1 Gut bacteria in Japanese people borrowed sushi -digesting genes from ocean bacteria By Ed Yong Japanese people have special tools that let them get more out of eating sushi than Americans can. They are probably raised with these utensils from an early age and each person wields millions of them. By now, you’ve probably worked out that I’m not talking about chopsticks. The tools in question are genes that can break down some of the complex carbohydrate molecules in seaweed, one of the main ingredients in sushi. The genes are wielded by the hordes of bacteria lurking in the guts of every Japanese person, but not by those in American intestines. And most amazingly of all, this genetic cutlery set is a loan. Some gut bacteria have borrowed their seaweed-digesting genes from other microbes living in the coastal oceans. This is the story of how these genes emigrated from the sea into the bowels of Japanese people. Within each of our bowels, there are around a hundred trillion microbes, whose cells outnumber our own by ten to one. This ‘gut microbiome’ acts like an extra organ, helping us to digest molecules in our food that we couldn’t break down ourselves. These include the large carbohydrate molecules found in the plants we eat. But marine algae – seaweeds – contain special sulphur-rich carbohydrates that aren’t found on land. Breaking these down is a tough challenge for our partners-in-digestion. The genes and enzymes that they normally use aren’t up to the task. Fortunately, bacteria aren’t just limited to the genes that they inherit from their ancestors. Individuals can swap genes as easily as we humans trade money or gifts. This ‘horizontal gene transfer’ means that bacteria have an entire kingdom of genes, ripe for the borrowing. All they need to do is sidle up to the right donor. And in the world’s oceans, one such donor exists – a seagoing bacterium called Zobellia galactanivorans. Zobellia is a seaweed-eater. It lives on, and digests, several species including those used to make nori. Nori is an extremely common ingredient in Japanese cuisine, used to garnish dishes and wrap sushi. And when hungry diners wolfed down morsels of these algae, some of them also swallowed marine bacteria. Suddenly, this exotic species was thrust among our own gut residents. As the unlikely partners mingled, they traded genes, including those that allow them to break down the carbohydrates of their marine meals. The gut bacteria suddenly gained the ability to exploit an extra source of energy and those that retained their genetic loans prospered. This incredible genetic voyage from sea to land was charted by Jan-Hendrik Hehemann from the University of Victoria. Hehemann was originally on the hunt for genes that could help bacteria to digest the unique carbohydrates of seaweed, such as porphyran. He had no idea where this quest would eventually lead. Mirjam Czjzek, one of the study leaders, said, “The link to the Japanese ...

1. 1
Gut bacteria in Japanese people borrowed sushi -digesting
genes from ocean bacteria
By Ed Yong
Japanese people have special tools that let them get more out of
eating sushi than Americans can. They are probably
raised with these utensils from an early age and each person
wields millions of them. By now, you’ve probably
worked out that I’m not talking about chopsticks.
The tools in question are genes that can break down some of the
complex carbohydrate molecules in seaweed, one of
the main ingredients in sushi. The genes are wielded by the
hordes of bacteria lurking in the guts of every Japanese
person, but not by those in American intestines. And most
amazingly of all, this genetic cutlery set is a loan. Some gut
bacteria have borrowed their seaweed-digesting genes from
other microbes living in the coastal oceans. This is the
story of how these genes emigrated from the sea into the bowels
of Japanese people.
Within each of our bowels, there are around a hundred trillion
microbes, whose cells outnumber our own by ten to
one. This ‘gut microbiome’ acts like an extra organ, helping us
to digest molecules in our food that we couldn’t break
down ourselves. These include the large carbohydrate molecules
found in the plants we eat. But marine algae –
seaweeds – contain special sulphur-rich carbohydrates that
aren’t found on land. Breaking these down is a tough

