General Microbiology Lab Briefing

Exercise 13:  Testing Disinfectants

• View the comic in Vancko Hall.
• Work in teams of three students.
• Each student prepares a lawn of differenct bacteria on the surface of a plate of agar following the directions. The bacteria are:
  • E. coli, Staphylococcus aureus, Salmonella sp.
• Then follow the directions and test the same set of disinfectants on each plate.
• Plates are then incubated at 37 degrees C for 48 hours and the zone of inhibition is measured to determine which worked the best against which bacterium.

Exercise 15:  Identification of Gram Negative Bacteria

• Work in groups.  Each lab will have 6 groups because we are using 6 species of bacteria:
  • E. coli
  • Enterobacter aerogenes
  • Alcaligenes faecalis
  • Salmonella sp.
  • Proteus vulgaris
  • Pseudomonas aeruginosa
    
• One of the most important things is to GET ORGANIZED — pick a person to keep a check-list of media and to be sure that all tubes are inoculated.
  • Be sure that all tubes are labeled in such a way that if the person doing the labeling is absent for the return lab, other members of the group can identify the tubes as to bacterium and type of medium.
• Each group will get a known gram negative bacterial culture and an unknown gram negative bacterial culture.
  • BE SURE TO RECORD THE NUMBER OR LETTER OF THE UNKNOWN.
• Then you will inoculate TWO sets of microbiological media:  one set with the known and the other with the unknown.
• Your inoculated cultures will be incubated for 48 hours and then you will collect results for your known and unknown.
• Basically you are looking for products of reactions that indicate the bacteria were able to utilize the substrate, i.e. sugar or amino acid, given them in the medium.
  • Sometimes you just look at the tube for a color change; for some media you must add reagents.
• Results of the knowns will be shared so that you can try and figure out what your unknown was.
• Media will include the following:
  • OF glucose — agar deeps (one with air and one shielded from air)
  • Fermentation Broths with phenol red containing sugars:
    • Glucose
    • Lactose
    • Sucrose
  • MR-VP Medium — a broth
  • Simmons Citrate Agar slants
  • Urea Broth
  • Phenylalanine agar slants
  • SIM medium (semi-solid agar deeps)
  • Nitrate broth

Exercise 12:  Determining the Number of Bacteria in Food

For this exercise you will work in a team to determine the number of bacteria per gram of hamburger.  Half of the teams will have meat that has been left out at room temperature for a number of hours and the other half will have meat that has been continuously refrigerated.  We will compare the results of the two teams for the return lab.

We are using the pour plate technique to mix a known portion of the food with agar, letting it incubate, and counting the number of resulting colonies.  This will give you an estimate of the number of bacteria in a gram of the food.

Dilution

• Mixing a gram of hamburger with agar will result in a huge number of colonies — clearly more than you can count.  A plate with more than 300 colonies is considered (and reported as) Too Numerous to Count (or TNTC).
  • Note that a plate with less than 30 colonies is considered Too Few to Count (TFTC).
• Sooo the hamburger must be diluted and then the dilution is placed in the agar.
• You are going to doing three dilutions with the hamburger:
  • 20 in 180 or 20/200 = 1 to 10 (or 1/10 or 1:10 or 0.1)
  • then that will be diluted 1 in 99 = 1 to 100 (or 1/100 or 1:100 or 0.01)  [total dilution 1/10 and 1/100 = 1/1,000]
  • and that will be diluted 1 in 99 = 1 to 100 (or 1/100 or 1:100 or 0.01)  [total dilution 1/1000 and 1/100 = 1/100,000]
• We’ll go over this at the start of lab.

Pour Plate

• You will be placing known quantities of your dilutions in empty sterile petri dishes.
  • We are duplicating everything this week.  [Why is replication necessary and important?]
• Then mixing sterile melted agar with your dilution in the plate, allowing it to solidify, and then incubating it at 37 degrees C for 48 hours.

Determining the Number of Bacteria:

• For the return lab you will count the number of colonies on those plates that can be accurately counted:
• those containing between 30 and 300 colonies.
• Then you will calculate the number of bacteria per gram of meat by the following formula:
  • # bacteria/gram = # colonies x 1/mL plated x 1/dilution plated

COME TO LAB PREPARED BY CAREFULLY READING THE LAB AND THIS BRIEFING!!!

There is NO Lab Quiz this week.  HOWEVER — there is a set of questions on dilutions that is due on your return lab on Wednesday or Thursday!!!  NO LATE ASSIGNMENTS WILL BE ACCEPTED WITHOUT A DOCTOR’S EXCUSE!!!!!  It is posted in Vancko Hall.

