International journal of systematic and evolutionary microbiology最新文献

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.

A novel Pseudonocardia strain DW16-2^T, isolated from duckweed (Spirodela polyrhiza), was taxonomically studied in detail. The analysis based on its 16S rRNA gene sequence revealed that the strain was most closely related to Pseudonocardia carboxydivorans Y8^T (98.8%), followed by Pseudonocardia tropica YIM 61452^T (98.7%), Pseudonocardia antarctica DVS 5a1^T (98.7%) and Pseudonocardia alni DSM 44104^T (98.7%). The average nucleotide identity (ANI) based on blast and digital DNA-DNA hybridization (dDDH) relatedness values between strain DW16-2^T and their closest type strains were below the threshold values for identifying a novel species. Morphological, physiological and chemotaxonomic features of strain DW16-2^T were typical for the genus Pseudonocardia by forming extensively branched substrate mycelium and aerial mycelium that fragmented into rod-shaped spore, with a smooth surface. The whole-cell hydrolysates of strain DW16-2^T contained meso-diaminopimelic acid as the diagnostic diamino acid, and the whole-cell sugars were arabinose, galactose, glucose and a trace amount of ribose. The polar lipids contained phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and unidentified phospholipids. The menaquinone (MK) was MK-8(H₄). The cellular fatty acids (>5 %) were iso-C_16 : 0, iso-C_16 : 1 H, summed feature 3: C_16 : 1 ω7c/C_16 : 1 ω6c; C_16 : 1 ω6c/C_16 : 1 ω7c, C_17 : 1 ω8c and anteiso-C_17 : 0. Characterization based on chemotaxonomic, phenotypic, genotypic and phylogenetic evidence demonstrated that strain DW16-2^T represents a novel species of the genus Pseudonocardia, for which the name Pseudonocardia spirodelae sp. nov. (type strain DW16-2^T = TBRC 16418^T = NBRC 115857^T) is proprosed. In addition, the comparison of the whole genome sequences suggested that P. alni and P. antarctica belong to the same species and P. carboxydivorans is a subspecies of P. alni. Therefore, it is proposed that P. antarctica Prabahar et al. 2004 is reclassified as a later heterotypic synonym of P. alni (Evtushenko et al. 1989) Warwick et al. 1994, and P. carboxydivorans Park et al. 2008 is proposed as a subspecies of P. alni (Evtushenko et al. 1989) Warwick et al. 1994.

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.

An obligately anaerobic, spore-forming sulphate-reducing bacterium, strain SB140^T, was isolated from a long-term continuous enrichment culture that was inoculated with peat soil from an acidic fen. Cells were immotile, slightly curved rods that stained Gram-negative. The optimum temperature for growth was 28 °C. Strain SB140^T grew at pH 4.0-7.5 with an optimum pH of 6.0-7.0 using various electron donors and electron acceptors. Yeast extract, sugars, alcohols and organic acids were used as electron donors for sulphate reduction. SB140^T additionally used elemental sulphur and nitrate as electron acceptors but not sulphite, thiosulphate or iron(III) provided as ferrihydrite and fumarate. The 16S rRNA gene sequence placed strain SB140^T in the genus Desulfosporosinus of the phylum Bacillota. The predominant cellular fatty acids were iso-C_15 : 0 (52.6%) and 5,7 C_15 : 2 (19.9%). The draft genome of SB140^T (5.42 Mbp in size) shared 77.4% average nucleotide identity with the closest cultured relatives Desulfosporosinus acididurans M1^T and Desulfosporosinus acidiphilus SJ4^T. On the basis of phenotypic, phylogenetic and genomic characteristics, SB140^T was identified as a novel species within the genus Desulfosporosinus, for which we propose the name Desulfosporosinus paludis sp. nov. The type strain is SB140^T (=DSM 117342^T=JCM 39521^T).

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.

Marine biofilms were newly revealed as a bank of hidden microbial diversity and functional potential. In this study, a Gram-stain-negative, aerobic, oval and non-motile bacterium, designated LMIT008^T, was isolated from the biofilm of concrete breakwater structures located in the coastal area of Shantou, PR China. Strain LMIT008^T was found to grow at salinities of 1-7% NaCl, at pH 5-8 and at temperatures 10-40 °C. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain LMIT008^T belonged to the genus Jannaschia and was closely related to the type strains Jannaschia aquimarina KCTC23555^T (96.03%) and Jannaschia marina SHC-163^T (95.31%). The draft genome size of the strain LMIT008^T was 3.67 Mbp, and the genomic DNA G+C content was 69.83 mol%. The average nucleotide identity value between strain LMIT008^T and the closely related type strain J. aquimarina KCTC23555^T was 74.82%. The predominant cellular fatty acids were identified as summed feature 8 (C_18 : 1  ω7c/C_18 : 1  ω6c) and C_18 : 0, and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. Ubiquinone-10 (Q-10) is the sole respiratory quinone. Further, genomic analysis of strain LMIT008^T showed that the strain harbours abundant genes associated with biofilm formation and environmental adaption, explaining the potential strategies for living on concrete breakwater structures. Based on the morphological, phylogenetic, chemotaxonomic and phenotypic characterization, the strain LMIT008^T was considered to represent a novel species in the genus of Jannaschia, for which the name Jannaschia maritima sp. nov. was proposed, with LMIT008^T (=MCCC 1K08854^T=KCTC 8321^T) as the type strain.

