1
|
Oren A, Göker M. Validation List no. 217. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38828845 DOI: 10.1099/ijsem.0.006275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
2
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 74, part 2 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38828851 DOI: 10.1099/ijsem.0.006301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
3
|
Tian X, Teo WFA, Yang Y, Dong L, Wong A, Chen L, Ahmed H, Choo SW, Jakubovics NS, Tan GYA. Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity. BMC Microbiol 2024; 24:185. [PMID: 38802738 PMCID: PMC11131293 DOI: 10.1186/s12866-024-03346-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences. RESULTS Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health. Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24. CONCLUSIONS Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health. SIGNIFICANCE This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.
Collapse
Affiliation(s)
- Xuechen Tian
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Wee Fei Aaron Teo
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Yixin Yang
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Linyinxue Dong
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
| | - Aloysius Wong
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA
| | - Li Chen
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Halah Ahmed
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK
| | - Siew Woh Choo
- College of Science, Mathematics and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Wenzhou Municipal Key Laboratory for Applied Biomedical and Biopharmaceutical Informatics, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Zhejiang Bioinformatics International Science and Technology Cooperation Center, Wenzhou-Kean University, Ouhai, Wenzhou, Zhejiang Province, 325060, China.
- Dorothy and George Hennings College of Science, Mathematics and Technology, Kean University, 1000 Morris Ave, Union, NJ, 07083, USA.
| | - Nicholas S Jakubovics
- School of Dental Sciences, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 4BW, UK.
| | - Geok Yuan Annie Tan
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia.
| |
Collapse
|
4
|
Sutcliffe IC, Rodriguez-R LM, Venter SN, Whitman WB. Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode. Syst Appl Microbiol 2024; 47:126498. [PMID: 38442686 DOI: 10.1016/j.syapm.2024.126498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of Archaea and Bacteria using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.
Collapse
Affiliation(s)
- Iain C Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle Upon Tyne, UK.
| | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innsbruck 60b0, Austria
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, GA C060b, USA
| |
Collapse
|
5
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 74, part 1 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38695346 DOI: 10.1099/ijsem.0.006271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
6
|
van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
Collapse
Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
7
|
Malhotra M, Bello S, Gupta RS. Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus. Syst Appl Microbiol 2024; 47:126499. [PMID: 38428338 DOI: 10.1016/j.syapm.2024.126499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/03/2024]
Abstract
To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.
Collapse
Affiliation(s)
- Megha Malhotra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Sarah Bello
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8N 3Z5, Canada.
| |
Collapse
|
8
|
Martinez-Romero E, Peix A, Hungria M, Mousavi SA, Martinez-Romero J, Young P. Guidelines for the description of rhizobial symbiovars. Int J Syst Evol Microbiol 2024; 74. [PMID: 38743471 DOI: 10.1099/ijsem.0.006373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024] Open
Abstract
Rhizobia are bacteria that form nitrogen-fixing nodules in legume plants. The sets of genes responsible for both nodulation and nitrogen fixation are carried in plasmids or genomic islands that are often mobile. Different strains within a species sometimes have different host specificities, while very similar symbiosis genes may be found in strains of different species. These specificity variants are known as symbiovars, and many of them have been given names, but there are no established guidelines for defining or naming them. Here, we discuss the requirements for guidelines to describe symbiovars, propose a set of guidelines, provide a list of all symbiovars for which descriptions have been published so far, and offer a mechanism to maintain a list in the future.
Collapse
Affiliation(s)
| | - Alvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain
- Interacción Planta-Microorganismo, Universidad de Salamanca, Unidad Asociada al CSIC por el IRNASA, Salamanca, Spain
| | | | | | | | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| |
Collapse
|
9
|
Berge A, Lundin J, Bläckberg A, Sunnerhagen T, Rasmussen M. Non-betahemolytic streptococcal bacteremia, cardiac implantable electronic device, endocarditis, extraction, and outcome; a population-based retrospective cohort study. Infection 2024:10.1007/s15010-024-02221-0. [PMID: 38634990 DOI: 10.1007/s15010-024-02221-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/19/2024] [Indexed: 04/19/2024]
Abstract
PURPOSE Patients with non-beta-hemolytic streptococcal bacteremia (NBHSB) are at risk of infective endocarditis (IE). Patients with cardiac implantable electronic device (CIED) have been described to have an increased risk of IE. The aim of the study was to describe a population-based cohort of patients with NBHSB and CIED and variables associated with IE and recurrent NBHSB. METHODS All episodes with NBHSB in blood culture from 2015 to 2018 in a population of 1.3 million inhabitants were collected from the Clinical Microbiology Laboratory, Lund, Sweden. Through medical records, patients with CIED during NBHSB were identified and clinical data were collected. Patients were followed 365 days after NBHSB. RESULTS Eighty-five episodes in 79 patients with CIED and NBHSB constituted the cohort. Eight patients (10%) were diagnosed with definite IE during the first episode, five of whom also had heart valve prosthesis (HVP). In 39 patients (49%) transesophageal echocardiography (TEE) was performed of which six indicated IE. Four patients had the CIED extracted. Twenty-four patients did not survive (30%) the study period. Four patients had a recurrent infection with NBHSB with the same species, three of whom had HVP and had been evaluated with TEE with a negative result during the first episode and diagnosed with IE during the recurrency. CONCLUSION The study did not find a high risk of IE in patients with NBHSB and CIED. Most cases of IE were in conjunction with a simultaneous HVP. A management algorithm is suggested.
Collapse
Affiliation(s)
- Andreas Berge
- Unit of Infectious Diseases, Department of Medicine, Solna, Karolinska Institutet, 171 76, Stockholm, Sweden.
