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Page 1: Lab manual 2009

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Page 2: Lab manual 2009

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Exercise No.____ Instrumentation

Microbiology as a science includes the study of bacteria (bacteriology), viruses (virology), fungi (Mycology), and animal parasites (Parasitology). After the discovery of microscopic life forms by Leeuwenhoek, other fields such as Immunology & Genetics are also classified as branches of Microbiology.

In the study of Microbiology, the single most important apparatus used in routine examinations is the compound microscope. The microscope is not only essential , it is also a must to master the proper usage and handling of this. Aside from the microscope comes many other laboratory equipment and glassware which are also needed in performing the daily tasks in a microbiology laboratory. This is the main goal of the initial chapter: To introduce to the dental students the basic instrumentation in the microbiology laboratory.

Objectives:

1. To familiarize the dental student with the common glassware & apparatus used in the microbiology laboratory.2. To be able to differentiate the functions of some of the common instruments & tools used in the performance of laboratory exercises in microbiology.

Part 1. The Compound Microscope:

Objectives:

a. To train the dental student in the use of the compound microscopeb. To enforce proper operation of the microscope specially with the Oil

Immersion objective

Materials:

a. Compound microscopeb. Prepared slide specimenc. Cedar wood oild. Xylol

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Part 2. Apparatus & Glassware

Objectives:

a. To acquaint the student with the various apparatus used in microbiology b. To know the different functions & uses of the different glassware in

microbiology.

Materials:

a. All apparatus & glassware checked & distributed to the studentsb. Apparatus in the Micro Lab ( GDLSC Stockroom )

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Illustration: (1) Draw and label properly all functional parts of the compound microscope.

(2)

Draw & give a use for each of the following :

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1. Plain slide: _______________________ 2. Depression slide: _____________________ _________________________________ ____________________________________

3. Candle jar:________________________ 4. Gas Pak: _____________________________ _________________________________ _____________________________________

5. Colony counter:____________________ 6. Wire basket: _______________________ _________________________________ __________________________________

7. Inoculating loop:___________________ 8. Inoculating needle:___________________ _________________________________ _________________________________

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9 Petridish : _______________________ 10. Coplin jar : _________________________ _________________________________ ____________________________________

11. Bunsen burner:___________________ 12. Waterbath: _________________________ __________________________________ _____________________________________

13.Dilution bottle :____________________ 14. Dropping bottle: _____________________ __________________________________ ____________________________________

15.Petridish can: ___________________ 16. Pipette can:_________________________ _________________________________ ____________________________________

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Review Questions:

1. Differentiate magnification , resolution & resolving power:

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2. Why is there a need for cedar wood oil & Xylol in the use of the Oil Immersion

Objective?_______________________________________________________________

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3. Briefly discuss the following:

a.Electron microscope: __________________________________________________

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b. Fluorescence Microscope: ______________________________________________

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c. Phase Contrast Microscope: ____________________________________________

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d. Inverted Microscope: _________________________________________________

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e. Darkfield Microscope: _______________________________________________

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4. Differentiate an autoclave from a hot air sterilizer. Which is more commonly used in

the microbiology laboratory? Which is usually used in the dental clinic?

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5. Why do you think is it necessary to take precautionary measures in handling your

specimen and for yourselves prior to coming in and out the laboratory as dental students?

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Exercise No.____Bacterial Cytology & Physiology

Bacteria are characteristically smaller than the more advanced microscopic eukaryotes and range in size from 0.2 um, in width , which is barely visible with the compound microscope, to some spiral-shaped species that reach 400-500 um in length. Generally speaking, most bacteria are 1 to 6 um in length with diameters between 0.2 to 1.5 um.

A typical bacterial cell taken apart could consist of a capsule, cell wall , cytoplasmic membrane, some organelles, nucleus, fimbriae & flagella plus the presence of spores. They could be classified according to shape into: spherical, rod shaped, curved or spiral and square, with variations in most types which is known as pleomorphism. They also have the ability to exhibit reproduction and in some cases motility and cellular interactions.

Objectives:

1. To study the basic structure of the bacterial cell.

2. To enable to student to distinguish the different morphological forms of the bacterial cell.

3. To fully understand the functions of the fundamental parts and the specialized structures contained in a bacterial cell.

Materials:

1. Compound microscope2. Prepared microscopic slides of the following :

a. Staphylococcus aureusb. Bacillus subtilis c. Vibrio cholera

3. Cedar wood oil 4. Xylol

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Illustrations:

(1) Draw a typical bacterial cell and label all its functional parts and structures:

(2) In the space provided , illustrate the different specialized structures which could be present in a bacterial cell and give their classifications:

(3) On the space provided , illustrate all pleomorphic forms of the cocci, bacilli

& spirilli:a. Cocci - diplococci, staphylococci, streptococci, sarcinae, tetradsb. Bacilli - single, diplococci, streptobacilli, palisadec. Spirilli - spiral, comma-shaped

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Review Questions:

(1) Give a specific function for each of the basic structures of the bacterial cell:

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__________________________________________________________________

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(2) Give the chemical composition of the cell wall and cell membrane of the

bacterial cell:

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(3) Name the specialized structures of the bacterial cell and give their functions:

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(4) Enumerate the different types of flagella based on number and location:

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(5) List down the different types of spores based on its location within the

bacterial cell:

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__________________________________________________________________

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(6) Aside from the three morphological forms ( cocci, bacilli & spirilli) , are there

other special morphological forms?

