Biology 560 - Interdisciplinary Explorations In Biology
Spring, 2015
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 (fall and Thanksgiving breaks) 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 the paperwork 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 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.


Office Location: 234F New Science Building
Office Phone: 4067
Office hours by Appointment: M,W,F 8:30 am - 9:30 am, M 3-4. Other Hours Gladly Set Up by Appointment. Walk-ins are always welcome!

Tweeting Available!: @Tobintc #SUMicrobz

Texting Hours: Nope, sorry. My minimal cell phone plan will not support them :-)

Email Policy ( Monday-Friday: I always respond to emails as quickly as I can (generally within a few hours during the work day). However, I am an early riser (5:00 am), so emails that are sent after 8:00 pm M-F will NOT receive a response until the next morning. Weekends/Holidays: Unless I am completely out of email contact (this is possible, as I am an avid hiker/camper) I will check my email daily during weekends and holidays and respond within 24 hours.



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. Exams 1 and 2 will 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 first two unit exams will be closed-book, individual efforts. Exam 3 will be a take-home, cumulative essay that will combine concepts and applications from all three units. It will be open book, but closed person. 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, 2015

Unit 1: The Microbiology of Beer

Week 1 (8/31-9/4)


Introduction to The Microbiology of Beer, Bread and Cheese

Syllabus Overview, Class Ground Rules

Introduction to Fermentation

Read: Brewing, A Legacy of Ancient Times

Week 1 Handout: Introduction to Fermentation

Week 2 (9/7-9/11)

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 (9/14-9/18)

The History and Culture of Beer

Reading #1: The Art of Fermentation, Chapter 9 (Available 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 (9/21-9/25)

9/21: Brewing Beer

Handout: How to Brew Beer - will be available as you arrive.

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).

9/25: No Class

Week 5 (9/28, 10/2) 9/28: Laboratory Explorations 1: How's the Beer Doing?

Handouts : The Chemistry of Beer, Chemistry of Beer Worksheet

10/2 Test 1

Test 1 Review Sheet

Week 6 (10/5-10/9)

10/5: An Introduction to the Microbiology of Bread


The sourdough microflora: biodiversity and metabolic interactions

Handout: An Introduction to The Microbiology of Sourdough Bread

10/9: 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.

Week 7 (10/12-10/16)

10/12 The Microbiology and Chemistry of Sourdough Bread


Flavour in sourdough breads: a review

Lactobacillus sanfrancisco a key sourdough lactic acid bacterium: a review

Handout: Flavor and Aroma in Sourdough Bread

10/16 Making Sourdough Starter Cultures

Handout: Making Sourdough Starter

Week 8 10/19 Fall Break!!
Week 8 10/21 Claritas Speaker!
Week 8 10/23

Laboratory Explorations 2: Making Sourdough Bread

Making Dough

Watch: Good Eats - Roll Call

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

Handout: No-Knead Sourdough Pizza Crust

Week 9 (10/26-10/30)

Laboratory Explorations 3: Beer and Bread

10/26: Baking Bread

Handout: Bring Last Friday's Handout

10/30 Lab Day: Chemical and Microscopic Analysis of Sourdough Starters

10/26 Schmidt Ethics Lectureship: "Stoned: A Doctor's Case for Medical Marijuana"
Week 10 (11/2-11/6

11/2: 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


Finish Bread Lecture

Exam Two Review

Week 11 (11/9) Exam Two
Week 11 (11/13)

An Introduction to the Fermentation of Milk


Making Great Cheeses, Part 1

Handout: Making Great Cheeses, Part I

Week 12 (11/16-11/20)

The Microbiome of Cheese


Recent Advances in Cheese Microbiology

11/16 - Handout: The Cheese Microbiome

11/20 - Making Ricotta Cheese: We will meet in the Biology student room to cook.

Week 13 (11/23)

The Biochemistry of Cheese


Biochemistry of Cheese Ripening

Flavor of Cheddar Cheese: A Chemical and Sensory Perspective

Handout: Making Great Cheeses, Part II

Week 13 (11/27) Thanksgiving Break!!
Week 14 (11/30-12/4)

History and Culture of Some Famous Cheeses:

Handout: World Culture of Cheese, Cheese Tasting

Week 15 (12/7-12/11)

Final Fermentation Essay Presentations

Final Exam Period (Mon Dec 14, 1:30 pm)

Final Exam Due via email.

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