2. challenge for our partners-in-digestion. The genes and enzymes
that they normally use aren’t up to the task.
Fortunately, bacteria aren’t just limited to the genes that they
inherit from their ancestors. Individuals can swap
genes as easily as we humans trade money or gifts. This
‘horizontal gene transfer’ means that bacteria have an entire
kingdom of genes, ripe for the borrowing. All they need to do is
sidle up to the right donor. And in the world’s oceans,
one such donor exists – a seagoing bacterium called Zobellia
galactanivorans.
Zobellia is a seaweed-eater. It lives on, and digests, several
species including those used to make nori. Nori is an
extremely common ingredient in Japanese cuisine, used to
garnish dishes and wrap sushi. And when hungry diners
wolfed down morsels of these algae, some of them also
swallowed marine bacteria. Suddenly, this exotic species was
thrust among our own gut residents. As the unlikely partners
mingled, they traded genes, including those that allow
them to break down the carbohydrates of their marine meals.
The gut bacteria suddenly gained the ability to exploit
an extra source of energy and those that retained their genetic
loans prospered.
This incredible genetic voyage from sea to land was charted by
Jan-Hendrik Hehemann from the University of
Victoria. Hehemann was originally on the hunt for genes that
could help bacteria to digest the unique carbohydrates
of seaweed, such as porphyran. He had no idea where this quest
would eventually lead. Mirjam Czjzek, one of the
study leaders, said, “The link to the Japanese human gut
bacteria was just a very lucky, opportunistic hit that we
clearly had no idea about before starting our project. Like so
often in science, chance is a good collaborative fellow!”

3. Hehemann began with Zobellia, whose genome had been
recently sequenced. This bacterium turned out to be the
proud owner of no fewer than five porphyran-breaking enzymes.
These enzymes were entirely new to science, they
are all closely related and they clearly originated in marine
bacteria. Their unique ability earned them the name of
‘porphyranases’ and the genes that encode them were named
PorA, PorB, PorC and so on.
They are clearly not alone. Using his quintet as a guide,
Hehemann found six more genes with similar abilities. Five of
them hailed from the genomes of other marine bacteria – that
was hardly surprising. But the sixth source was a far
bigger shock: the human gut bacterium Bacteroides plebeius.
What was an oceanic gene doing in such an unlikely
species? Previous studies provided a massive clue. Until then,
six strains of B.plebeius had been discovered, and all of
them came from the bowels of Japanese people.
Nori is, by far, the most likely source of bacteria with
porphyran-digesting genes. It’s the only food that humans eat
that contains any porphyrans and until recently, Japanese chefs
didn’t cook nori before eating it. Any bacteria that
lingered on the green fronds weren’t killed before they could
mingle with gut bacteria like B.plebius. Ruth Ley, who
sperrault
Highlight
sperrault
Highlight
sperrault
Highlight

4. sperrault
Highlight
sperrault
Highlight
sperrault
Highlight
sperrault
Highlight
sperrault
Line
2
works on microbiomes, says, “People have been saying that gut
microbes can pick up genes from environmental
microbes but it’s never been demonstrated as beautifully as in
this paper.”
In fact, B.plebeius seems to have a habit of scrounging genes
from marine bacteria. Its genome is rife with genes that
are more closely related to their counterparts in marine species
like Zobellia than to those in other gut microbes. All
of these borrowed genes do the same thing – they break down
the complex carbohydrates of marine algae.
To see whether this was a common event, Hehemann screened
the gut bacteria of 13 Japanese volunteers for signs of
porphyranases. These “gut metagenomes” yielded at least seven
potential enzymes that fitted the bill, along with six
others from another group with a similar role. On the other
hand, Hehemann couldn’t find a single such gene among

5. 18 North Americans. “We were trying at lunch to think about
where you might see patterns this clean,” says Ley.
“You’d have to find another group of people with a very
specialised diet. Because this involved seaweed and marine
bacteria, it might be one of the cleanest demonstrations you’d
get.”
For now, it’s not clear how long these marine genes have been
living inside the bowels of the Japanese. People might
only gain the genes after eating lots and lots of sushi but
Hehemann has some evidence that they could be passed
down from parent to child. One of the people he studied was an
unweaned baby girl, who had clearly never eaten a
mouthful of sushi in her life. And yet, her gut bacteria had a
porphyranase gene, just as her mother’s did. We already
known that mums can pass on their microbiomes to their
children, so if mummy’s gut bacteria can break down
seaweed carbs, then baby’s bugs should also be able to.
Are we what we eat?
This study is just the beginning. Throughout our history, our
diet has changed substantially and every mouthful of new
food could have acted as a genetic tasting platter for our gut
bacteria to sample. Personally, I’ve been eating sushi for
around two years ago and I was intrigued to know if my own
intestinal buddies have gained incredible new powers
since then. Sadly, Czjzek dispelled my illusions. “Today, sushi
is prepared with roasted nori and the chance of making
contact with marine bacteria is low,” she said. The project’s
other leader, Gurvan Michel, concurs. He notes that of all
the gut bacteria from the Japanese volunteers, only B.plebeius
as acquired the porphyranase enzymes. “This
horizontal gene transfer remains a rare event,” he says.
Michel also says that for these genes to become permanent