- Department of Infectious Diseases, Karolinska University Hospital, 171 76, Stockholm, Sweden.
| | - Johannes Lundin
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 00, Lund, Sweden
| | - Anna Bläckberg
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 00, Lund, Sweden
- Division for Infectious Diseases, Skåne University Hospital, 221 00, Lund, Sweden
| | - Torgny Sunnerhagen
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 00, Lund, Sweden
- Department of Clinical Microbiology, Infection Control and Prevention, Office for Medical Services, Region Skåne, 221 85, Lund, Sweden
| | - Magnus Rasmussen
- Department of Clinical Sciences Lund, Division of Infection Medicine, Lund University, 221 00, Lund, Sweden
- Division for Infectious Diseases, Skåne University Hospital, 221 00, Lund, Sweden
| |
Collapse
|
10
|
Deng A, Fu L, Mo P, Zheng Y, Tang T, Gao J. 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. Front Microbiol 2024; 15:1359021. [PMID: 38686110 PMCID: PMC11056570 DOI: 10.3389/fmicb.2024.1359021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
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.
Collapse
Affiliation(s)
- Aihua Deng
- Key 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, China
| | - Li Fu
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
| | - Ping Mo
- Key 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, China
| | - Yaxi Zheng
- Key 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, China
| | - Ting Tang
- Key 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, China
| | - Jian Gao
- School of Life and Health Sciences, Hunan University of Science and Technology, Xiangtan, Hunan, China
| |
Collapse
|
11
|
Deshmukh UB, Oren A. Proposal of Shuttleworthella gen. nov. and Nostocoides gen. nov. as replacement names for the illegitimate prokaryotic generic names Shuttleworthia and Tetrasphaera, respectively. Int J Syst Evol Microbiol 2024; 74. [PMID: 38573081 DOI: 10.1099/ijsem.0.006318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
The prokaryotic generic name Shuttleworthia Downes et al. 2002 is illegitimate because it is a later homonym of the plant genus Shuttleworthia Meisner 1840 and the mollusk genus Shuttleworthia Baker 1941 (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Shuttleworthella, with type species Shuttleworthella satelles comb. nov. The prokaryotic generic name Tetrasphaera Maszenan et al. 2000 is illegitimate because it is a later homonym of Tetrasphaera Popofsky 1913 (Protozoa, Radiolaria) and of Tetrasphaera Górka 1965 (a fossil dinoflagellate) (Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Nostocoides, with type species Nostocoides japonicum comb. nov.
Collapse
Affiliation(s)
- Umakant Bhoopati Deshmukh
- Institution of Higher Learning, Research and Specialized Studies Centre, Department of Botany, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| |
Collapse
|
12
|
Bläckberg A, Holm K, Liderot K, Nilson B, Sunnerhagen T. Eubacterium bacteremia - a retrospective observational study of a seldom found anaerobic pathogen. Diagn Microbiol Infect Dis 2024; 108:116185. [PMID: 38232640 DOI: 10.1016/j.diagmicrobio.2024.116185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/28/2023] [Accepted: 01/11/2024] [Indexed: 01/19/2024]
Abstract
BACKGROUND Human infections due to Eubacterium are rare and knowledge of the condition is limited. This study aimed to describe clinical characteristics and outcome in patients with Eubacterium bacteremia. METHODS Episodes of Eubacterium bacteremia were identified through the clinical microbiology laboratory in Lund, Sweden. Medical records were retrospectively reviewed. Blood isolates of Eubacterium were collected and antibiotic susceptibility testing was performed with agar dilution. RESULTS Seventeen patients with Eubacterium bacteremia were identified of whom six had monomicrobial bacteremia. The incidence was 1.7 cases of Eubacterium bacteremia per million inhabitants and year. The median age was 67 years (interquartile range 63-79 years), and six patients had some form of malignancy. Most of the patients an abdominal focus of infection and the 30-day mortality was low (n = 1). CONCLUSIONS Invasive infections with Eubacterium have a low incidence. The condition has a low mortality and an abdominal focus of infection, and malignancy, is common.
Collapse
Affiliation(s)
- Anna Bläckberg
- Department of Infectious Diseases, Skåne University Hospital Lund, Sweden; Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden
| | - Karin Holm
- Department of Infectious Diseases, Skåne University Hospital Lund, Sweden; Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden
| | - Karin Liderot
- Division of Clinical Microbiology, Karolinska Institutet and Karolinska University Hospital, Huddinge, Stockholm, Sweden
| | - Bo Nilson
- Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Lund, Sweden; Division of Medical Microbiology, Department of Laboratory Medicine Lund, Lund University, Lund, Sweden
| | - Torgny Sunnerhagen
- Division of Infection Medicine, Department of Clinical Sciences Lund, Lund University Sweden; Clinical Microbiology, Infection Prevention and Control, Office for Medical Services, Lund, Sweden.
| |
Collapse
|
13
|
Goo RY, Li MS. Proposal of Sphingobacterium allocomposti nom. nov., Mycobacterium chelonae subsp. bovistauri nom. nov. and Lactobacillus delbrueckii subsp. allosunkii nom. nov. as new names with replacement specific or subspecific epithets, respectively, for three illegitimate prokaryotic names Sphingobacterium composti Yoo et al. 2007, Mycobacterium chelonae subsp. bovis Kim et al. 2017 and Lactobacillus delbrueckii subsp. sunkii Kudo et al. 2012; proposal of Christiangramia oceanisediminis comb. nov. and Christiangramia crocea comb. nov. as replacement names respectively for two illegitimate prokaryotic names Gramella oceanisediminis Yang et al. 2023 and Gramella crocea Zhang et al. 2023. Int J Syst Evol Microbiol 2024; 74. [PMID: 38578275 DOI: 10.1099/ijsem.0.006319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024] Open
Abstract
As required by Rule 54 of the International Code of Nomenclature of Prokaryotes, the authors propose the replacement specific epithet 'allocomposti' for the illegitimate prokaryotic name Sphingobacterium composti Yoo et al. 2007, the replacement subspecific epithet 'bovistauri' for Mycobacterium chelonae subsp. bovis Kim et al. 2017 and the replacement subspecific epithet 'allosunkii' for Lactobacillus delbrueckii subsp. sunkii Kudo et al. 2012. Meanwhile, new combinations Christiangramia oceanisediminis and Christiangramia crocea are also proposed as replacements for the illegitimate prokaryotic names Gramella oceanisediminis Yang et al. 2023 and Gramella crocea Zhang et al. 2023, respectively.
