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ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Infectious Agents and Disease
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1494490
Identifying Potential Novel Widespread Determinants of Bacterial Pathogenicity using Phylogenetic-based Orthology Analysis
Provisionally accepted
Sara Ribeiro1,2*
Karine Alves1
Julien Nourikyan1
Jean-Pierre Lavergne2
Simon De Bernard1*
Laurent Buffat1- 1Altrabio, Lyon, Rhône-Alpes, France
- 2Structural and Molecular Basis of Infectious Systems (CNRS), Lyon, Rhône-Alpes, France
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The global rise in antibiotic resistance and emergence of new bacterial pathogens pose a significant threat to public health. Novel approaches to uncover potential novel diagnostic and therapeutic targets for these pathogens are needed. In this study, we conducted a large-scale, phylogenetic-based orthology analysis (OA) to compare the proteomes of pathogenic to humans (HP) and non-pathogenic to humans (NHP) bacterial strains across 734 strains from 514 species and 91 families. Using a dedicated workflow, we identified 4,383 hierarchical orthologous groups (HOGs) significantly associated with the HP label, many of which are linked to critical factors such as stress tolerance, metabolic versatility, and antibiotic resistance. Both known virulence factors (VFs) and potential novel widespread pathogenicity determinants were uncovered, supported by both statistical testing and complementary protein domain analysis. By integrating curated strain-level pathogenicity annotations from BacSPaD with phylogeny-based OA, we introduce a novel approach and provide a novel resource for bacterial pathogenicity research.
Keywords: Bacterial pathogenicity, Orthology analysis, comparative proteomics, therapeutic targets, diagnostic methods
Received: 10 Sep 2024; Accepted: 14 Apr 2025.
Copyright: © 2025 Ribeiro, Alves, Nourikyan, Lavergne, De Bernard and Buffat. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Sara Ribeiro, Altrabio, Lyon, 69007, Rhône-Alpes, France
Simon De Bernard, Altrabio, Lyon, 69007, Rhône-Alpes, France
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.