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BIOLOGY 211 Microbes and Humans Spring 2021

Microbes and Humans (BIO 211)


Spring 2021
Duke University

Day/Time Tuesday and Thursday, 10:00-11:30am


Location Gross Hall 103

Instructor Jeffrey Letourneau


PhD Candidate
Molecular Genetics and Microbiology
Email jeffrey.letourneau@duke.edu

Course overview

Microbes are everywhere: on every surface of our environment, in the air we breathe, inside
our bodies (the human microbiome), and in the food we eat. Microbes have inspired art and
literature, shaped history, and influenced human evolution. This course seeks to provide a
framework for students to understand what microbes are and how they function by placing
them in the context of human life and culture.

In addition to a basic understanding of what microbes are, microbiologists must be able to


design experiments, interpret data, and communicate scientific findings. Students in this
course will have the opportunity to hone these core skills over the course of three units:
Fermentation, Infectious Disease, and The Human Microbiome.

There is no prerequisite background for this introductory-level course, other than an


enthusiasm for science and a readiness to learn about microbes.

Course objectives

By the end of this course, students will be able to:


• Explain differences between types of microbes, including morphology and key
molecular functions
• Propose logical solutions to problems caused by microbes (e.g. disease treatment) as
well as ways we can use microbes as problem-solving tools themselves (e.g.
bioremediation)
• Evaluate the strengths and limitations of data on microbes
• Formulate hypotheses to answer questions about microbes and design experiments
to test those hypotheses
• Communicate knowledge about microbes to non-microbiologists by crafting
effective science communication pieces

In-class activities

Class will primarily consist of four types of activities:


• Discussion: This is a class about microbes and humans, so in addition to getting into
some of the microbiology, we will work together through discussions to better

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understand how microbes have shaped human society, how human attitudes towards
microbes develop and change, and the bioethics of microbiology.
• Group activities: In small groups, you will be asked to design experiments, plan
policies, or analyze data. We will then come back together as a class and discuss what
each group came up with.
• Peer review: We will devote some class time to peer reviewing SciComm pieces
(more on this below) at multiple points throughout the process so that the final
products can be well thought out and polished.
• Mini-lectures: Occasionally, I will lecture for 15-20 minutes to provide background
necessary for us to be able to discuss a topic in greater depth. You are highly
encouraged to interrupt me with questions!

Expectations

You are expected to attend and to actively participate in every class meeting. That includes
contributing to group activities and discussions and asking any questions you have. I believe
you all have valuable thoughts to share, so even (perhaps especially) if you think something
is a “wrong answer” or a “stupid question”, I want to hear it! Note that getting full credit for
participation does not require that you contribute to discussions every single class, but it
does require active engagement, participation in all in-class activities, and occasional high-
quality contributions to the entire class.

I also expect you will be fully respectful of your classmates, giving others the opportunity to
speak and refraining from personal attacks even in controversial discussions. All students of
all backgrounds and perspectives are welcome in this class. Remember that we are talking
about how microbes impact humans, so the diverse human perspectives you all bring will
enrich our discussions.

You are allowed one unexcused absence with no questions asked. After that, unexcused
absences will affect your class participation grade. Similarly, since your lowest problem set
grade is automatically dropped, you could skip one problem set with no effect on your grade.
(Of course, I encourage you to complete all problem sets, as they will challenge you to
deeply explore important questions in microbiology.) Otherwise, late work will only be
accepted except in cases of emergency, or at my discretion if you request an extension at
least 24 hours in advance of the deadline.

Assessments – problem sets

Problem sets are an opportunity for you to dive deeper into what we the topics covered in
each class and to prepare you for the next class. In general, they have been designed to
provide a smooth transition from one topic to the next. In the problem sets, I provide you
with multimedia resources (linked in the problem set or posted on Sakai) such as podcasts,
YouTube videos, and scientific papers. You are expected to read/watch/listen to these
resources in their entirety, as about half the questions will be based on them. For questions
that require you to do additional searching on your own, please make sure to cite these
sources using APA format. You are encouraged to collaborate with other students, provided
that all answers are in your own words.

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Everything you want to know about microbiology is out there (or waiting to be discovered).
These problem sets are like a guided scavenger hunt across the breadth of the Internet and
the depth of scientific papers and other resources I provide to accompany them. The skills
you gain by completing these will empower you to keep learning beyond this course.

