Microbiology 2031 Lecture Notes

Microbiology 2031 Lecture Notes in PDF Format

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Laboratory Notebook Procedures

Book: Use graph-lined, sewn composition notebooks (10″ x 7 7/8 “) so that you make a permanent record of your experiments and results. (Avoid glued books.)

Pen Options: Use a permanent black pen with a fine point, such as a Pilot Precise Rolling Ball V5 (my favorite), Tombow Roll Pen, Jr©, or Uni-ball Vision Micro. These are dark black, permanent, and duplicate (reproduce, copy) very well. A pencil or water soluble felt tipped pen are not acceptable. Ball point pens have ink which will dissolve under organic solvents.
Microbiology Page Numbering Illustration
llustration of the common features of all Micro Notebooks

1) Title the inside front cover LAB SCHEDULE. Number the facing page i, and title HANDOUT TABLE OF CONTENTS.
2) Mount the HANDOUTS (LAB SCHEDULE and HANDOUT TABLE OF CONTENTS) as shown. As each protocol is mounted in your notebook, enter its page number on the line provided to the left of its listing. It will look like this after you have referenced the handout pages. (Ready to turn in notebook for grading)
3) Number the next two pages ii, iii and iv. (for Micro, add iv, v and vi.) Title them MY TABLE OF CONTENTS I, II and III. You will mount your own table of contents here later.
4) Then number every right hand page at the top right with odd numbers: 1, 3, 5, etc.
5) If your handout packet contains a Slide List, title page 1 “LIST OF SLIDES.” Mount the list on this page. Label page 2 NOTEBOOK PROCEDURES. Mount those protocols on these pages.
6) Title the inside of the back cover “MY GRADESLIPS“. Mount sequential grade slips here. Title the facing page “NEW WORDSTEMS.” Earn two points by keeping a running table of wordstems given in lecture or lab, but which are not on the handout sheet and typing them up before NB grading.
7) Draw guide lines at lines 1, 3, 6 and 9 along the edge of your closed book.
8) Date each page in the upper left hand corner as soon as you begin an entry on that given page.
9) Title each page IN CAPITALS with a specific focused title between lines 1 & 3.
10) Begin the entries below line 9. Enter all data directly into the lab book. Here is a sample showing date, title, page, cross ref and entries below line 9.
11) Use a fresh page for each experiment . Neatness is of secondary importance, but leave adequate space for ease of future use. Do not tear out any pages.
12) Cross reference pages of related material on line 6 (three spaces below the title). Give the nature of the cross reference: protocol, data, graph, illustration, conclusion, etc. You may cross reference the location of illustrations to the right of the features listed in the protocol.
13) Permanently mount ALL handouts with clear contact paper. Keep intact if at all possible. Mount sequential grade slips inside back cover.
14) Use any excuse for an illustration, since it displays information or data in a manner comprehensible at a glance. (See Notebook Illustrations.) Prevent ink from bleeding through by placing illustrations on the R page, and handouts on the L (or vice versa).
15) For dissections, illustrate: 1) cuts made, 2) spatial & functional relations of organs.
16) For microscopic specimens, illustrate characteristic views to fill at least half a page. Clearly resolve all details observed with labels for all features mentioned in the protocol and/or in Lab. The illustration title goes above, magnification of the view at the lower right. The legend is below, indicating the source, treatment and staining procedure used. Do not hesitate to draw a second illustration to expand on the first.
17) For each new piece of apparatus: illustrate, label and explain all functional features.
18) Color may be added after illustrating with black pen. Use of appropriate color in illustrations can make them more meaningful as well as attractive.
19) Title your graphs precisely, cross reference, label coordinates, note significant phases, especially according to time. Give conditions under which experiment was performed. Show all effects observed, especially according to time or changing conditions. Here is a sample graph.
20) Indent protocols or recipes, leaving space above and below for clarity. Note in detail any changes made in the protocol, difficulties encountered, or future cautions.
21) Draw conclusions, noting the value of the exercise, and, if appropriate, making suggestions for improvement of the experiment. Include in your conclusions not only the “processed” data, but points which could be examined more closely in future experiments and questions which may have arisen as a result of the experiment. For an extra three points, type out your suggestions on a single page, cross reference them to the page of the experiment, and mount them in your notebook.

Compare these instructions with the Sample Notebook Grade Sheets which you have received. Note that points are awarded according to the completeness with which you have followed these instructions. Early effort applied to learning correct notebook procedure will pay dividends when your notebook is graded. (Lab work, as evidenced by your notebook comprises between 25 and 40% of your grade, depending on the course.)