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Exercise No._______Microscopic Study of Protozoans & Observation of True Motility

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Protozoans are unicellular, free living, in some cases parasitic microorganisms. They belong to the Kingdom Protista. Protozoa are excellent tools for research because they are easily cultivated in the laboratory. They reproduce asexually and clones are easily generated with the same genotype of the desired “parent”. The effects of environmental factors, such as radiation are easily analyzed in these organisms.

Protozoans are classified into the Sarcomastigophora, Sporozoa, Myxospora and the Ciliophora. Specific examples of protozoans include: Amoeba, Mastigamoeba, Euglena, Paramecia, Volvox, Bicoeca, Ochromonas, Opalina, Stentor, Hymenostomina & Pleuromona. Some of the morphological structures present on them are the pellicle, shell, mucocyst, cytosome, oral groove, cytopharynx, contractile & food vacuole, cytopyge, extrusomes & Uroid.

One of the most common characteristic of protozoans is the ability of movement or locomotion. This is brought about by organs of locomotion which are flagella and pili or fimbriae. True motility could easily be observed with a sample from any canal water

Objectives:

(1) To observe the actual living microorganisms present in the samples obtained from our present surroundings.

(2) To demonstrate and observe true motility as exhibited by the protozoans at the same time also study the organs for locomotion.

Materials:

1. Specimen from any canal water 2. Vials 3. Hanging - drop slide or depression slide4. cover slip5. Vaseline6. medicine dropper

Procedure:

1. Clean the concave slide and coverslip thoroughly.

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2. Take a drop of the specimen and carefully drop it on the center of the coverslip. Ring the coverslip with a thin layer of Vaseline.

3. Carefully invert the prepared coverslip over the concavity of the depression slide, making sure that the drop of specimen in the center is hanging into the concavity without touching the slide.

4. Study the preparation under low power objective with the diaphragm partly open and the condenser slightly lowered.

5. Switch the objective to high power and observe the specimen. The slide may be moved to have a wider field of coverage in searching for motile organisms.

6. Make a note of all the different types of motile organisms observed.

Note: After the exercise, remember to immerse the dropper used and the depression slide together with the coverslip into the disinfectant solution before washing with soap & water.

Observations: ________________________________________________________________________

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Illustration : ( Set-up)

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Review Questions:

(1) What do you think is the purpose of ringing the coverslip with Vaseline before

inverting it onto the depression slide?

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(2) What are the other methods of testing for bacterial motility?

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(3) Could there be other types of movement aside from true motility? What do you

attribute this to?

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________________________________________________________________________

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Exercise No._______Staining Techniques

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Staining is a technique used in the microbiology laboratory with the help of coloring dyes, indicator and reagents to enhance or distinguish a specific organism or a morphological structure to facilitate their study under the microscope. The most commonly used dyes in microbiological work are known as cationic dyes. The color containing portion of the molecule is known as chromatophore while the nonpigment containing part is known as auxochrome.

Before staining, one must first prepare a smear of the specimen by spreading a thin film of the bacterial suspension on a clean slide with the use of an inoculating loop. The smear is then air dried, heat fixed r immersed in chemical solutions. Stains could also be used in combination to produce contrasting colors and effects to distinguish 2 separate group of organisms in one sample.

Objectives:

1. To introduce the different types of staining procedures.

2. To differentiate and distinguish the functions of the individual reagents included in each staining procedure.

3. To have a realistic experience in the actual staining of microorganisms.

Materials:

1. Specimen of microorganisms to be provided in the lab.2. Different staining solutions3. Clean glass slides4. Inoculating loop5. Bunsen burner6. Dropping bottle7. Staining Rack

A. Simple Staining:

Procedure:

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Note : Inoculating loop must be flamed red hot before & after use.1. Prepare 2 smears with the inoculating loop for each of the microorganisms provided.2. Heat fix and allow the specimen to cool.3. Flood one set of the slides with Carbol fuchsin & the other set with

Methylene Blue.4. Allow the stain to remain for one minute.5. Wash with tap water and blot dry.6. Examine all specimen under oil immersion objective. 7. Note down all observations.

Observations:

B. Differential Staining:

I. Gram Stain:

Procedure:

1. Prepare a thin smear for all specimen provided.2. Fix & allow to cool.3. Flood the smear/s with a few drops of Crystal or Gentian Violet.4. Let the slide stand for 60 seconds then wash with tap water.5. Add a few drops of Gram’s Iodine.

6. Let the slide stand for 60 seconds then rinse with tap water.7. Add 95% alcohol to the smear until no more color comes off from the

alcohol (this may take 30 seconds to 2 minutes)8. Wash again with tap water.

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9. Add a few drops of Safranin10. Allow to stand for 30 seconds11. Wash off the excess stain.12. Blot dry and examine the specimen under Oil Immersion Objective.

Observations:

II. Acid Fast Staining:

Procedure:

1. Prepare a thin smear of the specimen provided.2. Heat fix and cool.3. Flood the slide with aqueous Carbol Fuchsin solution. Steam the slide

for 5 minutes over a flame. Do not allow the preparation to dry up by adding Carbol Fuchsin from time to time.