Assessments – science communication pieces

As a capstone project for each unit, you will be required to submit a total of three science
communication pieces in this course. For each one, you will select a recent (published in the
past 6 months) scientific paper, and discuss the findings of the paper in a way that is
accessible for non-microbiologists. Points to consider include:
• What is new and exciting here? How does this paper build on previous work in the
field?
• What are the limitations of this study? Are there any claims the authors made that
you were not 100% convinced about?
• What new questions does this raise? What future experiments would you like to see?

The format is flexible, but all submissions should essentially fall into the 800-1200 word
range, whether those words are written or spoken. A few examples include:
• Written article (800-1200 words)
• Podcast (5-10 minutes)
• Video (5-10 minutes)

You will have the option to have any or all of your science communication pieces posted on
the class blog. There is no grade incentive to share your work on the blog, and if you do
choose to publicize your work, you may choose to include your name or post anonymously.
The purpose of the blog is twofold – first, to share your scientific knowledge beyond your
immediate circle of peers, and second, to provide an opportunity for you to build a portfolio
of public science writing. Furthermore, if you are so inclined, we can talk about pitching
your work to science media outlets instead of posting on the blog. See “Science media
outlets to pitch” and “Guide to pitching articles” under the Resources tab in Sakai for more
information.

Final grade determination

Weight Assessment type How grade is determined


SciComm pieces will be evaluated using rubrics posted
40% SciComm pieces under the Resources section on Sakai, which we will also
discuss in class.
Individual problem sets are graded on a point-based
scale, with the point-value of each question noted in the
40% Problem sets
problem set. Your lowest problem set grade will be
automatically dropped.
Class participation will be assessed using a rubric posted
20% Class participation
on Sakai, which we will also discuss in class.

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Course feedback

I deeply value your feedback. In addition to the instructor evaluation form required by
Duke, I will ask you to complete additional surveys at the end of each unit so I can best
adapt instruction to meet your needs.

I consider myself very receptive to feedback on how the course is going, and am happy to
chat about any questions or concerns you may have in person or via email. If for any reason
you do not feel comfortable speaking with me directly about these concerns, you may
anonymously fill out this Google Form and I take your feedback into consideration.

Accommodations

Students with disabilities who believe that they may need accommodations in the class are
encouraged to contact the Student Disabilities Access Office at 919-668-1267 or
disabilities@aas.duke.edu as soon as possible to better ensure that such accommodations are
implemented in a timely fashion. There will never be any sort of penalty or judgment for
requiring specific environmental changes to perform at your very best.

Additionally, this course will cover several topics that may be sensitive for certain students,
including COVID-19, diet tracking, and alcohol. If you anticipate having any issues
researching or discussing these topics, please reach out to me in advance and we will find an
alternative.

Course schedule

Due by start of
Date Topic In-class activities
class
Introductions and expectations

Discussion: What would happen if all


Fermentation microbes suddenly disappeared?

The relationship Pre-class survey Workshop: Finding and interpreting


Thursday,
between microbiology research
Jan 7
microbes and Read syllabus
humans – past Discussion: What do modern humans
and present know and think about microbes?

Mini-lecture: History and pre-history of


fermented foods
Discussion: How has alcohol shaped
Saccharomyces
human society?
cerevisiae –
Tuesday, PS1: History of
microbial
Jan 12 bread and alcohol Group activity: Is beer a probiotic?
production of
alcohol
Mini-lecture: Yeast as a genetic tool

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Group activity: Designing yeast genetics


experiments
Mini-lecture: Major fungi used in
fermentation
Other types of PS2: Defining
Thursday, Group activity: Understanding fungal life
fungal features of
Jan 14 cycles
fermentation microbial fungi
Group activity: Preventing mold and
contamination
Discussion: The role of acidity in food
PS3: The role of
Tuesday, Lactic acid Group activity: Will it ferment?
pH in food
Jan 19 ferments
microbiology
Group activity: Designing a plant-based
cheese
PS4: Short-chain
fatty acids and Discuss selected papers with partner
other flavor
Thursday, Acetic acid metabolites Mini-lecture: History of vinegar
Jan 21 ferments
Identify 3 recent Group activity: Modulating SCFA
fermentation production
papers of interest
Mini-lecture: Microbe-microbe interactions
and diversity
Sourdough and
Group activity: Experimenting with
kombucha –
Tuesday, PS5: Intro to kombucha substrates
mixed
Jan 26 microbial ecology
community
Discussion: Starting a sourdough starter
ferments
Group activity: Effects of particle size on
diversity
PS6: Microbial
communities in Peer review intro paragraphs
Mycorrhizae and nature
Thursday,
agricultural Group activity: Where do truffles grow?
Jan 28
microbiology SciComm piece
#1 intro Discussion: Ethics of agricultural
paragraph microbiology
Mini-lecture: Wastewater treatment plants
PS7: Identification
Tuesday, and design of
Bioremediation Group activity: Designing a circuit to
Feb 2 bacteria for
break down plastic
bioremediation