Collapse
Affiliation(s)
- Ruo-Yun Goo
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Meng-Syun Li
- Department of Veterinary Medicine, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
| |
Collapse
|
14
|
Dong X, Jia H, Yu Y, Xiang Y, Zhang Y. Genomic revisitation and reclassification of the genus Providencia. mSphere 2024; 9:e0073123. [PMID: 38412041 PMCID: PMC10964429 DOI: 10.1128/msphere.00731-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Members of Providencia, although typically opportunistic, can cause severe infections in immunocompromised hosts. Recent advances in genome sequencing provide an opportunity for more precise study of this genus. In this study, we first identified and characterized a novel species named Providencia zhijiangensis sp. nov. It has ≤88.23% average nucleotide identity (ANI) and ≤31.8% in silico DNA-DNA hybridization (dDDH) values with all known Providencia species, which fall significantly below the species-defining thresholds. Interestingly, we found that Providencia stuartii and Providencia thailandensis actually fall under the same species, evidenced by an ANI of 98.59% and a dDDH value of 90.4%. By fusing ANI with phylogeny, we have reclassified 545 genomes within this genus into 20 species, including seven unnamed taxa (provisionally titled Taxon 1-7), which can be further subdivided into 23 lineages. Pangenomic analysis identified 1,550 genus-core genes in Providencia, with coenzymes being the predominant category at 10.56%, suggesting significant intermediate metabolism activity. Resistance analysis revealed that most lineages of the genus (82.61%, 19/23) carry a high number of antibiotic-resistance genes (ARGs) and display diverse resistance profiles. Notably, the majority of ARGs are located on plasmids, underscoring the significant role of plasmids in the resistance evolution within this genus. Three species or lineages (P. stuartii, Taxon 3, and Providencia hangzhouensis L12) that possess the highest number of carbapenem-resistance genes suggest their potential influence on clinical treatment. These findings underscore the need for continued surveillance and study of this genus, particularly due to their role in harboring antibiotic-resistance genes. IMPORTANCE The Providencia genus, known to harbor opportunistic pathogens, has been a subject of interest due to its potential to cause severe infections, particularly in vulnerable individuals. Our research offers groundbreaking insights into this genus, unveiling a novel species, Providencia zhijiangensis sp. nov., and highlighting the need for a re-evaluation of existing classifications. Our comprehensive genomic assessment offers a detailed classification of 545 genomes into distinct species and lineages, revealing the rich biodiversity and intricate species diversity within the genus. The substantial presence of antibiotic-resistance genes in the Providencia genus underscores potential challenges for public health and clinical treatments. Our study highlights the pressing need for increased surveillance and research, enriching our understanding of antibiotic resistance in this realm.
Collapse
Affiliation(s)
- Xu Dong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
| | - Huiqiong Jia
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Yuyun Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanghui Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Guangzhou, China
| |
Collapse
|
15
|
Peng Y, Mo P, Zheng Y, Li C, Huang K. Proposal of Streptomyces bellus Margalith and Beretta 1960 as a Later Heterotypic Synonym of Streptomyces coeruleorubidus (Preobrazhenskaya 1957) Pridham et al. 1958 and an Emended Description of Streptomyces coeruleorubidus. Curr Microbiol 2024; 81:121. [PMID: 38528205 DOI: 10.1007/s00284-024-03638-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 02/12/2024] [Indexed: 03/27/2024]
Abstract
In the present work, the taxonomic relationship between Streptomyces coeruleorubidus and Streptomyces bellus was reevaluated by a comprehensive comparison of phenotypic, chemotaxonomic and genomic characteristics, as well as phylogeny. In 1957 and 1960, Streptomyces coeruleorubidus and Streptomyces bellus were described as two novel Streptomyces species. The full-length 16S rRNA gene sequence analysis indicated that Streptomyces bellus JCM 4292T shared highest sequence identity with Streptomyces coerulescens ISP 5146T (100%). Phylogenetic analysis of 16S rRNA gene sequence showed that S. bellus JCM 4292T was most closely related to Streptomyces coerulescens ISP 5146T. Phylogenetic analysis of five housekeeping gene sequences demonstrated that S. bellus JCM 4292T was most closely related to S. coeruleorubidus ATCC 13740T. Nevertheless, the ANIm (average nucleotide identity based on MuMmer ultra-rapid aligning tool) and dDDH (digital DNA-DNA hybridization) values between them were 97.71% and 81.9%, respectively, greater than the threshold of 96.7% and 70% for the delineation of Streptomyces species, suggesting that they represent the same genomic species. In addition, phenotypic and chemotaxonomic characteristics, as well as phylogeny and genomic DNA-DNA correlation analysis also confirmed the above conclusion. Consequently, we proposed that S. bellus Margalith and Beretta 1960 is a later heterotypic synonym of S. coeruleorubidus (Preobrazhenskaya 1957) Pridham et al. 1958.
Collapse
Affiliation(s)
- Yi Peng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, 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, 415000, Hunan, People's Republic of China
| | - Ping Mo
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, 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, 415000, Hunan, People's Republic of China.
| | - Yaxi Zheng
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, 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, 415000, Hunan, People's Republic of China
| | - Chenxi Li
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, 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, 415000, Hunan, People's Republic of China
| | - Kerui Huang
- Key Laboratory of Agricultural Products Processing and Food Safety in Hunan Higher Education, 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, 415000, Hunan, People's Republic of China.
