Bacteria and Microfluidics

Overview: This seven day unit of study introduces seventh grade students to scientific research in the study of bacteria. Over the course of seven days students conduct research, experiment with live bacteria, and come to conclusions about how scientists may apply this study to solve real life problems.

Lesson Outline:

Day 1: Bacteria Research

  1. Show students a series of magnified bacteria. What are you looking at?
  2. Provide each student with the Bacteria Anticipation Guide. This is a pre-assessment. It will be given again at the conclusion of the unit.
  3. Before









    1.       It is easy to see bacteria.





    2.      All bacteria are dangerous.





    3.      Bacteria are found in healthy plants and animals.





    4.      Bacteria are alive.





    5.      Bacteria are found everywhere.





    6.      Bacteria are helpful for humans.





    7.      Bacteria can move.





    8.      I know how a microfluidic device works.





    9.      I know how a scientist might do an experiment to identify bacteria.





    10.  I am comfortable working in a science laboratory using science materials.





    11.  I think science is fun.


  4. When students are finished have them copy the Bacteria Frayer Model into their science notebooks.
  5.  bacteria

  6. Provide students multiple reading level appropriate texts to help them complete the Frayer model.

Bibliography of Student Research Texts:

Biskup, Agnieszka. The Surprising World of Bacteria with Max Axiom. Seattle, WA: Captstone Press, 2010. Bacteria. Milwaukee, WI: Gareth Stevens Pub., 2004. Print.

"Bacteria Rule!" National Geographic World Oct. 2000: 23. Ebscohost. Web.

de la Bedoyere, Guy. The Discovery of Penicillin. Pleasantvill, NY: World Almanac Library, 2006.

Favor, Lesli J. Bacteria. New York: Rosen Pub. Group, 2004. Print.

Facklam, Howard and Margery. Bacteria. New York: Twenty-First Century Books, 1994.

Friedman, B. Ellen. Bacteria. Mankato, MN: Creative Education, 1997. Print.

Goldsmith, Connie. Superbugs Strike Back. Minneapolis, MN: Twenty-First Century Books, 2007.

"It's Alive!" SuperScience Mar. 2001: 4-5. Ebscohost. Web.

Latta, Sara L., and Dennis Kunkel. The Good, the Bad, the Slimy: The Secret Life of Microbes. Berkeley Heights, NJ: Enslow, 2006. Print.

Levy, Janey. The World of Microbes: Bacteria, Viruses, and Other Microorganisms. New York: Rosen Pub., 2011. Print.

Mueller, Michelle. "Bacteria: The Good, the Bad, and the Itchy." Current Health Sept. 2002: 18. Ebscohost. Web.

Ollhoff, Jim. What Are Germs? Edina, MN: ABDO Pub., 2010. Print.

Snedden, Robert. The Benefits of Bacteria. Chicago, IL: Heinemann Library, 2000. Print.

"The Three Types of Bacteria." Microbiology Mar. 2000: 17. Ebscohost. Web.

Steffoff, Rebecca. The Moneran Kingdom. Tarrytown, NY: Marshall Cavendish Benchmark, 2009.

Wearing, Judy. Bacteria: Staph, Strep, Clostridium, and Other Bacteria. St. Catharines, Ont.: Crabtree Pub., 2010. Print.

Weir, Kirsten. "Uninvited Guests." Current Health Kids Apr.-May 2012: 9-11. Ebscohost. Web.

Day 2: Construction of smart phone microscope stands and Bac Chip sketch

  1. Prepare loose supplies for the construction of microscope stands
  2. Show students the youtube video showing how to construct the microscope stands. We originally found the plans on Link to video:
  3. When video is over, let students work in lab groups to construct a microscope stand at their lab station. When they are done constructing it encourage them to observe multiple different objects. I provided iPads for groups who did not have their own smart phone with camera. We looked at newspapers, maple leaves, and other small objects. d
  4. Distribute Bac Chips on glass slides. Students should sketch the basic structure of the Bac Chip in their notebook.
  5. On Promethean Board show the actual outline of the Bac Chip. Label the different parts. Have students take notes on the sugar configuration.

Day 3: Microfluidic Devices

There are 4 “outreach” microfluidic devices. By using the devices, food coloring, bulb pipettes, and glass microscope slides, students are able to gain a basic understanding of how microfluidic devices move very small amount of liquid through an imprint on a wafer of PDMS. We called the four devices by these names: Dragon, Rainbow, Gradient, and Laminar.

