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). The main text of the paper and the supplement can be found below, in the ‘Resources’ section of this assignment.

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 1 - with group in class

Estimated time: 30 min

2.5.4.1 Instructions

  1. Form working groups in class.
  2. Read the abstract and the introduction with your group and discuss the main objectives and purpose of the paper.
  3. Answer questions below.

2.5.4.2 Questions

1. Overview of the Paper

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. General Methods

2A. Discuss how many and what samples were used for this study? Are there any replicates?

2B. Discuss some methods used in this paper.

2C. Discuss steps authors used to ensure their data is available to the public.

3. Figure 1 Methods and Results

Figure Methods
Fig. 1B in class
Fig. 1C in class

Figure Main Findings
Fig. 1B in class
Fig. 1C in class

2.5.5 Activity 2 - with group homework

Estimated time: 60 min

2.5.5.1 Instructions

  1. With your working group for homework answer questions below.

2.5.5.2 Questions

  1. Methods
Figure Methods
Fig. 2 homework
Fig. 3A homework
Fig. 3B homework
Fig. 3C homework
  1. Results
Figure Main Findings
Fig. 2 homework
Fig. 3A homework
Fig. 3B homework
Fig. 3C homework

  1. Conclusions
3A. Read the discussion section. What were the main conclusions the authors made in this study?

3B. Do the figures agree with their conclusion?

  1. Future Directions
4A. Scientific work builds on previous studies. What do you believe could be the next step to further the work these researchers did?

4B. What might be the impact of this research area in general (or this study in particular?)

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

Last Revised: August 2025

All materials CC-BY unless noted otherwise.