Biology 560 - Interdisciplinary Explorations In Biology
Spring, 2013
The Microbiology of Beer, Bread and Cheese

Dr. Tammy Tobin




"God made yeast, as well as dough, and he loves fermentation just as dearly as he loves vegetation."
~Ralph Waldo Emerson

The goal of this course is to introduce you to the fundamental concepts and techniques of fermentation through a variety of disciplines. Gaining a complete understanding of the microbiology of beer, bread and cheese requires that you investigate not only their basic biological and chemical components, but also the amazing metabolic processes performed by the microbes that produce them. We will also explore the incredible ways in which fermentation has shaped (and been shaped by) human history, politics and religion. Ultimately, I hope that this course will help you savor the results of fermentation even more than you already do.

Prerequisites: Must have completed BIOL 101 or 102 AND have 2nd year standing or permission of instructor.  2 SH. 2 lecture hours. CC: Interdisciplinary

Spring 2011 Class at Penn Cheese Corporation

class photo 2011


After taking this course, students will be able to:

1. Demonstrate knowledge of the basic concepts and vocabularies central to:

a) The biology, chemistry and history of fermentation;
b) The scientific basis for the techniques and tools employed in the production of beer, bread and cheese;
c) The roles that different microbial species play in the production of beer, bread and cheese.

2.  Use multiple disciplines, including biology, chemistry, religion, history, poitical science, nutrition, and ecology and to explore and analyze the basics of fermentation science, as detailed above, and to explore the ways in which fermenation has shaped, and continues to shape human society.

3.  Articulate an understanding of the ways in which these disciplines can be brought together not only to supplement and reinforce each other, but also to highlight the complexities and ambiguities inherent to explaining issues central to the science and history of fermentation.

4. Perform biological and chemical tests to assay the results of microbial fermentations.



The final grade will be a composite of your performance in 3 Unit Exams (25% each), two fermentation worksheets (5% each), and one final fermentation essay (15%).

Your final grades will be based on the scale below:

A 94-100%
A- 90-93
B+ 87-89
B 84-86
B- 80-83
C+ 77-79
C 74-76
C- 70-73
D+ 67-69
D 64-66
D- 60-63
F All those numbers below 60


Attendance is required at all scheduled exams and lab sessions. You will receive a zero for all work performed during a class that you fail to attend. If you know in advance that you have a direct conflict with an upcoming class activity, please come speak with me about the nature of the conflict so that we can determine if a make-up assignment is possible. Note that this will not always be the case - particularly for laboratory experiments. In general, and unless something completely unforseen has happened (a natural disaster, etc.), you will only be allowed to arrange a make-up assignment for a missed class activity in advance of that activity. Please note that travel to and from vacation activities (Spring Break) will NOT qualify for a make-up activity, so plan accordingly.


Unless you have cleared it with me before class, all electronic communication devices must be off and in a closed container during the entire class. No texting is allowed for any reason. If any cell phone rings during class, I will answer it. Repeat offenders (more than one such offense) will be asked to leave class along with their cell phones until they can figure out where the off button is.


If you have a documented learning disability, I am happy to set up any appropriate arrangements for testing, classes, etc.  Simply provide me with a letter from the Center for Disability Services, and let me know what I can do to make the class work for you.


None Required. Readings will either be attached to the syllabus, emailed to you, available via eres and/or located in the class Blackboard Site. The syllabus will let you know where to find each assignment as it becomes available, so make sure to check the syllabus regularly.


234F New Science Building
Phone: 4067
Office hours: Open at all times. Just walk in if my door is open! The times during which I am available for scheduled appointments are Monday, Wednesday and Friday from 10-12. Please contact me if you wish to schedule an appointment during these times. Other appointments can be available on an as-needed basis.



Your final comprehension of the science concepts introduced in this class will be assessed during three unit exams, as indicated in the 'Schedule of Events' below. These exams will generally consist of two parts. The first part will contain 5-7 short answer questions that will be intended to assess your basic comprehension of unit concepts. You will be graded on all but one of the questions in this part, and you may choose which question to drop. The second part of the exam will contain one question that will evaluate your ability to synthesize and apply course concepts. All students will be required to complete part 2 in its entirety. The unit exams will be closed-book, individual efforts. If you are caught cheating on an exam you will receive a zero for that exam, and a letter will be sent to the Dean of Students.


Throughout the semester, you will be required to fill out short worksheets regarding your laboratory results. These worksheets will be team efforts.


Each student will write and present a final fermentation essay that will be due during the last week of class. More details will be provided in a separate handout.