4. Wash off the excess stain with tap water.5. Decolorize the smear with acid alcohol until no excess stain comes off.6. Counterstain with Methylene Blue for 30 seconds to one minute.7. Wash off excess stain with tap water.8. Blot dry and examine under Oil Immersion objective.

Observations:

III. Negative Staining:

Procedure:

1. Obtain gingival scrapings from crevices by means of a toothpick or a

periodontal scaler.

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2. Spread the scrapings on a glass slide and apply a drop of distilled water. 3. Mix Nigrosin with the smear and allow to dry.4. Wash the excess dye off , dry and examine under Oil Immersion objective. Use lead pencil in illustrating results.

Observations:

Review Questions:

(1) Enumerate and give the functions of the reagents used in Gram’s & Acid Fast

Stain:

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(2) What is the purpose of heating the bacterial smear before staining?

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(3) What is the factor behind an organism being gram (+) or gram (-)?

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________________________________________________________________________

(4) What is the purpose of steaming the smear in acid fast staining? ____________

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(5) Give examples of Acid fast bacteria:

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(6) Give the (+) and (-) color results of both the Gram’s stain & Acid fast stain:

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(7) Explain the reason why sometimes the color of the background of the specimen

is in contrast to that of the microorganism?

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(8) Give the importance and the circumstances when Negative staining is used:

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(9) What could be the possible explanation for you obtaining a result of having

both Gram positive and Gram negative results on one slide:

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Exercise No._____Media Preparation

Culture media refers to any artificial or natural substance or nutrients provided to the microorganism for it to obtain nourisment in order to sustain growth and reproduction.

An optimum balance of nutrients and a suitable growth environment are needed to culture a microbe in the laboratory. The culture media should contain all the necessary materials for the microbe to move quickly into the log phase of growth. Water, Carbon, Nitrogen, minerals and growth factors must be available in a usable form. Many growth media can be prepared by the dental student to isolate , grow and identify a particular specie of microbe in the laboratory.

In media preparation, the reagents and materials required may vary from one to the other but there a standard set of procedure to follow:

1. Gathering all the materials needed.2. Dissolving the ingredients in the proper solvents3. Adjusting the pH of the media4. Filtering the media5. Dispensing the media in their appropriate containers6. Cotton plugging the tubes7. Sterilizing the media8. Testing the sterility9. Storing the media.

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Objectives:

1. To develop the ability to prepare the different types of culture media based on the standard procedures and the requirements of the individual microorganisms.

2. To know the various nutrient requirements of various individual microorganisms

Materials:

1. Beef Extract 0.3 gm2. Peptone 2.0 gm3. Sodium Chloride 0.5 gm4. Distilled water 100 ml5. Erlenmeyer flask6. Pipettes, funnel, test tube7. Graduated cylinder8. Indicators9. Comparator block & pH standards

A. Nutrient Broth:

Procedure:

1. Mix the ingredients in a 100 ml flask. Add aliquot portion of distilled water.2. Dissolve by heating over flame.3. Adjust the pH to 7.4 - 7.5 using comparator block method.4. Filter the media if necessary.5. Dispense into 10 ml amount in test tubes, Plug with cotton plugs.6. Autoclave at 25 psi for 15 to 20 minutes7. Store in refrigerator for future use.

B. Nutrient Agar:

Procedure:

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1. Same as the above preparation but add 2 gram agar.2. Boil until all agar is completely dissolved.3. Dispense 10 cc into each test tube.4. Plug the test tube with non-absorbent cotton.5. Autoclave the tubes at 15 psi for 15 to 20 minutes.6. Slant 5 tubes and allow the other tubes to solidify in the upward position.7. Store the media in the refrigerator for future use.

Review Questions:

(1) What constituent in nutrient broth satisfy the essential requirements for energy,

cellular growth & repair?

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(2) Why is agar used in solid media preparation?

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(3) How would you adjust the pH of solid media ?

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(4) What are the different sterilizers available in the laboratory?

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(5) Is there danger or harmful effects in oversterilizing the media? _____ Explain:

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(6) What types of media are sterilized in the autoclave ?

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(7) Can all microorganisms grow in nutrient broth and media ? ________ Why or

why not?

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(8) Name the other types of media and give examples of organisms which grow in

them :

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(9) Give the differences between a butt culture and the slant culture aside from

their physical appearance:

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(10) Differentiate pure, stock & mixed culture. Give their uses and examples for

each:

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Exercise No. ______Aseptic Technique & Methods of Inoculation

One of the most important laboratory procedures in microbiology is to obtain pure cultures for the identification of organisms. When the samples from soil, water, food, or body are collected into nutrient containing petridishes, it is clear that each sample contains a variety of microbes. This is particularly true of specimens collected from the skin or the mucous membranes of patients with infection. The clinical specimens contain both the harmless microbes ( normal flora ) of the body and the microbes causing the disease ( pathogens ) . In order to accurately identify which microorganism is responsible for the illness, the many different types of microbes must be separated. After separation the individual microbes must be placed on the medium that will allow them to reproduce into a clearly visible population or colony containing only one specie. Samples from this colony can then be picked out and transferred to a separate culture for further growth and identification. The microbiologist will then be able to study such characteristics such as morphology, metabolism and antibiotic sensitivity.

Special wires known as the inoculating loop and needles are used in the transfer of specimen. Aseptic technique is followed to prevent both the mixing of cultures and contamination of the student or working area with pathogenic microbes or their toxins.

