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.

Judicial Opinion 129.

Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.

A long-awaited taxogenomic investigation of the family Halomonadaceae.

The family Halomonadaceae is the largest family composed of halophilic bacteria, with more than 160 species with validly published names as of July 2023. Several classifications to circumscribe this family are available in major resources, such as those provided by the List of Prokaryotic names with Standing in Nomenclature (LPSN), NCBI Taxonomy, Genome Taxonomy Database (GTDB), and Bergey's Manual of Systematics of Archaea and Bacteria (BMSAB), with some degree of disagreement between them. Moreover, regardless of the classification adopted, the genus Halomonas is not phylogenetically consistent, likely because it has been used as a catch-all for newly described species within the family Halomonadaceae that could not be clearly accommodated in other Halomonadaceae genera. In the past decade, some taxonomic rearrangements have been conducted on the Halomonadaceae based on ribosomal and alternative single-copy housekeeping gene sequence analysis. High-throughput technologies have enabled access to the genome sequences of many type strains belonging to the family Halomonadaceae; however, genome-based studies specifically addressing its taxonomic status have not been performed to date. In this study, we accomplished the genome sequencing of 17 missing type strains of Halomonadaceae species that, together with other publicly available genome sequences, allowed us to re-evaluate the genetic relationship, phylogeny, and taxonomy of the species and genera within this family. The approach followed included the estimate of the Overall Genome Relatedness Indexes (OGRIs) such as the average amino acid identity (AAI), phylogenomic reconstructions using amino acid substitution matrices customized for the family Halomonadaceae, and the analysis of clade-specific signature genes. Based on our results, we conclude that the genus Halovibrio is obviously out of place within the family Halomonadaceae, and, on the other hand, we propose a division of the genus Halomonas into seven separate genera and the transfer of seven species from Halomonas to the genus Modicisalibacter, together with the emendation of the latter. Additionally, data from this study demonstrate the existence of various synonym species names in this family.

The gender gap in names of prokaryotes honouring persons.

The aim of this study is to analyse prokaryotic names which honour persons, eponyms, from a gender perspective. Data were retrieved from the List of Prokaryotic names with Standing in Nomenclature. Excluding new combinations, the etymologies of 23 315 unique names at the rank of genus, species and subspecies were analysed. A total of 2018 (8.7 %) names honour persons (eponyms), for which the development of the female share over time was further investigated. Women started to be honoured very recently (1947) compared to men (1823). Moreover, only 14.8 % of all prokaryotic eponyms refer to females. This ratio has hardly improved since 1947, although the number of women whose contributions to microbiology could have been recognized has increased over time. In contrast, about 50 % of prokaryotic names derived from mythological characters refer to females. To reduce this gender gap, we encourage authors proposing new taxon names to honour female scientists who can serve as role models for new generations.

Judicial Opinion 128.

Judicial Opinion 128 addresses nomenclatural issues related to the names of classes validly published under the International Code of Nomenclature of Prokaryotes. It is confirmed that the common ending -proteobacteria of some class names is not indicative of a joint taxonomic or phylogenetic placement; that the nomenclatural type of Mollicutes Edward and Freundt 1967 (Approved Lists 1980) is Mycoplasmatales Freundt 1955 (Approved Lists 1980); and that the placement of a name on the list of rejected names does not imply that another name with the same spelling but a distinct rank is also placed on that list. The names at the rank of class Anoxyphotobacteria (Gibbons and Murray 1978) Murray 1988, Archaeobacteria Murray 1988, Bacteria Haeckel 1894 (Approved Lists 1980), Firmibacteria Murray 1988, Microtatobiotes Philip 1956 (Approved Lists 1980), Oxyphotobacteria (ex Gibbons and Murray 1978) Murray 1988, Photobacteria Gibbons and Murray 1978 (Approved Lists 1980), Proteobacteria Stackebrandt et al. 1988, Schizomycetes Nägeli 1857 (Approved Lists 1980), Scotobacteria Gibbons and Murray 1978 (Approved Lists 1980) are placed on the list of rejected names. For three common nominative singular suffixes of genus names their genitive singular and nominative plural forms are confirmed: -bacter (-bacteris, -bacteres); -fex (-ficis, -fices); and -genes (-genis, -genes). The class names Aquificae Reysenbach 2002, Chrysiogenetes Garrity and Holt 2002, Chthonomonadetes Lee et al. 2011, Gemmatimonadetes Zhang et al. 2003, Opitutae Choo et al. 2007 and Verrucomicrobiae Hedlund et al. 1998 are orthographically corrected to Aquificia, Chrysiogenia, Chthonomonadia, Gemmatimonadia, Opitutia and Verrucomicrobiia, respectively.

