International journal of systematic and evolutionary microbiology最新文献

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.C1^T=NVSL-WS92.C1^T=KIT0303^T), Leptospira cinconiae sp. nov. (type strain WS58.C1^T=NVSL-WS58.C1^T=KIT0304^T), Leptospira mgodei sp. nov. (type strain WS4.C2^T=NVSL.WS4.C2^T=KIT0305^T), Leptospira iowaensis sp. nov. (type strain WS39.C2^T=NVSL-WS39.C2^T=KIT0306^T) and Leptospira milleri sp. nov. (type strain WS60.C2^T=NVSL-WS60.C2^T=KIT0307^T) are proposed.

Subcommittee on the taxonomy of Chlamydiae: minutes of the closed meeting, Zoom meeting, 24 September 2024.

A polyphasic taxonomic study was carried out on strain T9W2-O^T, isolated from the roots of the aquatic plant Salvinia minima. This isolate is rod-shaped, forms yellow/orange pigmented colonies and produces the pigment flexirubin. Nearly complete 16S rRNA gene sequence homology related the strain to Chryseobacterium, with 98.8 and 98.5% similarity to Chryseobacterium profundimaris and Chryseobacterium takakiae, respectively. Average nucleotide identity and digital DNA-DNA hybridization with the closest phylogenetic neighbour of T9W2-O^T showed differences at the species level, further confirmed by differences in several physiological characteristics. The main fatty acids are iso C_{15 : 0}, iso C_{17:1 ω9c}, iso C_{17 : 0} 3-OH and summed feature 4 (iso-C_{15 : 0} 2-OH and/or C_{16:1 ω7c}). DNA G+C content is 37.2 mol%. MK-6 is the only menaquinone found, and phosphatidylethanolamine is the dominant polar lipid. Based on the results obtained, this bacterium is assigned to the genus Chryseobacterium as a new species with the name Chryseobacterium salviniae sp. nov., type strain T9W2-O^T (=NRRL B-65715^T =DSM 118061^T).

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 2.483^T (MycoBank MB 857072).

A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5^T 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 RB5^T had the highest similarity to Pseudomonas granadensis LMG27940^T (98.94%) and Pseudomonas gozinkensis IzPS32d^T (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5^T in a distinct branch alongside its closest relative, P. granadensis LMG27940^T. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5^T and its close relationship with P. granadensis LMG27940^T. 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 LMG27940^T. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5^T 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 RB5^T belongs to a unique evolutionary line. The genome of RB5^T, 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, RB5^T 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 RB5^T includes C_16:0, C_17:0 cyclo and the summed features 3 consisting of C_16:1 ω7c/_C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5^T was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5^T (=DSM 117471^T=LMG 33633^T=CIP 112482^T).

Following a proposal to emend Recommendation 6(7), Rule 64 and Appendix 9, Section D of the International Code of Nomenclature of Prokaryotes to regulate the formation of prokaryote names from personal names, I hereby report the outcome of the ballot on this proposal by the members of the International Committee on Systematics of Prokaryotes.

A bacterial strain, designated as A6^T, was isolated from the rhizosphere soil of a healthy muskmelon in Wenchang, Hainan Province, China. The cells of strain A6^T were Gram-negative, aerobic, short rod and motile with a single polar flagellum. Strain A6^T could tolerate up to 55.0 mM Al³⁺ and inhibited the growth of Fusarium oxysporum f. sp. melonis, which is the pathogen of muskmelon Fusarium wilt. Growth occurred at 15-37 ℃ (optimum at 30 ℃), pH 4.5-8.0 (optimum pH 6.5) and with 0-3.0 % NaCl (w/v; optimum, 0.5%). Strain A6^T shared the highest 16S rRNA gene sequence similarities with Dyella lutea Sa^T (98.0%), followed by Dyella thiooxydans ATSB10^T (98.0%), Frateuria edaphi 5GH9-34^T (97.9%), Dyella nitratireducens DHG59^T (97.7%), Frateuria defendens DHo^T (97.7%) and Frateuria soli 5GH9-11^T (97.7%). Phylogenetic trees based on 16S rRNA gene and genomic sequences indicated that strain A6^T belonged to the genus Dyella and formed a subclade with Dyella lutea Sa^T and Dyella thiooxydans ATSB10^T. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between A6^T and its closely related type strains were 78.8-80.8 %, 70.0-71.7 % and 20.5-22.1 %, respectively. The sole respiratory quinone was ubiquinone-8 (Q-8). The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified aminophospholipids (APL1-2) and three unidentified phospholipids (PL1-3). The major cellular fatty acids (≥5 %) were iso-C_17 : 0, C_16 : 0, summed feature 9 (iso-C_17 : 1  ω9c and/or C_16 : 0 10-methyl), iso-C_15 : 0, iso-C_16 : 0 and anteiso-C_17 : 0. The genome size of strain A6^T was 3.7 Mb with a DNA G+C content of 65.1%. Based on the phenotypic, phylogenetic, genotypic and chemotaxonomic features, strain A6^T represents a novel species in the genus Dyella, for which Dyella aluminiiresistens A6^T sp. nov. is proposed. The type strain is A6^T (= GDMCC 1.4640^T = KCTC 92542^T).