Objectives:

1. To develop the skill of proper inoculation of different kinds of culture media.

2. To be able to practice asepsis in the laboratory which will serve as a training ground for the dental students future practice in the clinic & actual practice.

3. To study bacterial growth in different types of culture media.

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Materials:

1. Culture mediaa. plain broth tubeb. plain agar buttc. plain agar slantd. agar plates

2. Inoculating loop and needle3. Bunsen burner4. Organism/specimen

Procedure:

A. Inoculation of Liquid media:

1. Hold the tube gently on the left hand and the loop or needle ( which must be previously heated ) with the right hand.

2. With the pinkie ( little finger) of the right hand, pull out the cotton plug of the tube.

3. Heat the mouth of the test tube and proceed with the actual inoculation by slightly rubbing the loop with the inoculum on the side of the

tube or simple just by twirling the loop to dislodge the inoculum.

4. Heat the mouth of the tube , put back the cotton plug onto the test tube before setting it down and reflame the loop or needle before

setting it down on the table.

B.Inoculation of Butt culture:

1. Repeat steps 1 & 2 from the previous instructions but this time use the inoculating needle.

2. Heat the mouth of the test tube and plunge the needle into the agar in one swift downward motion stabbing about 2/3 of the media. Pull out the needle, reheat the mouth of the tube and replace the cotton plug

onto the test tube.

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3. Flame the inoculating needle until red hot and cool before finally setting it down on the table.

C. Inoculation of Slant culture:

1. Repeat steps 1 & 2 of procedure A, but this time heat the inoculating loop.

2. With the little finger remove the cotton plug and heat the mouth of the test tube. 3. Starting from the butt end of the slant draw the loop over the surface in a

straight line towards the end of the slant.

4. Starting again from the butt end, trace a zigzag course from side to side, at the same time slowly drawing the loop towards the end of the

slant.

5. Heat the mouth of the test tube , replace the plug, heat the loop, cool and set it down on the table.

D. Inoculation of Plated Media:

I Interrupted Streak:

1. Flame the loop and pick up the specimen from the test tube after flaming the mouth of the tube. Reflame the mouth and replace the cotton

plug. Set down the test tube.

2. Hold the petridish with your left hand, with the cover side up. With the thumb and little finger, raise the lid up and proceed with the inoculation.

3. Start inoculation at the farther side of the plate tracing a zigzag course from side to side until you reach the middle of the plate or the

widest part of the petridish.

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4. Close the lid and rotate the plate 180 degrees. Repeat the procedure from the other end of the plate in the same manner.

II. Multiple Inoculation:

-This is done with the same steps as Procedure A except that this is a procedure done when the available media is insufficient for the

number of specimen. The plate is then divided into about 5 to 8 quadrants as that of a pizza pie, and each organism is streaked into each quadrant.

III. Overlap streak Method:

-This procedure is carried out in the same manner as above except that in the overlap method, we depend on the overlap zones to provide the

isolated colonies in the second & the third areas of inoculation.

IV. Radial Streak Method:

1. Follow all the preliminary steps as in procedure A.

2. Place a loopful of the broth culture near the edge of the agar plate.

3. From here make radial straight lines streaking towards the other side. Start from one side of the plate until the whole plate has been

inoculated. This method is usually used in culturing fungi.

V. Pour plate method:1. Prepare 3 sterile test tubes & petridishes .

2. Put 9 cc of sterile saline to each of the 3 test tubes.

3. To the first tube add 1 ml of the broth culture of Specimen A and mix.

4. Transfer 1 ml from the contents of the first tube into the second tube and mix. You now have a dilution of 1:10

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5. Transfer 1 ml from the contents of the 2nd tube into the 3rd tube and mix. You now have a dilution of 1:100

6. From each of the test tubes pipette out 1 ml of the contents separately and transfer them into a corresponding petridish.

7. Add about 10 - 12 cc of melted agar to each of the petridish.

8. Allow the agar to solidify then incubate.

Illustrations:

(1) Graphically present the different types of culture media used in inoculation:

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(2) On the space provided , graphically illustrate and label the 7 different methods of inoculation

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Review Questions:

(1) Why are the inoculated plates incubated in an inverted position ?

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(2) Differentiate a pure culture, mixed culture and a stock culture : _____________

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(3) What are the other ways of identifying microorganisms? ___________________

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(4) Assuming that the same serial dilution was carried out in a laboratory experiment in 10 tubes with 4 ml of saline in each . Pour plate method of

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inoculation was performed. It was later found out that on the 7th petridish cultured there was a total of 16 individual microorganisms found. Deduce a way based on the given and compute the total number of microorganisms present in tube one neglecting all chances of human error in the transferring process. ______________________

Show complete solution in the space provided:

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Exercise No. _____Biochemical Activities of Bacteria

Bacteria are capable of performing several biochemical activities, one of which is fermentation of many molecules including carbohydrates, amino acids & organic acids. These properties could serve as tools of identification since they demonstrates some metabolic capability of the microbe.

The set-up used in the laboratory to detect biochemical activity is with the use of Durham tubes inverted in test tubes containing different carbohydrates. The Durham tube would collect the gases such as Carbon Dioxide, Methane or Hydrogen that might be produced in the fermentation process. If gas is produced , a visible bubble will form clearly in the Durham tube. Some bacteria produce acid & gas as fermentation products and in some instances only one of the two is produced.

