Part I – Antibiotics and the Human Microbiome

1. Look at the figure that Amelia found in Wired pertaining to antibiotics and the microbiota.
What conclusions can you draw from this figure?
ANSWER: With accordance to the graph from Wired, it can be deduced that Antibiotics
indiscriminately kill ( both "good" and "bad" ) microbiome when misused and this could
lead to diseases. It can also disrupt the Microbiota biodiversity in a person's body and
could take years to fix.

2. Given the fact that Amelia found this article in an on-line pop-culture science magazine,
do you believe the data presented? Do some research on the impact of antibiotics on
the human microbiome using peer-reviewed literature. Summarize your findings from at
least three articles in a short paragraph.
ANSWER: Given the fact that the figures used in wired were sourced, then it can be
concluded that the data presented is indeed legitimate. Similar articles and other studies
have also tackled the impact of antibiotics on the human microbiome, and all those
references have a common conclusion which states that Antibiotics eventually disrupt
the normal (gut) microbiome in the body which is essential for fighting diseases and
maintaining homeostasis.

References:https://www.taconic.com/taconic-insights/microbiome-and-germ-free/antibiotics-
affect-microbiome.html

https://www.annualreviews.org/doi/abs/10.1146/annurev-micro-091313-103456

https://www.technologynetworks.com/biopharma/news/how-antibiotics-change-human-
microbiome-diversity-long-term-317454

3. Based on the figure from Wired and on your research, do you think that antibiotics
caused Amelia’s Crohn’s disease? Why or why not?
ANSWER: No, it is unlikely that antibiotics caused Amelia's Crohn's disease. it has been
stated in studies that Crohn's disease is mainly caused by the immune system attacking
bacteria in the Gastrointestinal tract of people, and the use of Antibiotics would have
killed the bacteria which would have initially triggered the immune system to respond in
that manner. It must be noted that Antibiotics are the first treatment or medicine
recommended by doctors to patients suffering Crohn's disease. But if misused or if a
patient uses the wrong type of antibiotic, it can trigger flares among people with Crohn's
disease and it can also cause diarrhea to people who do not even have this condition.

4. If a diverse gut microbiome is important for optimal health, what steps can you think of to
protect and/or reestablish gut flora following an illness like food poisoning?
ANSWER: The best and simplest step to protect gut flora is to avoid the unnecessary
intake of antibiotics. Additionally, people must also balance it out by also taking
Probiotics (live yeasts and bacteria which are goof for the digestive system).

Part II – Diseases of the Developed World

1. What are some possible reasons why Amelia got Crohn’s when her brother did not?
 ANSWER: This is because people's immune system vary greatly in how they react to
pathogens. Those with an overactive immune system are more susceptible to
autoimmune diseases. Another factor could be the fact that Crohn's disease is more
frequent with women compared to Men.

References: https://www.healthline.com/health/crohns-disease/facts-statistics-infographic#1
https://www.umcg.nl/EN/corporate/News/Paginas/why-every-immune-system-is-different.aspx

What patterns of disease occurrence can you observe from the table above and the
paper referenced?
ANSWER: Based on the table and the paper that was referenced, It can be observed or
deduced that Crohn’s disease is more frequent in developed/ industrialized countries
compared to underdeveloped countries.

2. List three hypotheses that might explain these patterns.

ANSWER:
1. The prevalence of Autoimmune Disease in industrialized countries are high and in
developing countries are low.
2. Frequent intake of Antibiotics can lead to the soaring frequency of Autoimmune
Diseases.
3. Underdeveloped countries commonly treat diseases with natural remedies and use
fewer antibiotics.

3. Note that the table above shows disease rates in terms of prevalence, while the
Economou and Pappas (2008) paper shows disease incidence. What is the difference
between incidence and prevalence?
ANSWER: The word "incidence" is used to identify the possibility of catching or contracting
a disease. Whereas, the word "prevalence" is used to indicate how prevalent or rampant the
disease is.

Part III –Exploring the Hygiene Hypothesis

1. Do you think the hygiene hypothesis could be applicable to Amelia’s case of Crohn’s
disease? Why or why or why not?
1. ANSWER: Yes, the hygiene hypothesis could be applicable to Amelia because she had little
exposure to bacteria considering that she lived in a well developed and hygienic country. It
must be noted that Amelia's Crohn’s disease only started acting up after she went on a trip to a
less-developed country. It is possible that Amelia had low exposure to bacteria back in America
which then lowered her tolerance for (new) bacteria or other diseases.

2. Develop a study that can test the hygiene hypothesis as a driver of allergic and
autoimmune disease. (Note that it might be easier to pick a single disease, like asthma
or Crohn’s.) Draw a graph of hypothetical data that would support the hygiene
hypothesis.
ANSWER:

Topic: Unraveling Hygiene Hypothesis and Autoimmunity: A study on Early germ

exposure and its Relationship to Asthma
 Problem: Is there a significant relationship between early germ exposure and Asthma?

