International Committee On Systematic Bacteriology Research Articles

Minutes of the closed plenary meeting of the International Committee on Systematics of Prokaryotes, 13 June 2024, via Zoom.

A closed virtual plenary meeting of the International Committee on Systematics of Prokaryotes (ICSP) was held online on 13 June 2024. The meeting was open to full, co-opted and life members of the ICSP and to members of the Judicial Commission. To comply with Articles 4(d) and 5(d)(1) of the Statutes of the ICSP, the minutes of this meeting are published here.

Proposals to revise the Statutes of the International Committee on Systematics of Prokaryotes.

The International Committee on Systematics of Prokaryotes serves to administer the rules of prokaryotic nomenclature via the International Code of Nomenclature of Prokaryotes, ensures the publication of the International Journal of Systematic and Evolutionary Microbiology, and works to represent the interests of the microbiological disciplines regarding prokaryotic nomenclature. The functions and mechanisms of operation of the International Committee on Systematics of Prokaryotes (ICSP) are defined in its Statutes, which were last revised in 2019. As members of the 2020-2023 and the 2023-2026 ICSP Executive Board and the Judicial Commission, we propose here some further revisions to help improve the clarity and functionality of the Statutes.

Minutes of the open plenary meetings of the International Committee on Systematics of Prokaryotes, 11 October 2022 and 14 December 2023.

Open virtual plenary meetings of the International Committee on Systematics of Prokaryotes (ICSP) were held on 11 October 2022 and on 14 December 2023. To comply with Articles 4(d) and 5(d)(1) of the statutes of the ICSP, the minutes of these meetings are published here.

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes.

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.

Minutes of the inaugural 25 October 2022 meeting of International Committee on Systematics of Prokaryotes (ICSP) Subcommittees on Taxonomy representatives: challenges, trends, and perspectives for microbial taxonomists.

Minutes of the inaugural 25 October 2022 meeting of International Committee on Systematics of Prokaryotes (ICSP) Subcommittees on Taxonomy representatives: challenges, trends, and perspectives for microbial taxonomists.

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

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.

International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae: Minutes of the closed meeting, 25 August 2022, ESCCAR Meeting Lausanne, Switzerland.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

Putting the cart before the horse: SeqCode’s attempt to solve systematics issues with changes to nomenclature

This opinion paper examines the recent proposal for a new nomenclatural code for prokaryotes (SeqCode). It addresses four problematic issues: (1) epistemological—failure of the SeqCode to acknowledge taxa as explanatory hypotheses, (2) conceptual—designating as a name-bearer a coded section of the genome of an organism, (3) operational—changing nomenclatural procedure as a means of resolving systematic challenges, and (4) political (policy)—SeqCode developed independent in opposition to the International Committee on Systematics of Prokaryotes (ICSP). Each of these matters should be alarms to the scientific community as the SeqCode proposal embodies many potentially negative consequences that would dramatically hinder systematics (science) and nomenclature (a tool in science) in other groups of organisms, e.g., animals, plants, fungi, if analogous proposals were sought.

Validation of the names Cyanobacterium and Cyanobacterium stanieri, and proposal of Cyanobacteriota phyl. nov.

The decision by the International Committee on Systematics of Prokaryotes (ICSP) to place the rank of phylum under the rules of the International Code of Nomenclature of Prokaryotes (ICNP), with phylum names ending in -ota based on the name of a type genus, enables the valid publication of the phylum name Cyanobacteriota with Cyanobacterium as the type genus. The names Cyanobacterium and its type species Cyanobacterium stanieri were effectively published in 1983 by Rippka and Cohen-Bazire, but the names were not validly published under the rules of the ICNP (then named the International Code of Nomenclature of Bacteria) or the rules of the ICN (International Code of Nomenclature for algae, fungi, and plants, then named the International Code of Botanical Nomenclature). We here propose the names Cyanobacterium gen. nov and Cyanobacterium stanieri sp. nov. for valid publication under the provisions of the ICN. Upon validation these names are also validly published under the ICNP according to General Consideration 5 and Rule 30. We also propose the phylum name Cyanobacteriota phyl. nov. under the rules of the ICNP.

Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping.

ABSTRACTLloyd and Tahon recently criticized proposed bacterial phylum nomenclature changes (K.G. Lloyd, G. Tahon, Nat Rev Microbiol 20:123-124, 2022, https://doi.org/10.1038/s41579-022-00684-2) precipitated by the International Committee on Systematics of Prokaryotes (ICSP)’s official recognition of phylum nomenclature rules. Here, we extend the critique. While we applaud bringing consistency to phylum names, we prognosticate what this minute but momentous change entails for the future of microbial nomenclature and how this will sow confusion among researchers. Several pitfalls of the proposed ICSP framework-based nomenclature are also detailed, including (i) improper type genus name and suffix usage, (ii) loss of Bacteria/Archaea distinctions, (iii) disruption of major phylum name prefixes, and (iv) absence of organism name prevalidation. Finally, we suggest new names for the key bacterial phyla Proteobacteria (Proteobacteriota), Firmicutes (Firmicuteota), Actinobacteria (Actinobacteriota), and Tenericutes (Tenericuteota), while keeping the archaeal phylum names Crenarchaeota, Thaumarchaeota, and Euryarchaeota. Together, these changes will help researchers attain chaos-free uniform nomenclature.

Current status and future perspectives of taxonomic subcommittees of the International Committee on Systematics of Prokaryotes (ICSP).

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

Valid publication of the names of forty-two phyla of prokaryotes.

After the International Committee on Systematics of Prokaryotes (ICSP) had voted to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes (ICNP), and following publication of the decision in the IJSEM, we here present names and formal descriptions of 42 phyla to effect valid publication of their names, based on genera as the nomenclatural types.

Recent trend, biases and limitations of cultivation-based diversity studies of microbes.

The current study attempts to analyze recent trends, biases and limitations of cultivation-based microbial diversity studies based on published, novel species in the past 6 years in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), an official publication of the International Committee on Systematics of Prokaryotes (ICSP) and the Bacteriology and Applied Microbiology (BAM) Division of the International Union of Microbiological Societies (IUMS). IJSEM deals with taxa that have validly published names under the International Code of Nomenclature of Prokaryotes (ICNP). All the relevant publications from the last 6 years were retrieved, sorted and analyzed to get the answers to What is the current rate of novel species description? Which country has contributed substantially and which phyla represented better in culturable diversity studies? What are the current limitations? Published data for the past 6 years indicate that 500-900 novel species are reported annually. China, Korea, Germany, UK, India and the USA are at the forefront while contributions from other nations are meager. Despite the recent development in culturomics tools the dominance of Proteobacteria, Bacteroidetes and Actinobacteria are still prevalent in cultivation, while the representation of archaea, obligate anaerobes, microaerophiles, synergistic symbionts, aerotolerant and other fastidious microbes is poor. Single strain-based taxonomic descriptions prevail and emphasis on objective-based cultivation for biotechnological and environmental significance is not yet conspicuous.

Microbial Taxonomy Run Amok.

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.

International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae, minutes of the closed meeting, 10 September 2020, via Zoom

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 20 March 2019, Seattle, WA, USA.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

International Committee on Systematics of Prokaryotes (ICSP) Subcommittee on the taxonomy of Chlamydiae. Minutes of the closed meeting, 5 July 2018, Woudschoten, Zeist, The Netherlands.

Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities.