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Discussion: Compost ethics


Mini-lecture: How to peer review

Peer review SciComm drafts


PS8: Discovering
novel antibiotics
Discussion: How do we isolate useful
Thursday, Microbes as in soil microbes
microbes?
Feb 4 disease fighters
SciComm piece
Mini-lecture: Phage therapy
#1 draft
Group activity: Optimizing antibody
production in bioreactors
Case study
Infectious disease
Tuesday, PS9: Viral vaccine Discussion: Effects of COVID-19 on
Feb 9 The world post- vectors social policy
COVID-19
Discussion: Pandemics in the movies
Case study
Listen to
Discussion: How has modern medicine
TPWKY: Plague
changed our attitudes towards microbes?
Thursday, How pandemics (no problem set)
Feb 11 shaped history
Mini-lecture: Plagues throughout history
SciComm piece
#1 final draft due
Group activity: Preparing for the next
pandemic
Case study

Mini-lecture: The innate immune system


PS10: The
Tuesday,
Innate immunity evolution of Group activity: Building an effective
Feb 16
immunity pathogen

Group activity: Dynamics of macrophage-


pathogen interactions
Case study

Discussion: How do doctors make


Tracking disease diagnoses?
Thursday, PS11: Differential
– diagnosis and
Feb 18 diagnosis
epidemiology Group activity: Finding the source of an
outbreak

Group activity: Is it an infection?

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Case study

Discussion: How and why do bacteria kill


PS12: each other?
Tuesday,
Antimicrobials Determining
Feb 23
disease etiology Mini-lecture: Classes of antimicrobials

Group activity: Designing a novel


antimicrobial
Case study
PS13: How
antibiotics work
Discuss selected papers with partner
Thursday, Antimicrobial
Feb 25 resistance Identify 3 recent
Discussion: The post-antibiotic era?
infectious disease
papers of interest
Group activity: Creative solutions to AMR
Case study

Group activity: Building adaptive


PS14: Host- immunity from scratch
Tuesday, Adaptive
pathogen
March 2 immunity
interactions Mini-lecture: Types of white blood cells

Group activity: Outwitting adaptive


immunity
PS15: Lymphocyte Peer review limitations
immunology
Thursday, Group activity: Analyzing vaccine data
Vaccines
March 4 SciComm piece
#2 limitations and Discussion: How do we improve public
confusing parts attitudes towards vaccines?
SPRING BREAK
NO CLASS
Case study

Discussion: Should I get a flu shot?


Individual
Tuesday, PS16: Variation in Group activity: Range of possible
variation in
March 16 vaccine efficacy responses to a pathogen
disease response
Discussion: How effective does a
treatment need to be in order to be good
enough?
Case study
What is an PS17: Epstein-
Thursday,
infectious disease Barr virus
March 18 Peer review SciComm drafts
anyway?

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SciComm piece Mini lecture: Types of infectious agents


#2 draft
Group activity: Classifying diseases
Discussion: What type of disease is NEC?
The human
microbiome PS18: Necrotizing
Group activity: What factors determine the
Tuesday, enterocolitis and
composition of our gut microbiome?
March 23 Where do our the infant gut
microbes come microbiome
Discussion: Are there benefits from giving
from?
“young” microbes to older adults?
Mini-lecture: Diet surveys

Group activity: Tracking diet


SciComm piece
Thursday, Diet and the gut
#2 final draft due
March 25 microbiome Discussion: How can we study effects of
(no problem set)
diet on health?

Group activity: Analyzing diet data


Group activity: How much fiber is too
much?
Tuesday, Probiotics and PS19: Dietary
March 30 prebiotics fiber Discussion: Ethics of supplement labeling

Group activity: Designing novel probiotics


Discussion: Ethics of FMT

Group activity: Antibiotics and gut


Effects of PS20: C. diff and
Thursday, microbial metabolic state
antibiotics on the fecal microbiota
April 1
gut microbiome transplants
Group activity: Assessing direct
antimicrobial effects of non-antimicrobial
drugs
Discussion: Are we more than just our
microbes?
PS21: Potential for
antibiotics to
Tuesday, The gut-brain Mini-lecture: State of gut-brain axis
cause and cure
April 6 axis research
neurological
disorders
Discussion: Ethics of modulating behavior
via the gut microbiome
Discuss selected papers with partner
PS22: The hygiene
The gut hypothesis
Discussion: Do you buy the hygiene
Thursday, microbiome and
hypothesis?
April 8 metabolic Identify 3 recent
disorders microbiome
Mini-lecture: How gut microbes shape the
papers of interest
immune system

