International journal of systematic and evolutionary microbiology最新文献

Six Gram-stain-positive and rod-shaped strains, designated FJAT-51614^T, FJAT-51639^T, FJAT-52054^T, FJAT-52991^T, FJAT-53654^T and FJAT-53711^T, were isolated from a mangrove ecosystem. The condition for growth among the strains varied (pH ranging 5.0-11.0 and temperature 15-45 °C). These strains showed the highest 16S rRNA gene sequence similarity to the genera Bacillus, Metabacillus and Psychrobacillus. Menaquinone MK-7 (100%) was present in all strains except strain FJAT-51614^T, which contained MK-7 (32%) and MK-8 (68%). The major fatty acids (>10%) in strains FJAT-52054^T and FJAT-51614^T were anteiso-C_15 : 0 and iso-C_14 : 0. The major fatty acid (>10%) in strain FJAT-53654^T was anteiso-C_15 : 0, while in strain FJAT-51639^T were iso-C_15 : 0 and iso-C_17 : 0. The major fatty acids in strains FJAT-52991^T and FJAT-53711^T were iso-C_15 : 0 and iso-C_16 : 0. The major polar lipids in strains FJAT-51639^T, FJAT-52991^T and FJAT-51614^T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, while strains FJAT-53711^T, FJAT-52054^T and FJAT-53654^T consist of diphosphatidylglycerol and phosphatidylglycerol. The genome-relatedness values among the present study strains and the closest species were below the recognized cutoff levels for species delineation. The polyphasic analysis comparison results represent six strains as novel species for which the names Bacillus bruguierae sp. nov. (FJAT-51639^T=GDMCC 1.3073^T=JCM 35615^T), Bacillus kandeliae sp. nov. (FJAT-52991^T=GDMCC 1.3069^T=JCM 35619^T), Bacillus yunxiaonensis sp. nov. (FJAT-53711^T=GDMCC 1.3068^T=JCM 35616^T), Metabacillus rhizosphaerae sp. nov. (FJAT-53654^T=GDMCC 1.3075^T=JCM 35614^T), Metabacillus sediminis sp. nov. (FJAT-52054^T=GDMCC 1.3074^T=JCM 35620^T) and Psychrobacillus mangrovi sp. nov. (FJAT-51614^T=GDMCC 1.3072^T=JCM35478^T) are proposed.

Four novel bacterial strains were isolated from stagnant water in a clump of Phragmites japonica Steud. The four Gram-negative, facultatively anaerobic, rod-shaped, non-motile and yellow-coloured strains were designated as DGU11^T, DGU38^T, DGU41^T and DGU99^T. The four novel strains exhibited 16S rRNA gene similarities with their closest type strains, ranging from 95.7 to 98.7%, average nucleotide identity values from 75.3 to 95.6% and digital DNA-DNA hybridization values between 17.9 and 59.6%. The cells of strain DGU11^T were non-motile and grew at 10-30°C (optimum 25 °C), a pH range of 4.0-12.0 (optimum 9.0) and in the presence of 0-1.0% sodium chloride (NaCl) (optimum 0%). The cells of strain DGU38^T were non-motile and grew at 10-35°C (optimum 30 °C), a pH range of 4.0-8.0 (optimum 7.0) and at 0 -2.0% NaCl (optimum 0%). The cells of strain DGU41^T were non-motile and grew at 15-50°C (optimum 30 °C), a pH range of 6.0-9.0 (optimum 7.0) and in the presence of 0% NaCl (optimum 0%). The cells of strain DGU99^T were non-motile and grew at 15-35°C (optimum 25 °C), a pH range of 6.0-12.0 (optimum 9.0) and in the presence of 0 -2.0% NaCl (optimum 0%). The major fatty acid composition of the four novel strains was iso-C_15:0 and C_16:1  ω7c/C1_6:1  ω6c, which is similar to other Flavobacterium species. The proposed names of the novel strains are Flavobacterium arundinis sp. nov. (type strain DGU11^T=KACC 23722^T=TBRC 19004^T), Flavobacterium calami sp. nov. (type strain DGU38^T=KACC 23723^T=TBRC 19005^T), Flavobacterium helocola sp. nov. (type strain DGU41^T=KACC 23724^T=TBRC 19006^T) and Flavobacterium flavipallidum sp. nov. (type strain DGU99^T=KACC 23725^T=TBRC 19007^T).

A polyphasic taxonomic study was carried out on strain T5W1^T, 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 T5W1^T showed differences at the species level, further confirmed by differences in several physiological characteristics. The main fatty acids are summed feature 3 (C_{16 : 1   ω7c} and/or C_{16 : 1   ω6c}), C_{18 : 1   ω7c}, and C_16 : 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 T5W1^T (=NRRL B-65714^T =DSM 118085^T).

