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.
Both the genera Suonthocola and Diplocloster are members of the family Lachnospiraceae. Their type species, both Suonthocola fibrivorans Sanger_33T and Diplocloster agilis ASD5720T, were isolated from human faeces. A comparison of their 16S rRNA gene sequences revealed 100% similarity, suggesting their close relatedness and the possibility of belonging to the same species. To clarify their taxonomic relationship, genome-based analyses were carried out. Overall genomic relatedness indices analyses indicated that S. fibrivorans Sanger_33T shared average amino acid identity and percentage of conserved proteins prediction values higher than the Lachnospiraceae-specific genus-level thresholds with D. agilis ASD5720T, as well as the other two existing species of the genus Diplocloster. Additionally, S. fibrivorans Sanger_33T formed a distinct branch with D. agilis ASD5720T, clustering with the other two species of the genus Diplocloster into the same clade in both the 16S rRNA gene phylogenetic tree and the core-genome phylogenomic tree. Essentially, both the average nucleotide identity and digital DNA-DNA hybridization prediction values between S. fibrivorans Sanger_33T and D. agilis ASD5720T were above the recommended species boundaries. It is thus clear that S. fibrivorans Sanger_33T and D. agilis ASD5720T constitute the same species. On the basis of the earliest valid publication, priority is given to D. agilis Chaplin et al. 2022. Based on this, the orphan species S. fibrivorans Hitch et al. 2022 is reclassified as a later heterotypic synonym of D. agilis Chaplin et al. 2022, along with the reclassification of the genus Suonthocola Hitch et al. 2022 as a later synonym of Diplocloster Chaplin et al. 2022.
In 1997, the name Skermania piniformis (Blackall et al. 1989) comb. nov. was proposed by Chun et al. on transfer of the species Nocardia pinensis to the newly established genus Skermania as its type species. The appearance of the epithet in S. piniformis was quite different from that in its basonym N. pinensis. This could be seen, at first glance, as an unnecessary epithet change that may render S. piniformis and its generic name Skermania illegitimate according to the International Code of Nomenclature of Prokaryotes (ICNP). But in this paper, the author argues that for this particular case, 'pinensis' and 'piniformis' are better treated as different spellings of the same epithet. And if so, the change from 'pinensis' to 'piniformis' will not give rise to a case of illegitimacy under Rule 41a of the ICNP. Several possible counterarguments are discussed, which are shown to be based on a misinterpretation of the ICNP, particularly in relation to Rule 20a. As this is a non-trivial issue, the author requests a final decision by the Judicial Commission according to Rule 58 of the ICNP. An additional request for clarifying Rule 54 is also made.
Two novel yeast strains, NYNU 236247 and NYNU 23523, were isolated from the leaves of Carpinus turczaninowii Hance, collected in the Tianchi Mountain National Forest Park, Henan Province, central China. Phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer (ITS) region revealed the closest relatives of the strains are three described Pseudobensingtonia species: Ps. fusiformis, Ps. musae and Ps. ingoldii. The novel species differed from the type strains of these three species by 12 to 22 nucleotide substitutions and 1 gap (~2.0-4.0%) in the D1/D2 domain and by 78 to 100 nucleotide mismatches (~12.0-16%) in the ITS region. Physiologically, the novel species differs from Ps. fusiformis and Ps. musae in its ability to assimilate dl-lactate and melezitose and from Ps. ingoldii by its inability to assimilate melibiose, soluble starch and ethanol. Pseudobensingtonia carpini sp. nov. is proposed for those two strains, with the holotype designated as GDMCC 2.483T (MycoBank MB 857072).
A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5T strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5T had the highest similarity to Pseudomonas granadensis LMG27940T (98.94%) and Pseudomonas gozinkensis IzPS32dT (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5T in a distinct branch alongside its closest relative, P. granadensis LMG27940T. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5T and its close relationship with P. granadensis LMG27940T. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940T. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5T represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5T belongs to a unique evolutionary line. The genome of RB5T, with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5T strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5T includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5T was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5T (=DSM 117471T=LMG 33633T=CIP 112482T).
Two Gram-stain-negative cocci anaerobes were isolated from pig faeces and designated as strains YH-vei2232T and YH-vei2233. Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates were most closely related to Veillonella rogosae KCTC 5967T, with 97.0% similarity. Analysis of housekeeping gene sequences (rpoB) revealed the strain formed a sub-cluster within the genus Veillonella. The average nucleotide identities between the two isolates and the most closely related strains within genus Veillonella were <75.0%. The major fatty acids were Summed Feature 8 and C16 : 1 ω9c. The cell wall peptidoglycan contained meso-diaminopimelic acid. The major metabolic end products of isolates were propionic and acetic acids. The genomic DNA G+C contents of both strains were 40.1 mol%. The chemotaxonomic, phenotypic and phylogenetic properties of YH-vei2232T (=KCTC 25748T=NBRC 116427T) and YH-vei2233 (=KCTC 25749=NBRC 116428) suggest that they represent a novel species of the genus Veillonella, for which the name Veillonella absiana sp. nov. is proposed.
