2.5 Project - Scientific Literature

2.5.1 Purpose

Examine research on metagenomic diversity by reading Xue, et al. Metagenome sequencing and 103 microbial genomes from ballast water and sediments. Scientific Data.2023 Aug 10;10(1):536. (pubmed.gov/37563185)

2.5.2 Learning Objectives

  • Understand the purpose and experimental setup of the paper
  • Understand the presented evidence (Figures and Tables) of the paper

2.5.3 Introduction

Understanding microbial composition and diversity in different environments is critical for assessing the benefits and threats of the bacterial community in that environment. In the publication by Xue, et al. 2023, the authors study microbial diversity in the ballast-tank water from two ships, with the idea that such a unique and isolated water environment may select for specific microbes. Luckily in their research they don’t find bacterium Vibrio cholerae, but that is exactly what they would find in the ballast water of cargo ships if they did the analysis during the cholera pandemic(s) of the 1800s.

2.5.4 Activity

Estimated time: 90 min

2.5.4.1 Instructions

Based on the study by Xue, et al.2023, answer the following questions. The main text of the paper and the supplement can be found below, in the ‘Resources’ section of this assignment.

2.5.4.2 Questions

2.5.4.2.1 Overview of the Paper
  • Suggestion: Answer questions below in class working in groups.
1A. What is the purpose of this study?

1B. What is the hypothesis in this study?

1C. Describe the knowledge gap. In essence, what did the scientific community not know that this study was trying to answer?

2.5.4.2.2 General Methods
  • Suggestion: Answer questions below in class working in groups.
1. Discuss how many and what samples were used for this study? Are there any replicates?

2. Discuss some methods used in this paper.

3. Discuss steps authors used to ensure their data is available to the public.

2.5.4.2.3 Figure Methods
  1. Explain in your own words the approach/methods used in each figure, focusing on how did the researchers tested their hypothesis?
  • Suggestion: For figure 1, work in groups in class to answer the questions. For homework, each group can be asigned a figure panel.
Figure Methods
Fig. 1B in class
Fig. 1C in class
Fig. 2 homework
Fig. 3A homework
Fig. 3B homework
Fig. 3C homework

2.5.5 Results (in class and Homework)

  1. What are the main results (findings) from each figure?
  • Suggestion: For figure 1, work in groups in class to answer the questions. For homework, each group can be asigned a figure panel.
Figure Main Findings
Fig. 1B in class
Fig. 1C in class
Fig. 2 homework
Fig. 3A homework
Fig. 3B homework
Fig. 3C homework

2.5.5.1 Conclusions

  1. Read the discussion section. What were the main conclusions the authors made in this study?

  2. Do the figures agree with their conclusion?

2.5.5.2 Future Directions

  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?
  1. 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?
  • Do you think there are risks associated with such studies?

2.5.6 Grading Criteria

  • Download as Microsoft Word (.docx) and upload on Canvas.

2.5.7 Footnotes

Resources

  • [Google Doc]

Contributions and Affiliations

  • Valeriya Gaysinskaya, Johns Hopkins University
  • Frederick Tan, Johns Hopkins University
All materials CC-BY unless noted otherwise.