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Group activity: Moving from correlation


to causation
Discussion: Ethics of model systems
PS23: Tools for
Tuesday, Gnotobiotic and
studying the gut
April 13 germ-free models Group-activity: Designing a collaborative
microbiome
microbiome study
PS24: Candida and
Peer review future experiments
opportunistic
Beyond the gut –
microbes
Thursday, microbiomes of Group activity: Preventing cavities
April 15 the skin, mouth,
SciComm piece
vagina, and more Group activity: Diet and the microbiome
#3 future
in pregnancy
experiments
Discussion: How do we maintain gut
health in the long run?
PS25: Are the
Individual microbes we have
Group activity: Analyzing human study
variation in evolved with
Tuesday, data
microbiome VANISHing?
April 20
composition and
Group activity: Designing studies to
function SciComm piece
account for variation
#3 draft
Peer review SciComm drafts
READING PERIOD
Tuesday, SciComm piece
April 27 #3 final draft due

Multimedia resources (podcasts, videos, scientific papers, news articles, book chapters, etc.) to
accompany problem sets (for me; would not be included in syllabus):
1. Ologies: Zymology (BEER) with Quinton Sturgeon
2. Gastropod: Meet Koji, your New Favorite Fungus
Salt Fat Acid Heat: Salt (just as a bonus since not everyone has Netflix)
3. Lactic Acid Fermentations (Steinkraus, 1992)
4. Aerobic submerged fermentation by acetic acid bacteria for vinegar production: Process and
biotechnological aspects (Gullo et al., 2014)
Fermentation Microorganisms and Flavor Changes in Fermented Foods (McFeeters, 2004)
5. Gastropod: Secrets of Sourdough
Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current
Knowledge on Their Impact on Human Health (Lavefve et al., 2019)
6. The known and the unknown in soil microbial ecology (Baldrian, 2019)
7. Understanding and Designing the Strategies for the Microbe-Mediated Remediation of
Environmental Contaminants Using Omics Approaches (Malla et al., 2018)
8. Kurzgesagt: The Deadliest Being on Planet Earth – The Bacteriophage

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Expanding Tiny Earth to genomics: a bioinformatics approach for an undergraduate class to


characterize antagonistic strains (Basalla et al., 2020)
9. TPWKY: COVID-19 Chapter 1-6
Everyone thinks they’re right about masks (Yong, 2020)
10. Kurzgesagt: The Immune System Explained I – Bacteria Infection
Kurzgesagt: Tiny Bombs in your Blood - The Complement System
11. Differential Diagnosis of Chikungunya, Dengue Viral Infection and Other Acute Febrile
Illnesses in Children (Laoprasopwattana et al., 2012)
12. Ologies: Disease Ecology (LYME/TICK-BORNE ILLNESSES) with Dr. Andrea Swei
13. Action and resistance mechanisms of antibiotics: A guide for clinicians (Kapoor et al., 2017)
14. Kurzgesagt: The Antibiotic Apocalypse Explained
Eicosanoid pathways regulate adaptive immunity to Mycobacterium tuberculosis (Divangahi
et al., 2010)
15. Identification of a major co-receptor for primary isolates of HIV-1 (Deng et al., 1996)
16. Kurzgesagt: The Side Effects of Vaccines - How High is the Risk?
Repeat vaccination reduces antibody affinity maturation across different influenza vaccine
platforms in humans (Khurana et al., 2019)
17. Epstein–Barr Virus Infection (Cohen, 2000)
18. Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and
fimbriae-encoding bacteria (Olm et al., 2019)
19. Kurzgesagt: How Bacteria Rule Over Your Body – The Microbiome
The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease (Makki et al.,
2018)
20. How Contaminated Stool Stored in a Freezer Left a Fecal Transplant Patient Dead (Jacobs,
2020)
21. Extensive impact of non-antibiotic drugs on human gut bacteria (Maier et al., 2018)
22. Ologies: Microbiology (GUT BIOME) with Dr. Elaine Hsiao
23. Effects of microbiota-directed foods in gnotobiotic animals and undernourished children
(Gehrig et al., 2019)
24. Candida auris: A rapidly emerging cause of hospital-acquired multidrug-resistant fungal
infections globally (Chowdhary et al., 2017)
25. Links between environment, diet, and the hunter-gatherer microbiome (Fragiadakis et al.,
2019)

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