6. fixtures of the B.plebeius repertoire, the bacterium would
have needed a strong evolutionary pressure to keep them. “Daily
access to ingested seaweeds as a carbon source”
would have provided such a pressure. My weekly nibbles on
highly sterile pieces of sushi probably wouldn’t.
That’s one question down; there are many to go. How did the
advent of agriculture or cooking affect this genetic
bonanza? How is the Western style of hyper-hygienic, processed
and mass-produced food doing so now? As different
styles of cuisines spread all over the globe, will our bacterial
passengers also become more genetically uniform?
The only way to get more answers is to accelerate our efforts to
sequence different gut microbiomes. Let’s take a look
at those of other human populations, including hunter-gatherers.
Let’s peer into fossilised or mummified stool
samples left behind by our ancestors. Let’s look inside the
intestines of our closest relatives, the great apes. These
investigations will tell us more about the intestinal genetic trade
that has surely played a big role in our evolution.
Reference: Hehemann, J., Correc, G., Barbeyron, T., Helbert,
W., Czjzek, M., & Michel, G. (2010). Transfer of
carbohydrate-active enzymes from marine bacteria to Japanese
gut microbiota Nature, 464 (7290), 908-912 DOI:
10.1038/nature08937
Source:
http://blogs.discovermagazine.com/notrocketscience/2010/04/07
/gut-bacteria-in-japanese-people-
borrowed-sushi-digesting-genes-from-ocean-bacteria/
http://dx.doi.org/10.1038/nature08937

7. http://blogs.discovermagazine.com/notrocketscience/2010/04/07
/gut-bacteria-in-japanese-people-borrowed-sushi-digesting-
genes-from-ocean-bacteria/
http://blogs.discovermagazine.com/notrocketscience/2010/04/07
/gut-bacteria-in-japanese-people-borrowed-sushi-digesting-
genes-from-ocean-bacteria/
sperrault
Highlight
sperrault
Highlight
UWP 011, Winter 2016 Assignments 1
UWP 011, Winter 2016
Assignments
Opening Impression, week 1
...............................................................................................
........... 2
Overviews and Comments (O&C), weeks 1-8
................................................................................. 3
Analyses & Plans (A&P), weeks 1-8
...............................................................................................
. 5
Terminology Quizzes, weeks 1-10
...............................................................................................
... 7

8. OCAP, weeks 8-9
...............................................................................................
.............................. 8
Closing Impression, Week 10
...............................................................................................
......... 10
Final Reflection, Exam
Week......................................................................................
................... 11
Appendix A: Overall Grading Standards
....................................................................................... 12
Appendix B: Calendar of All Assignment Due Dates
..................................................................... 13
UWP 011, Winter 2016 Assignments 2
Opening Impression, week 1
Opening Impression: Description
Read Folger’s “Foreword” to The Best American Science and
Nature Writing 2015.
Write at least 500 words about the Foreword, answering the
following questions: Folger asks
“What if the world’s political leaders met and engaged in the

9. same caliber of discourse that
scientists do, with the same spirit of collaborative problem
solving?” and goes on to say what
politicians would do as a result. What does this foreword
implying about science? About
politics? In what ways do you agree with him? In what ways do
you disagree? Why?
Opening Impression: Rationale
When learning, it helps to know where you are starting—what
you already know, what you
don’t know, what you want to know, what you assume, and so
on. This assignment gives you a
chance to pause and think about your knowledge and beliefs
before we leap into the readings
and rhetorical concepts of the quarter.
Opening Impression: Evaluation Criteria
Criteria Description
Completeness At least 500 words
Answers all the questions in the prompt
Clarity The writing is clear and unambiguous
throughout.
Professionalism The file is formatted according to the
instructions (i.e. with a header that includes
your name and so on).
The file is named according the file naming
conventions described in the syllabus.