Differential media is also used to differentiate microbes. One of the most important sets of tests is the IMViC Test. It is a series of biochemical test used to identify members of the Enterobacter family. Many members of this family produce diseases such as :

E. coli - Infantile diarrheaEnterobacter - Urinary tract infectionKlebsiella - PneumoniaSalmonella - Typhoid fever & GastroenteritisShigella - Bacillary Dysentery

An example would be two of the abovementioned organisms exhibits the same properties. E.coli & Enterobacter are both found in the colon of humans, they are both Gram negative rods, and also exhibit the same symptoms in parasitic relationships. The IMViC test would be the easiest way to distinguish them apart .

Objective :

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1. To understand the biochemical activity & metabolic capabilities of some closely related microbes.

2. To differentiate two groups of microorganisms based on their biochemical properties. (Escherichia coli & Enterobacter aerogenes)

3. To have an actual demonstration of the most common biochemical tests used in the microbiology laboratory.

Materials:

1. Broth culture of both E. coli & E. aerogenes2. Erlich’s reagent3. Clark & Lub’s media4. Ether5. Methyl red indicator6. Simon Citrate media7. 40 % KOH8. Test tubes

A. Indole Test:- demonstrates the production of indole based on the presence or absence of tryptophan

Procedure :

1. Prepare 2 test tubes containing Specimen A ( E. coli) & Specimen B ( E. aerogenes ) in broth culture.2. Add 1 ml of ether ( note: do not aspirate by mouth) to 48 hour broth

culture of both specimen A & B3. Shake well and allow to stand until ether rises to the surface.4. Gently add about 0.5 ml of Ehrlich’s reagent drop by drop down the side of the test tube so that it forms a ring between the medium and the

ether layer. The presence of indole is indicated by a cherry red or deep red color in the reagent layer at the top.

B. Methyl Red Test

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- a pH indicator ( Methyl Red ) is used to determine whether the microbe has produced acid or not.

Procedure:

1. Prepare 2 tubes containing Clark & Lub’s broth2. Inoculate specimen A & B into the tubes3. Incubate the tubes for 72 hours at 37 degrees4. After incubation, add 2 to 3 drops of Methyl Red.5. Red Color would be an indication for the production of acid and yellow color would be indicative of alkaline or negative results

C. Citrate Test- indicates whether or not the organism can utilize citrate as a sole source of Carbon.

Procedure:

1. Prepare two tubes with Simon Citrate media.2. Inoculate by streaking on the slant portion of the media.3. Incubate the tubes at 37 degrees for 24 hours.4. Blue color would be indicative of positive results and green color would be negative.

D. Voges-Proskauer Test- indicates the production of an organic molecule called acetyl- methylcarbinol or acetoin from glucose in microorganisms.

Procedure:

1. Prepare 2 tubes of Clark & Lubs media 2. Inoculate specimen A & B into the tubes3. Incubate the tubes at 37 degrees for 72 hours.4. After incubation add an equal amount of 40% KOH and shake vigorously for 2-5 min.5. Allow the tubes to stand and note the color reaction.

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6. Production of an Eosin like color up to 2 hours would be positive. Color would depend on the oxidation of acetoin.

Observations & Results: In the space provided, draw a 3 column table and tabulate your results:

Review

Questions:

1. Give the

positive

results & at

least 2

organisms

identified

by the

following tests:

a. Catalase test: ____________________________________________________

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b. Coagulase Test: __________________________________________________

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c. Oxidase Test ____________________________________________________

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d. Urease Test _____________________________________________________

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e. Hemolysis Test __________________________________________________

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_________________________________________________________________

_________________________________________________________________

f. Hydrogen Sulfide Test _____________________________________________

_________________________________________________________________

_________________________________________________________________

g. Greig’s Test _____________________________________________________

_________________________________________________________________

_________________________________________________________________

2. What is the API 20 system?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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Exercise No. _____Factors Influencing Bacterial Growth

Aside from the nutritional requirements of the microorganisms which are provided for in the culture media, different microbes require different environmental conditions for them to exist, grow and reproduce. Environmental factors such as temperature, pH, Osmotic pressure, salt concentration, Oxygen & Carbon Dioxide concentration and presence of moisture are all essential & should be taken into consideration as part of the whole living environment. This set of exercise is designed at altering and adjusting some of the variables and observing the effects of these variants on the behavior and growth of specific microbes.

Objectives:

1. To know the different factors behind the growth of microorganisms.

2. To differentiate microorganisms based on their ability to exist under different environmental conditions.

Materials:

1. Broth culture of different microorganisms2. 20 test tubes3. Candle jar or anaerobic jar4. Dessication chamber5. Mild acid & base6. Water bath

Procedure:

A. Temperature Requirement:

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1. For every specimen provided , inoculate each microorganism into 4 tubes and label them A, B, C, D.

2. Incubate all tube A’s at 37 degrees.3. Store all tube B’s in the refrigerator ( 4 - 12 degrees ) 4. Incubate all tube C’s in the incubator at 50 degrees.5. Store all tube D’s in the locker ( 25 degrees ) 6. After 24 hours check and tabulate results.