Start Morphological Unknowns! (Exercise 11)

The Setup

• You each get a tube with a mixed broth culture. Be sure to record your number.
• Each contains a mixture of 2 bacterial species which are visibly different either in shape, gram stain characteristics, or both.

Your Task (document everything with notes and drawings)

• Isolate each bacterial species by growing them on trypticase soy agar.
• Determine the following for each species:
  • Their colony characteristics.
  • Their shape and arrangement of cells.
  • Their gram stain characteristics.
  • Their motility.
• Document each of these characteristics with digital drawings or pictures.
• Write up your report and hand it in on time.
• You will have until Friday March 20 to work on your unknowns.
• Your report is due at the start of your lab session on Tuesday March 24th.

Day 1

• Isolate:  2 streak plates — one incubated at 37 degrees C, the other at 25 degrees C.
• Characterize from the broth cultures:
  • Motility — hanging drop or wet mount
  • Gram stain — prepare at least two slides for gram stains of you unknown.

Day 2

• Examine plates for isolated colonies (ideally with 2 different appearances).
  • Take a digital picture of your plate.
  • If you failed in your isolation attempt you may do one additional streak plate (that’s all, just one more).
  • If you do an additional plate it is your responsibility to incubate the plate and to remove it from the incubator.  Do not leave plates at 37 degrees C for more than 48 hours — they will dry out.  At least come in and put your plate in the refrigerator.
• Confirm isolation by doing a gram stain from each colony.
  • Don’t forget that a control (mixture of Gram + and Gram -) must be done with each and every gram stain.
• Negative stain if you didn’t do it on Day 1.

Due Dates etc.

• You have two weeks to complete your unknown project:
  • Both labs this week and one hour of the first lab next week.
  • You may come in on your own time to work on it until Friday October 30
• Your final paper (both digital and paper copies) is due before the start of your lab on Monday Nov. 2 or Tuesday Nov. 3rd (depending upon the date of your first lab of the week).
• The instructions for your paper are posted on the Lab Briefing Blog and there are sample papers posted in  lab.
  • NOTE:  do not go through the steps of the different stains and other procedures — just say that you did them and that you used aseptic technique throughout!

Continue Staining!

Even if you have completed all of your stains you still must attend lab.

Your instructor will check your drawings and your slides before you can leave lab.

1. You must save the reference slides that you made.
2. You might want to clean a few more slides in preparation for next week’s lab.  [I noticed that in my lab some of the negative stains tended to "puddle up" a bit too much which indicates that the slides were not clean enough.]

Next week it is Project 1:  Morphological Unknowns!   Be Prepared!

Exercise 9:  Staining Bacteria

We use three staining techniques in General Microbiology:

1. Simple Stain — uses one stain and all bacteria are the color of the stain.  Is not a differential stain.
   • Preparation of the specimen is the same as for the Gram Stain except that a control is not necessary because this is not a differential stain.  [Any technique that is differential distinguishes between two or more types of bacteria.]
2. Gram Stain — uses four reagents and results in distinguishing between bacteria with two types of cell wall structures (gram positive and gram negative).  This is a differential staining technique.
   • The preparation is the same as for the simple stain except that a known gram positive and gram negative are used as controls.
   • The control:  the control is a mixture of Gram + and Gram – bacteria of two shapes.
     • We use Staphylococcus aureus which is a Gram + spherical-shaped (coccoid) bacterium and Escherichia coli [E. coli] which is a Gram - rod-shaped (bacillus) bacterium.
     • Since we use bacteria of different shapes we can mix the two controls and do not have to do a separate + and - control.
   • Cells that are Gram + are purple and those that are Gram - are red (or pink).
3. Negative Stain — uses one stain (Congo Red) which has a negative charge and does not adhere to the negatively charged cells.
   • The background is stained, not the bacterium.  Hence if you use a black stain it looks like a photographic negative.  We don’t use a black stain, we use Congo Red, which is red because it works much better than Nigrosin which is a black negative stain.
     • NO HEAT is applied in the preparation of this stain.  Therefore the cells appear more “natural” — more their normal size and shape.
     • However, this means that they may still be viable and must be treated as such.  All slides with negative stain are disposed of in disinfectant and will be sterilized and recycled for your use.
     • NOTE that for the simple and gram stain, since the specimens are killed by heat fixing they are not to be discarded in the disinfectant.  You may keep them in your slide boxes OR you may clean and reuse them.  If you are going to discard the slides do so in the glass discard barrel NOT in the buckets under the hood.

All stained slides are to be viewed at 1000x total magnification.  Lower magnifications are not sufficient to really see and describe the bacteria accurately.

