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Whitman WB, Venter SN. Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names. Syst Appl Microbiol 2024; 47:126524. [PMID: 38878497 DOI: 10.1016/j.syapm.2024.126524] [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: 04/23/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/06/2024]
Abstract
Amendments were proposed to the International Code of Nomenclature of Prokaryotes (ICNP) in January [Arahal et al. (2024) Int. J Syst. Evol. Microbiol. 74: 006188] that would cause major changes in the treatment of Candidatus names. The amendments introduce Section 10 to name taxa whose names cannot be validly published under the ICNP because of the absence of type strains. This section creates a parallel 'pro-nomenclature' and formalizes alternative material which could serve as nomenclatural types. When conspecific isolates of taxa with Candidatus names are deposited in culture collections as type strains, the names can be validly published, and it is required that the same Candidatus name be used. While the amendments are promoted to provide stable names and rules of nomenclature for uncultivated taxa, the system is deeply flawed. It removes the permanent association between names and types, which will make the meaning of names imprecise and ambiguous. It creates 'pro-nomenclature', which is confusing and unnecessary. Since many taxa which cannot be validly named under the ICNP can already be named under the SeqCode, it duplicates and creates overlap with an established nomenclatural system without providing tangible benefits. As the SeqCode recognizes names formed under the ICNP, the ICNP should recognize names formed under the SeqCode as they have done for the Cyanobacteria named under the International Code of Nomenclature for algae, fungi and plants (ICN). For these reasons, we urge the members of the International Committee of Systematics of Prokaryotes (ICSP) to reject these amendments.
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Affiliation(s)
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
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Pragya K, Sreya P, Vighnesh L, Mahima D, Sushmita M, Sasikala C, Venkata Ramana C. Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds. Syst Appl Microbiol 2024; 47:126502. [PMID: 38458136 DOI: 10.1016/j.syapm.2024.126502] [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: 09/15/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 03/10/2024]
Abstract
Six metagenome-assembled genomes (JB008Ts, JB007, JB015, JB003, JB004, and JB002) belonging to the order Spirochaetales were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008Ts and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2-93.4 %, respectively with uncultivated Spirochaetaceae family members, and < 90 % identity with Marispirochaeta aestuari JC444T. While, the bin JB015 showed 99.1 % identity with Pleomorphochaeta naphthae SEBR 4209T. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008Ts confirmed that these members belong to the family Spirochaetaceae and bins JB015, JB002, JB003, and JB004 belong to the genus Pleomorphochaeta within the family Sphaerochaetaceae. The AAI values of the binned genomes JB007 and JB008Ts compared to other members of the Spirochaetaceae family were between 53.9- 56.8 % and 53.8-57.1 %, respectively. Furthermore, the comparison of ANI, dDDH, and POCP metrics of the binned genomes JB007 and JB008Ts, both among themselves and with the members of Spirochaetaceae, was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008Ts is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name Thalassospirochaeta sargassi gen. nov. sp. nov., in the family Spirochaetaceae while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other Pleomorphochaeta members.
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Affiliation(s)
- Kohli Pragya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Pannikurungottu Sreya
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Lakshmanan Vighnesh
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Dhurka Mahima
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Mallick Sushmita
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India
| | - Chintalapati Sasikala
- Bacterial Discovery Laboratory, Centre for Environment, IST, JNT University Hyderabad, Kukatpally, Hyderabad 500085, India.
| | - Chintalapati Venkata Ramana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, P.O. Central University, Hyderabad 500046, India.
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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.
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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
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Greub G, Pillonel T, Bavoil PM, Borel N, Campbell LA, Dean D, Hefty S, Horn M, Morré SA, Ouellette SP, Pannekoek Y, Puolakkainen M, Timms P, Valdivia R, Vanrompay D. Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae. New Microbes New Infect 2023; 54:101158. [PMID: 37416863 PMCID: PMC10320375 DOI: 10.1016/j.nmni.2023.101158] [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: 10/06/2021] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/08/2023] Open
Abstract
The International Committee on Systematics of Prokaryotes (ICSP) discussed and rejected in 2020 a proposal to modify the International Code of Nomenclature of Prokaryotes to allow the use of gene sequences as type for naming prokaryotes. An alternative nomenclatural code, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which considers genome sequences as type material for naming species, was published in 2022. Members of the ICSP subcommittee for the taxonomy of the phylum Chlamydiae (Chlamydiota) consider that the use of gene sequences as type would benefit the taxonomy of microorganisms that are difficult to culture such as the chlamydiae and other strictly intracellular bacteria. We recommend the registration of new names of uncultured prokaryotes in the SeqCode registry.
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Affiliation(s)
- Gilbert Greub
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Trestan Pillonel
- Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland
| | - Patrik M. Bavoil
- Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA
| | - Nicole Borel
- Department of Pathobiology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057, Zurich, Switzerland
| | - Lee Ann Campbell
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Deborah Dean
- Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, Oakland, CA, USA
| | - Scott Hefty
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090, Vienna, Austria
| | - Servaas A. Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research School GROW (School for Oncology & Developmental Biology), Faculty of Health, Medicine & Life Sciences, University of Maastricht, Maastricht, the Netherlands
- Dutch Chlamydia Trachomatis Reference Laboratory, Department of Medical Microbiology & Infection Control, VU University Medical Centre, Amsterdam, the Netherlands
| | - Scot P. Ouellette
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yvonne Pannekoek
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Mirja Puolakkainen
- Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Peter Timms
- Genecology Research Center, University of Sunshine Coast, Queensland, Australia
| | - Raphael Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA
| | - Daisy Vanrompay
- Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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Pu J, Yang J, Lu S, Jin D, Luo X, Xiong Y, Bai X, Zhu W, Huang Y, Wu S, Niu L, Liu L, Xu J. Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika. Microbiol Spectr 2023; 11:e0349522. [PMID: 37067438 PMCID: PMC10269723 DOI: 10.1128/spectrum.03495-22] [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: 08/31/2022] [Accepted: 02/13/2023] [Indexed: 04/18/2023] Open
Abstract
Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.
