Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species
The order <i>Lysobacterales</i> consists of three families (<i>Rhodanobacteraceae</i>, <i>Lysobacteraceae</i> and <i>Marinicellaceae</i>), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members withi...
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2025-05-01
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| author | Tengfei Ma Haijiao Liu Yafei Chen Juan Liu Chungen Piao Han Xue Risheng Xu Yong Li |
| author_facet | Tengfei Ma Haijiao Liu Yafei Chen Juan Liu Chungen Piao Han Xue Risheng Xu Yong Li |
| author_sort | Tengfei Ma |
| collection | DOAJ |
| description | The order <i>Lysobacterales</i> consists of three families (<i>Rhodanobacteraceae</i>, <i>Lysobacteraceae</i> and <i>Marinicellaceae</i>), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members within order <i>Lysobacterales</i> have relied heavily on 16S rRNA gene sequences, leading to taxonomic ambiguities at the familial level. With the advancement of sequencing technologies, an increasing number of whole-genome sequences have been available, providing an opportunity to revisit the taxonomy of families in <i>Lysobacterales</i>. In this study, we revisited the taxonomy of <i>Lysobacterales</i> by focusing on family-level reclassification based on phylogenomic frameworks. A total of 218 genome sequences, including 217 strains from <i>Lysobacterales</i> and 1 from <i>Nevskiales</i> (used as an outgroup), were collected for phylogenetic analysis. Phylogenetic relationships were inferred based on UBCG (up-to-date bacterial core gene) approach using 92 core genes and a concatenated protein phylogeney based on 227 single-copy orthologous proteins. Additionally, genomic similarity metrics, including average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI) and core-proteome average amino acid identity (cpAAI), were employed to assess the taxonomy of order <i>Lysobacterales</i>. Our results support the proposal of one novel family and the reassignment of six genera across different families within <i>Lysobacterales</i>, emphasizing the need for a refined family-level taxonomy. In addition, four novel species belonging to the family <i>Lysobacteraceae</i> were also confirmed. This study provides an updated familial framework for <i>Lysobacterales</i>, laying a robust foundation for future detailed taxonomic revisions at the genus and species levels. |
| format | Article |
| id | doaj-art-883ced6deaf748b7bb96193666f416d3 |
| institution | OA Journals |
| issn | 2076-2607 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | MDPI AG |
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| series | Microorganisms |
| spelling | doaj-art-883ced6deaf748b7bb96193666f416d32025-08-20T02:21:04ZengMDPI AGMicroorganisms2076-26072025-05-01136121210.3390/microorganisms13061212Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel SpeciesTengfei Ma0Haijiao Liu1Yafei Chen2Juan Liu3Chungen Piao4Han Xue5Risheng Xu6Yong Li7Peanut Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaPeanut Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaPeanut Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaPeanut Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaKey Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, ChinaKey Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, ChinaPeanut Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, ChinaKey Laboratory of Biodiversity Conservation of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, ChinaThe order <i>Lysobacterales</i> consists of three families (<i>Rhodanobacteraceae</i>, <i>Lysobacteraceae</i> and <i>Marinicellaceae</i>), many members of which are important pathogenic and beneficial bacteria. Previous classifications of members within order <i>Lysobacterales</i> have relied heavily on 16S rRNA gene sequences, leading to taxonomic ambiguities at the familial level. With the advancement of sequencing technologies, an increasing number of whole-genome sequences have been available, providing an opportunity to revisit the taxonomy of families in <i>Lysobacterales</i>. In this study, we revisited the taxonomy of <i>Lysobacterales</i> by focusing on family-level reclassification based on phylogenomic frameworks. A total of 218 genome sequences, including 217 strains from <i>Lysobacterales</i> and 1 from <i>Nevskiales</i> (used as an outgroup), were collected for phylogenetic analysis. Phylogenetic relationships were inferred based on UBCG (up-to-date bacterial core gene) approach using 92 core genes and a concatenated protein phylogeney based on 227 single-copy orthologous proteins. Additionally, genomic similarity metrics, including average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), average amino acid identity (AAI) and core-proteome average amino acid identity (cpAAI), were employed to assess the taxonomy of order <i>Lysobacterales</i>. Our results support the proposal of one novel family and the reassignment of six genera across different families within <i>Lysobacterales</i>, emphasizing the need for a refined family-level taxonomy. In addition, four novel species belonging to the family <i>Lysobacteraceae</i> were also confirmed. This study provides an updated familial framework for <i>Lysobacterales</i>, laying a robust foundation for future detailed taxonomic revisions at the genus and species levels.https://www.mdpi.com/2076-2607/13/6/1212<i>Lysobacterales</i>phylogenomicreannotation taxonomybacterial core genes |
| spellingShingle | Tengfei Ma Haijiao Liu Yafei Chen Juan Liu Chungen Piao Han Xue Risheng Xu Yong Li Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species Microorganisms <i>Lysobacterales</i> phylogenomic reannotation taxonomy bacterial core genes |
| title | Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species |
| title_full | Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species |
| title_fullStr | Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species |
| title_full_unstemmed | Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species |
| title_short | Familial Reclassification Within Order <i>Lysobacterales</i> and Proposal of Four Novel Species |
| title_sort | familial reclassification within order i lysobacterales i and proposal of four novel species |
| topic | <i>Lysobacterales</i> phylogenomic reannotation taxonomy bacterial core genes |
| url | https://www.mdpi.com/2076-2607/13/6/1212 |
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