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Cited by 10Bacteriophages and microbial interactionsGenomics and Phylogenetic StudiesEvolution and Genetic Dynamics

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A pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models

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Lee, Jeesu, Hunter, Branden, Shim, Hyunjin·2024·Frontiers in Molecular Biosciences
DOI 10.3389/fmolb.2024.1395450PMC PMC11224154

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Abstract

Bacteriophages are the most prevalent biological entities in the biosphere. However, limitations in both medical relevance and sequencing technologies have led to a systematic underestimation of the genetic diversity within phages. This underrepresentation not only creates a significant gap in our understanding of phage roles across diverse biosystems but also introduces biases in computational models reliant on these data for training and testing. In this study, we focused on publicly available genomes of bacteriophages infecting high-priority ESKAPE pathogens to show the extent and impact of this underrepresentation. First, we demonstrate a stark underrepresentation of ESKAPE phage genomes within the public genome and protein databases. Next, a pangenome analysis of these ESKAPE phages reveals extensive sharing of core genes among phages infecting the same host. Furthermore, genome analyses and clustering highlight close nucleotide-level relationships among the ESKAPE phages, raising concerns about the limited diversity within current public databases. Lastly, we uncover a scarcity of unique lytic phages and phage proteins with antimicrobial activities against ESKAPE pathogens. This comprehensive analysis of the ESKAPE phages underscores the severity of underrepresentation and its potential implications. This lack of diversity in phage genomes may restrict the resurgence of phage therapy and cause biased outcomes in data-driven computational models due to incomplete and unbalanced biological datasets.

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Metadata

Authors
Lee, J., Hunter, B., & Shim, H.
Affiliations
  • Ghent University Global Campus (KR)
  • California State University, Fresno (US)
Corresponding author
Shim, Hyunjin
ORCID
Venue
Frontiers in Molecular Biosciences
Publisher
Frontiers Media SA
Published
2024-06-21
Volume
11
Pages
1395450-1395450
ISSN
2296-889X (ISSN-L)
DOI
10.3389/fmolb.2024.1395450
PMC
PMC11224154
OpenAlex
W4399901391
Cited by
10
References
5
Citations by year
2026: 5 · 2025: 5
FWCI
2.74
Type
journal article
Language
en
Open access
Licence
Locations
  • Frontiers in Molecular Biosciences (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
California State University, Fresno
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords
bacteriophages, ESKAPE pathogens, pangenome analysis, core genes, phage clustering, lytic phages, phage therapy

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