Microbiology 2031

Microbiology 2031

Here are pdfs for lecture notes and lab protocols (please do not reproduce without written permission):
LECTURE NOTES: Here is a directory of informal lecture notes for my course. Please read the paragraph below.**
LABORATORY PROTOCOLS AND HANDOUTS: a directory of lab handouts.
The following protocols have been written by David Fankhauser for his Microbiology Course at the University of Cincinnati Clermont College.
They should not be reproduced without his express written permission. Thank you.

1) Table of Contents
2) Micro 2031 2015 Fall Semester Course Syllabus
3) How to Take a Fankhauser Course
4) Study Groups: Towards Effective Peer Education
5) Study Group Report Form
6) Micro Wordstems I, first half of quarter
7) Micro Wordstems II, second half of quarter
8) Micro Cumulative Wordstems List with meanings

9) Lab Schedule for Microbiology 2031, Spring 2015
10) Laboratory Notebook Procedure (Here is a pdf of the handout, 2012) Here is an illustrated page devoted to setting up your Microbiology Lab book.
11) Format for Table of Contents
12) Use of Contact Paper for Mounting Handouts
13) Sample First Notebook Gradesheet from previous year
14) Notebook Illustrations
15) Making Root Beer at Home
15b) Bacterial Colonies on Potato Slices a la Koch
16) Index to Micro Slides
17a) Binocular Microscope: Its Features and Care
17b) Microscope Storage Gradesheet
18a) How to View a Slide
18b) Bacterial Morphology for Microbiology Students
19) Sample Math Problems for Microbiology
20) Use of Oil Immersion Objective
21) Equipment for a Microbiology Workstation
22) Bacteriological Smear and Staining Protocol
23) Buccal Smear
24) Bacterial Flora of Teeth
25) Microbiological Media Preparation
26) Commonly Used Solid Media and Other Common Microbiological Media
27) Other Commonly Used Media for Phage Growth
28) Autoclave Use
29) Bacterial Growth Curve: E coli on various types of liquid media
30) Spectrophotometer Use
31) Graph Construction (Here is a pdf of an example notebook page demonstrating Graph Construction.)
32 & 33) Two sheets of three cycle semi-log paper
34) Preparation of Wet Mount Slide
35) Gram Stain Protocol
36) Milk Fermenters
37) Dilutions with Sample Problems
38) Serial Dilution, Pipetting Practice
39) Displacement Pipetters: Their Care and Use
40) Sterile Technique: Delivery of Liquids by Pipette
41) Spreading Technique for Plating Bacteria
42) Yeast Plate Count Protocol
43) Bacterial Anatomy (on Prepared Slides)
45) Table of Contents, Part 2
46) Lab Schedule for Microbiology 2031, Second half
47) Microbiology Wordstems, Second Half of Quarter
48) Sample Second Note Book Grade Sheet from previous year
49) Agar Overlay Technique
50) Demonstration of Bacterial Growth Inhibition
51) UV Killing of Bacteria
52) Additional Experiments with the UV Killing Assay
53) Hemolytic Streptococcus Detection by Throat Culture
54) Assay for Coliform Contamination in Ambient Water
55) Single Colony Isolation
56) Triple Sugar Iron Agar and Its Use
57) Triple Sugar Iron Agar: Interpretation of Results
58) Pour Plate Technique for Bacterial Enumeration
59) Bacterial Contamination of Milk: Pour Plate Assay
60) Bacterial Contamination of Meat: Pour Plate Assay
61) Meat and Milk Assay Setup
62) Protozoan and Helminth Parasites
63) Protozoan Phyla and Examples (not required for NB)
64) Salmonella Detection
Preparation of Media for Salmonella Detection
66) Coliform in Drinking Water Assay, p 1
67) Coliform in Drinking Water Assay, p 2
68) Preparation of Bacteriophage Stocks
69) Titering of Bacterial Viruses

LINKS: Questions about microbes? Here is a rich resource page of information about microbes at microbes.info

**Here is a directory containing some of my lecture notes in *.pdf form. Note that they are outline form, and informal. If you see errors in them please let me know. Even with these notes printed out, I urge students to take their own detailed notes in class for several reasons. First, the act of writing is very important in creating a long term memory in your brain. Second, my lecture notes are only guidelines for my lectures. My students soon recognize that I often go on a tangent which may not be in my prepared notes. Third, when you review your own handwritten notes, you will see areas which are not clear, and provide you an opportunity to clarify the question at the beginning of the next class.