| |
Collapse
|
16
|
Huang HJ, Zhang X, Sun XW, Chen B, Li XT, Zhou N, Abdugheni R, Cheng QY, Zhang TJ, Liu Y, Jiang Y, Deng Y, Liu SJ, Jiang CY. Xiashengella succiniciproducens gen. nov., sp. nov., a succinate-producing bacterium isolated from an anaerobic digestion tank in the family Marinilabiliaceae of the order Bacteroidales. Arch Microbiol 2024; 206:141. [PMID: 38441685 DOI: 10.1007/s00203-024-03909-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/24/2024] [Indexed: 03/07/2024]
Abstract
A strictly anaerobic, motile bacterium, designated as strain Ai-910T, was isolated from the sludge of an anaerobic digestion tank in China. Cells were Gram-stain-negative rods. Optimal growth was observed at 38 °C (growth range 25-42 °C), pH 8.5 (growth range 5.5-10.5), and under a NaCl concentration of 0.06% (w/v) (range 0-2.0%). Major cellular fatty acids were iso-C15 : 0 and anteiso-C15 : 0. The respiratory quinone was MK-7. Using xylose as the growth substrate, succinate was produced as the fermentation product. Phylogenetic analysis based on the 16 S rRNA gene sequences indicated that strain Ai-910T formed a distinct phylogenetic lineage that reflects a new genus in the family Marinilabiliaceae, sharing high similarities to Alkaliflexus imshenetskii Z-7010T (92.78%), Alkalitalea saponilacus SC/BZ-SP2T (92.51%), and Geofilum rubicundum JAM-BA0501T (92.36%). Genomic similarity (average nucleotide identity and digital DNA-DNA hybridization) values between strain Ai-910T and its phylogenetic neighbors were below 65.27 and 16.90%, respectively, indicating that strain Ai-910T represented a novel species. The average amino acid identity between strain Ai-910T and other related members of the family Marinilabiliaceae were below 69.41%, supporting that strain Ai-910T was a member of a new genus within the family Marinilabiliaceae. Phylogenetic, genomic, and phenotypic analysis revealed that strain Ai-910T was distinguished from other phylogenetic relatives within the family Marinilabiliaceae. The genome size was 3.10 Mbp, and the DNA G + C content of the isolate was 42.8 mol%. Collectively, differences of the phenotypic and phylogenetic features of strain Ai-910T from its close relatives suggest that strain Ai-910T represented a novel species in a new genus of the family Marinilabiliaceae, for which the name Xiashengella succiniciproducens gen. nov., sp. nov. was proposed. The type strain of Xiashengella succiniciproducens is Ai-910T (= CGMCC 1.17893T = KCTC 25,304T).
Collapse
Affiliation(s)
- Hao-Jie Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Xi Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Wei Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China
| | - Biao Chen
- Xuzhou Medical University, Xuzhou, 221004, China
| | - Xiu-Tong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nan Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rashidin Abdugheni
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiu-Yin Cheng
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Tie-Jun Zhang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yao Liu
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Yong Jiang
- Beijing Drainage Group Co., Ltd, Beijing, 100044, China
| | - Ye Deng
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266000, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Cheng-Ying Jiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, University of Chinese Academy of Sciences, Beijing, 100049, China.
- IMCAS-RCEES Joint Lab at CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| |
Collapse
|
17
|
Oren A, Göker M. Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74:006229. [PMID: 38546332 PMCID: PMC10995726 DOI: 10.1099/ijsem.0.006229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Indexed: 04/07/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
18
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 11 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38437003 DOI: 10.1099/ijsem.0.006213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
19
|
Cui HL, Hou J, Amoozegar MA, Dyall-Smith ML, de la Haba RR, Minegishi H, Montalvo-Rodriguez R, Oren A, Sanchez-Porro C, Ventosa A, Vreeland RH. Proposed minimal standards for description of new taxa of the class Halobacteria. Int J Syst Evol Microbiol 2024; 74:006290. [PMID: 38456846 PMCID: PMC10999741 DOI: 10.1099/ijsem.0.006290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 02/24/2024] [Indexed: 03/09/2024] Open
Abstract
Halophilic archaea of the class Halobacteria are the most salt-requiring prokaryotes within the domain Archaea. In 1997, minimal standards for the description of new taxa in the order Halobacteriales were proposed. From then on, the taxonomy of the class Halobacteria provides an excellent example of how changing concepts on prokaryote taxonomy and the development of new methods were implemented. The last decades have witnessed a rapid expansion of the number of described taxa within the class Halobacteria coinciding with the era of genome sequencing development. The current members of the International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Halobacteria propose these revisions to the recommended minimal standards and encourage the use of advanced technologies in the taxonomic description of members of the Halobacteria. Most previously required and some recommended minimal standards for the description of new taxa in the class Halobacteria were retained in the present revision, but changes have been proposed in line with the new methodologies. In addition to the 16S rRNA gene, the rpoB' gene is an important molecular marker for the identification of members of the Halobacteria. Phylogenomic analysis based on concatenated conserved, single-copy marker genes is required to infer the taxonomic status of new taxa. The overall genome relatedness indexes have proven to be determinative in the classification of the taxa within the class Halobacteria. Average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values should be calculated for rigorous comparison among close relatives.
Collapse
Affiliation(s)
- Heng-Lin Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Jing Hou
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, PR China
| | - Mohammad Ali Amoozegar
- Department of Microbiology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran 14178-64411, Iran
| | - Mike L. Dyall-Smith
- Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, University of Melbourne, Parkville, 3010, Australia
| | - Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Hiroaki Minegishi
- Department of Applied Chemistry, Faculty of Science and Engineering, Toyo University, Kawagoe, Japan
| | | | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Cristina Sanchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Russell H. Vreeland
- Eastern Shore Microbes, 15397 Merry Cat Lane, Post Office Box 216, Belle Haven, VA 23306, USA
| |
Collapse
|
20
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 12 of the IJSEM. Int J Syst Evol Microbiol 2024; 74:006243. [PMID: 38546333 PMCID: PMC10995960 DOI: 10.1099/ijsem.0.006243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Indexed: 04/07/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
21
|
Arahal DR, Göker M, Hahnke RL, Manaia CM, Moore ER, Oren A, Sutcliffe IC, Ventura S. Proposals to revise the Statutes of the International Committee on Systematics of Prokaryotes. Int J Syst Evol Microbiol 2024; 74:006291. [PMID: 38441551 PMCID: PMC10999737 DOI: 10.1099/ijsem.0.006291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
The International Committee on Systematics of Prokaryotes serves to administer the rules of prokaryotic nomenclature via the International Code of Nomenclature of Prokaryotes, ensures the publication of the International Journal of Systematic and Evolutionary Microbiology, and works to represent the interests of the microbiological disciplines regarding prokaryotic nomenclature. The functions and mechanisms of operation of the International Committee on Systematics of Prokaryotes (ICSP) are defined in its Statutes, which were last revised in 2019. As members of the 2020-2023 and the 2023-2026 ICSP Executive Board and the Judicial Commission, we propose here some further revisions to help improve the clarity and functionality of the Statutes.
