In silico Phage Hunting: Bioinformatics Exercises to Identify and Explore Bacteriophage Genomes

Abstract

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.

Four Novel Caudoviricetes Bacteriophages Isolated from Baltic Sea Water Infect Colonizers of Aurelia aurita

“…Lastly, our study demonstrated that phage research methods are still in their infancy, although several benchmarking studies on genomic and seasonal variation and diversity of tailed phages in the Baltic Sea were already published [ 84 , 85 ]. Bioinformatics tools specifically developed explicitly for phages still lag behind similar tools used in bacterial research [ 149 , 150 , 151 ]. However, some improved tools in recent years include Phaster, a web-based tool for identifying and annotating phage sequences in bacterial genomes and predicting their completeness [ 152 ].…”

Four novel Caudoviricetes bacteriophages isolated from Baltic Sea water infect colonizers of Aurelia aurita

“…Lastly, our study demonstrated that phage research methods are still in their infancy, although several benchmarking studies on genomic and seasonal variation and diversity of tailed phages in the Baltic Sea were already published (Jakubowska-Deredas et al, 2012;Nilsson et al, 2019). Bioinformatics tools specifically developed explicitly for phages still lag behind similar tools used in bacterial research (Coclet & Roux, 2021;Martinez-Vaz & Mickelson, 2020;Schackart III et al, 2023). However, some improved tools in recent years include Phaster, a web-based tool for identifying and annotating phage sequences in bacterial genomes and predicting their completeness (Arndt et al, 2016).…”

Development of computationally-guided workflow for designing therapeutic phage cocktail: targeting multidrug-resistant (MDR) bacteria

“…The small prophages having sizes below 11 kb are considered to be non-functional and unable to assemble a mature and viable bacteriophage because an intact phage with complete functional units can disrupt a target bacterium completely [30]. The prophages having size below 30 kb are also considered small and it is very di cult to differentiate between them and other mobile genetic elements [31]. This can pose a challenge when attempting to accurately identify and classify small prophages within prokaryotic genomes, therefore, we have included only those prophages in our study which had a size above 30 kb.…”