Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens
International audience The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurr...
Published in: | International Journal of Systematic and Evolutionary Microbiology |
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Main Authors: | , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2020
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Online Access: | https://hal.inrae.fr/hal-03319338 https://hal.inrae.fr/hal-03319338/document https://hal.inrae.fr/hal-03319338/file/2020_Nicholson_ijsem.pdf https://doi.org/10.1099/ijsem.0.003935 |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
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English |
topic |
Chryseobacterium extinction genus delineation taxonomy [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
spellingShingle |
Chryseobacterium extinction genus delineation taxonomy [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology Nicholson, Ainsley, Gulvik, Christopher, Whitney, Anne, Humrighouse, Ben, Bell, Melissa, Holmes, Barry Steigerwalt, Arnie, Villarma, Aaron Sheth, Mili Batra, Dhwani Rowe, Lori, Burroughs, Mark Pryor, Jessica, Bernardet, Jean-François Hugo, Celia Kämpfer, Peter Newman, Jeffrey, McQuiston, John Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
topic_facet |
Chryseobacterium extinction genus delineation taxonomy [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology |
description |
International audience The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov. |
author2 |
Centers for Disease Control and Prevention Atlanta (CDC) Centers for Disease Control and Prevention Health Protection Agency Virologie et Immunologie Moléculaires (VIM (UR 0892)) Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) University of the Free State South Africa Justus-Liebig-Universität Gießen (JLU) Lycoming College Advanced Molecular Detection (AMD) initiative. Lycoming College Professional Development Grants, NSF Grants 0960114 and 1248096 Fulbright Grant from the US State Department. INRAE |
format |
Article in Journal/Newspaper |
author |
Nicholson, Ainsley, Gulvik, Christopher, Whitney, Anne, Humrighouse, Ben, Bell, Melissa, Holmes, Barry Steigerwalt, Arnie, Villarma, Aaron Sheth, Mili Batra, Dhwani Rowe, Lori, Burroughs, Mark Pryor, Jessica, Bernardet, Jean-François Hugo, Celia Kämpfer, Peter Newman, Jeffrey, McQuiston, John |
author_facet |
Nicholson, Ainsley, Gulvik, Christopher, Whitney, Anne, Humrighouse, Ben, Bell, Melissa, Holmes, Barry Steigerwalt, Arnie, Villarma, Aaron Sheth, Mili Batra, Dhwani Rowe, Lori, Burroughs, Mark Pryor, Jessica, Bernardet, Jean-François Hugo, Celia Kämpfer, Peter Newman, Jeffrey, McQuiston, John |
author_sort |
Nicholson, Ainsley, |
title |
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
title_short |
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
title_full |
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
title_fullStr |
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
title_full_unstemmed |
Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens |
title_sort |
division of the genus chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus epilithonimonas, eleven species to the genus kaistella, and three species to the genus halpernia gen. nov., with description of kaistella daneshvariae sp. nov. and epilithonimonas vandammei sp. nov. derived from clinical specimens |
publisher |
HAL CCSD |
publishDate |
2020 |
url |
https://hal.inrae.fr/hal-03319338 https://hal.inrae.fr/hal-03319338/document https://hal.inrae.fr/hal-03319338/file/2020_Nicholson_ijsem.pdf https://doi.org/10.1099/ijsem.0.003935 |
genre |
Antarc* |
genre_facet |
Antarc* |
op_source |
ISSN: 1466-5026 EISSN: 1466-5034 International Journal of Systematic and Evolutionary Microbiology https://hal.inrae.fr/hal-03319338 International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, 2020, 70 (8), pp.4432 - 4450. ⟨10.1099/ijsem.0.003935⟩ https://www.microbiologyresearch.org/content/journal/ijsem |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1099/ijsem.0.003935 info:eu-repo/semantics/altIdentifier/pmid/32735208 hal-03319338 https://hal.inrae.fr/hal-03319338 https://hal.inrae.fr/hal-03319338/document https://hal.inrae.fr/hal-03319338/file/2020_Nicholson_ijsem.pdf doi:10.1099/ijsem.0.003935 PUBMED: 32735208 WOS: 000583797700003 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1099/ijsem.0.003935 |