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Affiliation(s)
- Ji Pu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jing Yang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Lu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Dong Jin
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuelian Luo
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiangning Bai
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wentao Zhu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuyuan Huang
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shusheng Wu
- Yushu Prefecture Center for Disease Control and Prevention, Yushu, China
| | - Lina Niu
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, Hainan Medical University, Haikou, China
| | - Liyun Liu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control and National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Public Health, Nankai University, Tianjing, China
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Kirdat K, Tiwarekar B, Sathe S, Yadav A. From sequences to species: Charting the phytoplasma classification and taxonomy in the era of taxogenomics. Front Microbiol 2023; 14:1123783. [PMID: 36970684 PMCID: PMC10033645 DOI: 10.3389/fmicb.2023.1123783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
Phytoplasma taxonomy has been a topic of discussion for the last two and half decades. Since the Japanese scientists discovered the phytoplasma bodies in 1967, the phytoplasma taxonomy was limited to disease symptomology for a long time. The advances in DNA-based markers and sequencing improved phytoplasma classification. In 2004, the International Research Programme on Comparative Mycoplasmology (IRPCM)- Phytoplasma/Spiroplasma Working Team – Phytoplasma taxonomy group provided the description of the provisional genus ‘Candidatus Phytoplasma’ with guidelines to describe the new provisional phytoplasma species. The unintentional consequences of these guidelines led to the description of many phytoplasma species where species characterization was restricted to a partial sequence of the 16S rRNA gene alone. Additionally, the lack of a complete set of housekeeping gene sequences or genome sequences, as well as the heterogeneity among closely related phytoplasmas limited the development of a comprehensive Multi-Locus Sequence Typing (MLST) system. To address these issues, researchers tried deducing the definition of phytoplasma species using phytoplasmas genome sequences and the average nucleotide identity (ANI). In another attempts, a new phytoplasma species were described based on the Overall Genome relatedness Values (OGRI) values fetched from the genome sequences. These studies align with the attempts to standardize the classification and nomenclature of ‘Candidatus’ bacteria. With a brief historical account of phytoplasma taxonomy and recent developments, this review highlights the current issues and provides recommendations for a comprehensive system for phytoplasma taxonomy until phytoplasma retains ‘Candidatus’ status.
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Affiliation(s)
- Kiran Kirdat
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Bhavesh Tiwarekar
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
| | - Shivaji Sathe
- Department of Microbiology, Tuljaram Chaturchand College, Baramati, India
| | - Amit Yadav
- National Centre for Cell Science, NCCS Complex, Savitribai Phule Pune University, Pune, India
- *Correspondence: Amit Yadav, ,
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Oren A. Naming new taxa of prokaryotes in the 21st century. Can J Microbiol 2023; 69:151-157. [PMID: 36852830 DOI: 10.1139/cjm-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.
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Affiliation(s)
- 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
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8
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Göker M, Moore ERB, Oren A, Trujillo ME. Status of the SeqCode in the International Journal of Systematic and Evolutionary Microbiology. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748408 DOI: 10.1099/ijsem.0.005754] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The recent publication of an alternative nomenclatural code that targets prokaryotes, the Code of Nomenclature of Prokaryotes Described from DNA Sequence Data (SeqCode), raises questions about how to treat names 'validly published' under that code in the International Journal of Systematic and Evolutionary Microbiology (IJSEM). Here, it is reiterated that the IJSEM must function in accordance with the International Code of Nomenclature of Prokaryotes (ICNP). It is also reiterated that the ICNP covers all prokaryotes and that it accordingly assigns a nomenclatural status to all names of prokaryotic taxa. This implies that the ICNP also assigns a status to names that are only 'validly published' under the SeqCode. It follows that the IJSEM must treat such names as not validly published, since 'validly published under the SeqCode' is not a nomenclatural status, under the ICNP. Such names should be marked accordingly as Candidatus names or printed in quotation marks. The same measures would need to be taken by other journals which intend to adhere to the ICNP.
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Affiliation(s)
- 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
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
| | - Martha E Trujillo
- University of Salamanca, Dpto de Microbiología y Genética, Campus Unamuno, 37007 Salamanca, Spain
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Towards a unifying system for the naming of cultured and uncultured prokaryotes. Nat Microbiol 2022; 7:1514-1515. [PMID: 36138167 DOI: 10.1038/s41564-022-01220-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
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Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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11
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It’s time for a new type of type to facilitate naming the microbial world. New Microbes New Infect 2022; 47:100991. [PMID: 35800027 PMCID: PMC9253472 DOI: 10.1016/j.nmni.2022.100991] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.
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12
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Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils. Proc Natl Acad Sci U S A 2021; 118:2025322118. [PMID: 34732568 DOI: 10.1073/pnas.2025322118] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.
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13
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Oren A. Nomenclature of prokaryotic ' Candidatus' taxa: establishing order in the current chaos. New Microbes New Infect 2021; 44:100932. [PMID: 34631108 PMCID: PMC8487987 DOI: 10.1016/j.nmni.2021.100932] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 11/18/2022] Open
Abstract
In the mid-1990s, the category 'Candidatus' was established for putative taxa of as yet uncultivated prokaryotes. The status of 'Candidatus' is not formally included in the rules of the International Code of Nomenclature of Prokaryotes. Thus, 'Candidatus' names do not have standing in the nomenclature. Curated annotated lists of 'Candidatus' names (not including phyla) have been published since 2020. By April 2021, about 2700 names of 'Candidatus' taxa had been published. The International Committee on Systematics of Prokaryotes recently rejected proposals to allow gene sequence data as nomenclatural types. An alternative code for naming uncultivated microorganisms (the 'SeqCode') is now being developed for naming the majority of prokaryotes that are as yet uncultivated. In the opinion of the author, there is no need for such a code, as the existing system, with nomenclature quality control also for 'Candidatus' names, fulfills the needs. Computer programs such as GAN which generates large numbers of correctly formed names from the short lists of Latin and Greek word elements and Protologger that produce descriptions directly from genome sequences will become important in the future for automated naming and description of large numbers of 'Candidatus' taxa from metagenomic and single cell genome data. However, the formation of interesting and meaningful names is encouraged whenever possible.
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Affiliation(s)
- A. Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
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14
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Abstract
The remarkable success of taxonomic discovery, powered by culturomics, genomics and metagenomics, creates a pressing need for new bacterial names while holding a mirror up to the slow pace of change in bacterial nomenclature. Here, I take a fresh look at bacterial nomenclature, exploring how we might create a system fit for the age of genomics, playing to the strengths of current practice while minimizing difficulties. Adoption of linguistic pragmatism-obeying the rules while treating recommendations as merely optional-will make it easier to create names derived from descriptions, from people or places or even arbitrarily. Simpler protologues and a relaxed approach to recommendations will also remove much of the need for expert linguistic quality control. Automated computer-based approaches will allow names to be created en masse before they are needed while also relieving microbiologists of the need for competence in Latin. The result will be a system that is accessible, inclusive and digital, while also fully capable of naming the unnamed millions of bacteria.
