5.3 Activity - Scientific Literature
5.3.1 Purpose
Examine research where a 16S rRNA-based approach is used to compare metagenomic diversity in children with Clostridioides difficile infection (CDI), before and after fecal microbiota transplantation (FMT) by reading: “Fecal transplant in children with Clostridioides difficile gives sustained reduction in antimicrobial resistance and potential pathogen burden” by Hourigan et al. (2019)
5.3.2 Learning Objectives
- Understand the purpose and experimental setup of the paper
- Understand the presented evidence (Figures and Tables) of the paper
5.3.3 Introduction
In this study, the effect of fecal transplantation on microbial composition and diversity in children with CDI is examined using short read shotgun metagenomics. Data visualization and taxonomic comparison between the samples was performed using R-based phyloseq, a tool you will use for 16S rDNA amplicon-seq analysis later in the course. Using phyloseq authors measure alpha diversity between samples, examine beta diversity with Principal Coordinate Analysis(PCoA) plots and use taxonomy barplots for comparing relative abundance of microbes.
5.3.4 Instructions
Based on the study, answer the following questions. The main text of the paper can be found below, in the ‘Resources’ section of this assignment.
5.3.5 Activity 1 - Overview of the paper
Estimated time: 30 minutes Determine the main objectives and purpose of the paper.
| 1. What is the purpose of this study? |
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| 2. What is the hypothesis in this study? |
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| 3. Describe the knowledge gap. In essence, what did the scientific community not know that this study was trying to answer? |
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| 4. What were the main conclusions the authors made in this study? |
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5.3.6 Activity 2 - Methods and Figure Analysis (in class and homework)
Estimated time: 45 minutes
5.3.6.1 Activity 2.1 – Examine the Methods and Data presented in this study
| 1. Summarize one aspect of sample-associated metadata used for this study? e.g. What is the range of subjects’ age; what is the spectrum of subjects’ medical problems? |
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| 2. Discuss one method or analysis used in this paper. |
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| 3. Summarize one figure presented in this paper. |
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5.3.6.2 Activity 2.2 - Figures and a Table
Describe the method/approach used to generate this data
| Method/Approach | |
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| Table 1 | |
| Fig. 2 | |
| Fig. 3A | |
| Fig. 3B |
Describe the main result/observation from each figure
| Main result/Observation | |
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| Table 1 | |
| Fig. 2 | |
| Fig. 3A | |
| Fig. 3B |
5.3.6.3 Activity 3 Conclusions
Estimated time: 10 min
1. Compare your conclusions to author conclusions.
- How similar are the conclusions you came up with to the authors?
- Were there any differences in interpreting the data?
- Do you think they are over-stating their findings? Do you think their conclusions are accurate and appropriate?
| Summarize one figure presented in this paper. |
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5.3.6.4 Activity 4 Future Directions
Estimated time: 10 min
1. Scientific work builds on previous studies. What do you believe could be the next step to further the work these researchers did? - What follow-up question(s) do you have for the authors?
2. What is the impact of this research area in general (or this study in particular?) - Do you believe further research in this area may benefit society? Can we build on what this study found?
5.3.7 Grading criteria
Download the assignment to your local computer as a .docx, complete it, and upload the assignment to your LMS (Blackboard, Canvas, Google Classroom).