The Microbiology of Beer, Bread and Cheese

Schedule of Events - Spring, 2013

Unit 1: The Microbiology of Beer

Week 1 (Jan 14, 18)


Introduction to The Microbiology of Beer, Bread and Cheese

Syllabus Overview, Class Ground Rules

Printer-Friendly Version of the Syllabus

Introduction to Fermentation

Read: The Art of Fermentation, Chapter 1 (Available in Blackboard Site under "Content"), Brewing, A Legacy of Ancient Times

Week 1 Handout: Introduction to Fermentation

Week 2 (Jan 21, 25)

The Microbiology and Chemistry of beer: Yeast, Barley, Hops, Water and Ageing

Read: Yeast Fermentation and the Making of Beer and Wine, Yeast's Epic Journey 500 Years Ago Gave Rise to Lager Beer, Tapping Chemistry: The Brewer's Art, Hop Chemistry: Homebrew Science, Iso-alpha-acids bitterness and loss of beer quality during storage.

Week 2 Handout: The Microbiology and Chemistry of Beer: Yeast, Barley, Hops, Water and Ageing

Week 3 (Jan 28, Feb 1)

The History and Culture of Beer

Reading #1: The Art of Fermentation, Chapter 9 (Available soon in Blackboard Site under "Content")

Reading #2: Fermentation Technology 3,000 Years Ago- The Archaeology of Ancient Egyptian Beer

Reading #3: Fermented Beverages of Pre- and Proto-Historic China

Week 3 Handout: History and Culture of Beer

Week 4 (Feb 4, 8)

Monday, February 4: Tour of Selin's Grove Brewing Company

Click on link to directions from campus here. Meet at 12:45 in back parking lot of the Brewing Company. Fear not! We will be done in plenty of time for you to get to your next classes.

Friday, February 8: Brewing Beer

Handout: How to Brew Beer

Note that this is an "all-day-ish activity". Each person in the class will sign up for brewing shifts during the day (beginning at 10:00 am and going until 3:00 pm).

Week 5 (Feb 11, 15) Feb 11: Test 1

Test 1 Review Sheet

Feb 15: An Introduction to the Microbiology of Bread


The sourdough microflora: biodiversity and metabolic interactions

Handout: An Introduction to The Microbiology of Sourdough Bread

Week 6 (Feb 18, 22)

The Microbiology and Chemistry of Sourdough Bread

Read (Feb 18):

Flavour in sourdough breads: a review

Lactobacillus sanfrancisco a key sourdough lactic acid bacterium: a review

Handout: Flavor and Aroma in Sourdough Bread

Bottling Beer (Feb 22)

Week 7 (Feb 25, March 1)

Laboratory Explorations 1: How's the Beer Doing?

Handouts : The Chemistry of Beer

Making Sourdough Starter Cultures

Handout: Making Sourdough Starter

March 4, 8

Spring Break!!

Week 8 (March 11, 15)

Laboratory Explorations 2: Baking Sourdough Bread

Monday: Making Dough

Watch: Good Eats - Roll Call

Read: The Secret of Great Bread, Letting Time do the Work

Handout: No-Knead Sourdough Pizza Crust

Friday: Baking Bread

Handout: Bring Monday's Handout

Week 9 (March 18, 22)

Laboratory Explorations 3: Beer and Bread

Lab Day: Chemical Analysis of Beer, Chemical Analysis of Beer Worksheet, and Microscopic Analysis of Sourdough Starters

The History and "Culture" of Bread

Read: Griddles, Ovens, and Agricultural Origins: An Ethnoarchaeological Study of Bread Baking in Highland Ethiopia,

Read: Cereal-based fermented foods and beverages (Focus on Idli, Injera, Kisra, Kishka and Pozol)

Handout: The History and "Culture" of Bread

Video: Making Injera

Week 10 (March 25)

Exam Two

Exam Two Review

Week 11 (April 5)

An Introduction to the Fermentation of Milk

Read: "About Cheese" From Course Blackboard Site under "Content"

Handout: An Introduction to Making Cheese

Week 12 (April 8, 12)

The Microbiome of Cheese

Read: Recent Advances in Cheese Microbiology

Monday - Handout: The Cheese Microbiome

Friday - Making Cottage Cheese: Watch Good Eats "Milk Made." We will meet in the Biology student room to cook.

Week 13 (April 15, 19)

The Biochemistry of Cheese

Read: Biochemistry of Cheese Ripening

Monday - No Class

Friday - Handout: The Biochemistry of Cheese (For a Short Week)

Week 14 (April 22, 26)

History and Culture of Some Famous Cheeses:

Handout: World Culture of Cheese, Cheese Tasting

Making Ricotta Cheese: Meet in the Biology Student Room to Cook

Week 15 (April 29, 30)

Final Fermentation Essay Presentations, Final Fermentation Essays Due

Monday, May 6, 8-10 am

Exam Three

Exam Three Review Sheet.

Back to Dr. Tobin's Home Page