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Affiliation(s)
- M.J. Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
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15
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Vázquez-Campos X, Kinsela AS, Bligh MW, Payne TE, Wilkins MR, Waite TD. Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. Front Microbiol 2021; 12:732575. [PMID: 34737728 PMCID: PMC8561730 DOI: 10.3389/fmicb.2021.732575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
During the 1960s, small quantities of radioactive materials were co-disposed with chemical waste at the Little Forest Legacy Site (LFLS, Sydney, Australia). The microbial function and population dynamics in a waste trench during a rainfall event have been previously investigated revealing a broad abundance of candidate and potentially undescribed taxa in this iron-rich, radionuclide-contaminated environment. Applying genome-based metagenomic methods, we recovered 37 refined archaeal MAGs, mainly from undescribed DPANN Archaea lineages without standing in nomenclature and 'Candidatus Methanoperedenaceae' (ANME-2D). Within the undescribed DPANN, the newly proposed orders 'Ca. Gugararchaeales', 'Ca. Burarchaeales' and 'Ca. Anstonellales', constitute distinct lineages with a more comprehensive central metabolism and anabolic capabilities within the 'Ca. Micrarchaeota' phylum compared to most other DPANN. The analysis of new and extant 'Ca. Methanoperedens spp.' MAGs suggests metal ions as the ancestral electron acceptors during the anaerobic oxidation of methane while the respiration of nitrate/nitrite via molybdopterin oxidoreductases would have been a secondary acquisition. The presence of genes for the biosynthesis of polyhydroxyalkanoates in most 'Ca. Methanoperedens' also appears to be a widespread characteristic of the genus for carbon accumulation. This work expands our knowledge about the roles of the Archaea at the LFLS, especially, DPANN Archaea and 'Ca. Methanoperedens', while exploring their diversity, uniqueness, potential role in elemental cycling, and evolutionary history.
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Affiliation(s)
- Xabier Vázquez-Campos
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Andrew S. Kinsela
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Mark W. Bligh
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
| | - Timothy E. Payne
- Environmental Research Theme, Australian Nuclear Science and Technology Organisation, Kirrawee DC, NSW, Australia
| | - Marc R. Wilkins
- NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - T. David Waite
- UNSW Water Research Centre, School of Civil and Environmental Engineering, The University of New South Wales, Sydney, NSW, Australia
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16
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Sutcliffe I, Rosselló-Móra R, Trujillo M. Addressing the sublime scale of the microbial world: reconciling an appreciation of microbial diversity with the need to describe species. New Microbes New Infect 2021; 43:100931. [PMID: 34484799 PMCID: PMC8408622 DOI: 10.1016/j.nmni.2021.100931] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/07/2021] [Accepted: 08/03/2021] [Indexed: 12/22/2022] Open
Abstract
There are fewer than 20,000 prokaryotic species with validly published names, meaning >99% of a reasonable estimate of microbial diversity remains formally unnamed. Here we explore the damaging consequences of the current practice in which each new species is described in a standardized publication, most typically a 'single strain species description'. This approach is both an impediment to scaling up progress in naming the microbial world and also a significant factor in the poor reputation of the discipline of microbial taxonomy. We conclude that significant changes in author habits are needed and make constructive suggestions as to how author practice should adapt.
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Affiliation(s)
- I.C. Sutcliffe
- Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, NE1 8ST, UK
| | - R. Rosselló-Móra
- Grup de Microbiologia Marina, IMEDEA (CSIC-UIB), C/Miquel Marques 21, 07190, Esporles, Illes Balears, Spain
| | - M.E. Trujillo
- Dpto. Microbiología y Genética, University of Salamanca, 37007, Salamanca, Spain
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17
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Tahon G, Patricia Geesink, Ettema TJG. Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. Annu Rev Microbiol 2021; 75:359-381. [PMID: 34351791 DOI: 10.1146/annurev-micro-040921-050212] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of the Archaea is a major scientific hallmark of the twentieth century. Since then, important features of their cell biology, physiology, ecology, and diversity have been revealed. Over the course of some 40 years, the diversity of known archaea has expanded from 2 to about 30 phyla comprising over 20,000 species. Most of this archaeal diversity has been revealed by environmental 16S rRNA amplicon sequencing surveys using a broad range of universal and targeted primers. Of the few primers that target a large fraction of known archaeal diversity, all display a bias against recently discovered lineages, which limits studies aiming to survey overall archaeal diversity. Induced by genomic exploration of archaeal diversity, and improved phylogenomics approaches, archaeal taxonomic classification has been frequently revised. Due to computational limitations and continued discovery of new lineages, a stable archaeal phylogeny is not yet within reach. Obtaining phylogenetic and taxonomic consensus of archaea should be a high priority for the archaeal research community. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Guillaume Tahon
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Patricia Geesink
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, 6700 EH Wageningen, The Netherlands; , ,
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18
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Hugenholtz P, Chuvochina M, Oren A, Parks DH, Soo RM. Prokaryotic taxonomy and nomenclature in the age of big sequence data. THE ISME JOURNAL 2021; 15:1879-1892. [PMID: 33824426 PMCID: PMC8245423 DOI: 10.1038/s41396-021-00941-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/01/2023]
Abstract
The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.
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Affiliation(s)
- Philip Hugenholtz
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Maria Chuvochina
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Aharon Oren
- grid.9619.70000 0004 1937 0538Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Edmond J. Safra campus, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Donovan H. Parks
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
| | - Rochelle M. Soo
- grid.1003.20000 0000 9320 7537Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD Australia
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19
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A standardized archaeal taxonomy for the Genome Taxonomy Database. Nat Microbiol 2021; 6:946-959. [PMID: 34155373 DOI: 10.1038/s41564-021-00918-8] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The accrual of genomic data from both cultured and uncultured microorganisms provides new opportunities to develop systematic taxonomies based on evolutionary relationships. Previously, we established a bacterial taxonomy through the Genome Taxonomy Database. Here, we propose a standardized archaeal taxonomy that is derived from a 122-concatenated-protein phylogeny that resolves polyphyletic groups and normalizes ranks based on relative evolutionary divergence. The resulting archaeal taxonomy, which forms part of the Genome Taxonomy Database, is stable for a range of phylogenetic variables including marker gene selection, inference methods, corrections for rate heterogeneity and compositional bias, tree rooting scenarios and expansion of the genome database. Rank normalization is shown to robustly correct for substitution rates varying up to 30-fold using simulated datasets. Taxonomic curation follows the rules of the International Code of Nomenclature of Prokaryotes while taking into account proposals to formally recognize the rank of phylum and to use genome sequences as type material. This taxonomy is based on 2,392 archaeal genomes, 93.3% of which required one or more changes to their existing taxonomy, mainly owing to incomplete classification. We identify 16 archaeal phyla and reclassify 3 major monophyletic units from the former Euryarchaeota and one phylum that unites the Thaumarchaeota-Aigarchaeota-Crenarchaeota-Korarchaeota (TACK) superphylum into a single phylum.