B. Oxygen

Requirement :

1. For every specimen provided, inoculate each into 3 sets of tubes2. Store the first set of tubes in the incubator.3. Store the second set of tubes in a candle jar or anaerobic jar4. Store the third set of tubes in the cabinet.5. Incubate for 24 hours. Check and tabulate the results

C. pH

Requirement:

1. To each of the specimen provided, inoculate each into three tubes.2. To the first set of tubes , add 1 ml of mild acid.

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3. To the second set of tubes, add 1 ml of mild base4. Use the third set of tubes as control.5. Incubate the tubes for 24 hours. 6. Check and tabulate your results.

D. Moisture

Requirement:

1. Inoculate the specimens provided in a set of tubes and store them in a desiccated chamber.2. Incubate for 24 hours.3. Observe and record the results.

Review

Questions:

1. Differentiate the following : Optimum growth temperature, minimum growth

temperature & maximum growth temperature:

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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________________________________________________________________________

________________________________________________________________________

2. Name the different types of microorganisms based on their oxygen requirement:

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. Different psychrophiles, mesophiles & thermophiles: _______________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. Aside from the factors discussed in the laboratory exercise, what other factors

do you think influence bacterial growth? ____________________________________

________________________________________________________________________

________________________________________________________________________

_______________________________________________________________________

(5) Is there an actual theoretical value for optimum growth temperature? Why or

why not? Justify your answer:

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

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__________________________________________________________________

__________________________________________________________________

Exercise No. _____Microbial Control

Microbes present in the environment which are harmful to us need to be controlled or eliminated. This is carried out by inhibiting their growth and mode of actions, destroying the microbes thereby eliminating them from the

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environment. This is carried out by elements known as antimicrobial agents. These agents could be classified into physical, chemical and through the process of filtration. The choice of a particular agent depends on the type of material to be treated, specific kind of microbe to be controlled and the environmental conditions present at the time of use.

Objective:

1. To have a general overview on the different methods of inhibiting & controlling microbes.

2. To distinguish the different physical & chemical agents used in microbial control

3. To be able to understand the bacteriostatic & bactericidal effects of some common agent used in microbial control

Materials:

1. Inoculating loops ( 3 ) 2. Nutrient broth3. Water bath4. Tripod5. Bunsen burner6. Broth culture of Staphylococcus aureus7. Hydrogen peroxide8. Phenol9. Clean test tubes

Procedure:

A. Effect of heat on Microorganisms:

1. Boil water in a water bath2. Label three test tubes nutrient broth as:

A - control

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B - dry heatC - moist heat

3. Expose the three tubes to the same environment ( to be given) 4. Dip one inoculating loop directly into tube A5. Flame another inoculating loop directly for 10 minutes then dip into tube B.6. Place the 3rd inoculating loop in boiling water for 10 minutes then dip in tube C.7. Incubate the three tubes for 24 hours.

Tabulate your results using the following symbols:( - ) no growth( +- ) slight growth or trace( + ) moderate growth( ++ ) heavy growth

Observations:

Using the symbols provided from the previous page draw a table & tabulate your results in the space provided below:

B. Effect of Chemical Agents on

Microorganisms :

1. Make dilutions of the following disinfectants:a. Phenolb. Hydrogen Peroxide

Prepare dilutions of 1:10, 1:100, 1:10002. Place all the tubes in a water bath at 20 degrees for 5 minutes3. Transfer 0.5 ml of the culture in each of the tubes4. Incubate the nutrient broth for 24 hours.

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Observations:

Using the same symbols given in part A, tabulate your results in the space provided below:

Review questions:

1. Name the

dental uses

of phenol :

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. What is phenol coefficient? ____________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. If results obtained were all ( ++ ) in all dilutions, what would be the most

sensible alternative or approach?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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4. Another method of microbial control is filtration. List down at least 5 kinds of

filters which could be used for this method? _________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

5. Define the following terms:

a. Antiseptic: ______________________________________________________

__________________________________________________________________

__________________________________________________________________

b. Asepsis:_________________________________________________________

_________________________________________________________________

__________________________________________________________________

c. Disinfectant : ____________________________________________________

_________________________________________________________________

d. Sterilization : ____________________________________________________

__________________________________________________________________

__________________________________________________________________

e. Bactericidal :_____________________________________________________

__________________________________________________________________

__________________________________________________________________

f. Bacteriostatic : ___________________________________________________

_________________________________________________________________

_________________________________________________________________

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Exercise No. _____Bacterial Growth Curve

Large population of bacterial cells are routinely used in the laboratory experiments in which bacterial growth and related processes are measured. A small inoculum of cells is usually introduced into the culture media and after a short period of time, when the cells have reached confluency, harvested. It is therefore of utmost importance to determine the time it takes for the organism to reach confluency and the stages of growth that the culture is in.

Cultures after being inoculated undergo several stages: A. Lag phase is a phase wherein cells are given ample time to react to their new environment and there is only increase in size, B. Log phase or the exponential phase is a stage of rapid growth and cell multiplication,

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C. Stationary phase is achieved after a period of time and the number of organisms remains constant due to the depletion of nutrients, pH

change from waste accumulation or simply overcrowding,D. Death or decline phase occurs when the organism starts to die off due to the increasingly irreversible effects from the stationary phase.

Objective:

1. To study the development of a bacterial culture from inoculation to its decline.

2. To be able to quantitatively measure the bacterial population at given points during culture.

3. To graphically illustrate the different stages of the bacterial growth curve based on the results obtained in the exercise.

