Chapter 10- Identification & Classification of Prokaryotic Organisms

taxonomy

the science that studies organisms in order to arrange them into groups

identification

process of characterizing an isolate to determine which taxon to which it belongs

classification

process of arranging organisms into similar or related groups, primarily to make it easier to study or identify them

nomenclature

system of assigning names to organisms

taxon

group or category used to classify an organism

phylogeny

determining evolutionary relatedness of two things, often determined by examining shared or unshared characteristics

Bergey’s Manual of Systemic Bacteriology

microbiologists classification bible— contains description of all known species, their properties, and ways to identify them

why is it more difficult to determine phylogeny of bacteria rather than plants & animals?

there are very few differences in bacterias size and shape. they also do not do sexual reproduction

species

in higher organisms, a group of morphologically similar organisms that are capable of interbreeding and producing viable, fertile offspring

What is the mnemonic for the taxonomic hierarchies?

Dumb Kids Prefer Candy Over Fancy Green Salad

Three Domain System

classifications of all organisms into three domains: bacteria, archaea, and eucarya

is there an official classification system of organisms?

No— but we do use the three domain system

what is the suffix of the order taxon?

-ales

what is the suffix of the family taxon?

-aceae

catalase biochemical test

detects activity of catalase, an enzyme that breaks down hydrogen peroxide to form O2 and water

what happens if the catalase test is positive?

reagant will bubble

citrate biochemical test

determines whether or not citrate can be used as a sole carbon source

what happens if the citrate test it positive?

growth occurs, usually with a color change of pH indicator

sugar fermentation biochemical test

detects the acidity resulting from fermentation of the sugar incorporated into the medium; also detects gas production

what happens if the sugar fermentation test is positive?

medium becomes acidic, causing pH indicator to change color

urease biochemical test

detects enzymatic degradation of urea to carbon dioxide and ammonia

what happens if the urease test is positive?

medium becomes alkaline, and the pH indicator will change color

what are two commercially available methods to identify bacteria?

API & Enterotube

dichotomous key

forking schematic for bacterial identification with two mutually exclusive choices at each step

serology

some bacteria produce distinct surface molecules that can be detected using antibodies

what is the phylogenetic tree of all living organisms called?

the tree of life

FAME (fatty acid methyl esters)

method using standardized bacteria treated with specific chemicals to extract their fatty acids in order to be quantified with gas chromatography. form of phenotypic identification

FISH

fluorescence in situ hybridization, genotypic identification

what are the phenotypic identification methods?

microscopic examination, biochemical tests, serology, phage typing, antibiotic resistances, FAME, and immunofluorescence

what are the genotypic identification methods?

FISH, NAAT, and ribosoma RNA gene sequencing

NAATs (nucleic acid amplification tests)

using PCR on mixed samples to amplify genes specific to an organism- genotypic identification method

what is one major way bacteria are classified?

phylogenetic analysis

phylogenetic analysis

using a mathematical composite of the DNA sequence of various slow evolving genes present on all bacterial chromosomes

what is almost always used during phylogenetic analysis?

16s rRNA gene

why is the 16s rRNA gene used in phylogenetic analysis?

because it is conserved and present in almost all bacterial chromosomes

domain

broadest taxonomic category. consists of either bacteria, archaea, or eucarya

what are the four techniques for identifying bacterial unknowns?

microscopic examination, culture characteristics, biochemical tests, and nucleic acid analysis

what are two examples of bacteria that can be identified by a microscopic exam alone?

Streptococcus pneumoniae and Neisseria gonorrhoeae

why does increased horizontal gene transfer in bacteria make it more difficult to do phylogenetic analysis?

certain tests may not be uniform among isolates of the same species

why is it useful to identify prokaryotes?

to detect contaminants and identify medically relevant bacteria

how are different species of prokaryotes determined?

by their functional roles and percent identity

serotype

cell structures used to distinguish different strains of members of the same family

most biochemical tests produce what?

color change

probe/FISH

labeled piece of DNA used as a testing agent for genotype

O, K, and H antigens are usually determine by what technique?

serology

antibiogram

plate of confluent bacteria tested with an antibiotic/s

In serology, the H antigen corresponds to what?

flagella

what does a large zone of inhibition on an antibiogram mean

the bacteria is sensitive to the antibiotic, or the antibiotic is very effective

in serology, the O antigen corresponds to what?

outer membrane

in serology, what does the K antigen correspond to?

capsule

what term pertains to evolutionary relatedness?

phylogen

genus

comes first in naming, always capitalized, often abbreviated as a letter

what is the species in “Streptococcus pyogenes” ?

pyogenes

species

second part of bacterial name, not capitalized, often ends in l, a or ii

strain or variety

often represented by capitalized letters and numbers

what are strains used for?

to denote minor genetic variations of a species

phylogenetic tree

figure that illustrates the relatedness of organisms included in the analysis