A machine-compiled microbial supertree from figure-mining thousands of papers

Background There is a huge diversity of microbial taxa, the majority of which have yet to be fully characterized or described. Plant, animal and fungal taxa are formally named and described in numerous vehicles. For prokaryotes, by constrast, all new validly described taxa appear in just one repository: the International Journal of Systematics and Evolutionary Microbiology (IJSEM). This is the official journal of record for bacterial names of the International Committee on Systematics of Prokaryotes (ICSP) of the International Union of Microbiological Societies (IUMS). It also covers the systematics of yeasts. This makes IJSEM an excellent candidate against which to test systems for the automated and semi-automated synthesis of published phylogenies. New information In this paper we apply computer vision techniques to automatically convert phylogenetic tree figure images from IJSEM back into re-usable, computable, phylogenetic data in the form of Newick strings and NEXML. Furthermore, we go on to use the extracted phylogenetic data to compute a formal phylogenetic MRP supertree synthesis, and we compare this to previous hypotheses of taxon relationships given by NCBI’s standard taxonomy tree. This is the world’s first attempt at automated supertree construction using data exclusively extracted by machines from published figure images. Additionally we reflect on how recent changes to UK copyright law have enabled this project to go ahead without requiring permission from copyright holders, and the related challenges and limitations of doing research on copyright-restricted material.

In memoriam –Scott Federhen (October 21, 1952 - May 5, 2016)

Scott (Herbert) Federhen passed away on May 5, 2016, after a short illness. Scott was well known for heading the National Center for Biotechnology Information’s (NCBI’s) Taxonomy project, which he started in 1991. Under his leadership it became an international standard for nomenclature and classification. Born in 1952, Scott obtained a MS degree in Computer Science, focused on denotational semantics of AI languages, from University of Maryland in 1980. An MS in Biology from MIT followed, with a focus on control structures in biological systems. He joined NCBI in 1990, shortly after its establishment. His dual training in both Computer Sciences and Biology served him well as he oversaw tremendous growth in the NCBI Taxonomy Database, developed numerous submission and database enhancements, and collaborated regularly with many other NCBI groups and members of the International Nucleotide Sequence Database Collaboration (INSDC). The INSDC continues to follow the NCBI Taxonomy Database classification. Under Scott’s guidance, the NCBI Taxonomy group was occasionally involved in scientific controversy, when underlying molecular data supported taxonomic changes. One example is the early inclusion of birds (Aves) under the Dinosauria in the NCBI classification. Scott also spearheaded NCBI’s efforts with the Barcode of Life project, an international initiative to identify and archive the barcode (a short genetic sequence from a standard part of the genome) for every species of life. Recently, Scott was instrumental in greatly expanding the annotation of type material in the NCBI taxonomic database. This allowed for improved taxonomic accuracy. Almost a year to the day before his death, he presented a proposal he developed for a groundbreaking change in how taxonomic names would be treated at NCBI. His sly sense of humor is evidenced in the title: “A Modest Proposal for making the Genomes of GenBank beneficial to the Publick, and preventing them from being a Burthen to the Curators and Taxonomists” (a nod to Johnathan Swift’s famous satire). The group he invited to the workshop included members of the International Committee on Systematics of Prokaryotes (ICSP) and the Judicial Commission on Prokaryotic Nomenclature, as well as bioinformaticians and taxonomists working with genomic similarity measures. Scott proposed a set of measures to represent a scaffold of reliably identified sequences that could be used to find and correct misidentified genomes. The invitees also agreed on a set of principles that will guide future efforts. It is anticipated that this project will continue and expand, but its inception was a testament to Scott’s drive and vision. Scott Federhen will be remembered as an adventurous eater, kind colleague and devoted Red Sox fan with an exceptionally broad intellectual range. He leaves behind his wife, Sheree, a daughter, Erica, a son, Luke, and many friends.

Sinorhizobium versus Ensifer: may a taxonomy subcommittee of the ICSP contradict the Judicial Commission?

In response to a Request for an Opinion, the Judicial Commission (Opinion 84) confirmed the earlier synonym, Ensifer, as the correct name for the genus better known as Sinorhizobium. The Judicial Commission considered that this decision would not cause sufficient confusion to justify the conservation of the latter name. The Subcommittee on the Taxonomy of Agrobacterium and Rhizobium of the International Committee on Systematics of Prokaryotes (ICSP) publicly disagreed with this conclusion. Was it justified in doing this?