And here is the directory of *pdf files of my Microbiology Lab protocols.

The following are pages which contain links to web images related to lectures presented.

The History of Microbiology
The History of the Germ Theory of Disease.
Essentials of microscopy and staining.
Prokaryotic Anatomy
Enzymology and Metabolism
Microbial Fermentation (Part of previous page…)
Requirements for Microbial Growth and Media
Control of Microbial Growth, Physical Means
Control of Microbial Growth, Chemical Means
Microbial Genetics
Microbial Taxonomy
Staphylococci and Streptococci
Spore Forming Bacteria
Gram Negative Rods and Cocci
Mycoplasmas, Rickettsias, Chlamydias, Spirochetes, Vibrios
Mammalian Pathogenic Viruses
Disease Processes
Non-specific Defences

Here is a page of illustrations related to the history of microbiology.

Microwave Popcorn, Home Made

My love of popcorn goes way back to my earliest childhood when my mother would make great bowls full on a weekend night when we lived in a garage… We owe a debt of gratitude to native Americans for this marvelous technological advance they made. I believe popcorn is one of the wonder foods for the following reasons:

The Wonders of Popcorn

  1. It is a whole grain, easily grown in substantial quantities.
  2. It contains the roughage often removed from processed grains. It also contains the same rich protein (though low in lysine, see “complimentary protein”), B complex vitamins and vitamin E of all whole grains.
  3. It is a live food, and sustains itself quite well for long storage periods.
  4. It has a very long storage period which makes it perfect for those who want to have a long-term well stocked pantry, or who are survivalists, or are awaiting the collapse of civilization…
  5. It is embarrassingly inexpensive, especially when bought in bulk (I typically buy a 40 pound bag at a time). I immediately house it in large air-tight containers such as gallon milk jugs, etc. Air-tight is extremely important so that the kernels do not lose moisture and therefore popping ability.
  6. It is DELICIOUS as well as nutritious.
  7. And now, it is SO easy to whip up a bowlful in five minute any or every evening you desire.

Problems with Commercial Microwave Popcorn
Commercial microwave popcorn may be convenient, but you probably know the problems with it:

  1. It contains LARGE amounts of hydrogenated fats. You have noticed the thick grease after you eat a bag… (Look it up if you don’t know the problem with hydrogenated oils.)
  2. It contains artificial flavoring (notably diacetyl: so-called “butter-flavor… This is associated with popcorn workers lung disease) and artificial colors.
  3. It contains much more salt than one might desire (200-355 mg/bag), and you cannot control the quantity.
  4. It costs three to four times what it would cost if you made your own as below. (How much more DOES it cost? I haven’t bought it for so long, I have no idea.)
  5. It generates waste in the form of an oily heavy bag which remains after you have made it.

I am delighted to have devised the following “appropriate technology” for making microwave popcorn at home and believe that many will find it useful. What do you think?


Microbiology 2031 Lab Handouts Directory

Microbiology 2031 Lab Handouts Directory









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Bacterial Colonies on Potato Slices a la Koch

Bacterial Colonies on Potato Slices a la Koch

Robert Koch is famous for being the first scientist to conclusively identify the etiological agent of any disease (anthrax in this instance). He established a set of criteria which must be satisfied in order to do this, called “Koch’s Postulates.” They are:

1) All diseased animals must display the putative pathogen.
2) The putative pathogen must be isolated in pure culture.
3) The pure culture, when inoculated into a healthy animal, must cause the disease.
4) The putative pathogen must be reisolated from the experimentally diseased animal.

The major challenge in these criteria is to isolate “the putative pathogen” (bacterium) in pure culture. Koch was familiar with the work of Joseph Schroeter, who observed that the surface of a potato slice would develop small colored raised circular spots when left open to the air. Koch reasoned that each of these raised spots must have arisen from a single contaminating cell. As it multiplied, the single cell produced a visible clone of identical cells (a colony) .

He realized that these colonies were pure cultures (clones) of bacteria because each arose from a single cell.

Fortuitously, Bacillus anthracis, the etiological agent of anthrax, was able to grow on potato, and would yield a pure culture by which he was able to satisfy his postulates.


sterile petri dishes, one per two students
clean cutting board
sharp paring knife
Bunsen burner
tweezers in an EtOH beaker
37°C incubator


95% ethanol in a deep beaker
cooked potatoes (not too soft)
Q tips

1) Pre experiment (understand the experiment and lay it out!):

a) Cross reference in your Notebook the protocol you are following.
b) Describe the specimen with which you are going to inoculate your potato.
c) Label your petri dish in small letters ar the edge of the plate:
i) your initials
ii) the date
iii) the specimen being tested.