Ten novel Gram-negative, aerobic, non-sporulating, yellow-pigmented rod-shaped bacterial strains motile by gliding were isolated from marine organisms/environments in French Polynesia. Three of them designated as 190524A05cT, 190524A02bT and 190130A14aT were retrieved from orbicular batfish (Platax orbicularis) mucus. Online database comparisons using 16S rRNA amplicons resulted in over 95% similarity to the genus Tenacibaculum. Phylogenetic analyses based on 679 concatenated core protein sequences revealed that strains 190524A05cT, 190524A02bT and 190130A14aT showed the highest similarity to Tenacibaculum skagerrakense DSM 14836T, Tenacibaculum xiamenense LMG 27422T and Tenacibaculum holothuriorum S2-2T, respectively. Digital DNA-DNA hybridization and average nt identity values between strains 190524A05cT, 190524A02bT and 190130A14aT and other type strains were less than 76.25 and 24.1%, respectively. The DNA G+C content was 31.48, 30.66 and 31.98 mol% for strains 190524A05cT, 190524A02bT and 190130A14aT, respectively. Menaquinone-6 was detected as the major isoprenoid quinone in these three strains. The major polar lipids (phosphatidylethanolamine and aminophospholipid) were similar to the chemotaxonomic profile of other species of the genus Tenacibaculum. Strain 190524A05cT contained summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:1 G, iso-C15:0 and iso-C17:0 3-OH as the major cellular fatty acids. Strain 190524A02bT contained summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:0, iso-C15:1 G and iso-C17:0 3-OH as the major cellular fatty acids. Strain 190130A14aT contained iso-C15:1 G, summed feature 3 (comprising C16:1 ω7c and/or iso-C15:0 2-OH), iso-C15:0 and iso-C17:0 3-OH as the major cellular fatty acids. Based on the phenotypic and molecular features, these three strains represent novel species of the genus Tenacibaculum for which the names Tenacibaculum platacis sp. nov., with 190524A05cT (= CIP 112470T = DSM 118113T) as the type strain; Tenacibaculum vairaonense sp. nov., with 190524A02bT (= CIP 112469T = DSM 118112T) as the type strain; and Tenacibaculum polynesiense sp. nov., with 190130A14aT (= CIP 112468T = DSM 118111T) as the type strain, are proposed.
Two Gram-stain-negative, motile, non-spore-forming, aerobic or facultative anaerobic and short rod-shaped bacterial strains, 25B02-3T and BH-R2-4, were isolated from surface seawater collected from the Bering Sea and Chukchi Sea, respectively. The 16S rRNA gene sequences of the two strains were identical. The phylogenetic analysis of the 16S rRNA gene sequences indicated that they were related to the genus Tistrella and shared 99.6 and 98.2% sequence similarity with T. bauzanensis BZ78T and T. mobilis IAM 14872T, respectively. Both 16S rRNA gene and genome sequence-based phylogenetic analyses showed that the two strains formed a monophyletic clade within the genus Tistrella, indicating that they may represent a novel species. The digital DNA‒DNA hybridization (dDDH) values and average nucleotide identities (ANI) between the two strains were 93 and 99%, respectively, indicating that they are different strains. The dDDH and ANI values between the two strains and the type strains of the genus Tistrella were 22.4-58.3% and 81.0-95.0%, respectively. These data clearly demonstrated that the two strains represent a separate genomic species of the genus Tistrella. The principal fatty acids were Sum In Feature 8 (C18 : 1 ω7c or C18 : 1 ω6c), C19 : 0 cyclo ω8c, Sum In Feature 2 (C12 : 0 aldehyde or unknown 10.928) and C16 : 0. The predominant respiratory quinone was Q-10, with a minor Q-9. The polar lipids included phosphatidylethanolamine, aminolipids and phospholipids. The genomic DNA G+C contents of strains 25B02-3T and BH-R2-4 were 67.3 mol% and 67.4 mol%, respectively. On the basis of the polyphasic evidence presented in this study, the two strains represent a novel species within the genus Tistrella, for which the name Tistrella arctica sp. nov. is proposed. The type strain is 25B02-3T (=MCCC 1A07333T=KCTC 8340T).
Isolates of Leptospira spp. were cultured from water sources at five different sites in central Iowa in the Midwestern United States and characterized by whole-genome sequencing. Isolates were helix-shaped and motile. Genome sequence analyses determined that the isolates could be clearly distinguished from other species described in the genus Leptospira and included one species that belonged to the pathogen subclade P1, one species that belonged to the pathogen subclade P2 and three species that belonged to the saprophyte subclade S1. The names Leptospira gorisiae sp. nov. (type strain WS92.C1T=NVSL-WS92.C1T=KIT0303T), Leptospira cinconiae sp. nov. (type strain WS58.C1T=NVSL-WS58.C1T=KIT0304T), Leptospira mgodei sp. nov. (type strain WS4.C2T=NVSL.WS4.C2T=KIT0305T), Leptospira iowaensis sp. nov. (type strain WS39.C2T=NVSL-WS39.C2T=KIT0306T) and Leptospira milleri sp. nov. (type strain WS60.C2T=NVSL-WS60.C2T=KIT0307T) are proposed.
A polyphasic taxonomic study was carried out on strain T5W1T, isolated from the roots of the aquatic plant Spirodela polyrhiza. This isolate is Gram-negative, rod-shaped, motile, aerobic and non-pigmented. Nearly complete 16S rRNA gene sequence homology related the strain to Pseudomonas, with 98.4% similarity to P. guineae, P. peli and P. leptonychotis. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbour of T5W1T showed differences at the species level, further confirmed by differences in several physiological characteristics. The main fatty acids are summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C18 : 1 ω7c, and C16 : 0. The DNA G+C content is 59.3 mol%. Q-9 is the primary ubiquinone found, and phosphatidylethanolamine is the dominant polar lipid, with lesser amounts of phosphatidylglycerol, diphosphatidylglycerol and phosphatidylserine. Based on the results obtained, this bacterium is assigned to the genus Pseudomonas as a new species with the name Pseudomonas spirodelae sp. nov., type strain T5W1T (=NRRL B-65714T =DSM 118085T).
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