Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species

Marin, MG, Quinones-Olvera, N, Wippel, C, Behruznia, M, Jeffrey, BM, Harris, M, Mann, BC, Rosenthal, A, Jacobson, KR, Warren, RM, Li, H, Meehan, CJ ORCID: https://orcid.org/0000-0003-0724-8343 and Farhat, MR, 2025. Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species. Bioinformatics, 41 (5): btaf219. ISSN 1367-4803

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Abstract

Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, a clonally evolving bacterium with a small accessory genome, as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read versus hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.

Item Type:	Journal article
Publication Title:	Bioinformatics
Creators:	Marin, M.G., Quinones-Olvera, N., Wippel, C., Behruznia, M., Jeffrey, B.M., Harris, M., Mann, B.C., Rosenthal, A., Jacobson, K.R., Warren, R.M., Li, H., Meehan, C.J. and Farhat, M.R.
Publisher:	Oxford University Press (OUP)
Date:	8 May 2025
Volume:	41
Number:	5
ISSN:	1367-4803
Identifiers:	Number Type 10.1093/bioinformatics/btaf219 DOI 2487826 Other
Rights:	© The Author(s) 2025. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Divisions:	Schools > School of Science and Technology
Record created by:	Jeremy Silvester
Date Added:	22 Aug 2025 07:57
Last Modified:	22 Aug 2025 07:57
URI:	https://irep.ntu.ac.uk/id/eprint/54241

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