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

HiBC: a publicly available collection of bacterial strains isolated from the human gut

Numerous bacteria in the human gut microbiome remain unknown and/or have yet to be cultured. While collections of human gut bacteria have been published, few strains are accessible to the scientific community. We have therefore created a publicly available collection of bacterial strains isolated from the human gut. The Human intestinal Bacteria Collection (HiBC) ( https://www.hibc.rwth-aachen.de ) contains 340 strains representing 198 species within 29 families and 7 phyla, of which 29 previously unknown species are taxonomically described and named. These included two butyrate-producing species of Faecalibacterium and new dominant species associated with health and inflammatory bowel disease, Ruminococcoides intestinale and Blautia intestinihominis, respectively. Plasmids were prolific within the HiBC isolates, with almost half (46%) of strains containing plasmids, with a maximum of six within a strain. This included a broadly occurring plasmid (pBAC) that exists in three diverse forms across Bacteroidales species. Megaplasmids were identified within two strains, the pMMCAT megaplasmid is globally present within multiple Bacteroidales species. This collection of easily searchable and publicly available gut bacterial isolates will facilitate functional studies of the gut microbiome.

A blueprint for contemporary studies of microbiomes

This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.

Request for conserving the generic name Methylacidiphilum Awala et al. 2023 over Methylacidiphilum Ratnadevi et al. 2023 to resolve the illegitimacy of Methylacidiphilum Awala et al. 2023, Methylacidiphilum caldifontis Awala et al. 2023, Methylacidiphilaceae Awala et al. 2023 and Methylacidiphilales Awala et al. 2023. Request for an Opinion

The generic name Methylacidiphilum Awala et al. 2023 contravenes Rule 51b(5) of the International Code of Nomenclature of Prokaryotes (ICNP) for being a later homonym of Methylacidiphilum Ratnadevi et al. 2023, leading to the illegitimacy of Methylacidiphilum caldifontis Awala et al. 2023, Methylacidiphilaceae Awala et al. 2023 and Methylacidiphilales Awala et al. 2023. Previous taxonomic analyses revealed that the names Methylacidiphilum Awala et al. 2023 and Methylacidiphilum Ratnadevi et al. 2023 happen to be heterotypic synonyms as well, which makes sense since both the names are derived from Candidatus Methylacidiphilum. And therefore, to resolve the illegitimacy and prevent nomenclatural instability, we refrain from proposing replacement names and here call for action by the Judicial Commission to conserve Methylacidiphilum Awala et al. 2023 over Methylacidiphilum Ratnadevi et al. 2023 according to Rule 23a Note 4(1) and Rule 56b of the ICNP. The conservation of the generic name Methylacidiphilum Awala et al. 2023 will retain the usage of the family name Methylacidiphilaceae and the order name Methylacidiphilales in prokaryotic taxonomy.

Preparing the 2025 revision of the International Code of Nomenclature of Prokaryotes

The editorial Board of the International Code of Nomenclature of Prokaryotes (ICNP) - the Prokaryotic Code - has compiled already ratified proposed emendations of the ICNP, together with additional editorial changes and clarifications. These were implemented in a draft 2025 revision of the Prokaryotic Code. To comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Systematics of Prokaryotes (ICSP), a public discussion of the document will start on 1 January (or later if required) 2025, to last for 6 months. Here, we present the basis for the revision and the procedure for the discussion. The discussion will be followed by the balloting of the ICSP members.

Addition of Section 10, Rules 66-73 for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes

Following a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes, I here report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes.

International Committee on Systematics of Prokaryotes: minutes of the open plenary meeting, Tuesday, 22 October 2024, Sesto Fiorentino, Florence, Italy, and via Teams

A hybrid in-person and online open plenary meeting of the International Committee on Systematics of Prokaryotes (ICSP) was held on 22 October 2024 at the Consiglio Nazionale delle Ricerche, Sesto Fiorentino, Florence, Italy, and via Teams just prior to the IUMS 2024 Congress. To comply with Articles 4(d) and 5(d) (1) of the statutes of the ICSP, the minutes of this meeting are published here.

Options and considerations for validation of prokaryotic names under the SeqCode

Stable taxon names for Bacteria and Archaea are essential for capturing and documenting prokaryotic diversity. They are also crucial for scientific communication, effective accumulation of biological data related to the taxon names and for developing a comprehensive understanding of prokaryotic evolution. However, after more than a hundred years, taxonomists have succeeded in valid publication of only around 30 000 species names, based mostly on pure cultures under the International Code of Nomenclature of Prokaryotes (ICNP), out of the millions estimated to reside in the biosphere. The vast majority of prokaryotic species have not been cultured and are becoming increasingly known to us via culture-independent sequence-based approaches. Until recently, such taxa could only be addressed nomenclaturally via provisional names such as Candidatus or alphanumeric identifiers. Here, we present options and considerations to facilitate validation of names for these taxa using the recently established Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Community engagement and participation of relevant taxon specialists are critical and encouraged for the success of endeavours to formally name the uncultured majority.