Guidelines for interpreting the International Code of Nomenclature of Prokaryotes and for preparing a Request for an Opinion.

In this paper the Judicial Commission provides general guidance for interpreting the International Code of Nomenclature of Prokaryotes (ICNP) and specific assistance to authors, reviewers and editors of a Request for an Opinion, or of other suggestions related to the ICNP. The role of the Judicial Commission is recapitulated, particularly with respect to the processing of such Requests. Selected kinds of nomenclature-related proposals are discussed that are unsuitable as the basis for a Request. Particular emphasis is put on Requests for placing names or epithets on the list of nomina rejicienda, and a dichotomous identification key is provided to guide potential authors of a Request that targets the name of a species or subspecies because of issues with its type strain. To this end, the criteria for the valid publication of such names under the ICNP are revisited. Aspects of other kinds of Requests are also addressed. The study is based on a comprehensive review of all Judicial Opinions issued since the publication of the Approved Lists in 1980. One goal of this paper is to assist potential authors in deciding whether their concern should be the subject of a Request, and if so, in composing it with the greatest chance of success. It is also clarified how to obtain additional help regarding nomenclature-related issues.

Judicial Opinions 112-122.

Opinion 112 denies the request to place Seliberia Aristovskaya and Parinkina 1963 (Approved Lists 1980) on the list of rejected names because the information provided is insufficient. For the same reason, Opinion 113 denies the request to reject Shewanella irciniae Lee et al. 2006 and Opinion 114 denies the request to reject the name Enterobacter siamensis Khunthongpan et al. 2014. Opinion 115 rejects the epithet of Moorella thermoautotrophica (Wiegel et al. 1981) Collins et al. 1994, which is regarded as a nomen confusum. To assess the consequences of Rule 8, Opinion 116 revisits names of taxa above the rank of genus which should comprise the stem of the name of a nomenclatural type and a category-specific ending but fail to do so. Such names should be orthographically corrected if the sole error is the inadvertent usage of an incorrect stem or be regarded as illegitimate if otherwise. The necessary corrections are made for a number of names. In Opinion 117, the request to designate Methylothermus subterraneus Hirayama et al. 2011 as the type species of the genus Methylothermus is denied because an equivalent action compatible with the Code was already conducted. In Opinion 118, the possible orthographical correction of the name Flaviaesturariibacter is treated, as are the analogous cases of Fredinandcohnia and Hydrogeniiclostidium. The genus names are corrected to Flaviaestuariibacter, Ferdinandcohnia and Hydrogeniiclostridium, respectively. Opinion 119 concludes that assigning Actinomycetales Buchanan 1917 (Approved Lists 1980) as nomenclatural type of the class Actinobacteria Stackebrandt et al. 1997 would not render that name legitimate if Rule 8 remained retroactive. The request is granted but Actinomycetales is also assigned as type of Actinomycetes Krassilnikov 1949 (Approved Lists 1980). In Opinion 120, the possible orthographical correction of the name Amycolatopsis albidoflavus is treated. It is grammatically corrected to Amycolatopsis albidoflava. Six names which could according to Rule 61 be grammatically corrected by anyone are also corrected. Opinion 121 denies the request to revise Opinion 69 and notes that Opinion 69 does not have the undesirable consequences emphasized in the request. In Opinion 122, the request to reject various taxon names of Mollicutes proposed in 2018 is denied because it is based on misinterpretations of the Code, which are clarified. Alternative ways to solve the perceived problems are outlined. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Parvicella tangerina gen. nov., sp. nov. (Parvicellaceae fam. nov., Flavobacteriales), first cultured representative of the marine clade UBA10066, and Lysobacter luteus sp. nov., from activated sludge of a seawater-processing wastewater treatment plant.