A novel Corynebacterium species, strain BD556^T, isolated from blood, was identified at Mayo Clinic, Rochester, MN, USA. After failing definitive identification using MALDI-ToF MS and partial 16S rRNA gene sequencing, BD556^T was characterized using a polyphasic approach, including phenotypic, biochemical and whole-genome sequencing methods. BD556^T was a Gram-positive rod with clubbed ends, facultatively anaerobic, catalase-positive, oxidase-negative and non-motile. Colonies were white, opaque and non-haemolytic with halo-like edges. BD556^T grew at 35 °C in room air, with CO₂ and under anaerobic conditions. BD556^T grew well in 0 and 6% NaCl and weakly in 10% NaCl. The genome size was 2 349 779 bp with a G+C content of 60.39%. Phylogenetic analysis using 16S rRNA gene sequence analysis, average nucleotide identity and digital DNA-DNA hybridization between the genome of BD556^T and the closest type strains from the Type Strain Genome Server database yielded separation values well beyond those required for species delineation. Chemotaxonomic analyses of BD556^T revealed ribose, arabinose and galactose as whole-cell sugars and an A1γ meso-diaminopimelic acid-direct peptidoglycan type. The major cellular fatty acids were C_15 : 0 (21.0%), C_16 : 0 (14.8%), C_17 : 1 ω9c (26.2%), C_17 : 0 (13.3%) and C_18 : 1 ω9c (18.3%). Polar lipids included diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids and phospholipids. BD556^T also contained mycolic acids (32-36 carbons) typical of corynebacteria. The respiratory quinones were dominated by MK-8(H₂) (71.2%) and MK-9(H₂) (25.9%), with smaller amounts of MK-7(H₂) and MK-10(H₂). The results presented support the tenet that BD556^T (=TSD 427^T=NCTC 15078^T) is a novel species for which the name Corynebacterium mayonis sp. nov. is proposed.

Six Gram-reaction-positive, strictly aerobic, mycelium-forming actinobacteria were isolated from soils collected from a natural cave in Jeju, Republic of Korea. The isolates produced well-developed, branched, substrate mycelia and white aerial mycelia that differentiated into straight or flexuous chains of smooth-surfaced spores. Cells showed growth at 15-30 °C, pH 3.5-8.0 and 0-1% (w/v) NaCl. Most of the isolates also grew at pH 10.0. The cell-wall peptidoglycan in common contained ll-diaminopimelic acid, galactose, glucose, mannose and rhamnose. The major menaquinone was MK-9(H₆) and MK-9(H₈). The polar lipids in common contained phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid, with the presence of diphosphatidylglycerol and phosphatidylethanolamine in some strains. The predominant fatty acids in common were anteiso-C_15 : 0, iso-C_16 : 0 and C_16 : 0. Strains N1-1^T, N1-3 and N1-12 contained genomes of 8.44-8.77 Mbp, and strains N1-5 and N1-10^T consisted of genomes of 9.00-9.17 Mbp, while strain N8-3^T contained the smallest genome (7.33 Mbp) among the isolates. The genomic DNA G+C contents of the isolates were 71.5-72.2%. Three representatives of the isolates encompassed 16-29 biosynthetic gene clusters predicted to encode for secondary metabolites. The core genome-based phylogenomic tree showed that they formed three distinct clusters within the genus Streptacidiphilus, with the closest relative, the type strain of Streptacidiphilus carbonis, which was also supported by 16S rRNA gene phylogeny. The orthologous average nucleotide identity (≤88.2%) and digital DNA-DNA hybridization (≤30.3%) between three representatives of the isolates and members of the genus Streptacidiphilus and among them supported that the isolates represent three new species of the genus Streptacidiphilus, for which the names Streptacidiphilus alkalitolerans [type strain, N1-1^T (=KCTC 19224^T=DSM 45080^T)], Streptacidiphilus cavernicola [type strain, N8-3^T (=KCTC 29470^T=DSM 117389^T)] and Streptacidiphilus jeojiensis sp. nov. [type strain, N1-10^T (=KCTC 19257^T=DSM 117391^T=NRRL B-24556^T)] are proposed.

A clinical isolate, R131, was isolated from the peritoneal swab of a patient who suffered from ruptured appendicitis with abscess and gangrene in Hong Kong in 2018. Cells are facultatively anaerobic, non-motile, Gram-positive coccobacilli. Colonies were small, grey, semi-translucent, low convex and alpha-haemolytic. The bacterium grew on blood agar but not on Brain Heart Infusion (BHI) and Mueller-Hinton agars. It was negative for catalase, oxidase, indole and aesculin hydrolysis. The initial identification attempts via matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S rRNA gene sequencing yielded inconclusive results. The 16S rRNA gene analysis showed that R131 shared >99% nucleotide identity with certain uncultured Actinomycetales bacteria. In this retrospective investigation, a complete genome of R131 was constructed, disclosing a DNA G+C content of 64%. Phylogenetic analysis showed that the bacterium was mostly related to Scrofimicrobium canadense WB03_NA08, which was first described in 2020. However, its 16S rRNA gene shared only 94.15% nucleotide identity with that of S. canadense WB03_NA08. Notably, the orthoANI between R131 and S. canadense WB03_NA08 was 67.81%. A pan-genome analysis encompassing R131 and 4 Scrofimicrobium genomes showed 986 core gene clusters shared with the Scrofimicrobium species, along with 601 cloud genes. The average nucleotide identity comparisons within the pan-genome analysis ranged from 59.78 to 62.51% between R131 and the other Scrofimicrobium species. Correspondingly, the dDDH values ranged from 19.20 to 22.30%, while the POCP values spanned from 57.48 to 60.94%. Therefore, a novel species, Scrofimicrobium appendicitidis sp. nov., is proposed. The type strain is R131^T (=JCM 36615^T=LMG 33627^T).