Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae

Gilbert Greub; Trestan Pillonel; Patrik M Bavoil; Nicole Borel; Lee Ann Campbell; Deborah Dean; Scott Hefty; Matthias Horn; Servaas A Morré; Scot P Ouellette; Yvonne Pannekoek; Mirja Puolakkainen; Peter Timms; Raphael Valdivia; Daisy Vanrompay

doi:10.1016/j.nmni.2023.101158

Use of gene sequences as type for naming prokaryotes: Recommendations of the international committee on the taxonomy of chlamydiae

New Microbes New Infect. 2023 Jun 21:54:101158. doi: 10.1016/j.nmni.2023.101158. eCollection 2023 Sep.

Authors

Gilbert Greub¹, Trestan Pillonel¹, Patrik M Bavoil², Nicole Borel³, Lee Ann Campbell⁴, Deborah Dean⁵, Scott Hefty⁶, Matthias Horn⁷, Servaas A Morré^{8

9

10}, Scot P Ouellette¹¹, Yvonne Pannekoek¹², Mirja Puolakkainen¹³, Peter Timms¹⁴, Raphael Valdivia¹⁵, Daisy Vanrompay¹⁶

Affiliations

¹ Centre for Research on Intracellular Bacteria, Institute of Microbiology, University Hospital Centre and University of Lausanne, Bugnon 48, 1011, Lausanne, Switzerland.
² Department of Microbial Pathogenesis, University of Maryland School of Dentistry, Baltimore, MD, USA.
³ Department of Pathobiology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 268, CH-8057, Zurich, Switzerland.
⁴ Department of Global Health, University of Washington, Seattle, WA, USA.
⁵ Departments of Medicine and Pediatrics, University of California San Francisco School of Medicine, Oakland, CA, USA.
⁶ Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA.
⁷ Centre for Microbiology and Environmental Systems Science, University of Vienna, 1090, Vienna, Austria.
⁸ Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands.
⁹ 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.
¹⁰ Dutch Chlamydia Trachomatis Reference Laboratory, Department of Medical Microbiology & Infection Control, VU University Medical Centre, Amsterdam, the Netherlands.
¹¹ Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA.
¹² Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands.
¹³ Department of Virology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
¹⁴ Genecology Research Center, University of Sunshine Coast, Queensland, Australia.
¹⁵ Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, 27710, USA.
¹⁶ Department of Animal Science and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.

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.

Keywords: Chlamydia; Chlamydiales; Intracellular bacteria; SeqCode; Taxogenomics.