SeqCode: A Nomenclatural Code for Prokaryotes

SeqCode is a nomenclatural code for naming prokaryotes based on genetic information. With the majority of prokaryotes being inaccessible as pure cultures, they are not eligible for naming under the International Code of Nomenclature of Prokaryotes. To address this challenge, a new concept that is SeqCode, which assign names to prokaryotes on the basis of genome sequence, has been announced in 2022. The valid publication of names for prokaryotes based on isolated genome, metagenome-assembled genomes, or single-amplified genome sequences. It operates through a registration portal, SeqCode Registry, where metadata is linked to names and nomenclatural types. This code provides a framework for reproducible nomenclature for all prokaryotes, either culturable or not and facilitates communication across all microbiological disciplines. Additionally, the SeqCode includes provisions for updating and revising names as new data becomes available. By providing a standardized system for naming and classifying these microorganisms based on their genetic information, the SeqCode will facilitate the discovery, understanding and comparison of these microorganisms, helping us to understand their role in the environment and how they contribute to the functioning of the Earth.

Harmonious naming across nomenclature codes exemplified by the description of bacterial isolates from the mammalian gut

A dual system for naming prokaryotes is currently in place based on the well-established International Code of Nomenclature of Prokaryotes (ICNP) and the newly created Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Whilst recent creation of the SeqCode opened an avenue to accelerate the naming of uncultured taxa, the existence of two codes increases the risk of species being assigned multiple validly published names. In this work we present a workflow that aims to limit conflicts by firstly naming novel cultured taxa under the SeqCode, and secondly under the ICNP, enhancing the traceability of the taxa across the two codes. To exemplify this workflow, we describe four novel taxa isolated from the intestine of pigs: Intestinicryptomonas porci gen. nov., sp. nov. (strain CLA-KB-P66T, genome accession GCA_033971905.1TS) within a novel family, Intestinicryptomonaceae; Grylomicrobium aquisgranensis gen. nov., sp. nov. (CLA-KB-P133T, GCA_033971865.1TS); Absicoccus intestinalis sp. nov. (CLA-KB-P134T, GCA_033971885.1TS); and Mesosutterella porci sp. nov. (oilRF-744- wt-GAM-9T, GCF_022134585.1TS).

Advancements in prokaryotic systematics and the role of Bergey's International Society for Microbial Systematicsin addressing challenges in the meta-data era

Prokaryotes are ubiquitous in the biosphere, important for human health and drive diverse biological and environmental processes. Systematics of prokaryotes, whose origins can be traced to the discovery of microorganisms in the 17th century, has transitioned from a phenotype-based classification to a more comprehensive polyphasic taxonomy and eventually to the current genome-based taxonomic approach. This transition aligns with a foundational shift from studies focused on phenotypic traits that have limited comparative value to those using genome sequences. In this context, Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB) and Bergey's International Society for Microbial Systematics (BISMiS) play a pivotal role in guiding prokaryotic systematics. This review focuses on the historical development of prokaryotic systematics with a focus on the roles of BMSAB and BISMiS. We also explore significant contributions and achievements by microbiologists, highlight the latest progress in the field and anticipate challenges and opportunities within prokaryotic systematics. Additionally, we outline five focal points of BISMiS that are aimed at addressing these challenges. In conclusion, our collaborative effort seeks to enhance ongoing advancements in prokaryotic systematics, ensuring its continued relevance and innovative characters in the contemporary landscape of genomics and bioinformatics.

Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names

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.

SeqCode in the golden age of prokaryotic systematics

The SeqCode is a new code of prokaryotic nomenclature that was developed to validate taxon names using genome sequences as the type material. The present article provides an independent view about the SeqCode, highlighting its history, current status, basic features, pros and cons, and use to date. We also discuss important topics to consider for validation of novel prokaryotic taxon names using genomes as the type material. Owing to significant advances in metagenomics and cultivation methods, hundreds of novel prokaryotic species are expected to be discovered in the coming years. This manuscript aims to stimulate and enrich the debate around the use of the SeqCode in the upcoming golden age of prokaryotic taxon discovery and systematics.