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20
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Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME COMMUNICATIONS 2021; 1:30. [PMID: 36739331 PMCID: PMC9723677 DOI: 10.1038/s43705-021-00032-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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Affiliation(s)
- Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Gagen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
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21
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Dijkshoorn L. Minutes of the International Committee on Systematics of Prokaryotes. Minutes of the miniplenary meeting, 11 July 2019, Glasgow, Scotland. Int J Syst Evol Microbiol 2021; 71. [PMID: 33709897 DOI: 10.1099/ijsem.0.004706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lenie Dijkshoorn
- Dept. of Infectious Diseases C5-P, Leiden University Medical Center, Albinusdreef 2, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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22
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Sanford RA, Lloyd KG, Konstantinidis KT, Löffler FE. Microbial Taxonomy Run Amok. Trends Microbiol 2021; 29:394-404. [PMID: 33546975 DOI: 10.1016/j.tim.2020.12.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/20/2020] [Accepted: 12/22/2020] [Indexed: 11/28/2022]
Abstract
DNA sequencing has led to an explosion in discovery of microbial phylogenetic novelty, especially that represented by uncultivated taxa, to which the traditional system of prokaryotic taxonomy has not adapted. A lack of expansion of the International Code of Nomenclature of Prokaryotes (ICNP, 'the Code') to effectively capture this information has created a 'wild west' situation where names are published or appear in popular reference databases without further verification or validation. The rapid propagation of variant and questionable naming methods has led to widespread confusion and undermines prior accomplishments. We exemplify inconsistencies that have arisen from this practice and endanger the interoperability of scientific findings. The immediate solution to this problem is to develop and adopt universal best practices that are accepted by expert researchers, major publishers, the International Committee on Systematics of Prokaryotes (ICSP), and international microbiological societies.
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Affiliation(s)
- Robert A Sanford
- Department of Geology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA; Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN 37996, USA; Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, TN 37996, USA; Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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23
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Borel N, Greub G. International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae, minutes of the closed meeting, 10 September 2020, via Zoom. Int J Syst Evol Microbiol 2021; 71. [PMID: 33332256 DOI: 10.1099/ijsem.0.004620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Nicole Borel
- Institute of Veterinary Pathology, Department of Pathobiology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057 Zurich, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland
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24
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Alcorta J, Alarcón-Schumacher T, Salgado O, Díez B. Taxonomic Novelty and Distinctive Genomic Features of Hot Spring Cyanobacteria. Front Genet 2020; 11:568223. [PMID: 33250920 PMCID: PMC7674949 DOI: 10.3389/fgene.2020.568223] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/15/2020] [Indexed: 01/06/2023] Open
Abstract
Several cyanobacterial species are dominant primary producers in hot spring microbial mats. To date, hot spring cyanobacterial taxonomy, as well as the evolution of their genomic adaptations to high temperatures, are poorly understood, with genomic information currently available for only a few dominant genera, including Fischerella and Synechococcus. To address this knowledge gap, the present study expands the genomic landscape of hot spring cyanobacteria and traces the phylum-wide genomic consequences of evolution in high temperature environments. From 21 globally distributed hot spring metagenomes, with temperatures between 32 and 75°C, 57 medium- and high-quality cyanobacterial metagenome-assembled genomes were recovered, representing taxonomic novelty for 1 order, 3 families, 15 genera and 36 species. Comparative genomics of 93 hot spring genomes (including the 57 metagenome-assembled genomes) and 66 non-thermal genomes, showed that the former have smaller genomes and a higher GC content, as well as shorter proteins that are more hydrophilic and basic, when compared to the non-thermal genomes. Additionally, the core accessory orthogroups from the hot spring genomes of some genera had a greater abundance of functional categories, such as inorganic ion metabolism, translation and post-translational modifications. Moreover, hot spring genomes showed increased abundances of inorganic ion transport and amino acid metabolism, as well as less replication and transcription functions in the protein coding sequences. Furthermore, they showed a higher dependence on the CRISPR-Cas defense system against exogenous nucleic acids, and a reduction in secondary metabolism biosynthetic gene clusters. This suggests differences in the cyanobacterial response to environment-specific microbial communities. This phylum-wide study provides new insights into cyanobacterial genomic adaptations to a specific niche where they are dominant, which could be essential to trace bacterial evolution pathways in a warmer world, such as the current global warming scenario.
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Affiliation(s)
- Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
| | - Tomás Alarcón-Schumacher
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Oscar Salgado
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Laboratorio de Bioinformática, Facultad de Educación, Universidad Adventista de Chile, Chillán, Chile
| | - Beatriz Díez
- Department of Molecular Genetics and Microbiology, Biological Sciences Faculty, Pontifical Catholic University of Chile, Santiago, Chile
- Center for Climate and Resilience Research (CR)2, University of Chile, Santiago, Chile
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25
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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26
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Sutcliffe IC, Dijkshoorn L, Whitman WB, Executive Board OBOTI. Minutes of the International Committee on Systematics of Prokaryotes online discussion on the proposed use of gene sequences as type for naming of prokaryotes, and outcome of vote. Int J Syst Evol Microbiol 2020; 70:4416-4417. [PMID: 32628106 PMCID: PMC7657488 DOI: 10.1099/ijsem.0.004303] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The International Committee on Systematics of Prokaryotes has held an electronic discussion on proposals to amend the International Code of Nomenclature of Prokaryotes in order to allow the use of gene sequence data as type. The scientific discussion is reported. Subsequently members of the International Committee on Systematics of Prokaryotes voted on these proposals, which were rejected.
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Affiliation(s)
| | - Lenie Dijkshoorn
- Department of Infectious Diseases, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens GA 30602-2605, USA
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27
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Hussein WE, Huang E, Ozturk I, Somogyi Á, Yang X, Liu B, Yousef AE. Genome-Guided Mass Spectrometry Expedited the Discovery of Paraplantaricin TC318, a Lantibiotic Produced by Lactobacillus paraplantarum Strain Isolated From Cheese. Front Microbiol 2020; 11:1381. [PMID: 32760356 PMCID: PMC7372301 DOI: 10.3389/fmicb.2020.01381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
The quest for potent alternatives to the currently used antimicrobials is urged by health professionals, considering the rapid rise in resistance to preservatives and antibiotics among pathogens. The current study was initiated to search for novel and effective bacteriocins from food microbes, preferably lactic acid bacteria (LAB), for potential use as preservatives. Advances in genome-guided mass spectrometry (MS) were implemented to expedite identifying and elucidating the structure of the recovered antimicrobial agent. A LAB strain, OSY-TC318, was isolated from a Turkish cheese, and the crude extract of the cultured strain inhibited the growth of various pathogenic and spoilage bacteria such as Bacillus cereus, Clostridium sporogenes, Enterococcus faecalis, Listeria monocytogenes, Salmonella enterica ser. Typhimurium, and Staphylococcus aureus. The antimicrobial producer was identified as Lactobacillus paraplantarum using MS biotyping and genomic analysis. Additionally, L. paraplantarum OSY-TC318 was distinguished from closely related strains using comparative genomic analysis. Based on in silico analysis, the genome of the new strain contained a complete lantibiotic biosynthetic gene cluster, encoding a novel lantibiotic that was designated as paraplantaricin TC318. The bioinformatic analysis of the gene cluster led to the prediction of the biosynthetic pathway, amino acid sequence, and theoretical molecular mass of paraplantaricin TC318. To verify the genomic analysis predictions, paraplantaricin TC318 was purified from the producer cellular crude extract using liquid chromatography, followed by structural elucidation using Fourier transform ion cyclotron resonance MS analysis. This genome-guided MS analysis revealed that the molecular mass of paraplantaricin TC318 is 2,263.900 Da, its chemical formula is C106H133N27O22S4, and its primary sequence is F-K-S-W-S-L-C-T-F-G-C-G-H-T-G-S-F-N-S-F-C-C. This lantibiotic, which differs from mutacin 1140 at positions 9, 12, 13, and 20, is considered a new member of the epidermin group in class I lantibiotics. In conclusion, the study revealed a new L. paraplantarum strain producing a novel lantibiotic that is potentially useful in food and medical applications.
