BIMM121 – Spring 2021
Pre-lab: Jove video
In this pre-lab you will learn the importance of some of the microbiology techniques that are
routinely used by governmental agencies, such as the Food and Drug Administration (FDA)
and the Environmental and Protection Agency (EPA), to test food and water that are used for
human consumption. The largest source of potentially pathogenic microbes is fecal material
from domestic and farm animals as well as humans, since animals harbor the highest
diversity of microorganisms in their intestines, and that is daily shed in feces. That fecal
material can be easily distributed to a large number of individuals through water (via the
fecal-oral route), thus, increasing the danger of such polluting events.
Government agencies cannot test for each individual pathogen, however, they test for
indicator organisms whose presence indicates water unfit for human consumption and
possible pathogens.
1. Watch “Isolation of fecal bacteria from water samples by filtration”:
You may have to create an account by signing in with your UCSD Google credentials or
Before lab:
• Watch the Jove video “Isolation of fecal bacteria from water samples by filtration”
• Come up with 2 questions or things you didn’t understand in the video, and write about
them in your notebook (NB1)
• Answer NB2
During lab:
Jove video discussion:
• In your group, discuss your questions from NB1 & NB2
• Share the answer to NB1 & NB2 within your group and answer NB3
Simulation lab:
• Watch the ‘bacteria sampling’ simulation lab and answer NB4
• Watch the ‘Gram staining’ simulation lab and answer NB5 & NB6
• Watch the ‘under the microscope’ simulation lab and answer NB7 & NB8
• Discuss your answers with the whole group
©UC San Diego, do not copy or distribute without permission 1
BIMM121 – Spring 2021
access the link via UCSD Easy Connect VPN (
To access the video with your UCSD Google credentials: 1) click on the Jove video link; 2)
click on ’sign in’ on the top right of the Jove video window 3) sign in with Google by using
your UCSD Google credentials (you will see the ‘G’ Google icon and ‘Sign in’ at the bottom
of the pop up sign in window). More details can be found in Canvas > Week 7.
This Jove video covers some of the techniques that are used to detect indicator organisms,
such as coliform and fecal coliforms. Coliforms are organisms that are inhabitants of the
animal gut (the word coli comes from Latin and means colon, large intestine), are classified
as Gram negative rods, ferment lactose and produce acids and gas in presence of bile. To
be classified as fecal coliform, a coliform must also be able to grow at 44oC and ferment
lactose, producing a high amount of acids and gas. E. coli, the most common indicator
fecal coliform, can also produce a metallic – green sheen or blue color on specific selective
If there are words or terms you do not recognize while watching the video (you will learn
names of different media, tests, and microbial species/genera), use outside sources to look
them up. It is ok if you do not understand everything described in the video, in fact, that will
help you with your pre-lab notebook assignment:
NB1: Come up with two questions or things you didn’t understand in the video, and
write about them in your notebook.
NB2: Based on what you learned through the Jove video, list two reasons why
you think a fecal coliform as E. coli is commonly used as indicator organism when
assessing quality of food or water. (List them in your notebook).
During lab: Jove Video Discussion
1. Starting with the manager, share one of your questions or confusing points of the video with
the group. If someone in the group thinks she knows the answer or has an opinion, she should
offer it! Otherwise, work together as a group to try to figure it out (you can use outside sources
to find out). Once you think you have a satisfactory explanation, you can move on to the next
person. If you have a question, use the ‘ask for help button’ and an IA or the instructor will
come to your room (but it may not be right away – so move on to the next question in the
2. Once everyone has had a chance to ask one question and discuss it with the group, take a
moment to record the answer to one of your questions in your notebook.
©UC San Diego, do not copy or distribute without permission 2
BIMM121 – Spring 2021
o NB3: record the answer, in your own words, to one of the questions you had written
in your notebook.
During lab: Simulation Lab
In lab today you will do three simulation labs (in this order): 1) bacteria sampling, 2) Gram
staining, 3) using the microscope. They can be found here:
Since this is a brand – new simulation lab developed in Beta, it might have glitches. Please wait
until the narrating voice has finished talking before clicking ‘continue’. If you see other boxes,
such as ‘info’ or ‘photo’, wait until the narrating voice has finished talking and then click on
them. Do not click on the video at the bottom of the screen, you want to actively do the
simulation, not just passively watch the video.
1. Individually start the “bacteria sampling” simulation lab (click ‘Continue’). You will learn
what type of routine microbiological tests are performed in a milk plant to test for
contamination. Do not click on the video at the bottom of the screen, you want to
actively do the simulation, not just passively watch the video.
After doing the simulation, answer the following question in your notebook. You may discuss
the answer with your teammates.
NB4. In the ‘bacteria sampling’ simulation, you learned how 3M Petrifilm coliform count
plates can be used to identify coliforms that may be present in contaminated milk
samples. Using outside sources, identify how coliforms are isolated and identified on
Petrifilm plates.
2. Individually start the “Gram staining” simulation lab (you can access it from the Virtual lab
banner on top of the screen). You will learn how to manually perform a Gram stain and its
significance as a routine microbiological test to identify contamination in yogurt. Do not
©UC San Diego, do not copy or distribute without permission 3
BIMM121 – Spring 2021
click on the video at the bottom of the screen, you want to actively do the simulation,
not just passively watch the video.
After doing the simulation, answer the following questions in your notebook. You may discuss
the answers with your teammates.
NB5. In the Gram stain simulation, you learned how air bubbles toward the bottom of a
yogurt bottle may indicate a sign of contamination. Based on what you know about the
common lactic acid bacteria used for yogurt production and their metabolism, explain why
you do not expect air bubbles production by those microbes.
NB6. At the end of the Gram stain simulation you learned how this technique is a starting
point to look for contamination. We can do further tests to figure out the species that
contaminated a yogurt sample. Considering the culture-dependent and cultureindependent methods that we have learned in this course so far, list at least two specific
techniques per each of those methods.
3. Individually start the “under the microscope” simulation lab. You will learn how to manually
use a bright field microscope to observe the slides prepared in the previous simulation. Do
not click on the video at the bottom of the screen, you want to actively do the
simulation, not just passively watch the video.
After doing the simulation, answer the following questions in your notebook. You may discuss
the answer with your teammates.
NB7. In the ‘under the microscope’ simulation, you learned how we use immersion oil with
the 100X objective lens. Why is immersion oil necessary at this point? Why is 100X the
only objective lens that requires oil?
NB8. When all team members have completed the simulation labs, starting with the
manager, discuss two things that you have learned during this whole lab (including the
pre-lab) that have surprised you.
4. Return to the main room for discussion. The reporter should be prepared to share your
group’s answers with the class.
©UC San Diego, do not copy or distribute without permission 4

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