Collapse
Affiliation(s)
- David R. Arahal
- Departamento de Microbiología y Ecología, Universitat de València, 46100 Burjassot (Valencia), Spain
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Bioinformatics and Databases, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Richard L. Hahnke
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Department of Microorganisms, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Célia M. Manaia
- Universidade Católica Portuguesa, CBQF – Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Edward R.B. Moore
- Department of Infectious Disease, and Culture Collection University of Gothenburg, Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, P.O. Box 7193, SE0492 34, Gothenburg, Sweden
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | | | - Stefano Ventura
- IRET-CNR, Research Institute on Terrestrial Ecosystems, National Research Council, Via Madonna del Piano 10, 50019 Sesto Fiorentino, and NBCF, National Biodiversity Future Center, Palermo, Italy
| |
Collapse
|
22
|
Oren A, Göker M. Validation List no. 215. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299482 DOI: 10.1099/ijsem.0.006173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
23
|
Novoa EAM, Deshmukh UB, Oren A. Reclassification of Allomuricauda and Muricauda species as members of the genus Flagellimonas Bae et al. 2007 and emended description of the genus Flagellimonas. Int J Syst Evol Microbiol 2024; 74. [PMID: 38421264 DOI: 10.1099/ijsem.0.006286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
The recently proposed genus Allomuricauda Deshmukh and Oren 2023 is illegitimate because it includes the type species of the genera Flagellimonas Bae et al. 2007 and Spongiibacterium Yoon and Oh 2012, contravening Rule 51b(1) of the International Code of Nomenclature of Prokaryotes. As Flagellimonas Bae et al. 2007 is the earlier described genus, we here reclassify 36 species earlier described as belonging to the illegitimate genus Muricauda as species of Flagellimonas. We also present an emended description of the genus Flagellimonas.
Collapse
Affiliation(s)
- Eduardo A Molinari Novoa
- Chess Consulting & Project, Lima 15039, and 'La Molina' National Agrarian University, Lima 15024, Peru
| | - Umakant Bhoopati Deshmukh
- Institution of Higher Learning, Research and Specialized Studies Centre, Department of Botany, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| |
Collapse
|
24
|
Arahal DR, Bull CT, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Ventosa A, Young P, Göker M. Judicial Opinion 129. Int J Syst Evol Microbiol 2024; 74. [PMID: 38376502 DOI: 10.1099/ijsem.0.006064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024] Open
Abstract
Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.
Collapse
Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, QLD 4072, Australia
| | - Svetlana N Dedysh
- Research Center of Biotechnology RAS, Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| |
Collapse
|
25
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 10 of the IJSEM. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299470 DOI: 10.1099/ijsem.0.006172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures,, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
26
|
Bello S, McQuay S, Rudra B, Gupta RS. Robust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers. Int J Syst Evol Microbiol 2024; 74. [PMID: 38319314 DOI: 10.1099/ijsem.0.006247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
The family Peptostreptococcaceae, which contains 15 genera including Clostridioides, presently lacks proper circumscription. Using 52 available genomes for Peptostreptococcaceae species, we report comprehensive phylogenomic and comparative analyses to reliably discern their evolutionary relationships. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, the examined species formed a strongly supported clade designated as Peptostreptococcaceae sensu stricto. This clade encompassed the genera Peptostreptococcus (type genus), Asaccharospora, Clostridioides, Intestinibacter, Paeniclostridium, Paraclostridium, Peptacetobacter, Romboutsia and Terrisporobacter, and two misclassified species (viz. Eubacterium tenue and 'Clostridium dakarense'). The distinctness of this clade is strongly supported by eight identified conserved signature indels (CSIs), which are specific for the species from this clade. Based on the robust evidence provided by presented studies, we are proposing the emendment of family Peptostreptococcaceae to only the genera within the Peptostreptococcaceae sensu stricto clade. We also report 67 other novel CSIs, which reliably demarcate different Peptostreptococcaceae species clades and clarify the classification of some misclassified species. Based on the consistent evidence obtained from different presented studies, we are making the following proposals to clarify the classification of Peptostreptococcaceae species: (i) transfer of Eubacterium tenue, Paeniclostridium ghonii and Paeniclostridium sordellii as comb. nov. into the genus Paraclostridium; (ii) transfer of Clostridioides mangenotii as a comb. nov. into Metaclostridioides gen. nov.; (iii) classification of 'Clostridium dakarense' as a novel species Faecalimicrobium dakarense gen. nov., sp. nov. (type strain FF1T; genome and 16S rRNA accession numbers GCA_000499525.1 and KC517358, respectively); (iv) transfer of two misclassified species, Clostridium paradoxum and Clostridium thermoalcaliphilum, into Alkalithermobacter gen. nov.; and (v) proposals for two novel families, Peptoclostridiaceae fam. nov. and Tepidibacteraceae fam. nov., to accommodate remaining unclassified Peptostreptococcaceae genera. The described CSIs specific for different families and genera provide novel and reliable means for the identification, diagnostics and biochemical studies on these bacteria.
Collapse
Affiliation(s)
- Sarah Bello
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Ontario, Canada
| | - Sarah McQuay
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Ontario, Canada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Ontario, Canada
| | - Radhey S Gupta
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, L8N 3Z5, Ontario, Canada
| |
Collapse
|
27
|
Oren A, Göker M. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of Changes in Taxonomic Opinion no. 39. Int J Syst Evol Microbiol 2024; 74. [PMID: 38299467 DOI: 10.1099/ijsem.0.006145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
28
|
Arahal D, Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Duim B, Emler S, Figge M, Göker M, Moore ERB, Nemec A, Nørskov-Lauritsen N, Nübel U, On SLW, Vandamme P, Ventosa A. The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38180015 DOI: 10.1099/ijsem.0.006188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024] Open
Abstract
The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.