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Affiliation(s)
- Walaa E Hussein
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology and Immunology, National Research Center, Giza, Egypt
| | - En Huang
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Ismet Ozturk
- Faculty of Fine Arts, Department of Gastronomy and Culinary Arts, Istanbul Arel University, Istanbul, Turkey
| | - Árpád Somogyi
- Campus Chemical Instrument Center, Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH, United States
| | - Xu Yang
- Nutrition and Food Science Department, California State Polytechnic University Pomona, Pomona, CA, United States
| | - Baosheng Liu
- College of Animal Science Technology, Jiangxi Agricultural University, Nanchang, China
| | - Ahmed E Yousef
- Department of Food Science and Technology, The Ohio State University, Columbus, OH, United States.,Department of Microbiology, The Ohio State University, Columbus, OH, United States
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28
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Alejandre-Colomo C, Viver T, Urdiain M, Francis B, Harder J, Kämpfer P, Amann R, Rosselló-Móra R. Taxonomic study of nine new Winogradskyella species occurring in the shallow waters of Helgoland Roads, North Sea. Proposal of Winogradskyella schleiferi sp. nov., Winogradskyella costae sp. nov., Winogradskyella helgolandensis sp. nov., Winogradskyella vidalii sp. nov., Winogradskyella forsetii sp. nov., Winogradskyella ludwigii sp. nov., Winogradskyella ursingii sp. nov., Winogradskyella wichelsiae sp. nov., and Candidatus "Winogradskyella atlantica" sp. nov. Syst Appl Microbiol 2020; 43:126128. [PMID: 32977081 DOI: 10.1016/j.syapm.2020.126128] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 11/18/2022]
Abstract
Evaluation of bacterial succession with cultivation-dependent strategies during a spring phytoplankton bloom in the North Sea led to the isolation of 41 strains that affiliated with the genus Winogradskyella. Fifteen of the strains were selected for a taxonomic study after discarding clonal cultures. A thorough phylogenetic, genomic and phenotypic analysis of the isolates indicated that they represented eight new species that coexisted in North Sea waters. Molecular data revealed the existence of an as yet uncultivated novel species recurrently binned from the North Sea metagenomes. The metagenome-assembled genomes (MAGs) of this new Winogradskyella were used to classify it as a new Candidatus species. This study represented a new example of the use of the tandem approach of whole cell mass spectrometry linked to 16S rRNA gene sequencing in order to facilitate the discovery of new taxa by high-throughput cultivation, which increases the probability of finding more than a single isolate for new species. In addition, we demonstrated the reasons for classifying MAGs representing recurrently retrieved heterotrophic species that evade cultivation even after an important high-throughput effort. The taxonomic study resulted in the classification of eight new species and one new Candidatus species of the genus Winogradskyella for which we propose the names W. schleiferi sp. nov., W. costae sp. nov., W. helgolandensis sp. nov., W. vidalii sp. nov., W. forsetii sp. nov., W. ludwigii sp. nov., W. ursingii sp. nov., W. wichelsiae sp. nov., and Candidatus "W. atlantica" sp. nov.
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Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Mercedes Urdiain
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Justus Liebig Universität Giessen, IFZ-Heinrich-Buff-Ring, Giessen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, D-28359 Bremen, Germany
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), 07190 Esporles, Illes Balears, Spain.
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29
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Oren A, Garrity GM, Parker CT, Chuvochina M, Trujillo ME. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2020; 70:3956-4042. [DOI: 10.1099/ijsem.0.003789] [Citation(s) in RCA: 782] [Impact Index Per Article: 195.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.
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Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- NamesforLife, LLC, PO Box 769, Okemos MI 48805-0769, USA
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | | | - Maria Chuvochina
- Australian Centre for Ecogenomics, University of Queensland, St. Lucia QLD 4072, Brisbane, Australia
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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30
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Oren A, Garrity GM, Trujillo ME. Registration of names of prokaryotic Candidatus taxa in the IJSEM. Int J Syst Evol Microbiol 2020; 70:3955. [DOI: 10.1099/ijsem.0.003791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J Safra Campus, 9190401 Jerusalem, Israel
| | - George M. Garrity
- Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
| | - Martha E. Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, Universidad de Salamanca, 37007, Salamanca, Spain
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31
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Hildebrand F, Pallen MJ, Bork P. Towards standardisation of naming novel prokaryotic taxa in the age of high-throughput microbiology. Gut 2020; 69:1358-1359. [PMID: 31203204 PMCID: PMC7306977 DOI: 10.1136/gutjnl-2019-319045] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/30/2019] [Indexed: 12/08/2022]
Affiliation(s)
- Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK,Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mark J Pallen
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, UK
| | - Peer Bork
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany
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32
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Murray AE, Freudenstein J, Gribaldo S, Hatzenpichler R, Hugenholtz P, Kämpfer P, Konstantinidis KT, Lane CE, Papke RT, Parks DH, Rossello-Mora R, Stott MB, Sutcliffe IC, Thrash JC, Venter SN, Whitman WB, Acinas SG, Amann RI, Anantharaman K, Armengaud J, Baker BJ, Barco RA, Bode HB, Boyd ES, Brady CL, Carini P, Chain PSG, Colman DR, DeAngelis KM, de Los Rios MA, Estrada-de Los Santos P, Dunlap CA, Eisen JA, Emerson D, Ettema TJG, Eveillard D, Girguis PR, Hentschel U, Hollibaugh JT, Hug LA, Inskeep WP, Ivanova EP, Klenk HP, Li WJ, Lloyd KG, Löffler FE, Makhalanyane TP, Moser DP, Nunoura T, Palmer M, Parro V, Pedrós-Alió C, Probst AJ, Smits THM, Steen AD, Steenkamp ET, Spang A, Stewart FJ, Tiedje JM, Vandamme P, Wagner M, Wang FP, Yarza P, Hedlund BP, Reysenbach AL. Roadmap for naming uncultivated Archaea and Bacteria. Nat Microbiol 2020; 5:987-994. [PMID: 32514073 PMCID: PMC7381421 DOI: 10.1038/s41564-020-0733-x] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 05/01/2020] [Indexed: 11/09/2022]
Abstract
The assembly of single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) has led to a surge in genome-based discoveries of members affiliated with Archaea and Bacteria, bringing with it a need to develop guidelines for nomenclature of uncultivated microorganisms. The International Code of Nomenclature of Prokaryotes (ICNP) only recognizes cultures as 'type material', thereby preventing the naming of uncultivated organisms. In this Consensus Statement, we propose two potential paths to solve this nomenclatural conundrum. One option is the adoption of previously proposed modifications to the ICNP to recognize DNA sequences as acceptable type material; the other option creates a nomenclatural code for uncultivated Archaea and Bacteria that could eventually be merged with the ICNP in the future. Regardless of the path taken, we believe that action is needed now within the scientific community to develop consistent rules for nomenclature of uncultivated taxa in order to provide clarity and stability, and to effectively communicate microbial diversity.
