Article
Microbiology
Aharon Oren, David R. Arahal, Markus Goeker, Edward R. B. Moore, Ramon Rossello-Mora, Iain C. Sutcliffe
Summary: This article proposes amendments to the International Code of Nomenclature of Prokaryotes, focusing on the nomenclatural type of taxa, the suitability of names published in supplementary material or in papers published on e-print servers, the number of culture collection designations for validating a species name, the kinds of restrictions on type strain deposits, and the establishment of new combinations through elevation or lowering of taxonomic ranks.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Aharon Oren, Maria Chuvochina
Summary: Section E of Appendix 9 of the International Code of Nomenclature of Prokaryotes gives guidelines on forming adjectival specific and subspecific epithets reflecting the organism's geographical location. However, it does not cover naming genera after geographical locations. We propose amending Appendix 9 by providing recommendations on forming such names and discussing the implementation of the current wording.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Aharon Oren, George M. Garrity, Edward R. B. Moore, Iain C. Sutcliffe, Martha E. Trujillo
Summary: The International Journal of Systematic and Evolutionary Microbiology (IJSEM) will transition to true continuous publication in early 2021, with a new article citation method. Changes in the workflow and nomenclature rules are necessary to adapt to this new system.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Adyasha Panda, Salim T. Islam, Gaurav Sharma
Summary: In this article, Lloyd and Tahon criticize the proposed changes in bacterial phylum nomenclature and highlight several pitfalls of the new framework. They suggest new names for key bacterial phyla while keeping the archaeal phylum names. These changes aim to achieve a consistent and chaos-free nomenclature for researchers.
Article
Microbiology
Adyasha Panda, Salim T. Islam, Gaurav Sharma
Summary: This article criticizes the proposed changes in bacterial phylum nomenclature by the International Committee on Systematics of Prokaryotes and discusses the potential problems and suggestions for improvement.
Editorial Material
Microbiology
Aharon Oren, David R. Arahal, Ramon Rossello-Mora, Iain C. Sutcliffe, Edward R. B. Moore
Summary: The Editorial Board for the International Code of Nomenclature of Prokaryotes has compiled proposed revisions of the ICNP, and a public discussion of the document will start on July 1, 2021, lasting for 6 months.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Aharon Oren
Summary: The nomenclature of prokaryotes is regulated by the International Code of Nomenclature of Prokaryotes (ICNP) based on the Linnaean binomial system. However, the current rules only cover the nomenclature of cultivated prokaryotes, while proposals to include the uncultivated majority were rejected. The provisional rank of Candidatus can be used to name uncultivated prokaryotes, but now their names can be validated under the SeqCode for the uncultivated majority. Automated programs like GAN and Protologger can assist in naming and describing newly discovered prokaryotes, but knowledge of Latin and Greek is still necessary for quality control of names.
CANADIAN JOURNAL OF MICROBIOLOGY
(2023)
Article
Infectious Diseases
A. Oren
Summary: In the mid-1990s, the category 'Candidatus' was established for putative taxa of as yet uncultivated prokaryotes. As of April 2021, around 2700 'Candidatus' names have been published, but they do not have formal standing in nomenclature. A new code for naming uncultivated prokaryotes ('SeqCode') may be developed in the future.
NEW MICROBES AND NEW INFECTIONS
(2021)
Article
Microbiology
Alei Geng, Meng Jin, Nana Li, Daochen Zhu, Rongrong Xie, Qianqian Wang, Huaxing Lin, Jianzhong Sun
Summary: The study found that glycoside hydrolase families are more common in bacteria and showed strong or moderate-strong correlations among certain microbial collections. Additionally, particular GHFs were progressively enriched in certain types of microbes.
Editorial Material
Microbiology
Aharon Oren, Markus Goeker
Summary: Occasionally, there are attempts to validate the name of a prokaryotic taxon under the ICNP even if the original proposal does not meet all requirements. In such cases, a corrigendum must be published, but it should include the full description of the taxon. Modifying the original article is not allowed under the ICNP. Effective publication of a taxon name requires it to be a permanent record, and journals that modify articles after publication are not considered acceptable sources of effective publications.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Brian Dehlinger, Jared Jurss, Karson Lychuk, Catherine Putonti
Summary: The Codon Bias Database (CBDB) and the Dynamic Codon Biaser (DCB) are tools used to calculate codon usage bias in bacterial genomes, aiding in research on gene expression control, guiding protein structure, evolutionary studies, and phage-host predictions.
MICROBIAL GENOMICS
(2021)
Article
Environmental Sciences
E. Rahav, A. Paytan, B. Herut
Summary: The atmosphere plays a crucial role in transporting prokaryotic microorganisms across the oceans and land. Despite harsh conditions, a significant fraction of airborne prokaryotes survives and remains viable upon deposition, impacting the receiving environment. This study estimates the potential viability of airborne prokaryotic cells in the Southeastern Mediterranean coast, finding that marine-origin aerosols have higher viability compared to predominantly terrestrial trajectories, and that dust storms reduce viability while mineral dust particles enhance it.
FRONTIERS IN ENVIRONMENTAL SCIENCE
(2022)
Article
Agriculture, Multidisciplinary
Tian Xue-liang, Liu Jia-jia, Liu Quan-cheng, Xia Xin-yao, Peng Yong, Alejandra I. Huerta, Yan Jian-bing, Li Hui, Liu Wen-de
Summary: In this study, the impact of maize production cropping systems, soil properties, and geographic location on soil prokaryotic communities in four different maize production regions in China was investigated. The results showed that soil pH, cropping system, and geographic location significantly influenced the composition and function of the soil prokaryotic community.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Article
Plant Sciences
Sergei L. Mosyakin
Summary: The proposals by Wright and Gillman to amend the International Code of Nomenclature for algae, fungi, and plants (ICN) by allowing the retroactive replacement of scientific names with indigenous names have been met with criticism. Their definition of Indigenous People is different from internationally recognized definitions, and their arguments regarding chronological priority and the use of indigenous diacritics have been deemed irrelevant and impractical. The proposals have also been criticized for being potentially discriminatory and biased. Consequently, the international taxonomic community should reject these proposals.
Article
Microbiology
Li Ma, Weiyu She, Geng Wu, Jian Yang, Dorji Phurbu, Hongchen Jiang
Summary: The distribution and diversity of sulfate/sulfite reduction prokaryotic communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, were reported for the first time. The study found that the SRP populations were diverse and correlated with environmental factors. Temperature played a significant role in affecting the distribution and diversity of the dsrB gene in these geothermal areas.