Oil is applied directly to the dry stained slide.  No cover slip is used.

BE SURE TO READ THE COMIC BOOK ON STAINING — IT GOES THOUGH THE PROCEDURE IN DETAIL.

Practice is the key to successful staining technique.

In lab do these stains:

1. One simple stain
2. One negative stain
3. The following gram stains

• Do a gram stain from your thioglycollate broth from the soil lab. What do you expect to see here?
• Create reference slides (slides you will keep to refer to as you do your unknown) of the following:
  • Staphylococcus [gram + cocci in clusters]
  • Micrococcus luteus [gram + cocci in a sarcinate arrangement]
  • Streptococcus faecalis [gram + cocci in a string; note these sometimes look like slightly elongated cocci]
  • Bacillus subtilis or B. megaterium (whichever one we have out)
    • fairly large gram + rods; can form endospores
    • older cultures of Bacillus can sometimes be “gram variable” which means that some will look gram negative.
  • Eschericia coli (E. coli) [gram - rods]
  • Salmonella sp. [The "sp." means "species" -- I'm not sure what species we have.]  [gram - rods]

  Save your reference slides by dabbing off the oil and placing them in your blue slide box.

• Remember that for each and every gram stain you do, you must include a control mixture.
  • If you wish you can fit three samples on 1 slide:  one control and two other kinds of bacteria in each of two other circles.
  • Exercise 10 Isolation of Bacteria

Exercise 10 Isolation of Bacteria

In order to isolate bacteria you must spread the sample so thinnly that it separates individual cells which can then grow into visible colonies.   This is done in order to make a pure culture which can then be used for identification of the bacteiral species that is isolated.  [See Koch's postulates for the importance of this procedure.]

We use the “Streak Plate Technqiue”.

READ THE COMIC BOOK AS WELL AS YOUR LAB BOOK FOR THIS TECHNIQUE.

Each student will be doing two streak plates using a mixed culture that we provide:

1. One on a general-purpose medium:  Trypticase Soy Agar (TSA)
2. One on a selective medium  [Be sure you know what this means.]
   • Mannitol Salt Agar (MSA)*
   • Eosin Methyleneblue Agar (EMB)*
   • Phenylethylalcohol Agar (PEA)

• *These are also differential media.

These plates will be incubated for 48 hours at 37 degrees C and evaluated in the comeback lab period.

Aseptic technqiue is crutial in this process!  Review your aseptic technqiue.

Be sure to follow the directions exactly.

For what these media are used for and their ingredience see the lab book and the microbiological media information sheet in Vancko Hall.

Exercise 7 — Microbiological Media and  Aseptic Technique

Microbiological media comes in three forms:  broth (liquid), semisolid agar, and agar (solid)

• Trypicase soy broth and agar are the nutritionally the same; the latter has agar added (15 gm/l) to make it solid.
  • Remember that agar alone has no nutritional value for most bacteria; it is just a solid medium to which nutrients must be added to support bacterial growth.
  • You can find a listing of kinds of media that we use and their composition in the introductory module in Vancko Hall Lab.
• Broth is usually dispensed in tubes and it is what we use for our pure cultures of bacteria.
• Semisolid agar is usually dispensed in “deep” tubes — about 10ml per tube.  It is used for detecting motility.
• Agar may be dispenses in tubes as agar deeps or slants (allowed to cool at an angle so a slanted surface forms) or into plates.

You will take one of three available species of bacteria and aseptically transfer it to one tube of broth, one tube of semisolid agar, and one agar slant.  You are inoculating these sterile media.  The three species are:

• Staphylococcus aureus
• E. coli
• Proteus vulgaris

Aseptic Technique enables you to safely transfer bacteria from a culture to a sterile medium without contaminating the culture with another bacterium and without contaminating you or your work place.  It is second only to the use of the microscope in importance in microbiology.

Be sure to read the lab book AND the comic book on this laboratory exercise.  You may even find it helpful to print the comic.

Exercise 8 — Isolation of Soil Bacteria

The bacteria found in soil often form resistant structrures called endospores.  These resist drying and other hazards (like oxygen if it is an anerobic organism).

• In this exercise you will heat a soil sample to kill any vegetative (living) cells that are present and presumably leaving on the endospores.
• After heating you will inoculate a tube of specialized medium (thioglycollate medium) which promotes the growth of anaerobes.
• Next week you will stain your soil cultures.

Exercise 5 — Organisms in the Environment.

