Data_Sheet_8_In silico Phage Hunting: Bioinformatics Exercises to Identify and Explore Bacteriophage Genomes.PDF

Bioinformatics skills are increasingly relevant to research in most areas of the life sciences. The availability of genome sequences and large data sets provide unique opportunities to incorporate bioinformatics exercises into undergraduate microbiology courses. The goal of this project was to develop a teaching module to investigate the abundance and phylogenetic relationships amongst bacteriophages using a set of freely available bioinformatics tools. Computational identification and examination of bacteriophage genomes, followed by phylogenetic analyses, provides opportunities to incorporate core bioinformatics competencies in microbiology courses and enhance students’ bioinformatics skills. The first activity consisted of using PHASTER (PHAge Search Tool Enhanced Release), a bioinformatics tool that identifies bacteriophage sequences within bacterial chromosomes. Further computational analyses were conducted to align bacteriophage proteins, genomes, and determine phylogenetic relationships amongst these viruses. This part of the project was carried out using the Clustal omega, MAFFT (Multiple Alignment using Fast Fourier Transform), and Interactive Tree of Life (iTOL) programs for sequence alignments and phylogenetic analyses. The laboratory activities were field tested in undergraduate directed research, and microbiology classes. The learning objectives were assessed by comparing the scores of pre and post-tests and grading final presentations. Post-tests were higher than pre-test scores at or below p = 0.002. The data suggest in silico phage hunting improves students’ ability to search databases, interpret phylogenetic trees, and use bioinformatics tools to examine genome structure. This activity allows instructors to integrate key bioinformatic concepts in their curriculums and gives students the opportunity to participate in a research-directed learning environment in the classroom.

生物信息学技能在生命科学绝大多数研究领域中的重要性与日俱增。基因组序列与大型数据集的公开获取，为将生物信息学实训融入本科微生物学课程提供了独特契机。本项目旨在开发一套教学模块，借助多款免费开源的生物信息学工具，探究噬菌体的丰度及其系统发育关系。通过对噬菌体基因组开展计算鉴定与分析，再进行系统发育研究，可将核心生物信息学能力培养融入微生物学课程，同时提升学生的生物信息学实操技能。第一项实训环节采用了PHASTER（PHAge Search Tool Enhanced Release）——一款可在细菌染色体中识别噬菌体序列的生物信息学工具。后续的计算分析环节用于比对噬菌体蛋白与基因组序列，并明确这类病毒间的系统发育关联。本环节借助Clustal Omega、MAFFT（Multiple Alignment using Fast Fourier Transform）以及iTOL（Interactive Tree of Life，交互式生命之树）三款软件完成序列比对与系统发育分析。本实验室实训环节已在本科定向研究课程与微生物学课堂中进行了实地测试。项目通过对比课前测试与课后测试的得分，以及对结课汇报进行评分，来评估教学目标的达成情况。课后测试得分显著高于课前测试，差异具有统计学意义（p≤0.002）。实验数据表明，计算机模拟噬菌体筛选可提升学生检索数据库、解读系统发育树以及运用生物信息学工具分析基因组结构的能力。该实训模块可帮助教师将核心生物信息学理念融入课程体系，同时为学生提供在课堂中参与科研导向型学习的机会。