody (Ab)

-protein produced by the body in response to an Ag, which is capable of combining specifically with that introduced Ag

Antigen-Antibody complex

-is the combination of Ag with the Ab that is specific for it
-This is the basis of immune protection and many diagnostic tests

Serotypes (serovars)

-strains within a clone that are genetically different and can be identified by their distinct surface antigens

Slide agglutination test

-Combine an antiserum consisting of known antibodies (Abs) with and unkown bacterium
-An interaction between the antibody and antigens on the surface of the unkown bacterium causes the bacteria to clump (agglutinate) and is a positive result. (clumpy)
-In a negative test, the antigen and antibody do not intereact and the bacteria are remain evenly distributed in the suspension of antiserum. (creamy mixture)

ELISA

-Enzyme-linked immunosorbent assay
-Known antibodies
-uknown type of bacterium
-antibodies linked to enzyme
-enzyme substrate
-very accurate
-primary blood test for HIV
-clear= negative
-color= positive

ELISA (test)

-looks for bacterial antigens present in the sample by detecting interactions with known antibodies
-primary antibody (Ab)= known antibody that recognizes specific bacterium
-Antigen (Ag)= unknown bacterium
-Secondary antibody: same antibody and specificity as primary antibody, but attached to an enzyme
-If enzyme is present, clearn substrate is changed into a visible product by the enzyme.

The Western Blot

-looks for the presence of Abs in the patient's serum against a wide range of proteins (Ags) found on the surface of a microorganism that is suspected of causing disease
-Antigen (Ag): commercially prepared proteins obtained from Borellia burgdorferi, the causative bacterium of Lyme disease
-Primary Antibody (Ab)= Antibodies obtained from the serum of a patient suspected to be infected with Borrelia burdoferi
-Secondary Anitbody=anti-human Antibody (Anti-H Ab)= commercially prepared antibodies and are tagged with an enzyme that allows visualization
-pos. result: black line (enzyme converts sibstrate)

Dichotomous key

-widely used in identification
-successive questions with 2 answers

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