Two strains isolated from a sample of activated sludge that was obtained from a seawater-based wastewater treatment plant on the southeastern Mediterranean coast of Spain have been characterized to achieve their taxonomic classification, since preliminary data suggested they could represent novel taxa. Given the uniqueness of this habitat, as this sort of plants are rare in the world and this one used seawater to process an influent containing intermediate products from amoxicillin synthesis, we also explored their ecology and the annotations of their genomic sequences. Analysis of their 16S rRNA gene sequences revealed that one of them, which was orange-pigmented, was distantly related to Vicingus serpentipes (family Vicingaceae) and to other representatives of neighbouring families in the order Flavobacteriales (class Flavobacteriia) by 88-89 % similarities; while the other strain, which was yellow-pigmented, was a putative new species of Lysobacter (family Xanthomonadaceae, order Xanthomonadales, class Gammaproteobacteria) with Lysobacter arseniciresistens as closest relative (97.3 % 16S rRNA sequence similarity to its type strain). Following a polyphasic taxonomic approach, including a genome-based phylogenetic analysis and a thorough phenotypic characterization, we propose the following novel taxa: Parvicella tangerina gen. nov., sp. nov. (whose type strain is AS29M-1T=CECT 30217T=LMG 32344T), Parvicellaceae fam. nov. (whose type genus is Parvicella), and Lysobacter luteus sp. nov. (whose type strain is AS29MT=CECT 30171T=LMG 32343T).

Complete genome sequences of Lacticaseibacillus paracasei INIA P272 (CECT 8315) and Lacticaseibacillus rhamnosus INIA P344 (CECT 8316) isolated from breast-fed infants reveal probiotic determinants.

Lacticaseibacillus paracasei INIA P272 and Lacticaseibacillus rhamnosus INIA P344, isolated from breast-fed infants, are two promising bacterial strains for their use in functional foods according to their demonstrated probiotic and technological characteristics. To better understand their probiotic characteristics and evaluate their safety, here we report the draft genome sequences of both strains as well as the analysis of their genetical content. The draft genomes of L. paracasei INIA P272 and L. rhamnosus INIA P344 comprise 3.01 and 3.26 Mb, a total of 2994 and 3166 genes and a GC content of 46.27 % and 46.56 %, respectively. Genomic safety was assessed following the EFSA guidelines: the identification of both strains was confirmed through Average Nucleotide Identity, and the absence of virulence, pathogenic and antibiotic resistance genes was demonstrated. The genome stability analysis revealed the presence of plasmids and phage regions in both genomes, however, CRISPR sequences and other mechanisms to fight against phage infections were encoded. The probiotic abilities of both strains were supported by the presence of genes for the synthesis of SCFA, genes involved in resistance to acid and bile salts or a thiamine production cluster. Moreover, the encoded exopolysaccharide biosynthesis genes could provide additional protection against the deleterious gastrointestinal conditions, besides which, playing a key role in adherence and coaggregation of pathogenic bacteria together with the high number of adhesion proteins and domains encoded by both genomes. Additionally, the bacteriocin cluster genes found in both strains, could provide an advantageous ability to compete against pathogenic bacteria. This genomic study supports the probiotic characteristics described previously for these two strains and satisfies the safety requirements to be used in food products.