Materials:

1. Broth culture of Staphylococcus aureus & Escherichia coli2. Spectrophotometer3. Cuvette4. Graphing paper

Procedure:

1. Prepare the broth culture of the different specimen provided in serial dilutions of 1:10, 1:100 and 1:1000 labeled as tube A, B, & C.2. Prepare a control by storing broth in a tube without any specimen.3. Incubate the tubes at 37 degrees.4. Take the readings of the tubes with a spectrophotometer at the given intervals: 0 minutes, 30 minutes, 2 hours, 4 hours , 8 hours, 12 hours, 24 hours , 48 hours5. Take the reading of the control and subtract the value from the values obtained in all tubes at all times.6. Tabulate all results and plot with a graphing paper.

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Review Questions:

1. What are the stages of the bacterial growth curve? Discuss Briefly. ___________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2.. What are the factors influencing the decline of a bacterial culture? ___________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. Would all microorganisms exhibit the same bacterial growth curve? ______

Why?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

__________________________________________________________________

4. Why is there an existence of a stationary phase? Is it really because the

microorganisms “stop” growing ?

_____________________________________________________________________

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________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

5. What are the other methods of determining cell population? _________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

Exercise No. _____Antibiotic Susceptibility Test

The single most important clinical test performed by many microbiologists is the culture and susceptibility test because the results would provide the physician, dentist or any medical personnel with significant information regarding the pathogen and a possible means of controlling it.

A culture and susceptibility test is the growth of a known pathogen in pure culture and its exposure to known antibiotics of different concentration to determine which drug will kill or inhibit the growth of the microorganism.

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Objectives:

1. To understand the principle behind a culture and sensitivity test.

2. To illustrate the effects of different antibiotics on a given microorganism

3. To quantitatively measure the delimiting power of a specific antibiotic to a given microbe.

Materials:

1. Broth cultures of specimen provided2. Agar plates3. Antibiotic paper discs4. Sterile swabs5. Sterile forceps6. Transparent ruler

Procedure:

1. Prepare one agar plate for each specimen provided. Label properly.2. Inoculate the agar plates.3. Using flamed forceps, place the antibiotic discs on the agar surface . Gently press down the discs to ensure contact with the agar.4. Incubate the plates in an inverted manner at 37 degrees for 48 hours.5. Measure the clearing zone or zone of inhibition with your rulers.6. Record and tabulate your results in millimeters.

Observations:

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Review Questions:

1. What is the Kirby-Bauer method in susceptibility testing? ___________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. What are the three ranges of inhibition zones? How are they interpreted? _____

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. How do you differentiate a broad from a narrow spectrum antibiotic?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. What is MIC in relation to antibiotic susceptibility? How does it affect the

choice of antibiotic prescription? __________________________________________

________________________________________________________________________

________________________________________________________________________

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________________________________________________________________________

________________________________________________________________________

5. Would the same procedure done above be applicable in determining allergies in

man? _______________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

6. Pick out any one microorganism which you have studied and try to classify it in

terms of susceptibility to any 10 common antibiotics used in Microbiology or

Pharmacology:

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

7. What is the basis of determining a microorganism in being susceptible or

resistant to a specific antibiotic? _______________________________________

__________________________________________________________________

__________________________________________________________________

__________________________________________________________________

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Exercise No. _____Normal Flora of the Oral Cavity

There are more than 30 species of microorganisms that have been isolated from the oral cavity. From shortly after birth till death, the individual supports a relatively stable oral microbiota. Its composition depends upon the introduction of various microorganisms from the external environment and more importantly upon the various inherent and acquired factors that control the environment within the oral cavity.

Although there are many factors which make it difficult to obtain valid information concerning the kinds and number of microorganisms in the oral cavity at a given time, this exercise is designed to only identify indigenous organisms present. Some examples of these organisms are lactobacilli, streptococci, veillonella, spirochetes, filamentous forms, fusiform bacilli & vibrios. They are constantly present in large numbers.

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Objectives:

1. To confirm the presence of microorganisms in the normal flora of the oral cavity

2. To identify the organisms present in the oral cavity by studying the saliva.

3. To practically apply the different laboratory procedures introduced in the laboratory to be used in the identification of the microorganisms.

Materials:

1. Broth culture of salivary secretions.2. Agar plates3. Methyl violet4. Gram’s Stain5. Nigrosin Dye6. Inoculating loop and needle7. Bunsen burner8. Glass slides

Procedure:

1. Using clean glass slides perform the following staining procedures:a. Direct methyl violet stainingb. Gram’s Stainc. Negative staining

2. Inoculate the agar plate with the broth culture of saliva3. Invert the plate and incubate for 48 hours.4. Observe and record your results for all procedures performed.

Observations:

Review Questions:

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1. What are the microorganisms most commonly found in the healthy oral cavity?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. What is the nature of the oral environment of the infant at birth ? _____________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. Name the factors that regulate the oral microbiota: _________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. What is commonly known as the indicator microorganism in the oral cavity?

Why?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

__________________________________________________________________

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Exercise No. _____Microbiota of Dental Caries

The teeth, because of their composition, inertness and environment are particularly susceptible to destruction. Caries is a destructive disease of the teeth of man and all other forms of life that possess calcified dentition, the etiology of which is intimately associated with the oral microbial flora.

