What are the three types of taxonomy?

Biologic

Numeric

DNA

Taxonomy

Nomenclature

Identification

ales: order

aceae: family

• It is to provide useful ways for identifying and comparing organisms.
• Another goal is to asses the extent of diversity of different types of organisms.

What is numeric taxonomy and what is usually used to chart it?

Numeric taxonomy is a Phenetic system that uses observable characteristics (gram stain, cell shape, motility, size, cell wall chemistry etc....) to group organisms

A Similarity Matrix is used to group the organisms by greatest number of characteristics in common and a dendogram is used to graphically display similarity coefficients. 

What is a phenon?

it is a group of organisms with great similarity

*In numeric taxonomy >%80 similarity= same species

This groups organisms based on shared evolutionary heritage. 

*DNA and RNA sequencing techniques are considered to give the most meaningful phylongenies

How much Guanine and Cytosine in a  strand of DNA 

Determined by: G+C/ G+C+T+A

What is the purpose of a thermalstability test?

o   two organisms are considered to be in the same molecular species if they exhibit 70% or greater relatedness and the related sequences contain 5% or fewer unpaired bases

What is Multilocus Sequence Typing (MLST)

the seqeuncing and comparison of 5-7 housekeeping genes done to prevent misleading results from analysis of one gene introduced by lateral gene transfer.

** also used for microbial classification and determination of phylogenetic relationships

 a.a. sequencing of a protien is a reflections of mRNA seqeunce and therefore of the gene which encodes that protien. 

[cytochrome, histones, and heatshock proteins provided relevant taxonomic and phylogentic info]

when comparing rRNA sequences between 2 organisms, their relatedness is represented by an associatin coefficient of Sab value, the higher the Sab value…..

Who was Carl Linne (Carlus Linnaeus)?

By:

1. Discoverer
2. Habitat
3. Morphology
4. Physiologic characteristics
5. Pathogenicity
6. Cultural Characteristics
7. Pigmentation

1. Streak plate - serial dilution on plate
2. Pour Plate various colonies in molten agar (45-55 C)
3. Colony Subculure - transfer colony from one environment to another
4. Special Indentification Methods: Spore vs. veg cells (85 deg celsius, 5 min, kills veg but not spores) Add antimicrobials (screen out certain organisms) add dyes instead of antimicrobials (CV, brillant green), serial dilutions, single cell isolator (research lab)

Gas Environment (second test in Identification)

Are they strict aerobes?

microaerophiles? facultative anaerobe? etc?

Step 3- Microscopic & Macroscopic Mophology

Determine colony formation, bacterial shape, on unadulturated organisms (close to orginal environment as possible)

1.Carbohydrate Dissimilation: Fermentation, Voges-Prokauer, and Fermentation and Proteolysis of Milk.

2. Proteolysis- Nutrient gelatin, gelatin hydrolysis, H2S production, Indole production, Nitrate Reduction, and rapid tests

1. Durham Tube

2. Phenol Red broth base

3. Specific Carbohydrate

Nutrient broth + 10% gelatin incubated at 20C or 35C (melts at this temp so always read at 20C)

read as liquifiers, weak liquifiers, or non liqufiers

petri dish with nutrient gelatin, add frazier glacial acetic acid/ HCl-HgCl2 after innoc. and incub. then look for clearing zone

reduction of thiol(sulfur containing) AAS

add Pb or Fe, it will turn black

the trytophan will reduce to Indole + pyruciv acid

detect indole with Kovacks reagent

-n-amyl alcohol

-HCl

-PABA

you will get a red color

in a liquid media with a peptone to start it. 

Na, KNO2

(can organisms use nitrate as H acceptor?)

·      due to ultrastructure most microorganisms are capable of acting as antigens to the human immune system

even with all the previous test, sometimes the microorganisms still cant be identified so they innoculate an animal (kochs 3rd postulate)

issues with this are: time, cost, and space

-because bacteria are able to have their own parasites, bacteriophages, this test is done

**it needs to be narrowed down to 2 bacterias

-bc it is very host specific, you place the bacterias in a petri dish, add the bacteriophage that targets one, and if it "eats" the bacteria, the bacteria is host specific for that bacteriophage

What is DNA  probe/Homology in Identification of microorganisms?

to be able to tell the organisms apart by their DNA

-need to have a good idea what you are looking for, a specific reason why

-some tests/labs may start with this

1. Isolation
2. Gas environment
3. Microscopic & Macroscopic Morphology
4. Biochemical Characteristics
5. Serologic Characteristics
6. Pathophysiologic Characteristics
7. Phage Testing
8. DNA probes/homology
9. PCR