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Affiliation(s)
- Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA.
| | - John Freudenstein
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Roland Hatzenpichler
- Department of Chemistry and Biochemistry, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Peter Kämpfer
- Department of Applied Microbiology, Justus-Liebig-Universität, Giessen, Germany
| | | | - Christopher E Lane
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - R Thane Papke
- Department of Molecular and Cellular Biology, University of Connecticut, Storrs, CT, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Ramon Rossello-Mora
- Mediterranean Institute for Advanced Studies, CSIC-UIB, Illes Balears, Spain
| | - Matthew B Stott
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Iain C Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - J Cameron Thrash
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institut de Ciènces del Mar, CSIC, Barcelona, Spain
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | | | - Jean Armengaud
- CEA Technological Innovations for Detection and Diagnosis Laboratory, CEA Pharmacology and Immunoanalysis Unit (SPI), Bagnols-sur-Cèze, France
| | - Brett J Baker
- Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port Aransas, TX, USA
| | - Roman A Barco
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany.,Senckenberg Society for Nature Research, Frankfurt am Main, Germany
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | - Paul Carini
- Department of Environmental Science, University of Arizona, Tuscon, AZ, USA
| | - Patrick S G Chain
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | | | | | | | - Christopher A Dunlap
- National Center for Agricultural Utilization Research, Crop Bioprotection Research Unit, Peoria, IL, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, Department of Medical Microbiology and Immunology, University of California, Davis, CA, USA
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, the Netherlands
| | | | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Ute Hentschel
- GEOMAR-Helmholtz Centre for Ocean Research, RD3-Marine Ecology, RU-Marine Microbiology, Kiel, Germany
| | | | - Laura A Hug
- Department of Biology, University of Waterloo, Waterloo, Canada
| | - William P Inskeep
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA
| | - Elena P Ivanova
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Karen G Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, TN, USA
| | - Frank E Löffler
- Departments of Microbiology and Civil & Environmental Engineering, Center for Environmental Biotechnology, University of Tennessee, Knoxville, TN, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Duane P Moser
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, NV, USA
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | | | | | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute for Environment and Natural Resources, Zürich University for Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Andrew D Steen
- Departments of Microbiology and Earth and Planetary Sciences, University of Tennessee, Knoxville, TN, USA
| | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Anja Spang
- Department for Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, the Netherlands.,Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Frank J Stewart
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - James M Tiedje
- Center for Microbial Ecology, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Feng-Ping Wang
- International Center for Deep Life Investigation, School of Oceanography and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA.
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33
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Huang CH, Chen CC, Liou JS, Lee AY, Blom J, Lin YC, Huang L, Watanabe K. Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. Int J Syst Evol Microbiol 2020; 70:3755-3762. [DOI: 10.1099/ijsem.0.003969] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Taxonomic relationships between
Lactobacillus casei
,
Lactobacillus paracasei
and
Lactobacillus zeae
have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains
L. casei
ATCC 393T and
L. zeae
ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that
L. casei
could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the
L. zeae
strains, and supported an emended the description of the name of
Lactobacillus zeae
(ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- General Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan, Taiwan, ROC
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10673, Taiwan, ROC
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34
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35
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Parks DH, Chuvochina M, Chaumeil PA, Rinke C, Mussig AJ, Hugenholtz P. A complete domain-to-species taxonomy for Bacteria and Archaea. Nat Biotechnol 2020; 38:1079-1086. [DOI: 10.1038/s41587-020-0501-8] [Citation(s) in RCA: 518] [Impact Index Per Article: 129.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/26/2020] [Indexed: 12/30/2022]
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36
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Janda JM. Proposed nomenclature or classification changes for bacteria of medical importance: taxonomic update 5. Diagn Microbiol Infect Dis 2020; 97:115047. [PMID: 32321664 DOI: 10.1016/j.diagmicrobio.2020.115047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 01/23/2023]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy continues to change at a very rapid rate in the era of molecular diagnostics including whole genome sequencing. This update focuses on taxonomic changes and proposals that may be of medical importance from 2018 to 2020.
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Affiliation(s)
- J Michael Janda
- Public Health Laboratory, Public Health Services Department, Kern County, Bakersfield, CA 93306-3302.
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37
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Inderbitzin P, Robbertse B, Schoch CL. Species Identification in Plant-Associated Prokaryotes and Fungi Using DNA. PHYTOBIOMES JOURNAL 2020; 4:103-114. [PMID: 35265781 PMCID: PMC8903201 DOI: 10.1094/pbiomes-12-19-0067-rvw] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Species names are fundamental to managing biological information. The surge of interest in microbial diversity has resulted in an increase in the number of microbes that need to be identified and assigned a species name. This article provides an introduction to the principles of DNA-based identification of Archaea and Bacteria traditionally known as prokaryotes, and Fungi, the Oomycetes and other protists, collectively referred to as fungi. The prokaryotes and fungi are the most commonly studied microbes from plants, and we introduce the most relevant concepts of prokaryote and fungal taxonomy and nomenclature. We first explain how prokaryote and fungal species are defined, delimited, and named, and then summarize the criteria and methods used to identify prokaryote and fungal organisms to species.