Four novel nontuberculous mycobacteria were discovered from a historical strain collection at the International Reference Laboratory of Mycobacteriology at Statens Serum Institut in Copenhagen, Denmark. Phylogenetic analysis combining the 16S rrs, internal transcribed spacer and 23S rrl elements, as well as a single-copy core-gene (hsp65, rpoB+C, secA and tuf) analysis of these freeze-dried mycobacteria, clinically isolated from gastric lavage samples between 1948 and 1955, showed to be associated with type strains grouping within the Terra and Fortuitum-Vaccae clade. Phenotypic characteristics, biochemical properties and fatty acid and mycolic acid profiles supported the classification as novel strains. A genomic comparison to the closest related type strain was done by calculating average nucleotide identity and in silico DNA:DNA hybridization values, which showed 87.9% and 33.0% for Mu0050, 85.2% and 27.4% for Mu0053, 85.3% and 27.6% for Mu0083 and 93.3% and 50.1% for Mu0102, respectively. The names proposed for the new species are Mycobacterium wendilense sp. nov. (Mu0050^T=ITM 501390^T=CCUG 77525^T), Mycobacterium burgundiense sp. nov. (Mu0053^T=ITM 501391^T=CCUG 77526^T), Mycobacterium kokjensenii sp. nov. (Mu0083^T=ITM 501392^T=CCUG 77527^T) and Mycobacterium holstebronense sp. nov. (Mu0102^T=ITM 501393^T=CCUG 77528^T).

Yeast strains representing a novel asexual ascomycetous species were isolated from seven Malva sylvestris flowers. Sequencing of the chromosomal regions coding for the D1/D2 domains of the large subunit ribosomal RNA, the ITS1-5.8S-ITS2 segments and parts of the gene coding for the small subunit ribosomal RNA showed that the isolates were conspecific. Comparative analysis of these sequences and the corresponding sequences of the type strains of ascomycetous yeasts revealed that the strains represent a hitherto undescribed species belonging to the sensu stricto subclade of the genus Starmerella. The new species is osmotolerant and can develop invasive pseudohyphae, but does not form spores. For the new species, the name Starmerella aleppica f.a. (forma asexualis) is proposed. The holotype, preserved in a metabolically inactive state, is CBS 12960^T (extype cultures: 2-1361 and CCY 90-2-1, NCAIM Y.02123). The GenBank accession numbers of barcode sequences are JX515983 (D1/D2 domain), JX515985 (ITS1-5.8S-ITS2 and partial 18S rRNA gene), PQ613837 (TEF1 partial sequence) and PQ613838 (RPB2 partial sequence). MycoBank: MB855459. The analysis of the D1/D2 and internal transcribed spacer (ITS) sequences of the type strains of species of the genus identified multiple multinucleotide indels that can be used as taxonomic markers (InDel markers). The indel patterns of the subclades are very different and homogeneous within the subclades. This result reinforces the idea raised, but also refuted, in previous studies that the Starmerella subclades may represent different genera.

Two Gram-stain-negative cocci anaerobes were isolated from pig faeces and designated as strains YH-vei2232^T and YH-vei2233. Phylogenetic analysis using 16S rRNA gene sequences revealed that the isolates were most closely related to Veillonella rogosae KCTC 5967^T, 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 C_16 : 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-vei2232^T (=KCTC 25748^T=NBRC 116427^T) 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 190524A05c^T, 190524A02b^T and 190130A14a^T 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 190524A05c^T, 190524A02b^T and 190130A14a^T showed the highest similarity to Tenacibaculum skagerrakense DSM 14836^T, Tenacibaculum xiamenense LMG 27422^T and Tenacibaculum holothuriorum S2-2^T, respectively. Digital DNA-DNA hybridization and average nt identity values between strains 190524A05c^T, 190524A02b^T and 190130A14a^T 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 190524A05c^T, 190524A02b^T and 190130A14a^T, 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 190524A05c^T contained summed feature 3 (comprising C_16:1 ω7c and/or iso-C_15:0 2-OH), iso-C_15:1 G, iso-C_15:0 and iso-C_17:0 3-OH as the major cellular fatty acids. Strain 190524A02b^T contained summed feature 3 (comprising C_16:1 ω7c and/or iso-C_15:0 2-OH), iso-C_15:0, iso-C_15:1 G and iso-C_17:0 3-OH as the major cellular fatty acids. Strain 190130A14a^T contained iso-C_15:1 G, summed feature 3 (comprising C_16:1 ω7c and/or iso-C_15:0 2-OH), iso-C_15:0 and iso-C_17:0 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 190524A05c^T (= CIP 112470^T = DSM 118113^T) as the type strain; Tenacibaculum vairaonense sp. nov., with 190524A02b^T (= CIP 112469^T = DSM 118112^T) as the type strain; and Tenacibaculum polynesiense sp. nov., with 190130A14a^T (= CIP 112468^T = DSM 118111^T) as the type strain, are proposed.

Two Gram-stain-negative, motile, non-spore-forming, aerobic or facultative anaerobic and short rod-shaped bacterial strains, 25B02-3^T 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 BZ78^T and T. mobilis IAM 14872^T, 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 (C_{18 : 1} ω7c or C_{18 : 1} ω6c), C_{19 : 0} cyclo ω8c, Sum In Feature 2 (C_{12 : 0} aldehyde or unknown 10.928) and C_{16 : 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 25B02-3^T 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 25B02-3^T (=MCCC 1A07333^T=KCTC 8340^T).

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.