This exercise is pretty straight forward:

You will sample two environments — your body and any non-body environment.  For each:

• Swab the environment with a sterile swab; if the environmental surface is dry, moisten the swab with sterile water.
• Zig-zag the swab over the surface  of a trypticase soy agar plate.  [Don't forget to label the plate!]
• Then swish the swab in a tube of sterile broth.  [NOTE:  broth is just a liquid medium.]
  • What do you do with the swab?????
• Place the plate in the appropriate bin for incubation:
  • 37 degrees C for the body
  • 25 degrees C for room temperature
• Place both tubes of broth in a test tube rack which will be incubated at 37 degrees C.

Exercise 6 — Hand Washing Experiment

About the Scientific Method:

• All scientific investigations start out with observations.  These may include observations in nature or information from sources such as advertising claims and scientific reports and papers in refereed scientific  journals.
  • Do some background reading before you come to lab!!!!
• Such observations lead to questions that may be answered by good experimental design.  They lead first to objectives of the investigation overall.  For example, in this exercise your objective clearly is to determine the effectiveness of some method [you fill in the method] of hand cleansing.
• From this comes your hypothesis.  The hypothesis is based on observations.  It is a statement of the expected results of your experiment.  [It is not a question.]  It should be stated in a way that it can be affirmed or denied by the experiment you are designing.
• Your experimental design should follow from your hypothesis.
  • It should clearly test the hypothesis.  And must contain a control as well as one or more experimental variables.
  • For example an unwashed hand would be a control for most of your experiments.
  • If you were testing the effectiveness of water temperature you would have cold and hot water washing as your experimental variables.
• Your experiment must be replicated to insure that your results are dependable.
  • In this case each member of your group conduct exactly the same experiment.  That way each person is replicating the experiment.
• Your experimental results must be quantified in some way so that you can calculate a mean (average) of the replicated results!
  • The easiest way to do this is to use a scale of your design which will assign a numerical score (say 0 to 3) to the amount of growth on the agar plate.
• Your results will be “published” in a PowerPoint report!

Practicalities:

• Work in groups.  Four members is ideal.  Three is too few to get good replication and 5 is really too many.
  • Five will be allowed only with approval of your lab instructor and only when there is no other way to formulate groups.
• Each person gets one plate of agar.
• Test methods by lightly pressing a finger on the surface of the agar.
  • You can easily divide a plate into 4 sections:  one a control and one for each variation on a method.  [For example, time would be 1 minutes, 5 minutes, 10 minutes, 15 minutes.]
  • Remember that each person does exactly the same thing.
• Don’t overlap variables.  For example:  washing both hands with cold water, testing, then washing with hot water and testing is examining the effect of double washing not the differences between the two!
  • You can remedy this by using different fingers for different treatments OR by recontaminating your hands between treatments.
• All plates will be incubated at 37 degrees C for approximately 48 hours.
• Results will be collected and pictures taken of plates during the return lab.
  • Note the computer int he lab has a digital camera attached or you can use your own cameras.
• Completed reports will be  in one week — the date depending upon the date of Exam 1 to avoid having the exam and the reports due on the same day.
  • Reports will include PowerPoint with narration and a written abstract.  [Instructions on Vancko Hall.]

Here’s a presentation (no voice) on the fungi we’re looking at in lab this week:

Exercise 3:  Kingdom Myceteae

Be sure to view the sort on-line lecture on the fungi in Vancko Hall Laboratory.  This will be a short introduction to the group since I won’t be getting to it in lecture before you have lab.

You will be examining fungi that are unicellular (yeasts) as well as those that are filamentous (molds).

Filamentous Fungi — Three representative genera are Penicillium, Rhizopus, and Aspergillus.

• View and draw these as they appear in an agar plate of Sabauroud Dextrose Agar.  Do not open the petri dishes — spores will escape and contaminate everything for the rest of the semester!!!!!
• View and draw them from a prepared slide that contains all three genera.  They are located on the slide in the order they are listed on the label.  View:
  • Aspergillus and Rhizopus at 100x
  • Penicillium at 400x
• The spores you see are asexual spores — either conidiospores or sporangiospores depending upon the genus.

Yeast:

• View yeast of two genera — make wet mounts — Candida (opportunistic pathogen) and Saccharomyces (bread and brewing yeast).
• Make a wet mount of my sourdough “sponge”.
  • A sponge is a culture of yeast (and in this case bacteria).
  • You will see abundant yeast and small rod-shaped bacteria between the cells of yeast.  The yeast breakdown carbohydrates and produce alcohol and the bacteria (Lactobacillus ) produce acid from the alcohol.  Hence the sour taste of sourdough bread!
• Try to culture some yeast from your tongue.  Follow directions in your lab book.  We’ll incubate them at 37 degrees C and you’ll check them on Thursday and maybe into next week.

