2.5 Activity: 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 scope of the paper
- 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 Part 1 - Paper Overview
Estimated time: 30 min
2.5.4.1 Instructions
- Form working groups in class
- Read the abstract and the introduction with your group
- Discuss the main objectives and purpose of the paper
- Answer questions below
2.5.4.2 Questions
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? 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.
2.5.5 Part 2 - Methods and Figure Analysis
Estimated time: 60 min
2.5.5.1 Questions
What methods did researchers use? Describe in your own words the methods used in each figure.
Figure Methods/Approach Fig. 1A With instructor Fig. 1B With instructor Fig. 1C With instructor Fig. 2 Homework Fig. 3A Homework Fig. 3B Homework Fig. 3C Homework What are the main findings from each figure?
Figure Result/Observation Fig. 1A With instructor Fig. 1B With instructor Fig. 1C With instructor Fig. 2 Homework Fig. 3A Homework Fig. 3B Homework Fig. 3C Homework
2.5.6 Part 3 - Conclusions
Estimated time: 30 min
Conclusions
1A. Read the discussion section. What were the main conclusions the authors made in this study? 1B. Do the figures agree with their conclusion? Future Directions
2A. 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 questions(s) do you have for the authors? 2B. What might be the impact of this research area in general (or this study in particular?)