BIO3334 Microbiology

Assignment – Reading Science Research articles

Dr. Joel Funk
10 pts.
Name: Handel Justus
Date: 1/13/2024

1. Describe one or more key characteristics of a science research article (primary literature), like the article listed
above, that is different from a review article that could be published in the same journal.
A primary literature (science research article) is different from a review article that could be published in
the same journal in the following ways:
 The primary literature is the original work or research of the researcher, while the secondary
literature (review article) is material that references or condenses the work of primary
literature.
 The secondary literature mostly does not include the methods and results section, which is an
essential part of the primary literature.
2. Write down the complete citation for this paper using CSE “Name–Year” format. (Hint: the above citation
needs to be reformatted in the CSE style). These websites give examples of the CSE Name–Year format:
https://writing.wisc.edu/Handbook/DocCSE_NameYear.html
http://www.scientificstyleandformat.org/Tools/SSF-Citation-Quick-Guide.html

Yeoh YK, et al. 2021. Gut microbiota composition reflects disease severity and dysfunctional immune responses
in patients with COVID-19. Gut. 70(4):698-706.

3. What was the authors’ hypothesis?

The authors hypothesize that the gut microbiota is associated with host inflammatory immune responses
in COVID-19.
4. How many subjects (people) participated in the study? Briefly describe the subjects used in this study. Where
did you find this information?
In this study, 100 subjects participated with either COVID-19 or up to 30 days of recovery. The 27 out of
100 individuals were patients that had a clearance of Sars-Cov-2 for up to 30 days. The subjects with COVID-19
were used from the Prince of Wales and United Christian Hospitals in Hong Kong. The patients were also
laboratory-confirmed Sars-Cov-2 positive. On the other hand, the non-Covid-19 subjects were employed before
COVID-19 as part of a Hong Kong population gut microbiome survey or non-disease controls from colonoscopy
Trials. This information can be found under the “Materials and Methods” section.

5. What were the main methods used in this research?

The main methods used in this research are:
 Subject recruitment and sample collection
 Stool DNA extraction and sequencing
 Sequence data processing, inferring gut microbiota composition and statistical analysis
 Measuring SARS-CoV-2 load in stool samples
 Plasma cytokine measurements

6. What institutions are the authors affiliated with? (List first and last author only).
1. Department of Microbiology (First)
10. Li Ka Shing Institute of Health Sciences (Last)

7. Summarize the authors’ findings in your own words in a short paragraph (five sentences or more).
The authors find a possibility that the gut microbiota has a direct correlation to the plasma concentrations
of several cytokines, chemokines, and inflammation markers, resulting in the modulation of the host immune
response. This modulation of the immune system then influences the disease severity and outcome. They find the
depletion of certain species of microorganisms that also link to the increase in concentrations of pro-inflammatory
cytokines (TNF-α, CXCL10, CCL2, and IL-10). The absence of the depleted taxa of microorganisms may also
play a role in overaggressive inflammation. Additionally, the researchers found that there is no difference in
outcomes with or without antibiotics, suggesting that antibiotics do not improve patient outcomes.

8. Did the authors find support for their hypothesis? Briefly explain.
Yes, the authors find support for their hypothesis because they find a correlation between the presence of
inflammatory cytokines and the composition of gut microbiota in COVID-19 patients. However, the
authors could not determine if these microorganisms actually play an active part in the disease or just
opportunistically grow in the absence of other microorganisms. Therefore, further research can confirm if
the inflammatory microorganisms play a direct role in COVID-19.

9. What future work do the authors propose?

Some future works that the authors propose include:
 A longer follow-up with patients of COVID-19 to determine whether the gut microbiota
composition relates to the long-term symptoms and microbiota dysbiosis.
 Whether the change in the gut microbiota predisposes patients and recovered individuals to future
health problems.
10. Save your answers as a MS Word or pdf document. Upload the assignment document to Blackboard Week 1
folder. This assignment is due on Wed. by 6 pm.