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Affiliation(s)
| | - Barbara Robbertse
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
| | - Conrad L. Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892
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38
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Rossello-Mora R, Konstantinidis KT, Sutcliffe I, Whitman W. Opinion: Response to concerns about the use of DNA sequences as types in the nomenclature of prokaryotes. Syst Appl Microbiol 2020; 43:126070. [PMID: 32081606 DOI: 10.1016/j.syapm.2020.126070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022]
Abstract
In the current Opinion we respond to the major concerns by Bisgaard et al. (2019) and Overmann et al. (2019) and conclude that the adoption of sequences as types for the names of prokaryotes will allow for improvements of the taxonomic framework, increased stability of names derived from robust phylogenomic methods, and enable a full circumscription of the microbial world rather than just the cultivated minority.
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Affiliation(s)
- Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Bacterial Diversity, IMEDEA (CSIC-UIB), 07190 Esporles, Balearic Islands, Spain.
| | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Iain Sutcliffe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - William Whitman
- Department of Microbiology, University of Georgia, Athens, GA, USA
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39
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Konstantinidis KT, Rosselló‐Móra R, Amann R. Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy. Environ Microbiol 2020; 22:819-822. [DOI: 10.1111/1462-2920.14934] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 01/27/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Konstantinos T. Konstantinidis
- School of Civil and Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology Atlanta GA USA
| | - Ramon Rosselló‐Móra
- Marine Microbiology Group, Institut Mediterrani d'Estudis Avançats (IMEDEA; CSIC‐UIB) E‐07190 Esporles Spain
| | - Rudolf Amann
- Max Planck Institute for Marine Microbiology D‐28359 Bremen Germany
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40
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Borel N, Horn M, Greub G. International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 20 March 2019, Seattle, WA, USA. Int J Syst Evol Microbiol 2019; 69:3654-3656. [PMID: 31592763 DOI: 10.1099/ijsem.0.003738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Nicole Borel
- Institute of Veterinary Pathology, Department of Pathobiology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057 Zurich, Switzerland
| | - Matthias Horn
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstr. 14, A-1090 Vienna, Austria
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne, Bugnon 48, CH-1011 Lausanne, Switzerland
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41
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Huang CH, Wang CL, Liou JS, Lee AY, Blom J, Huang L, Watanabe K. Reclassification of Micrococcus aloeverae and Micrococcus yunnanensis as later heterotypic synonyms of Micrococcus luteus. Int J Syst Evol Microbiol 2019; 69:3512-3518. [DOI: 10.1099/ijsem.0.003654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Chun-Lin Wang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Lina Huang
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Bioresource Collection and Research Center (BCRC), Food Industry Research and Development Institute, 331 Shih-Pin Rd., Hsinchu 30062, Taiwan, ROC
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, No. 50, Ln. 155, Sec. 3, Keelung Rd., Taipei 10673, Taiwan, ROC
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42
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Whitman WB, Sutcliffe IC, Rossello-Mora R. Proposal for changes in the International Code of Nomenclature of Prokaryotes: granting priority to Candidatus names. Int J Syst Evol Microbiol 2019; 69:2174-2175. [DOI: 10.1099/ijsem.0.003419] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- William B. Whitman
- 1Department of Microbiology, University of Georgia, Athens GA 30602-2605, USA
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43
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Bisgaard M, Christensen H, Clermont D, Dijkshoorn L, Janda JM, Moore ERB, Nemec A, Nørskov-Lauritsen N, Overmann J, Reubsaet FAG. The use of genomic DNA sequences as type material for valid publication of bacterial species names will have severe implications for clinical microbiology and related disciplines. Diagn Microbiol Infect Dis 2019; 95:102-103. [PMID: 30981555 DOI: 10.1016/j.diagmicrobio.2019.03.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 03/18/2019] [Indexed: 01/19/2023]
Affiliation(s)
| | - Henrik Christensen
- University of Copenhagen, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, Frederiksberg, Denmark.
| | | | - Lenie Dijkshoorn
- Department of Infectious Diseases C5-P, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Edward R B Moore
- Department of Infectious Diseases and Culture Collection University of Gothenburg (CCUG), Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Alexandr Nemec
- Laboratory of Bacterial Genetics, National Institute of Public Health, Prague and Department of Laboratory Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | | | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany; Microbiology, Braunschweig University of Technology, Braunschweig, Germany
| | - Frans A G Reubsaet
- Diagnostic Laboratory for Bacteriology and Parasitology, Center for Infectious Disease Research, Diagnostics and laboratory Surveillance, National Institute of Public Health and the Environment, Bilthoven, The Netherlands
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44
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Rinke C, Rubino F, Messer LF, Youssef N, Parks DH, Chuvochina M, Brown M, Jeffries T, Tyson GW, Seymour JR, Hugenholtz P. A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). THE ISME JOURNAL 2019; 13:663-675. [PMID: 30323263 PMCID: PMC6461757 DOI: 10.1038/s41396-018-0282-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/24/2018] [Accepted: 09/01/2018] [Indexed: 01/08/2023]
Abstract
Marine Group II (MGII) archaea represent the most abundant planktonic archaeal group in ocean surface waters, but our understanding of the group has been limited by a lack of cultured representatives and few sequenced genomes. Here, we conducted a comparative phylogenomic analysis of 270 recently available MGII metagenome-assembled genomes (MAGs) to investigate their evolution and ecology. Based on a rank-normalised genome phylogeny, we propose that MGII is an order-level lineage for which we propose the name Candidatus Poseidoniales (after Gr. n. Poseidon, God of the sea), comprising the families Candidatus Poseidonaceae fam. nov. (formerly subgroup MGIIa) and Candidatus Thalassarchaeaceae fam. nov. (formerly subgroup MGIIb). Within these families, 21 genera could be resolved, many of which had distinct biogeographic ranges and inferred nutrient preferences. Phylogenetic analyses of key metabolic functions suggest that the ancestor of Ca. Poseidoniales was a surface water-dwelling photoheterotroph that evolved to occupy multiple related ecological niches based primarily on spectral tuning of proteorhodopsin genes. Interestingly, this adaptation appears to involve an overwrite mechanism whereby an existing single copy of the proteorhodopsin gene is replaced by a horizontally transferred copy, which in many instances should allow an abrupt change in light absorption capacity. Phototrophy was lost entirely from five Ca. Poseidoniales genera coinciding with their adaptation to deeper aphotic waters. We also report the first instances of nitrate reductase in two genera acquired via horizontal gene transfer (HGT), which was a potential adaptation to oxygen limitation. Additional metabolic traits differentiating families and genera include flagellar-based adhesion, transporters, and sugar, amino acid, and peptide degradation. Our results suggest that HGT has shaped the evolution of Ca. Poseidoniales to occupy a variety of ecological niches and to become the most successful archaeal lineage in ocean surface waters.