Collapse
Affiliation(s)
- David Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | | | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Dominique Clermont
- Institut Pasteur, Université Paris Cité, CRBIP, CIP-Collection of Institut Pasteur, F-75015 Paris, France
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, Albinusdreef 2, Leiden / Torensteelaan 68, 3281 MA Numansdorp, Netherlands
| | - Birgitta Duim
- Department Biomolecular Health Sciences, Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CS Utrecht, Netherlands
| | - Stefan Emler
- SmartGene Services SARL, EPFL Innovation Park, PSE-C, CH-1015 Lausanne, Switzerland
| | - Marian Figge
- Westerdijk Fungal Biodiversity Institute Uppsalalaan 8 3584 CT, Utrecht, Netherlands
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Edward R B Moore
- Department of Infectious Disease and Culture Collection University of Gothenburg (CCUG), Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, SE-402 34 Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Srobarova 48, 100 00 Prague 10, Czech Republic
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, V Úvalu 84, 150 06 Prague 5, Czechia
| | | | - Ulrich Nübel
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
| | - Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Faculty of Agricultural Science, Lincoln University, Lincoln 7647, Christchurch, New Zealand
| | - Peter Vandamme
- BCCM/LMG, Laboratorium voor Microbiologie, Universiteit Gent (UGent) K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| |
Collapse
|
29
|
Goodfellow M, Oren A, Sangal V, Sutcliffe IC. Is the bacterial genus name Rhodococcus Zopf 1891 illegitimate? Request for an Opinion. Int J Syst Evol Microbiol 2024; 74. [PMID: 38265282 DOI: 10.1099/ijsem.0.006251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024] Open
Abstract
In 2014, it was reported that the bacterial genus name Rhodococcus Zopf 1891 was illegitimate due to the priority of the cyanobacterial genus name Rhodococcus Hansgirg 1884. Since that time, the consequences of this conclusion have been largely ignored, whilst changes have been made to relevant Rules of the International Code of Nomenclature of Prokaryotes, including significant changes to the way in which the Code treats the names of members of Cyanobacteriota. Given the complexity of the nomenclatural issues, we request the opinion of the Judicial Commission of the International Committee on Systematics of Prokaryotes as to whether the genus name Rhodococcus Zopf 1891 (Approved Lists 1980) is illegitimate.
Collapse
Affiliation(s)
- Michael Goodfellow
- School of Natural and Environmental Sciences, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
| | - Vartul Sangal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| | - Iain C Sutcliffe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST, UK
| |
Collapse
|
30
|
Pallen MJ. Formation of prokaryote names from personal names: a review of current practice and a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38226641 DOI: 10.1099/ijsem.0.006233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
The practice of naming elements from the natural world after notable individuals stretches back to ancient times. This practice of creating eponyms-terms derived from personal names-has been carried forward into prokaryotic nomenclature, where the International Code of Nomenclature of Prokaryotes (ICNP) sets guidelines for creating scientific names from personal names. However, these guidelines can be seen as culturally biased, disjointed and, on occasion, misguided. Here, with the goal of modernizing these recommendations to render them more user-friendly, coherent and inclusive, I review current practice in the light of precedents and key linguistic and cultural principles, while questioning the applicability of the first-name/last-name paradigm for many cultural traditions. Procedural challenges include romanization of the personal name (including handling of diacritics), creation of a short and agreeable latinized stem, assignment of the stem to a declension and addition of suffixes or compound word components to create genus names or species epithets, customizing the approach for names and stems that end in a vowel. I review the pros and cons of stem augmentation, which involves addition of an extra 'i' to the original stem. Next, I formulate a coherent workflow, which I incorporate into a Python script to enable computer-based automation of name creation. Rather than following the ICNP in limiting discussion to a few dozen mainly European names, I examine how these principles work out when applied to the tens of thousands of last names under which scientists publish in the PubMed database, focusing on edge cases where conventional approaches fail, particularly very short and very long names. Drawing on these explorations and analyses, I propose emendations to the advice currently presented in the ICNP to usher in a modern, consistent, pragmatic and globally inclusive approach to the creation of prokaryotic eponyms.
Collapse
Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
31
|
Oren A. Emendation of Appendix 9 of the International Code of Nomenclature of Prokaryotes to provide guidelines for naming genera after geographical locations. Int J Syst Evol Microbiol 2024; 74. [PMID: 38289226 DOI: 10.1099/ijsem.0.006252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Following a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes with guidelines for the naming of genera after geographical locations, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes and present the guidelines to be incorporated in Appendix 9.
Collapse
Affiliation(s)
- Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| |
Collapse
|
32
|
Göker M, Oren A. Valid publication of names of two domains and seven kingdoms of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38252124 DOI: 10.1099/ijsem.0.006242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.
Collapse
Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
| |
Collapse
|
33
|
Lawhon SD, Burbick CR, Munson E, Thelen E, Zapp A, Wilson A. Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022. J Clin Microbiol 2023; 61:e0083923. [PMID: 37889054 PMCID: PMC10729710 DOI: 10.1128/jcm.00839-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023] Open
Abstract
Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the implications of those changes. Here, we describe additions of novel taxa from domestic animals published in 2022 that are validly published per the International Code of Nomenclature of Prokaryotes. These included new members of Staphylococcaceae, Moraxella nasovis sp. nov. in sheep with respiratory disease, three additions to Campylobacteraceae (including one from chickens with spotty liver disease), and multiple additions of organisms from the microbiota of dogs, pigs, and especially honeybees and other important pollinators. Noteworthy additions were associated with diseases of cattle, including mastitis, endocarditis, orchitis, and endometritis. Also described in 2022 was Pseudochrobactrum algeriense sp. nov., a member of the Brucellaceae family, isolated from the mammary lymph nodes of cows.