10. UWP 011, Winter 2016 Assignments 3
Overviews and Comments (O&C), weeks 1-8
O&C: Description
For each O&C, write:
x A 150-200 word objective overview of the article. Include its
main point(s), and write
this entirely in your own words (no quoting). Use a signal
phrase that refers to the
article in each sentence; this will help you develop or hone a
habit of always attributing
information or ideas to the source they come from.
x A 150-200 word subjective commentary to the article in which
you share your personal
reactions to or thoughts about any aspect of the article. Write
this entirely in your own
words (no quoting).
Use the following headings to separate the sections:
x Overview (# words)
x Comment (# words)
For “# words,” include the number of words in that section.
O&C: Rationale

11. Writing Overviews and Commentaries will help you practice:
x Identifying main ideas in articles
x Shifting between two stances toward a text: An objective
stance in which you simply
report what the article says, and a subjective stance in which
you offer personal
reactions.
x Attributing each source’s ideas to that source
x Writing concisely and clearly
The O&Cs will also help us (the teaching team) identify who
needs help with the readings, and
make sure that you get credit for doing the readings.
O&C: Evaluation Criteria
Over all Clarity The writing throughout is clear and
unambiguous.
Attributions It is clear at all points which ideas are yours and
whom other
ideas are from.
Professionalism The document heading includes your name and
the date.
The file is named according the file naming conventions
described
in the syllabus.

12. UWP 011, Winter 2016 Assignments 4
The O&C is written and formatted according to instructions
(i.e.,
with a heading and word count for each section).
Overview Objectivity The overview is completely objective.
Accuracy The overview includes the article’s main
points/ideas.
Originality The overview is in your own word (no quoting).
Length The overview is 150-200 words
Comment Focus The comment is your reactions or thoughts
about the article.
Originality The comment is in your own words (no quoting).
Length The comment is 150-200 words.
UWP 011, Winter 2016 Assignments 5
Analyses & Plans (A&P), weeks 1-8
A&P: Description
The A&P has two parts. For the analysis, consider the article
using ONLY the current theoretical

13. lens and, based on that lens:
x Make an overall claim about how good a job the article does.
x Make a claim about one STRENGTH the article has, offer
supporting evidence from the
article, and explain how the evidence supports the claim.
x Make a claim about one WEAKNESS the article has, offer
supporting evidence from the
article, and explain how the evidence supports the claim.
For the plan:
x Describe how the writer could improve the piece to overcome
that weakness.
x Find and cite an outside (not from UWP 11) source the writer
could use in doing so, and
explain how the information or ideas from that source would
overcome the article’s
weakness.
x Include an “ASPECT” evaluation of the outside source.
Please use the provided template provided on SmartSite
(SmartSite > Resources > Handouts >
A&P_Template_For_Students.docx). Remember to change the
file name, following the file
naming conventions described in the syllabus:
YourLastName-YourFirstName_ProjectTitle_mm-dd.doc
A&P: Rationale
Writing Analyses & Plans will help you practice:

14. x Making a claim and supporting it with evidence
x Explaining how the evidence supports the claim
x Finding and evaluating relevant sources
x Attributing each source’s ideas to that source and citing
sources
x Writing concisely and clearly
A&P: Evaluation Criteria
Overall Clarity Writing throughout is clear and unambiguous
Professionalism File is named according the file naming
conventions described in
the syllabus
UWP 011, Winter 2016 Assignments 6
Document is formatted according to instructions
Analysis Claims Has a clear claim about one strength the article
has based on the
theoretical lens
Has a clear claim about one weakness the article has based on
the
theoretical lens
Support Supports each claim with evidence from the article
Explains how the evidence supports each claim

