New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis
At present, it is widely believed that a 95–96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA–DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-04-01
|
| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1359021/full |
| _version_ | 1797208800922435584 |
|---|---|
| author | Aihua Deng Li Fu Ping Mo Yaxi Zheng Ting Tang Jian Gao |
| author_facet | Aihua Deng Li Fu Ping Mo Yaxi Zheng Ting Tang Jian Gao |
| author_sort | Aihua Deng |
| collection | DOAJ |
| description | At present, it is widely believed that a 95–96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA–DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95–96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis. |
| first_indexed | 2024-04-24T09:44:34Z |
| format | Article |
| id | doaj.art-936616c745c2479193ce0ada2df7a905 |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-04-24T09:44:34Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-936616c745c2479193ce0ada2df7a9052024-04-15T04:13:37ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2024-04-011510.3389/fmicb.2024.13590211359021New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysisAihua Deng0Li Fu1Ping Mo2Yaxi Zheng3Ting Tang4Jian Gao5Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, ChinaSchool of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, ChinaKey Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, ChinaKey Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, ChinaKey Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, Hunan Provincial Engineering Research Center for Fresh Wet Rice Noodles, Science and Technology Innovation Team for Efficient Agricultural Production and Deep Processing at General University in Hunan Province, Hunan Provincial Key Laboratory for Health Aquaculture and Product Processing in Dongting Lake Area, Hunan Provincial Key Laboratory for Molecular Immunity Technology of Aquatic Animal Diseases, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, Hunan, ChinaSchool of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, ChinaAt present, it is widely believed that a 95–96% average nucleotide identity (ANI) value is equivalent to a 70% digital DNA–DNA hybridization (dDDH) value in the prokaryotic taxonomy. However, in the present study, comparative genome analysis of 29 pairs of Amycolatopsis type strains revealed that a 70% dDDH value did not correspond to a 95–96% ANI based on the MuMmer ultra-rapid aligning tool (ANIm) but approximately corresponded to a 96.6% ANIm value in the genus Amycolatopsis. Based on this corresponding relationship, phenotypic and chemotaxonomical characteristics, as well as phylogenetic analysis, an actinobacterial strain HUAS 11-8T isolated from the rhizosphere soil of Cynara scolymus, was subjected to a polyphasic taxonomic characterization. Based on EzBioCloud alignment, it was found that strain HUAS11-8T had the 16S rRNA gene similarities of 99.78% with A. rhizosphaerae JCM 32589T, 97.8% with A. dongchuanensis YIM 75904T, and < 97.8% sequence similarities to other Amycolatopsis species. Phylogenetic analysis of 16S rRNA gene sequences and whole-genome sequences revealed that strain HUAS 11-8T was closely related to A. rhizosphaerae JCM 32589T. ANIm and dDDH values between strains HUAS 11-8T and A. rhizosphaerae JCM 32589T were 96.3 and 68.5%, respectively, lower than the 96.6 and 70% thresholds recommended for the delineation of a novel Amycolatopsis species. Consequently, strain HUAS 11-8T should represent a novel Amycolatopsis species, for which the name Amycolatopsis cynarae sp. nov. (type strain HUAS 11-8T = MCCC 1K08337T = JCM 35980T) is proposed. Furthermore, based on comparative genomic analysis and rule 42 of the Prokaryotic Code, we propose that Amycolatopsis niigatensis is a later heterotypic synonym of Amycolatopsis echigonensis.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1359021/fullInternational Streptomyces ProjectANIm and dDDHcorresponding relationshipAmycolatopsis cynarae sp. nov.synonymAmycolatopsis niigatensis |
| spellingShingle | Aihua Deng Li Fu Ping Mo Yaxi Zheng Ting Tang Jian Gao New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis Frontiers in Microbiology International Streptomyces Project ANIm and dDDH corresponding relationship Amycolatopsis cynarae sp. nov. synonym Amycolatopsis niigatensis |
| title | New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis |
| title_full | New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis |
| title_fullStr | New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis |
| title_full_unstemmed | New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis |
| title_short | New insights into the relationship between the average nucleotide identity and the digital DNA–DNA hybridization values in the genus Amycolatopsis and Amycolatopsis cynarae sp. nov., a novel actinobacterium from the rhizosphere soil of Cynara scolymus, and proposal of Amycolatopsis niigatensis as a synonym of Amycolatopsis echigonensis based on comparative genomic analysis |
| title_sort | new insights into the relationship between the average nucleotide identity and the digital dna dna hybridization values in the genus amycolatopsis and amycolatopsis cynarae sp nov a novel actinobacterium from the rhizosphere soil of cynara scolymus and proposal of amycolatopsis niigatensis as a synonym of amycolatopsis echigonensis based on comparative genomic analysis |
| topic | International Streptomyces Project ANIm and dDDH corresponding relationship Amycolatopsis cynarae sp. nov. synonym Amycolatopsis niigatensis |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1359021/full |
| work_keys_str_mv | AT aihuadeng newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy AT lifu newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy AT pingmo newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy AT yaxizheng newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy AT tingtang newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy AT jiangao newinsightsintotherelationshipbetweentheaveragenucleotideidentityandthedigitaldnadnahybridizationvaluesinthegenusamycolatopsisandamycolatopsiscynaraespnovanovelactinobacteriumfromtherhizospheresoilofcynarascolymusandproposalofamycolatopsisniigatensisasasy |