container_title |
International Journal of Systematic and Evolutionary Microbiology |
container_volume |
70 |
container_issue |
8 |
container_start_page |
4432 |
op_container_end_page |
4450 |
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1766260981165457408 |
spelling |
ftccsdartic:oai:HAL:hal-03319338v1 2023-05-15T13:54:50+02:00 Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens Nicholson, Ainsley, Gulvik, Christopher, Whitney, Anne, Humrighouse, Ben, Bell, Melissa, Holmes, Barry Steigerwalt, Arnie, Villarma, Aaron Sheth, Mili Batra, Dhwani Rowe, Lori, Burroughs, Mark Pryor, Jessica, Bernardet, Jean-François Hugo, Celia Kämpfer, Peter Newman, Jeffrey, McQuiston, John Centers for Disease Control and Prevention Atlanta (CDC) Centers for Disease Control and Prevention Health Protection Agency Virologie et Immunologie Moléculaires (VIM (UR 0892)) Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE) University of the Free State South Africa Justus-Liebig-Universität Gießen (JLU) Lycoming College Advanced Molecular Detection (AMD) initiative. Lycoming College Professional Development Grants, NSF Grants 0960114 and 1248096 Fulbright Grant from the US State Department. INRAE 2020 https://hal.inrae.fr/hal-03319338 https://hal.inrae.fr/hal-03319338/document https://hal.inrae.fr/hal-03319338/file/2020_Nicholson_ijsem.pdf https://doi.org/10.1099/ijsem.0.003935 en eng HAL CCSD Microbiology Society info:eu-repo/semantics/altIdentifier/doi/10.1099/ijsem.0.003935 info:eu-repo/semantics/altIdentifier/pmid/32735208 hal-03319338 https://hal.inrae.fr/hal-03319338 https://hal.inrae.fr/hal-03319338/document https://hal.inrae.fr/hal-03319338/file/2020_Nicholson_ijsem.pdf doi:10.1099/ijsem.0.003935 PUBMED: 32735208 WOS: 000583797700003 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 1466-5026 EISSN: 1466-5034 International Journal of Systematic and Evolutionary Microbiology https://hal.inrae.fr/hal-03319338 International Journal of Systematic and Evolutionary Microbiology, Microbiology Society, 2020, 70 (8), pp.4432 - 4450. ⟨10.1099/ijsem.0.003935⟩ https://www.microbiologyresearch.org/content/journal/ijsem Chryseobacterium extinction genus delineation taxonomy [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology info:eu-repo/semantics/article Journal articles 2020 ftccsdartic https://doi.org/10.1099/ijsem.0.003935 2021-12-18T23:57:12Z International audience The genus Chryseobacterium in the family Weeksellaceae is known to be polyphyletic. Amino acid identity (AAI) values were calculated from whole-genome sequences of species of the genus Chryseobacterium, and their distribution was found to be multi-modal. These naturally-occurring non-continuities were leveraged to standardise genus assignment of these species. We speculate that this multi-modal distribution is a consequence of loss of biodiversity during major extinction events, leading to the concept that a bacterial genus corresponds to a set of species that diversified since the Permian extinction. Transfer of nine species ( Chryseobacterium arachidiradicis , Chryseobacterium bovis, Chryseobacterium caeni, Chryseobacterium hispanicum, Chryseobacterium hominis, Chryseobacterium hungaricum,, Chryseobacterium pallidum and Chryseobacterium zeae ) to the genus Epilithonimonas and eleven ( Chryseobacterium anthropi , Chryseobacterium antarcticum , Chryseobacterium carnis , Chryseobacterium chaponense , Chryseobacterium haifense, Chryseobacterium jeonii, Chryseobacterium montanum , Chryseobacterium palustre , Chryseobacterium solincola , Chryseobacterium treverense and Chryseobacterium yonginense ) to the genus Kaistella is proposed. Two novel species are described: Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. Evidence is presented to support the assignment of Planobacterium taklimakanense to a genus apart from Chryseobacterium, to which Planobacterium salipaludis comb nov. also belongs. The novel genus Halpernia is proposed, to contain the type species Halpernia frigidisoli comb. nov., along with Halpernia humi comb. nov., and Halpernia marina comb. nov. Article in Journal/Newspaper Antarc* Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) International Journal of Systematic and Evolutionary Microbiology 70 8 4432 4450 |