Judicial Opinions 103-111.

In Opinion 103, the request to place the name Spirillum volutans Ehrenberg 1832 (Approved Lists 1980) on the list of rejected names is denied because a neotype may be designated. Similarly, because a neotype may be designated, in Opinion 104 the request to place the name Beijerinckia fluminensis Döbereiner and Ruschel 1958 (Approved Lists 1980) on the list of rejected names is denied. In Opinion 105, it is emphasized that the name Rhodoligotrophos Fukuda et al. 2012 does not contravene the Code. The request to orthographically correct Rhodoligotrophos Fukuda et al. 2012 to Rhodoligotrophus corrig. Fukuda et al. 2012 is denied. Opinion 106 addresses two Requests for an Opinion and results in the placement of the epithet hoagii in Corynebacterium hoagii (Morse 1912) Eberson 1918 (Approved Lists 1980) and Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014 on the list of rejected specific and subspecific epithets. Since this removes all known available earlier synonyms of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 (Approved Lists 1980), the request to conserve the epithet equi in this name is denied. In Opinion 107, Thermomicrobium fosteri Phillips and Perry 1976 (Approved Lists 1980) is placed on the list of rejected names as a nomen dubium et confusum. Opinion 108 denies the request to place Hyphomonas rosenbergii Weiner et al. 2000 on the list of rejected names because the information provided to the Judicial Commission is not sufficient to draw a conclusion on this matter. In Opinion 109, which addresses three Requests for an Opinion, the Judicial Commission denies the requests to place the names Bacillus aerius Shivaji et al. 2006, Bacillus aerophilus Shivaji et al. 2006 and Bacillus stratosphericus Shivaji et al. 2006 on the list of rejected names. Instead, it is concluded that these three names had not met the requirements for valid publication. Likewise, the Judicial Commission concludes in Opinion 110 that the name Actinobaculum massiliense corrig. Greub and Raoult 2006 had not met the requirements for valid publication. The Judicial Commission reaffirms in Opinion 111 that Methanocorpusculum parvum Zellner et al. 1988 is the nomenclatural type of Methanocorpusculum Zellner et al. 1988 and further emphasizes that the species was not in danger of losing this status. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Proposals to emend Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a, and Appendix 7 of the International Code of Nomenclature of Prokaryotes.

To complete the ongoing revision of the International Code of Nomenclature of Prokaryotes, we here propose emendation of Rules 8, 15, 22, 25a, 30(3)(b), 30(4), 34a and Appendix 7. These proposed emendations deal with: the nomenclatural type of taxa above genus; the suitability of names published in supplementary material or in papers published on e-print servers for effective publication; the number of culture collection designations to be included in an effective publication of a name of a species or subspecies to qualify for validation of the name; the kinds of restrictions that may be attached to deposits of type strains; and the question whether elevation of a subspecies to the rank of species or lowering of a species to the rank of subspecies establish new combinations. Some of these emendations change the meaning of the Code while others are mere textual clarifications.

Judicial Opinions 123-127.

Opinion 123 places the epithet of the name Aeromonas punctata on the list of rejected epithets and clarifies the citation of authors of selected names within the genus Aeromonas. Opinion 124 denies the request to place Borreliella on the list of rejected names because the request is based on a misinterpretation of the Code, which is clarified. There are alternative ways to solve the perceived problem. Opinion 125 denies the request to place Lactobacillus fornicalis on the list of rejected names because the provided information does not yield a reason for rejection. Opinion 126 denies the request to place Prolinoborus and Prolinoborus fasciculus on the list of rejected names because a relevant type strain deposit was not examined. Opinion 127 grants the request to assign the strain deposited as ATCC 4720 as the type strain of Agrobacterium tumefaciens, thereby correcting the Approved Lists. These Opinions were ratified by the voting members of the International Committee on Systematics of Prokaryotes.

Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems.

