Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut
Abstract Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any p...
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Nature Portfolio
2025-05-01
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| Online Access: | https://doi.org/10.1038/s41598-025-99981-y |
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| author | Gérard Guédon Florence Charron-Bourgoin Thomas Lacroix Toufik Hamadouche Nicolas Soler Badreddine Douzi Hélène Chiapello Nathalie Leblond-Bourget |
| author_facet | Gérard Guédon Florence Charron-Bourgoin Thomas Lacroix Toufik Hamadouche Nicolas Soler Badreddine Douzi Hélène Chiapello Nathalie Leblond-Bourget |
| author_sort | Gérard Guédon |
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| description | Abstract Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14–23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe3+, carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes. |
| format | Article |
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| issn | 2045-2322 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Nature Portfolio |
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| spelling | doaj-art-3947c4c7028e41f1b33cfe88bc4813f82025-08-20T02:32:08ZengNature PortfolioScientific Reports2045-23222025-05-0115111310.1038/s41598-025-99981-yMassive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gutGérard Guédon0Florence Charron-Bourgoin1Thomas Lacroix2Toufik Hamadouche3Nicolas Soler4Badreddine Douzi5Hélène Chiapello6Nathalie Leblond-Bourget7Université de Lorraine, INRAE, DynAMicUniversité de Lorraine, INRAE, DynAMicUniversité Paris-Saclay, INRAE, MaIAGEUniversité de Lorraine, INRAE, DynAMicUniversité de Lorraine, INRAE, DynAMicUniversité de Lorraine, INRAE, DynAMicUniversité Paris-Saclay, INRAE, MaIAGEUniversité de Lorraine, INRAE, DynAMicAbstract Faecalibacterium is one of the most abundant bacteria of the human gut microbiota of healthy adults and is recognized to have positive effects on health. Here, we precisely and comprehensively analyzed the conjugative mobilome of four complete Faecalibacterium genomes. Despite lacking any plasmid, these bacteria harbor a vast arsenal of 130 elements, including 17 integrative and conjugative elements (ICEs) and 83 integrative and mobilizable elements (IMEs), collectively comprising 14–23% of the genome. Genome comparison of two strains isolated from the same fecal sample (Faecalibacterium and Roseburia strains) revealed almost identical elements indicating that transfer of ICEs and IMEs shape gut microbiome. ICEs and IMEs from Faecalibacterium encode many and diverse predicted functions such as defense and stress response (phages, multidrug, antibiotics, oxidative stress, biliar salts, antimicrobial peptides), nutrient import and metabolisms (Fe3+, carbohydrates) and riboflavin synthesis. This hints at their important role in the survival and adaptation of Faecalibacterium strains to the gut ecosystem. A rapid survey of 29 additional Faecalibacterium genomes uncovered many putative ICEs and IMEs, reinforcing their role in the rapid and massive evolution of Faecalibacterium genomes.https://doi.org/10.1038/s41598-025-99981-yICEIMEHorizontal gene transferTn1549FaecalibacteriumNutrient import |
| spellingShingle | Gérard Guédon Florence Charron-Bourgoin Thomas Lacroix Toufik Hamadouche Nicolas Soler Badreddine Douzi Hélène Chiapello Nathalie Leblond-Bourget Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut Scientific Reports ICE IME Horizontal gene transfer Tn1549 Faecalibacterium Nutrient import |
| title | Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut |
| title_full | Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut |
| title_fullStr | Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut |
| title_full_unstemmed | Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut |
| title_short | Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut |
| title_sort | massive acquisition of conjugative and mobilizable integrated elements fuels faecalibacterium plasticity and hints at their adaptation to the gut |
| topic | ICE IME Horizontal gene transfer Tn1549 Faecalibacterium Nutrient import |
| url | https://doi.org/10.1038/s41598-025-99981-y |
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