15. Includes in-text citations for the article
Plan Claim Makes a claim about how to improve the article.
Support Supports the claim with evidence from an outside
source you found
Explains how the evidence supports the claim
Includes in-text citations for the outside source
Citation Give a full citation for the source using a standard
academic
citation format (MLA, APA, CBE, etc.)
ASPECT Includes a completed ASPECT table for the source
UWP 011, Winter 2016 Assignments 7
Terminology Quizzes, weeks 1-10
Terminology Quizzes: Description
Twelve times during the quarter you will be asked to define a
term. This may be during lecture,
and it may be during a discussion.
The quiz format will be simple:
x You will be given two of the terms from a running list of
terms.
x You will be asked to define one of them in your own words.
The terms will be explained during lectures, and each lecture’s

16. slides will end with a list of
terms from that day.
You are welcome to discuss definitions with the professor, TAs,
and each other. You are
welcome to ask about terms on the SmartSite chat.
Terminology Quizzes: Rationale
These quizzes are intended to help you stay up to date with the
technical vocabulary we use in
UWP 11.
Terminology Quizzes: Evaluation Criteria
Each quiz is worth ½ point, and the lowest two quiz grades will
be dropped.
They will be evaluated on accuracy of how the term is used in
UWP 11.
Many fields (academic and non-academic) use the same words
to mean different things, so it is
important to understand how a given term is being used in a
given context. Thus, if you are
asked to define rhetoric, we will not be looking for a dictionary
definition of rhetoric, or even
the definition you may have learned in a previous writing
course, but for what is meant by
“rhetoric” in the context of UWP 011.

17. UWP 011, Winter 2016 Assignments 8
OCAP, weeks 8-9
Choose one article from The Best American Science and Nature
Writing 2015, and two lenses.
Write a combined Overview, Comment, Analysis, and Plan
(OCAP).
Use at least five new outside sources, and submit the ASPECT
form for each with your OCAP.
OCAP will be evaluated using these criteria:
Completeness The OCAP is complete, meaning:
x It uses two lenses
x It uses at least five sources in addition to the article being
analyzed.
x It uses those sources to make a research-based argument for
how
your selected article could be improved according to those
lenses.
Development The OCAP:
x Makes clear, specific claims and subclaims.
x Uses the rhetorical vocabulary from this course whenever
appropriate.
x Convincingly argues that the article has weaknesses according
to the

18. lenses you chose.
x Explains how the article it could be more improved according
to those
lenses. Suggestions are specific, relevant, and supported by
research.
x Explains how each piece of evidence supports a given point,
and how
each suggestion would improve the article.
x Explains how conclusions follow from the claims or
suggestions and
evidence.
Sources Choice
x Each of the five sources is appropriate for use in a scholarly
paper.
x Each of the five sources meets the “ASPECT” criteria for this
topic.
Citations & Attributions
x Each of the five sources is cited both in the text and in a
works cited
section using an academic citation format (such as MLA, APA,
CBE,
etc.).
x It is clear at all points which ideas are yours and whom other
ideas are

19. UWP 011, Winter 2016 Assignments 9
from.
Readability The writing is well organized and the pieces are
connected together:
x Each paragraph addresses one main point.
x Topic are sentences easy to identify.
x Ideas follow each other logically, with the connections
between ideas
explained.
The writing is clear and unambiguous throughout.
Professionalism The document header includes your name, the
date, and the title of the
article you are writing about.
The file is named according the file naming conventions
described in the
syllabus.
UWP 011, Winter 2016 Assignments 10
Closing Impression, Week 10
This assignment description will be given during week 10. It

20. will ask you to write approximately
500 words, and it will not require outside sources.
UWP 011, Winter 2016 Assignments 11
Final Reflection, Exam Week
Write a letter of at least 600 words reflecting on what you
learned this quarter.
First, please fill in the following, providing specific information
and examples:
� I used to think ______ [elaborate].
� But now I think ________ [elaborate].
Next, please answer the following questions:
� How do two of the lenses apply to some other part of your
life (other classes,
books or articles you have read, your work, your hobbies, or
other interests)? Be
specific and provide examples (even hypothetical ones).
� What did you learn from this class that surprised you? Why
did it surprise you?
� What are you still left wondering? What else would you like
to have learned
about?
To answer these questions, you should draw on class
discussions and lecture materials about