A novel bacterium, designated 19SA41, was isolated from the air of the Icelandic volcanic island Surtsey. Cells of strain 19SA41 are Gram-stain-negative, strictly aerobic, non-motile rods and form pale yellow-pigmented colonies. The strain grows at 4-30 °C (optimum, 22 °C), at pH 6-10 (optimum, pH 7.5) and with 0-4% NaCl (optimum, 0.5%). Phylogenetic analyses based on 16S rRNA gene sequences showed that 19SA41 belonged to the genus Flavobacterium and is most similar to Flavobacterium xinjiangense DSM 19743^T, with a sequence similarity of 96.52%. The new strain contained iso-C_15 : 0 (22%) and summed feature 3 (C_16∶1ω6c/C_16∶1ω7c) (20%) as the predominant fatty acids. The major respiratory quinone was menaquinone-6 (100%). The polar lipid profile consisted of phosphatidylethanolamine and several uncharacterized amino lipids, glycolipids and lipids. The genome of the new strain was 4.01 Mbp, and its G+C content was 33.2 mol%. Based on characterization and comparative results, using a polyphasic taxonomic approach, we propose that the new isolate represents a novel species of the genus Flavobacterium with the name Flavobacterium aerium sp. nov. The type strain is ISCaR-07695^T (=DSM 116640^T =UBOOC-M-3567^T).

A Gram-stain-positive, facultatively anaerobic, rod-shaped strain, designated SPB1-3^T, was isolated from tree bark. This strain exhibited heterofermentative production of dl-lactic acid from glucose. Optimal growth was observed at 25-40 °C, pH 4.0-7.0, and in the presence of 3% (w/v) NaCl. The cell wall peptidoglycan contained lysine and aspartic acid. The predominant fatty acids identified were C_16:0 and the Summed feature 7 (C_19 :1  ω7c/C_19:1  ω6c and/or C_19:1  ω6c/ω7c/19cy). The polar lipid profile included phosphatidylglycerol, diphosphatidylglycerol and phosphatidylinositol, along with two unidentified phospholipids, two unidentified amino lipids and two unidentified lipids. Phylogenetic analysis based on 16S rRNA gene sequences positioned strain SPB1-3^T within the genus Lentilactobacillus, showing a close relation to Lentilactobacillus kosonis NBRC 111893^T (99.86%) and Lentilactobacillus curieae CCTCC M 2011381^T (98.65%). The whole genome of strain SPB1-3^T comprised 1 932 998 base pairs with 1955 coding genes and a DNA G+C content of 37.8%. Digital DNA-DNA hybridization between strain SPB1-3^T and closely related type strains ranged from 19.50 to 27.20%. The average nucleotide identity ranged from 84.21 to 85.56%, and the average amino acid identity ranged from 57.25 to 85.99%, both falling below the established thresholds for species delineation. Strain SPB1-3^T was clearly distinguishable from related Lentilactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and whole genome analysis. Additionally, the strain exhibited radical scavenging activity at 66.92% and demonstrated 82.32% inhibition in the tyrosinase inhibitory assay. These findings support the classification of strain SPB1-3^T as a novel species within the genus Lentilactobacillus, for which the name Lentilactobacillus terminaliae sp. nov. is proposed. The type strain is SPB1-3^T (=JCM 35081^T=TISTR 10005^T).

A new alkaliphilic strain of a purple sulphur bacterium designated as Um2 (=KCTC 25734=VKM B-3893=UQM 41073) with bacteriochlorophyll b and internal photosynthetic membranes of tubular type was isolated from the Umhei hydrothermal system (40 °C, pH 9.3 and salinity 0.42 g l^-1) located in the Baikal rift zone (Russia). Based on morphological and physiological characteristics, this bacterium was classified as Thioalkalicoccus limnaeus. The 16S rRNA gene sequence similarity of strain Um2 was 96.69% with the type strain of Tac. limnaeus A26^T, 95.41% with 'Thioflavicoccus mobilis' 8321^T and 95.34% with Thiococcus pfennigii 4250. The level of similarity of the ribulose 1,5-bisphosphate carboxylase sequences of strain Um2 and known strains of Thioalkalicoccus showed that they belong to the same species. Comparison of the genome nt sequences of strain Um2 revealed that the new isolate was remote from all other described Chromatiaceae species both in digital DNA-DNA hybridization (21.5%) and in average nt identity (76.7%) at the genus level. However, a genome nt sequence had not been determined for any of the known Thioalkalicoccus strains; therefore, the first genome sequence of a member of the genus Thioalkalicoccus is presented here. Tac. limnaeus Um2 is proposed as the neotype, as strain A26^T has been lost from culture collections.