Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions
Abstract Background Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary rela...
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09945-7 |
| _version_ | 1797363553997422592 |
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| author | Dae Gyu Choi Ju Hye Baek Dong Min Han Shehzad Abid Khan Che Ok Jeon |
| author_facet | Dae Gyu Choi Ju Hye Baek Dong Min Han Shehzad Abid Khan Che Ok Jeon |
| author_sort | Dae Gyu Choi |
| collection | DOAJ |
| description | Abstract Background Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. Results E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. Conclusions Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions. |
| first_indexed | 2024-03-08T16:22:56Z |
| format | Article |
| id | doaj.art-00a9828a8a49443d9de3d00c33323d77 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T16:22:56Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-00a9828a8a49443d9de3d00c33323d772024-01-07T12:12:32ZengBMCBMC Genomics1471-21642024-01-0125111710.1186/s12864-023-09945-7Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitionsDae Gyu Choi0Ju Hye Baek1Dong Min Han2Shehzad Abid Khan3Che Ok Jeon4Department of Life Science, Chung-Ang UniversityDepartment of Life Science, Chung-Ang UniversityDepartment of Life Science, Chung-Ang UniversityAtta‑ur‑Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST)Department of Life Science, Chung-Ang UniversityAbstract Background Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species. Results E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans. Conclusions Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.https://doi.org/10.1186/s12864-023-09945-7Enterococcus faeciumEnterococcus lactisPangenomeAdaptive evolutionHorizontal gene transferAntibiotic resistance |
| spellingShingle | Dae Gyu Choi Ju Hye Baek Dong Min Han Shehzad Abid Khan Che Ok Jeon Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions BMC Genomics Enterococcus faecium Enterococcus lactis Pangenome Adaptive evolution Horizontal gene transfer Antibiotic resistance |
| title | Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| title_full | Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| title_fullStr | Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| title_full_unstemmed | Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| title_short | Comparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| title_sort | comparative pangenome analysis of enterococcus faecium and enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions |
| topic | Enterococcus faecium Enterococcus lactis Pangenome Adaptive evolution Horizontal gene transfer Antibiotic resistance |
| url | https://doi.org/10.1186/s12864-023-09945-7 |
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