Collapse
Affiliation(s)
- Sara D. Lawhon
- Department of Veterinary Pathobiology, Texas A&M University, College Station, Texas, USA
| | - Claire R. Burbick
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, Washington, USA
| | - Erik Munson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Elizabeth Thelen
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Amanda Zapp
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| | - Anastasia Wilson
- Department of Medical Laboratory Science, Marquette University, Milwaukee, Wisconsin, USA
| |
Collapse
|
34
|
Lee SD, Yang HL, Kim IS. Four new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium. Front Microbiol 2023; 14:1299950. [PMID: 38164402 PMCID: PMC10757982 DOI: 10.3389/fmicb.2023.1299950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024] Open
Abstract
The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species. Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the "Microbacterium agarici clade", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.
Collapse
Affiliation(s)
- Soon Dong Lee
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - Hong Lim Yang
- Institute of Jeju Microbial Resources, BioPS Co., Ltd., Jeju, Republic of Korea
| | - In Seop Kim
- Department of Biological Sciences and Biotechnology, Hannam University, Daejon, Republic of Korea
- BioPS Co., Ltd., Daejeon, Republic of Korea
| |
Collapse
|
35
|
Pallen MJ. Use of connecting vowels after stems ending in the same vowel: a proposal to emend Appendix 9 of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 38054495 DOI: 10.1099/ijsem.0.006191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023] Open
Abstract
The International Code of Nomenclature of Prokaryotes (ICNP) provides guidance on the formation of names from compound words. This includes recommendations on the use of connecting vowels, which are meant to make names easier to pronounce. However, deployment of a connecting vowel when the preceding word element ends in the same vowel can make a name harder to spell or say, bringing us into conflict with the recommendations that we should avoid names that are disagreeable and difficult to pronounce. Given that there are many precedents where connecting vowels are not used in this context, particularly in names formed from the term 'alkali', I hereby propose an emendation to the ICNP to drop the connecting vowel when the preceding word element ends in the same vowel.
Collapse
Affiliation(s)
- Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- University of East Anglia, Norwich Research Park, Norwich, UK
| |
Collapse
|
36
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 8 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 38038642 DOI: 10.1099/ijsem.0.006094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
37
|
Oren A, Göker M. Validation List no. 214. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 38038645 DOI: 10.1099/ijsem.0.006080] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
38
|
de la Haba RR, Arahal DR, Sánchez-Porro C, Chuvochina M, Wittouck S, Hugenholtz P, Ventosa A. A long-awaited taxogenomic investigation of the family Halomonadaceae. Front Microbiol 2023; 14:1293707. [PMID: 38045027 PMCID: PMC10690426 DOI: 10.3389/fmicb.2023.1293707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 12/05/2023] Open
Abstract
The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.
Collapse
Affiliation(s)
- Rafael R. de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - David R. Arahal
- Departament of Microbiology and Ecology, University of Valencia, Valencia, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Stijn Wittouck
- Research Group Environmental Ecology and Applied Microbiology, Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, Spain
| |
Collapse
|
39
|
Freese HM, Giner-Pérez L, Oren A, Göker M, Arahal DR. The gender gap in names of prokaryotes honouring persons. Int J Syst Evol Microbiol 2023; 73. [PMID: 37909279 DOI: 10.1099/ijsem.0.006115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
The aim of this study is to analyse prokaryotic names which honour persons, eponyms, from a gender perspective. Data were retrieved from the List of Prokaryotic names with Standing in Nomenclature. Excluding new combinations, the etymologies of 23 315 unique names at the rank of genus, species and subspecies were analysed. A total of 2018 (8.7 %) names honour persons (eponyms), for which the development of the female share over time was further investigated. Women started to be honoured very recently (1947) compared to men (1823). Moreover, only 14.8 % of all prokaryotic eponyms refer to females. This ratio has hardly improved since 1947, although the number of women whose contributions to microbiology could have been recognized has increased over time. In contrast, about 50 % of prokaryotic names derived from mythological characters refer to females. To reduce this gender gap, we encourage authors proposing new taxon names to honour female scientists who can serve as role models for new generations.
Collapse
Affiliation(s)
- Heike M Freese
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - Lola Giner-Pérez
- Departament of Microbiology and Ecology, Universitat de València, 46100 Burjassot (Valencia), Spain
- Laboratory of Lactic Acid Bacteria and Probiotics, Department of Biotechnology, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), 46980 Paterna (Valencia), Spain
- Laboratory of Neurobiology, Centro de Investigación Principe Felipe, 46012 Valencia, Spain
| | - Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Department of Bioinformatics and Databases, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| | - David R Arahal
- Departament of Microbiology and Ecology, Universitat de València, 46100 Burjassot (Valencia), Spain
| |
Collapse
|
40
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 9 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37937952 DOI: 10.1099/ijsem.0.006158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
41
|
Straková D, Galisteo C, de la Haba RR, Ventosa A. Characterization of Haloarcula terrestris sp. nov. and reclassification of a Haloarcula species based on a taxogenomic approach. Int J Syst Evol Microbiol 2023; 73. [PMID: 37990990 DOI: 10.1099/ijsem.0.006157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
An extremely halophilic archaeon, strain S1AR25-5AT, was isolated from a hypersaline soil sampled in Odiel Saltmarshes Natural Area (Huelva, Spain). The cells were Gram-stain-negative, motile, pleomorphic rods. Cell growth was observed in the presence of 15-30 % (w/v) NaCl [optimum, 25 % (w/v) NaCl], at pH 6.0-9.0 (optimum, pH 6.5-7.5) and at 25-50 °C (optimum, 37 °C). Based on the 16S rRNA and rpoB' gene sequence comparisons, strain S1AR25-5AT was affiliated to the genus Haloarcula. Taxogenomic analysis, including comparison of the genomes and the phylogenomic tree based on the core-orthologous proteins, together with the genomic indices, i.e., orthologous average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity, confirmed that strain S1AR25-5AT (=CCM 9249T=CECT 30619T) represents a new species of the genus Haloarcula, for which we propose the name Haloarcula terrestris sp. nov. The major polar lipids were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulphate and an unidentified glycolipid, which correlated with the lipid profile of species of the genus Haloarcula. In addition, based on the modern approach in description of species in taxonomy of prokaryotes, the above mentioned genomic indexes indicated that the species Haloarcula tradensis should be considered as a heterotypic synonym of Haloarcula argentinensis.