2) Sterilize a paring knife by dipping into 95% EtOH, shake off the excess, then briefly flame to burn off the alcohol.


3) Slice a cooked potato about 1/4 inch thick and, using tweezers dipped to sterilize in EtOH and flamed to remove excess EtOH, place the slice on the bottom of a sterile petri dish.


4) Inoculate the surface of the potato with a sample of your choice: wipe a finger across it, lick it, swab the floor with a Q tip, sample your nose with a Q tip, (or pick your nose and wash afterwards…), or leave open to the air for several minutes, etc
Place in 37 C incubator

Petri dish going in an incubator

5) Cover the Petri dish and place in the 37°C incubator in your assigned spot according to your seat number.


6) Incubate for 48 hours, and examine the surface of the potato for any growth.


7) Describe the colonies which appear, and, time permitting, smear and stain to see their morphology. Illustrate what it looks like. Then, if you like, take a picture?

Additional images of incubated plates:


Gallery of Micrographs

Gallery of Micrographs of Prepared Slides of Microbes


Bacterial Capsules:

Clostridium botulinum

Clostridium tetani

Giardia lamblia

Mycobacterium tuberculosis

Neisseria gonorrhoeae

Plasmodium vivax

Bacterial flagella

Rhizobium leguminosarum

Rhodospirillum rubrum

Staphylococcus aureus

Trichinella spiralis

Trichomonas vaginalis

Trypanosoma gambiense

Directory of Microbiology Illustrations

Directory of Microbiology Illustrations


Rennet, Home Made, Illustrated

Here are the results of an experiment at producing home made rennet.

Rennin is an enzyme which, in an acid environment, digests the water soluble milk protein casein into insoluble products. When these precipitate out of solution, the milk coagulates. The test is the famous “clean break” of cheese making.

Here, the abomasum of a suckling kid was cleaned, salted and dried. A small piece (0.75 gm) of it was suspended in warm water (30 C), and added to 1 gallon of inoculated milk. While a clean break was not achieved in three hours, by the evening (about 7 hours) the milk had formed a very firm coagulant.

This is my first attempt at using home made rennet.  I am sure that the process and conditions can be improved.  Let me know if you have suggestions.

See the bottom of the page for suggestions from Mr. Wolfgang Pachschwöll, of “Hundsbichler company Austria – producer of natural rennet.”

Here are some points of expert advice on making rennet from Wolfgang Pachschwöll of “Hundsbichler company Austria – producer of natural rennet”, sent in response to my initial posting of this page. (Thank you very much Wolfgang!)

1) Do not thoroughly clean out the inside of the abomasum. The “slime” inside contains rennin. Therefore, also no washing nor squeezing.

2) Lightly salt the abomasum, store undried with 30% salt in a closed container to activate the enzyme over three months. (Pepsin, another stomach enzyme, is also secreted in the inactive form (pemsinogen), and activated by acid or enzymatic action.)

3) The traditional way to then dry the abomasum is to inflate it like a balloon and dry by hanging in a cool dark place.

4) Dissolving and activation of rennin occurs best in acid conditions at a cool temperature.



Saccharomyces cerevisiae
Saccharomyces cerevisiae (Brewer’s yeast–well… if not a mushroom, it is a fungus…)

Hmmm… NOT Chicken of the Woods… I think it is probably Pleurotus ostreatus.

Chlorophyllum molybdites (Poisonous when eaten raw. Take my word for it…)

Chlorophyllum molybdites
Chlorophyllum molybdites

Coprinus comatus (Shaggy Mane)

Coprinus micaceus

Ustilago maydis (Corn Smut) A delicacy to many Mexicans, here prepares as a stuffing for quesidillas.

Lepiota Americana 

Morchella esculanta and its spores

Morchella semilibera (Semifree Morels)

Pleurotus ostreatus (Oyster mushroom)

Pleuteus sp.

Polyporus squamousus (I call it “Black leg”)

Calvatea gigantia (Giant puffball, and its spores.)

Hmmm… who knows what this one is???

Auricularia auricula (Wood Ears–used in Oriental soups, etc.  Its consumption may be linked with low coronary disease rate in China!))