A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them revealed that strains CECT 9293T and CECT 9393T could perhaps be related at the species level as they shared 99.5 % similarity. However, whole genome sequencing was performed and the subsequent calculation of relatedness indices, average nucleotide identity and estimated DNA-DNA hybridization, ruled out that possibility and confirmed instead that each of the strains should be considered a separate species in the genus Chryseobacterium. Having clarified their status, we also performed phylogenomic analyses and searched for possible environmental or non-type material sequences that could be related to any of them at the species level. In parallel, the strains were characterized phenotypically and compared to their closest relatives to determine diagnostic traits to support their formal proposal. The proposed species are Chryseobacterium potabilaquae sp. nov. with the type strain CECT 9293T (=LMG 32084T), Chryseobacterium aquaeductus sp. nov. with the type strain CECT 9390T (=LMG 32085T) and Chryseobacterium fistulae sp. nov. with the type strain CECT 9393T (=LMG 32086T).

Rapid and improved identification of drinking water bacteria using the Drinking Water Library, a dedicated MALDI-TOF MS database.

According to the European Directives (UE) 2020/2184 and 2009/54/EC, which establishes the sanitary criteria for water intended for human consumption in Europe, water suitable for human consumption must be free of the bacterial indicators Escherichia coli, Clostridium perfringens and Enterococcus spp. Drinking water is also monitored for heterotrophic bacteria, which are not a human health risk, but can serve as an index of bacteriological water quality. Therefore, a rapid, accurate, and cost-effective method for the identification of these colonies would improve our understanding of the culturable bacteria of drinking water and facilitate the task of water management by treatment facilities. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is potentially such a method, although most of the currently available mass spectral libraries have been developed in a clinical setting and have limited environmental applicability. In this work, a MALDI-TOF MS drinking water library (DWL) was defined and developed by targeting bacteria present in water intended for human consumption. This database, made up of 319 different bacterial strains, can contribute to the routine microbiological control of either treated drinking water or mineral bottled water carried out by water treatment and distribution operators, offering a faster identification rate compared to a clinical sample-based library. The DWL, made up of 96 bacterial genera, 44 of which are not represented in the MALDI-TOF MS bacterial Bruker Daltonics (BDAL) database, was found to significantly improve the identification of bacteria present in drinking water.

Emendation of General Consideration 5 and Rules 18a, 24a and 30 of the International Code of Nomenclature of Prokaryotes to resolve the status of the Cyanobacteria in the prokaryotic nomenclature.

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to resolve the status of the Cyanobacteria in the prokaryotic nomenclature, we announce here the results of the ballot. We also present the emended versions of General Consideration 5 and Rules 18a, 24a and 30, based on the outcome of the ballot, to be included in the new revision of the International Code of Nomenclature of Prokaryotes.

Public discussion on a proposed revision of the International Code of Nomenclature of Prokaryotes.

The Editorial Board for the International Code of Nomenclature of Prokaryotes (ICNP) has compiled proposed revisions of the ICNP. As outlined previously (Oren et al., Int J Syst Evol Microbiol 2021;71:004598; https://doi.org/10.1099/ijsem.0.004598) and to comply with Articles 13(b)(4) and 4(d) of the statutes of the International Committee on Systematics of Prokaryotes, a public discussion of the document will start on 1 July 2021, to last for 6 months. Here, we present the procedure for this discussion.

Emendation of Rules 5b, 8, 15 and 22 of the International Code of Nomenclature of Prokaryotes to include the rank of phylum.

Following the International Committee on Systematics of Prokaryotes electronic discussion and vote on proposals to include the rank of phylum in the rules of the International Code of Nomenclature of Prokaryotes, we here announce the results of the ballot. We also present draft versions of the emended Rules 5b, 8, 15 and 22, based on the outcome of the ballot, to be included in the proposal for the preparation of a new revision of the International Code of Nomenclature of Prokaryotes.