Take home Midterm Exam for Microbiomes Fall 2014

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Choose 4 of these findings and use what we have studied to help explain why the results are as they are.
Please make sure you explain what the mechanisms, compounds involved are.
a. Explain Why
Hunter-gatherers had really good teeth," says Alan Cooper director of the Australian Centre for Ancient DNA. "[But]
as soon as you get to farming populations, you see this massive change. Huge amounts of gum disease. And cavities
start cropping up.
b. Explain the mechanism why:
Biologists removed bacteria from the guts of four pairs of human twins in which one was obese and the other was
lean. The researchers then transplanted those microbes into the guts of lab mice that didn't have any of their own
microbes. The mice that got microbes from the obese twins gained more weight and accumulated more fat than
those who got microbes from the lean twin, even when the mice ate identical diets.
c. An experiment involved replacing the gut bacteria of anxious mice with bacteria from fearless mice. The mice
became less anxious, more gregarious. It worked the other way around, too bold mice became timid when they
got the microbes of anxious ones. And aggressive mice calmed down when the scientists altered their microbes by
changing their diet, feeding them probiotics or dosing them with antibiotics. Researchers then measured brain
chemistry in mice.
d. Researchers found that the 65 babies whose mother or father sucked on their pacifiers to cleanse them were
significantly less likely to get eczema and asthma, two conditions caused by allergic reactions, than babies whose
parents did not use the cleaning technique.
e. Alzheimers disease was first discovered 100 years ago. In a small study, nine out of ten patients who were treated
with a complete lifestyle overhaul displayed improvements in memory that began within three to six months. The
results were so significant that six patients who were struggling at work or had stopped working entirely because of
cognitive problems associated with Alzheimers disease were able to return to their jobs or demonstrated improved
performance at their jobs. Some of the critical lifestyle and diet changes that is said to have improved the symptoms
of Alzheimers disease

Eliminating processed food

Eliminating all simple carbohydrates and gluten
Eating more vegetables and fruits
Eating wild-caught fish
Meditating twice a day
Starting yoga
Increasing sleep to between seven and eight hours each night
Daily supplementation of coenzyme Q10, fish oil, melatonin, methylcobalamin, and vitamin D3
Improving oral hygiene by introducing an electric flossing tool and an electric toothbrush
Reinstating hormone replacement therapy as needed
Fasting for a minimum of 12 hours between dinner and breakfast
Not eating at least three hours before bedtime
Exercising for at least 30 minutes, up to six days each week

The major side effects of this therapeutic system are improved health and an improved body mass index, a stark
contrast to the side effects of many drugs. This study documents for the first time how memory improvements in
nine patients with Alzheimers disease occurred without drugs.

f. Nutritional deficiencies right at the time of conception can alter a baby's genes permanently. An environmental
factor during the first few days of development can change DNA long term. Tagging the DNA with a special tag,
during a process called methylation, controls this on-and-off switch. When several of these nutrients, including
vitamin B2, were at lower levels in mom's blood, the six genes had less methylation. The team also found a link
between the DNA methylation and mom's body mass index at the time of conception. The heavier the mother, the
less methylation. But there's growing evidence from other studies that similar types of genetic changes may help
determine a child's risk for some diseases, including diabetes, mental disorders and autism.

Here are the 15 questions for the in-class portion of the exam. Answer all 15 thoroughly. You can work
collaboratively with your friends on coming up with the answers (or not). However you will need to know all
the answers on your own in the end. Most all of the material should come from the presentations or papers
we read. In a few cases, maybe only 1 I think of possibly will you need to do a bit of additional research. You
really should consider going back to your bio 1 book to get additional understanding of the systems (or use
the one in the library) if you didn't cover all the human body systems. Read through the
physiology/structure sections, as Im not sure all the presentors had the time to clearly explain the parts
and how they function. Hard to do when you are also discussing the microbiome parts.
1. Potential question for in class part of exam.
So far this semester we have discussed the microbiomes of the 1. Mouth, 2. airway, 3. gut, 4. skin, 5. brain-CNS 6.
immune system, and 7. vaginal areas. Discuss how the microbiomes of each one of these seven areas impacts at
least 1-2 other areas. In other words how are they all interconnected? Create a big map showing how they
interconnect and what compounds permit that connection.
2. Potential question for In class part of exam.
What is diabetes? Be specific. Give evidence that connects gut microflora to type 2 diabetes. What foods work
against those fighting diabetes- what shouldn't they be eating? What foods should diabetes be eating? Does food
eaten impact the microbiota-diabetes interconnection?
3. Potential question for In-class part of exam.
How are SCFA created, what they are and how do they impact the human body? What foods support higher SCFA
production?
4. Potential question for in class part of exam.
Explain what the 3 molecular means for communication are between the gut and the brain. Explain how microbiota
can influence these communications and the resulting impact on the host or offspring.
5. Potential question for in class part of exam.
How do L cells, gut mucus, gut motility protect the gut? How do microbiota effect each of these structures or how are
they involved in increasing or decreasing their levels.
6. Potential question for in class part of exam.
Describe the layers of the skin. How does the skin protect our bodies from bacteria and fungi? How do the
microbiome populations defend the skin?
7. Potential question for in class part of exam.
The immune system is complex. Describe how the 3 lines of immune defense systems differ and how they work to
protect the body. What types of protective cells can be found in each of these systems and how they function in the
immune reaction. How does the microbiota directly work with or against the immune system?
8. Potential question for in class part of exam.
How does the vaginal microbiome directly and indirectly help protect their hosts? Give several mechanisms. Why do
vaginal diseases occur?
9. Potential question for in class part of exam.
The number of births through C-sections is increasing work worldwide. Why is this an issue? What are some
potential ramifications to a child who was delivered through a C vs natural birth process?

10. Potential question for in class part of exam.

The gut has multiple sections all that serve different functions and house different microbiomes. Explain how these
sections differ structurally and functionally and then how their microbiota serve different functions in each of these
areas.
11. Potential question for in class part of exam
Explain how the structure of the airway is designed to allow exchange of gases. From the nose to alveoli/bronchioles.
Then explain how the mucus layer in the different sections can help protect or alternatively cause disease and how
this mucus layer in each of the different sections can impact the microbiome.
12. Potential question for in class part of exam
One of our first talks was on the mouth microbiome. How can different species of the same microbiome cause both
positive and negative effects? Give examples of both positive impacts of the microbiome as well as bad ones.
13. Potential question for in class part of exam
How core is the core microbiota in different parts of the body? What is more important, species composition
(specific species) or their function? Give examples.
14. Potential question for in class part of exam
How are fecal transplants used to test how microbiota and human/mice interact? A number of researchers and even
individuals on their own are advocating fecal transplants to help resolve diseases or gut issues. What are potential
benefits? What are potential dangers?
15. Potential question for in class part of exam
Where you live can impact your exposure to microbes that may be harmful or actually helpful. Gives examples
where you want to keep your home clean. THEN explain why keeping your children too clean, too far from microbial
exposure can be equally harmful.