21. the various lenses and other concepts.
The final reflection will be graded on completeness, clarity, and
professionalism, as defined
throughout this document.
UWP 011, Winter 2016 Assignments 12
Appendix A: Overall Grading Standards
Written work will be evaluated for each criterion as “Good,”
“Mostly Good,” “Needs Some
Work” or “Need Work” for each criterion.
The overall grade for each assignment will be a combination of
the criteria, such that:
• “A” work is Good for all criteria.
• “B” work is Mostly Good or Good for all criteria.
• “C” work is Mostly Good for most criteria but Needs Some
Work in a few.
• “D” work Needs Work for at least half of the criteria.
Plus and minus grades will be used.
Grades are not divided with points per category. “A” work must
be “Good” in all areas.
Attention to detail matters.
Late work may be marked down one full letter grade for each
calendar day it is late.
We do not curve grades.

22. UWP 011, Winter 2016 Assignments 13
Appendix B: Calendar of All Assignment Due Dates
What When Where Grade
%
Opening Impression 3:00 p.m. on Thursday, January
07
Upload to SmartSite
Assignments
2
O&C 1 on Yong, draft The start of your discussion
section on Friday, January 8
Bring to discussion --
O&C-01 on Yong 3:00 p.m. on Monday, January 11 Upload to
SmartSite
Assignments
2
O&C-02 on Margulis & Case 3:00 p.m. on Tuesday, January 12
Upload to SmartSite
Assignments

23. 2
O&C-03 on Steingraber 3:00 p.m. on Thursday, January 14
Upload to SmartSite
Assignments
2
A&P-01 on Cold & Hot 1 in
Yong (draft)
The start of your discussion
section on Friday, January 15
Bring to discussion --
A&P-01 on Cold & Hot 1 Yong 3:00 p.m. on Monday, January
18 Upload to SmartSite
Assignments
10
O&C-04 on Kintisch 3:00 p.m. on Tuesday, January 19 Upload
to SmartSite
Assignments
2
O&C-05 on Mnookin 3:00 p.m. on Thursday, January 21 Upload
to SmartSite
Assignments
2
A&P-02 on Background &
Definitions in Specter

24. 3:00 p.m. on Monday, January 25 Upload to SmartSite
Assignments
10
O&C-06 on Freedman 3:00 p.m. on Tuesday, January 26
Upload to SmartSite
Assignments
2
O&C-07 on Maxmen 3:00 p.m. on Thursday, January 28 Upload
to SmartSite
Assignments
2
UWP 011, Winter 2016 Assignments 14
A&P-03 on Study in
Schweizter
3:00 p.m. on Monday, February 1 Upload to SmartSite
Assignments
10
O&C-08 on Goodell 3:00 p.m. on Tuesday, February 2 Upload
to SmartSite
Assignments

25. 2
O&C-09 on Jarvis 3:00 p.m. on Thursday, February 4 Upload to
SmartSite
Assignments
2
AP-04 on Cold & Hot 2 in
Boyle
3:00 p.m. on Monday, February 8 Upload to SmartSite
Assignments
10
O&C-10 on Yeoman 3:00 p.m. on Tuesday, February 9 Upload
to SmartSite
Assignments
2
O&C-11 on Nijhuis 3:00 p.m. on Thursday, February
11
Upload to SmartSite
Assignments
2
A&P-05 on Expertise in
Yeoman
3:00 p.m. on Monday, February
15

26. Upload to SmartSite
Assignments
10
O&C-12 on Hamilton 3:00 p.m. on Tuesday, February 16
Upload to SmartSite
Assignments
2
O&C-13 on Keith 3:00 p.m. on Thursday, February
18
Upload to SmartSite
Assignments
2
A&P-06 on Epideictic in
Context in Jacobsen
3:00 p.m. on Monday, February
22
Upload to SmartSite
Assignments
10
OCAP 3:00 p.m. on Thursday, March 3 Upload to SmartSite
Assignments
15
Concluding Impression 3:00 p.m. on Thursday, March 10

27. Upload to SmartSite
Assignments
2
Reflection 10:00 a.m. on Tuesday, March 15 Upload to
SmartSite
Assignments
2