Dental caries begins most often in areas of coronal enamel where saliva may stagnate, food debris may impact, and the oral microbial flora may find a suitable environment for growth such as enamel pits & fissures, and near the point of interproximal areas. Microbial activity initiates the destruction of enamel by converting carbohydrates to organic acids which demineralize the enamel or by chelation of enamel calcium by a variety of bacterial metabolites.

Objectives:

1. To confirm the presence of specific microorganism present in dental caries

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2. To compare the microbiota of patients with rampant dental caries from those without..

Materials:

1. Saliva from a patient with rampant dental caries2. Saliva from a patient without caries3. Rogosa’s agar slant4. Sterile test tubes5. Clean slides6. Reagents for gram and negative staining

Procedure:

1. Collect a small amount of saliva from both types of patients and store in sterile tubes

2. Inoculate the Rogosa;s agar slant. Incubate for 48 hours at 37 degrees.3. Perform Gram and negative staining procedures.4. Examine under oil immersion objective.

Observations::

Review Questions:

1. What are

the

microorganism which are predominant in the occurrence of dental caries?

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________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. Discuss the factors that mediate dental caries: _____________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. What is Snyder’s colorimetric test? ______________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. What is the DMF index ? _______________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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Exercise No. _____Microbiota of Dental Plaque

Dental plaque is the mass of bacteria in a matrix of organic material which adheres tenaciously to the tooth surface. It is made up largely of protein and polysaccharide which is partly derived from saliva and partly produced by the organism . Plaque does not include food debris or exfoliated epithelial cells which are only transient features.

Dental plaques are composed of about 20% precipitated salivary mucoid or mucin and about 80% microorganisms.

Objectives:

1. To identify the presence of microorganisms in dental plaque

2. To know the different types of plaque.

Materials:

1. Clean glass slides2. Reagents for Gram’s and Negative staining procedure3. Toothpick

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Procedure:

1. Collect plaque from the enamel and dentin with the use of a toothpick.2. Prepare a bacterial smear from the collected sample.3. Perform Gram’s and negative staining procedure.4. Wash and dry stained smears.5. Examine specimen under OIO.6. Record your results and observations.

Observations:

Review Questions:

1. What

organisms

make up

the

considerable bulk of the microbial flora of the dental plaque?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. .How are plaque formed? ______________________________________________

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________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

3. Name the bacterial species which are predominant in superficial enamel decay.

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. What are the three types of dental plaque? ________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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Exercise No. _____Microbiota of the Periodontal Pocket & Root Canal

The tissues that surround and support the teeth like the gingival tissues, alveolar bone, periodontal membrane are subject to various diseases, collectively known as periodontal diseases. In these pathological processes, the oral microbial flora is greatly involved.

Bacteria do not produce disease simply by their physical presence, although their adequate multiplication is essential to infection. To produce a disease, some constituents or products of bacteria like toxins and enzymes must react with the tissues or cells to destroy them or interfere with their normal functions.

Objectives:

1. To distinguish the microorganisms present in the periodontal pocket and the root canal.

2. To identify the predominating organisms generally causing periodontal diseases.

Materials:

1. Sample from a periodontal pocket & infected root canal2. Brain Heart Infusion broth ( BHI )3. Reagents for gram’s and negative staining .4. Clean glass slides

Procedure:

1. Inoculate the collected specimen in BHI2. Incubate at 37 degrees for 48 hours

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3. Perform Gram’s and negative staining procedures.4. Examine under OIO.5. Record your results and observations.

Observations:

Review Questions:

1. What factors

influence the

initiation &

progression

of periodontal

diseases? __

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

2. What is Vincent’s angina? Ludwig’s angina? ______________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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3. Name the enzymes produced by the members of the oral microbial flora? ______

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

4. Why is BHI commonly used in culturing root canal specimen? _______________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

5. What is the microbiota of an infected root canal? ___________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

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Exercise No. ______The Study of Fungi

Mycology is the study of fungi which are non-photosynthetic microorganisms that grow typically in filaments and reproduce by sporulation. Example of this group of organisms would include the lichens, mushrooms, toadstools, puffballs and the microscopic plants known as molds and yeast. Some of them have evolved into true pathogens and are able to actively infect, cause harm and be transmitted from one suitable host to another.

Infections caused by fungi is known as mycoses. The types of clinical mycoses could be divided into cutaneous, subcutaneous & systemic. These different types of fungi that are clinically significant could be acquired from soil or are opportunistic normal flora of the body.

Objectives:

1. To study the microscopic appearance of a common fungi.

2. To enumerate the cultural characteristics and mode of reproduction of fungi

Materials:

1. An old piece of bread2. Hand lens3. Clean glass slide

Procedure:

1. Moisten a little piece of old bread and incubate2. Study the bread from the incubator.3. With the hand lens, examine the bread and identify the colonies.4. Prepare a wet mount using the fresh state, and focus under the microscope.5. Draw and label all parts observed

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Observations:

Review

Questions:

(1) Why are

fungi

considered

plant-like

organism

and yet studied

under

microbiology?

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

(2) Give the different types of mycoses and examples of each: _________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

(3) Name some of the members of the fungi family which are beneficial to

mankind & give their uses: _______________________________________________

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________________________________________________________________________

________________________________________________________________________

________________________________________________________________________

71