Here is the procedure provided to the students.

  1. Get clean glass microscope slide. Hold the edges to avoid finger prints.
  2. Unwrap the device. Find the device side. Put his side down on the glass slide. Press edges onto glass to make a seal.
  3. Choose 2 colors of food coloring. Add one drop to each inlet hole. Use bulb pipette to pull liquid through the device. Observe! Try all 4 devices. Sketch at least one in your science notebook. In one or two sentences write about how the microfluidic device works.
  4. Clean up by rinsing each device and slide with water and paper towels. Tape wrap each microfluidic device.


Day 4: E. coli Sugar Metabolism Test

To open the lesson we provide students with a short lecture about bacteria, how they are grown in LB by scientists in lab, and how phenol red works as a pH indicator. Phenol red can be added to LB that is used to grow bacteria. Students learn that bacteria eat and produce waste. This waste is acidic. When phenol red comes into contact with acids, it changes color. Certain species of bacteria prefer to consume different types of sugar than other species. If bacteria grown in LB with phenol red are introduced to sugar and the bacteria eat it, the acidic waste will change the color of the LB. As scientists, students can use this color change to test to see what types of sugars a type of bacteria consume. In this experiment students will determine what sugars E. coli prefer to consume. At the end of the brief lecture students are introduced to the Bacteria Identification Page. They view pictures, see sugar metabolism profiles for, and learn pertinent information about different bacteria types. Students should notice that the metabolism profile for E. coli is blank. They must determine it through testing.

This procedure was presented to students:

Be sterile in lab. Wash your hands with soap when you are done with the lab.

  1. Sketch the Bac Chip Sugars Orientation in your notebook.

    Bac Chip Sugars

  2. Align the vials of sugar like you saw in the sketch. Write your names on the tape and put it on the plastic vial holder.
  3. Avoid contamination! During this process do not talk and keep your mouth closed.
  4. Dip the end of a clean toothpick into the vial of E. coli.
  5. Open one sugar vial. Inoculate it with bacteria. Close the top.
  6. Get a new toothpick and inoculate a different vial with bacteria. Continue until all eight vials have been inoculated.
  7. Put into incubator to grow overnight.

At the conclusion of the lab portion of this lesson, we delivered a Bacteria information lesson. Students were directed to take some notes about bacteria during this activity.

Bacteria Lecture

Source: Singleton, Paul. Introduction to Bacteria, John Wiley & Sons, 2nd Edition, Chichester 1992.

Bacteria: really small organisms that live almost everywhere. Prokaryotic

  • Bacteria were unknown until the 17th century when microscopes were invented
  • Bacteria are known as prokaryotic cells. These are simple cells—DNA float around in the cell with no nuclear membrane, in direct contact with cytoplasm. Plant and animal cells are more complex and not bacteria. They are called Eukaryotic cells.

Other Microorganisms:

fungi, lichens, protozoa, viruses, archaea

Fossils of bacteria are some of the oldest known on Earth. Cyanobacteria may have been the dominant form of life on Earth from 2500-570 million years ago. These bacteria were probably responsible for creating much of Earth’s atmospheric oxygen (stromatolites).

Why should we study bacteria? Why are bacteria important?

  • Bacteria are the source of many diseases. While most bacteria are not harmful or can even be helpful to humans, some are dangerous pathogens. The study of bacteria can lead to medical breakthroughs in the treatment of diseases.
  • Many bacteria are useful to humans:
    • Digest food
    • Make foods: yogurt, butter, cheese
    • Make vinegar
    • Soil based bacteria are required for plants to obtain nutrients—bacteria in soil affix nitrogen to roots
    • Some strains aid in the production of antibiotics
    • Some can be placed in plants and act as an insecticide

Bacteria are prokaryotic cells.

prokaryotic cells

Bacteria are really small! You can’t see a single cell using your eyes. They are too small. The smallest are about 0.2 micrometers long. Largest are about 250 micrometers. 250 micrometers is ¼ the length of a millimeter. Bacteria are so small that 500 cells could line up side by side in a single millimeter.