Collapse
Affiliation(s)
- Dáša Straková
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Cristina Galisteo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, 41012 Sevilla, Spain
| |
Collapse
|
42
|
Oren A. Emendation of Principle 8, Rules 5b, 8, 15, 33a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes to include the categories of kingdom and domain. Int J Syst Evol Microbiol 2023; 73. [PMID: 37909283 DOI: 10.1099/ijsem.0.006123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Following an electronic discussion on proposals to emend Principle 8, Rules 5b, 8, 15, 33a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes (ICNP), I here report the outcome of the ballot on these proposals by the members of the International Committee on Systematics of Prokaryotes. These emendations enact the addition of the categories of kingdom and domain to the ICNP.
Collapse
Affiliation(s)
- Aharon Oren
- Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| |
Collapse
|
43
|
Val-Calvo J, Vázquez-Boland JA. Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. mBio 2023; 14:e0220723. [PMID: 37796005 PMCID: PMC10653829 DOI: 10.1128/mbio.02207-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE A robust taxonomy is essential for the organized study of prokaryotes and the effective communication of microbial knowledge. The genus rank is the mainstay of biological classification as it brings together under a common name a group of closely related organisms sharing the same recent ancestry and similar characteristics. Despite the unprecedented resolution afforded by whole-genome sequencing in defining evolutionary relationships, a consensus approach for phylogenomics-based prokaryotic genus delineation remains elusive. Taxonomists use different demarcation criteria, sometimes leading to genus rank over-splitting and the creation of multiple new genera. This work reports a simple, reliable, and standardizable method that seeks to minimize subjectivity in genomics-based demarcation of prokaryotic genera, exemplified through application to the order Mycobacteriales. Formal descriptions of proposed taxonomic changes based on our study are included.
Collapse
Affiliation(s)
- Jorge Val-Calvo
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - José A. Vázquez-Boland
- Microbial Pathogenesis Laboratory, Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Edinburgh, Scotland, United Kingdom
| |
Collapse
|
44
|
Yabe S, Muto K, Abe K, Yokota A, Staudigel H, Tebo BM. Correction: Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum "Eremiobacterota", is a metabolically versatile aerobic anoxygenic phototroph. ISME COMMUNICATIONS 2023; 3:102. [PMID: 37848514 PMCID: PMC10582173 DOI: 10.1038/s43705-023-00301-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Affiliation(s)
- Shuhei Yabe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 980-0845, Japan.
- Hazaka Plant Research Center, Kennan Eisei Kogyo Co., Ltd., Sendai, Miyagi, 989-1311, Japan.
| | - Kiyoaki Muto
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 980-0845, Japan
| | - Keietsu Abe
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 980-0845, Japan
| | - Akira Yokota
- Department of Microbial Resources, Graduate School of Agricultural Sciences, Tohoku University, Sendai, Miyagi, 980-0845, Japan
| | - Hubert Staudigel
- Institute of Geophysics and Planetary Physics, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bradley M Tebo
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA
| |
Collapse
|
45
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 6 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787066 DOI: 10.1099/ijsem.0.006009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B38124, Braunschweig, Germany
| |
Collapse
|
46
|
Oren A, Göker M. Validation List no. 213. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787078 DOI: 10.1099/ijsem.0.005997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures,, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
47
|
Molinari Novoa EA, Oren A. Proposal of Allopseudospirillum gen. nov. as a replacement name for the illegitimate prokaryotic generic name Pseudospirillum Satomi et al. 2002. Int J Syst Evol Microbiol 2023; 73. [PMID: 37882658 DOI: 10.1099/ijsem.0.006129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023] Open
Abstract
The prokaryotic generic name Pseudospirillum Satomi et al. 2002 is illegitimate because it is a later homonym of Pseudospirillum Alexeieff 1917, a genus of uncertain affiliation, possibly belonging to the Mesomycetozoa (Principle 2 and Rule 51b(5) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Allopseudospirillum, with type species Allopseudospirillum japonicum.
Collapse
Affiliation(s)
- Eduardo A Molinari Novoa
- Chess Consulting & Project, Lima 15039, and 'La Molina' National Agrarian University, Lima 15024, Peru
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 9190401, Israel
| |
Collapse
|
48
|
Oren A, Göker M. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 73, part 7 of the IJSEM. Int J Syst Evol Microbiol 2023; 73. [PMID: 37906095 DOI: 10.1099/ijsem.0.006041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, 38124 Braunschweig, Germany
| |
Collapse
|
49
|
Whitman WB, Hedlund BP, Palmer M, Sutcliffe I, Chuvochina M. Request for public discussion and ballot to amend SeqCode rules on priority of Candidatus names and correction of typographic and orthographic errors. ISME COMMUNICATIONS 2023; 3:96. [PMID: 37709936 PMCID: PMC10502122 DOI: 10.1038/s43705-023-00303-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/05/2023] [Indexed: 09/16/2023]
Affiliation(s)
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Iain Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| |
Collapse
|
50
|
Deshmukh UB, Oren A. Proposal of Allomuricauda gen. nov. and Allofranklinella gen. nov. as replacement names for the illegitimate prokaryotic generic names Muricauda and Franklinella, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37747448 DOI: 10.1099/ijsem.0.006023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023] Open
Abstract
The prokaryotic generic names Muricauda Bruns et al. 2001 and Franklinella Bernard et al. 2022 are illegitimate because they are later homonyms of the genus names Muricauda Small 1903 (synonym of Arisaema; Tracheophyta - Liliopsida - Araceae) and Franklinella Stewart and Hendrix 1945 (a Devonian ostracod genus) and Franklinella Lenz 1973 (a Devonian brachiopod genus), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Allomuricauda and Allofranklinella, with type species Allomuricauda ruestringensis and Allofrankinella schreckenbergeri, respectively.
Collapse
Affiliation(s)
- Umakant Bhoopati Deshmukh
- Department of Botany, Institution of Higher Learning, Research and Specialized Studies Centre, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 9190401, Israel
| |
Collapse
|