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Affiliation(s)
- Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia.
| | - Francesco Rubino
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Lauren F Messer
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Noha Youssef
- Department of Microbiology and Molecular Genetics, Oklahoma State University Stillwater, Stillwater, OK, USA
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mark Brown
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Thomas Jeffries
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, NSW, Australia
| | - Gene W Tyson
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Justin R Seymour
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, Australia
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45
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Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5-14. [DOI: 10.1016/j.syapm.2018.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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46
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Ramos-Barbero MD, Martin-Cuadrado AB, Viver T, Santos F, Martinez-Garcia M, Antón J. Recovering microbial genomes from metagenomes in hypersaline environments: The Good, the Bad and the Ugly. Syst Appl Microbiol 2018; 42:30-40. [PMID: 30528276 DOI: 10.1016/j.syapm.2018.11.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 11/06/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
Abstract
Current metagenomic tools allow the recovery of microbial genomes directly from the environment. This can be accomplished by binning metagenomic contigs according to their coverage and tetranucleotide frequency, followed by an estimation of the bin quality. The public availability of bioinformatics tools, together with the decreasing cost of next generation sequencing, are democratizing this powerful approach that is spreading from specialized research groups to the general public. Using metagenomes from hypersaline environments, as well as mock metagenomes composed of Archaea and Bacteria frequently found in these systems, we have analyzed the advantages and difficulties of the binning process in these extreme environments to tackle microbial population diversity. These extreme systems harbor relatively low species diversity but high intraspecific diversity, which can compromise metagenome assembly and therefore the whole binning process. The main goal is to compare the output of the binning process with what is previously known from the analyzed samples, based on years of study using different approaches. Several scenarios have been analyzed in detail: (i) a good quality bin from a species highly abundant in the environment; (ii) an intermediate quality bin with incongruences that can be solved by further analyses and manual curation, and (iii) a low-quality bin to investigate the failure to recover a very abundant microbial genome as well as some possible solutions. The latter can be considered the "great metagenomics anomaly" and is mainly due to assembly problems derived from the microdiversity of naturally co-existing populations in nature.
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Affiliation(s)
| | - Ana-B Martin-Cuadrado
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Tomeu Viver
- Department of Animal and Microbial Biodiversity, Marine Microbiology Group, Mediterranean Institute for Advanced Studies (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Manuel Martinez-Garcia
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain; Multidisciplinary Institute of Environmental Studies Ramon Margalef, University of Alicante, Alicante, Spain.
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47
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Oren A, Garrity GM. Proposal to modify Rules 27 and 30(3)(b) of the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2018; 68:3951-3953. [PMID: 30307385 DOI: 10.1099/ijsem.0.003063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We propose to modify Rules 27 and 30(3)(b) of the International Code of Nomenclature of Prokaryotes so that the formal description of new taxa (the 'protologue') will include a statement about the nomenclatural type, so that this information will be linked to the name of the taxon, the derivation (etymology) of the name, and the properties of the taxon.
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Affiliation(s)
- Aharon Oren
- 1The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- 2Department of Microbiology and Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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48
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Hao L, McIlroy SJ, Kirkegaard RH, Karst SM, Fernando WEY, Aslan H, Meyer RL, Albertsen M, Nielsen PH, Dueholm MS. Novel prosthecate bacteria from the candidate phylum Acetothermia. THE ISME JOURNAL 2018; 12:2225-2237. [PMID: 29884828 PMCID: PMC6092417 DOI: 10.1038/s41396-018-0187-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/09/2018] [Accepted: 03/20/2018] [Indexed: 02/05/2023]
Abstract
Members of the candidate phylum Acetothermia are globally distributed and detected in various habitats. However, little is known about their physiology and ecological importance. In this study, an operational taxonomic unit belonging to Acetothermia was detected at high abundance in four full-scale anaerobic digesters by 16S rRNA gene amplicon sequencing. The first closed genome from this phylum was obtained by differential coverage binning of metagenomes and scaffolding with long nanopore reads. Genome annotation and metabolic reconstruction suggested an anaerobic chemoheterotrophic lifestyle in which the bacterium obtains energy and carbon via fermentation of peptides, amino acids, and simple sugars to acetate, formate, and hydrogen. The morphology was unusual and composed of a central rod-shaped cell with bipolar prosthecae as revealed by fluorescence in situ hybridization combined with confocal laser scanning microscopy, Raman microspectroscopy, and atomic force microscopy. We hypothesize that these prosthecae allow for increased nutrient uptake by greatly expanding the cell surface area, providing a competitive advantage under nutrient-limited conditions.
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Affiliation(s)
- Liping Hao
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Simon Jon McIlroy
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Rasmus Hansen Kirkegaard
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Søren Michael Karst
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | | | - Hüsnü Aslan
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Rikke Louise Meyer
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Mads Albertsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per Halkjær Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
| | - Morten Simonsen Dueholm
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark.
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49
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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996-1004. [PMID: 30148503 DOI: 10.1038/nbt.4229] [Citation(s) in RCA: 1830] [Impact Index Per Article: 305.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 07/27/2018] [Indexed: 02/07/2023]
Abstract
Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.
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50
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Overmann J, Huang S, Nübel U, Hahnke RL, Tindall BJ. Relevance of phenotypic information for the taxonomy of not-yet-cultured microorganisms. Syst Appl Microbiol 2018; 42:22-29. [PMID: 30197212 DOI: 10.1016/j.syapm.2018.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 12/12/2022]
Abstract
To date, far less than 1% of the estimated global species of Bacteria and Archaea have been described and their names validly published. Aside from these quantitative limitations, our understanding of phenotypic and functional diversity of prokaryotes is also highly biased as not a single species has been described for 85 of the 118 phyla that are currently recognized. Due to recent advances in sequencing technology and capacity, metagenomic datasets accumulate at an increasing speed and new bacterial and archaeal genome sequences become available at a faster rate than newly described species. The growing gap between the diversity of Bacteria and Archaea held in pure culture and that detected by molecular methods has led to the proposal to establish a formal nomenclature for not-yet-cultured taxa primarily based on sequence information. According to this proposal, the concept of Candidatus species would be extended to groups of closely related genome sequences and their names validly published following established rules of bacterial nomenclature. The corresponding sequences would be deposited in public databases as the type. The suggested alterations of the International Code of Nomenclature of Prokaryotes raise concerns regarding (1) the reliability and stability of nomenclature, (2) the technological and conceptual limitations as well as availability of reference genomes, (3) the information content of in silico functional predictions, and (4) the recognition of evolutionary units of microbial diversity. These challenges need to be overcome to arrive at a meaningful taxonomy of not-yet-cultured prokaryotes with so far poorly understood phenotypes.
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Affiliation(s)
- Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany; German Center for Integrative Biodiversity Research (iDiv) Jena Halle Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Sixing Huang
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Deutsches Zentrum für Infektionsforschung (DZIF), Standort Braunschweig-Hannover, Braunschweig, Germany
| | - Richard L Hahnke
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Brian J Tindall
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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