Hypothesis: There is an inverse relationship between early germ exposure and the
possibility of contracting Asthma.

(Hypothetical) Graph with Hypothetical data:

3.5

3
Possibility of Contracting Asthma

2.5

1.5 Asthma
Linear (Asthma)
1

0.5

0
0 5 10 15 20 25 30 35
Early Germ Exposure

3. Think about all of the ways that a scientist could test the hygiene hypothesis. If you were
doing a correlational study in humans, what independent variables would you need to
consider? If you were doing a manipulative study in mice, what variables would you
need to control? What dependent variable would you measure?

ANSWER: The Hygiene Hypothesis could be tested by setting Environmental hygiene level
of a country as an variable, and (probability of getting) Asthma as the other independent
variable in the study. A Correlational research could then be conducted to check the
relationship between the two variables.

As for the manipulative study using mice, certain variables such as variation of its
environments (from insanitary, sterile, and untreated) could be manipulated to test mice's
incidence to Asthma.

Part IV– Exploring Options

1. Steroids, fecal transplants, and helminth therapy are three very different approaches to
the same disease. If you were deciding on a treatment plan, what additional information
would you need to make an informed choice?
 ANSWER: Even though these treatments have a common denominator of solving the
same disease, different patients might receive it differently depending on the treatment
and their body. First and foremost, it must be verified first if these tretments are verified
by the FDA for implementation. It would also be better to identify first if the patient has
any allergies to certain components or substances which would be used in each
treatment plan. Thirdly, it would be better to identify the type of bacteria that is present
in the patient. And lastly, it would be better to gather information on whether the patient
has other medical conditions that could be negatively affected upon using the
treatments.

2. Based on your understanding of Crohn’s so far, what do you think the major differences
are in these three different approaches? For example, think about the target and the
underlying goal of each treatment.
ANSWER:
1.) Steroids: It treats the symptoms but not the cause or source of those symptoms.
2. Fecal Transplants: Attempts to treat the cause, but can involuntarily deteriorate the
immune response to an increase in bacteria
3.) Helminth Transplant: On the other hand, this is the sole treatment which specifically
treats autoimmune diseases. But it has not been approved by the FDA yet and has room
for further studies.

3. How does FDA approval influence your decision on treatment options? Should it be a
consideration? (Here is a link to the FDA website for more information on the drug
approval process: http://www.fda.gov/Drugs/ DevelopmentApprovalProcess/.)
ANSWER: FDA approval is a significant influence on the deciding between treatment
options. This is because the FDA sets safety protocols to ensure reliability and mitigate
risk factors in the said treatments.

4. If you had a severe autoimmune disorder, would you consider helminth therapy as a
possible treatment? Why or why not?
ANSWER: The student would only consider it as a last option treatment when no other
FDA approved treatments will work. The introduction of a parasite in treatment is not a
current norm in treatment and could be dangerous. There has to be an assurance first
that it will not have negative long term effects.

5. A database of current clinical trials is found here: https://clinicaltrials.gov/. Look for

examples of clinical trials for Crohn’s. Are there any trials using fecal transplant or
helminth therapy that Amelia might consider? Are there alternative treatments not on the
list above that she might add to her table?
ANSWER: At present, There haven't been many clinical trials or studies which used
helminth and fecal transplantation treatment. Although Stem Cell Transplant, Drug
Testing, and Radiation therapy are also therapies currently being tested by doctors
which that could provide alternative treatment solutions to Amelia's condition.

Part V –The Human Body as an Ecosystem

1. What impact do you think the factors listed above have on human biodiversity?
ANSWER: They have more contact with Bacteria and live in a less sterile environment,
which means they get in touch and learn to deal with more diseases. Additionally,
Human biodiversity is continuously challenged by the use of antibiotics , as well as by
the low exposure of particular microorganisms.
2. If we think of the human body as an ecosystem, what ecological parallels can you draw
between the consequences of decreased biodiversity in nature and your body? For
example, if you think back to the initial graph from the Wired article in Part I, imagine you
were looking at fish species in a coral reef or species of birds in a tropical forest rather
than species of bacteria in the gut of a person.
ANSWER: Antibiotics are like deforestation. It opens doors to invasive plants and the
mass extinction of animals, the same way that misuse of antibiotics can open doors for
the death of bacteria needed by our body to fight diseases. Autoimmune diseases are as
if one's own immune system were an invasive species that destroys everything because
they don't have anything else to prey on left (actual bacteria).

3. What are some possible implications of decreased biodiversity for human health?
ANSWER: A possible implication is that the frequency of the reactions to new bacteria
will be more severe. Loss of diversity can inflict unnecessary burdens on the normal
immune response.

4. Should this information change our attitudes about microbes?

ANSWER: At the very least, people should be aware that microbes are in some cases
vital to our life and are not necessarily pathogenic all the time.

5. Why do you think 1950 is the time period around which the incidence of many
autoimmune diseases beganto increase?
ANSWER: This may be because the use of antibiotics became common in the year
1950 and the population expanded rapidly.