Exercise 4:  Helminths (Multicellular Parasites)

Be sure to view the online lecture on Helminths in Vancko Hall — lecture section.

You will be looking at and drawing the following:

Here is the table from Microbiology Perspectives by Wistreich.  [Note this book will be very handy this week so if you have it, bring it to lab.]

• Cestodes (tape worms)
  • Slides:
    • Scolex and immature proglottids
    • Gravid proglottids
  • Whole or part tapeworms in bioplastic
• Trematodes (flukes):
  • Slides:
    • Chinese liver fluke (Clinorchis senensis) [I took invertebrate zoology with my fiance and we were going to name our first son Clinorchis -- good thing we never had kids, huh?]
      • Whole mount (w.m.)
      • Ova (eggs)
  • Sheep liver fluke (Fasciola hepatica)
    • These you do not need to look at because they are in the pictures on the diagram above.  They include:
      • cercarium
      • metacercarium
      • miracidium
  • Blood fluke (Schistosoma japonicum)
    • male
    • female
    • eggs
  • Also various whole flukes in bioplastic or other preservative.
• Nematodes (roundworms)
  • Trichinella spiralis slides:
    • muscle section
    • isolated larvae

This week we’re doing Exercise 2:  The Kingdom Protista

• Be sure to read the introductory portion of the lab book for this lab before you come to lab.  It is also a good idea to review the lecture information that we have gone over.  [NOTE that the Protista lecture (with pictures) is posted in the lecture portion of Vancko Hall.]
• The Protista consists of two subkingdoms:  Algae and Protozoa
• Be sure to draw and label your drawings.  Also include a brief description of what you see.

Here is what you’ll be looking at of the Protozoa

• Live Cultures of the following — all can be easily viewed at 100x and 400x (draw them at either magnification):
  • Paramecium — these are kind of speedy you may want to slow them down with some Protoslo solution — a drop of it on your slide then some of the culture.
  • Amoeba — your instructor may need to fish these out for you — they are a bit hard to capture with a pipet because they are kind of sparse in the culture.
  • Vorticella – a stalked ciliated protozoan that looks like a wine goblet!  The cilia create a vortex or mini-whorlpool that draws the bacteria in the water toward the gullet.
  • NOTE:  be sure to view the live protozoans in your first lab — they probably will not live to Wednesday or Thursday!
• Prepared slides of
  • Trichomonas vaginalis — causes an STD.  These are small and are stained pink or lavender. [400x]
  • Trypanosoma – are hemoparasites causing sleeping sickness.  So this is a blood slide — best viewed at 1,000x.  The parasites look kind of like worms between the red blood cells. Why are they wavy on one side? What is that called?
    • Be sure to listen to the podcast on Trypanosoma available in Vancko Hall lecture section.
  • Paramecium – 100x or 400x.
  • Amoeba – 100x or 400x — the colors are due to stains that have been used in the preparation of the slides.
  • For all of these make a note about what group of Protozoa they belong to — Mastigophora, Sarcodina, Ciliata, or Apicomplexa!

Algae:

• Live cultures of (mostly can be viewed at 100x but for some you may need 400x):
  • Closterium – a green alga that looks like a green cigar or new moon (some will have a curve to them).
  • Spirogyra - a filamenouts green alga with a spiral-shaped chloroplast.
  • Variety of live algae from various habitats.  I’ll let you know where from after I collect them!
• Prepared slides of (100x and 400x):
  • Volvox
  • Various diatoms — these are slides I prepared for my master’s degree work on a small stream.  I’ll include my thesis so you can look at the pictures of these as well.
    • What you are looking for are regular shapes — round or lancet shaped usually.  These have been “cleaned” so all you are seeing is their silica cell walls.

Cyanobacteria:

• I include the Cyanobacteria here because they are metabolically similar to the algae because they generate oxygen during the light reactions of photosynthesis.  In addition they are found in aquatic habitats like the algae.  They also tend to be green(ish) — actually they are sometimes called “Bluegreen Algae”.  They contain chlorophyll a and a red pigment (phycoerythrin) and a blue pigment (phycocyanin).  Note that they do not have any internal structure (no chloroplasts).  For this reason they are classified with the bacteria.
• Live cultures of
  • Oscillatoria (400x)
  • There may be some Cyanobacteria in the mixed cultures from streams or ponds.
• Prepared slides of
  • Oscillatoria (400x)

  For more information on Cyanobacteria see this website:  http://www.ucmp.berkeley.edu/bacteria/cyanolh.html