A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses
Abstract Background Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far....
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BMC
2025-01-01
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| Online Access: | https://doi.org/10.1186/s12864-024-11201-5 |
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| author | Elhem Yacoub Vincent Baby Pascal Sirand-Pugnet Yonathan Arfi Helmi Mardassi Alain Blanchard Salim Chibani Boutheina Ben Abdelmoumen Mardassi |
| author_facet | Elhem Yacoub Vincent Baby Pascal Sirand-Pugnet Yonathan Arfi Helmi Mardassi Alain Blanchard Salim Chibani Boutheina Ben Abdelmoumen Mardassi |
| author_sort | Elhem Yacoub |
| collection | DOAJ |
| description | Abstract Background Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far. Results Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas. Conclusion This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks. |
| format | Article |
| id | doaj-art-0a9ec84a790e4811b1b0ccceda8c6173 |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-0a9ec84a790e4811b1b0ccceda8c61732025-01-12T12:09:21ZengBMCBMC Genomics1471-21642025-01-0126112810.1186/s12864-024-11201-5A sweeping view of avian mycoplasmas biology drawn from comparative genomic analysesElhem Yacoub0Vincent Baby1Pascal Sirand-Pugnet2Yonathan Arfi3Helmi Mardassi4Alain Blanchard5Salim Chibani6Boutheina Ben Abdelmoumen Mardassi7Unit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University Tunis El ManarCentre de Diagnostic Vétérinaire de L’Université de Montréal (CDVUM), Faculty of Veterinary Medecine, Université de MontréalUniv. Bordeaux, INRAE, UMR BFPUniv. Bordeaux, INRAE, UMR BFPUnit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University Tunis El ManarUniv. Bordeaux, INRAE, UMR BFPUnit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University Tunis El ManarUnit of Mycoplasmas, Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Institut Pasteur de Tunis, University Tunis El ManarAbstract Background Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far. Results Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas. Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas. Conclusion This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks.https://doi.org/10.1186/s12864-024-11201-5Avian mycoplasmasComparative genomicsPan/core genomePhylogenyEnergy metabolismVirulence |
| spellingShingle | Elhem Yacoub Vincent Baby Pascal Sirand-Pugnet Yonathan Arfi Helmi Mardassi Alain Blanchard Salim Chibani Boutheina Ben Abdelmoumen Mardassi A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses BMC Genomics Avian mycoplasmas Comparative genomics Pan/core genome Phylogeny Energy metabolism Virulence |
| title | A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| title_full | A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| title_fullStr | A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| title_full_unstemmed | A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| title_short | A sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| title_sort | sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses |
| topic | Avian mycoplasmas Comparative genomics Pan/core genome Phylogeny Energy metabolism Virulence |
| url | https://doi.org/10.1186/s12864-024-11201-5 |
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