Bacteria Cell Shapes:

  • Round—Cocci (coc-si)
  • Elongated, rod shaped—Baccili
  • Spiral—Spirilla and Spirochetes

Notable Cocci:

  • Staphylococcus aureus (Staph infection)
  • Streptococcus pneumonia (pneumonia)
  • Streptococcus salivarius (cheese)
  • Neisseria gonorrhoeae (gonorrhea)

Notable Baccili

  • Escherichia coli (E. coli) found in your intestines, digest your food
  • Bacillus subtilis (common bacteria found in soil)
  • Pseudomonas Aeruginosa (pneumonia)
  • Lactobacillus Acidophilus (yogurt production)
  • Rhizobium leguminosarum (affix nitrogen to roots of plants)

Notable Spirilla

  • Borrelia burgdorferi (Lyme Disease)
  • Magnetospirillum (magnetic bacteria found in wetlands)
  • Treponema pallidum (Syphilis)

E. coli structure and sketch:

E. coli structure and sketch

Cell wall- encases the cell

Chromosome- DNA loop

Cytoplasm- water based liquid inside the cell

Flagellum- tail like appendage used for cell movement

Ribosome- very small structures where proteins are made

Motile-many bacteria are motile. This means that they can actively move through liquids

Bacteria are Alive-

  • They eat, live, and poop out waste just like you

Lysogeny Broth

  • Nutrient rich liquid scientists use to grow bacteria in. Made of tryptone, yeast, and salt. This is the liquid that we will use to grow bacteria in our lab here at school.

Day 5: Bac Chip Test

First students should check their sugar tests from the day previous. They should record the coloration of the cells in their Eppendorf vials in their science notebook. As a class students discussed their findings and came to an agreement about the correct sugar configuration.

day 5 Bac Chip Test

After reviewing the functionality of a Bac Chip, I proposed a hypothetical story of how the Bac Chip might Be applied to a real life situation. Here is the story presented to students:

The Cave

You are on a mission to explore the Crystal Caves near Chihuahua, Mexico. The caves are dark and humid. They have a musty smell of heat and old rock. It is silent in the caves—the only thing you can hear are the echoes and quiet talking you and your troop make as you descend deeper into the darkness. The only way you can see anything is by the lights of your headlamps.

Your troop is trying to find new passages in the caves and take pictures of the legendary Mother Crystal which is said to be 45 feet long and a perfect ruby red. Your troop is being led by an experienced guide named Jose. You are the medic on this mission. Your job is to make sure that everyone is healthy in the cave environment. Other people on this mission include a journalist, photographer, and two geologists.

After 4 hours of descending deeper into the caves everyone is hot. Sweat clings to your face. You notice that Jose has begun to breathe heavily and his skin is becoming pale. You ask him if he is okay. He looks down at his leg. Around his leg is a dirty white rag. He unwraps it from his calf to reveal a deep festering wound. He has obviously been cut by a crystal and the wound is cut deep into his muscle. It is clearly infected and puss is oozing down the side of his leg.

As medic, it is your responsibility to save Jose by treating his infection. But what type of bacteria is causing his infection? You must find out. Fortunately in your medical kit you brought vacuumed Bac Chips and antibiotics. If you can determine what type of bacteria is causing Jose’s infection you can give him the correct type and dose of antibiotics to heal his wound. However, if Jose is unable to lead the group, you may be stuck in the depths of the Crystal Caves forever……………

At the conclusion of the story we presented students with the following laboratory procedure:

Identifying Bacteria Using the Bac Chip

 identifying bacteria using the bac chip

Students can watch the microfluidic devices fill before placing them in the incubator. Actual bacterial identification takes around 4 hours. For the purpose of middle school science, we waited overnight.

Day 6: Identify Bacteria

Students were presented the following procedure and were given copies of the Bacteria Identification page.

  1. Get Bac Chip out of incubator
  2. Color sugar metabolism results in your notebook
  3. Use Bacteria ID page to determine type of bacteria

Following this students discussed their findings. Unfortunately, of our twelve lab groups, only two were able to use the Bac Chip to correctly identify the type of bacteria.

Students then completed the ‘after’ section of the Bacteria Anticipation Guide.

We culminated the day by watching this youtube video about how bacteria is all over everything.

After the video, students were given this lab procedure to complete:

  1. Get plate of agar
  2. Use a Sharpie marker to draw lines on the outside of the plate to divide it into four equal pieces. Label each zone 1, 2, 3, and 4.
  3. Draw agar diagram in notebook
  4. Use Q tip to swab a surface of your choice
  5. Swab the Q tip on agar in your plate in the correct zone
  6. Record your swab location in your notebook


    The plates of agar were left to sit on the bench overnight. The next day students were able to take a look at what bacteria grew.








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