- Volume 73, Issue 1, 2023
Volume 73, Issue 1, 2023
- Validation Lists
-
- Notification Lists
-
- List of Changes in Taxonomic Opinion
-
- New Taxa
-
- Actinomycetota
-
-
Streptomyces rhizoryzae sp. nov., isolated from paddy rhizosphere soil and formal proposal to reclassify Streptomyces albulus as a later heterotypic synonym of Streptomyces noursei
More LessThe taxonomic position of a novel actinomycete, designated strain RS10V-4T, was determined using a polyphasic approach. Strain RS10V-4T was isolated from paddy rhizosphere soil of rice plant (Oryzae sativa L.). The morphological, physiological and chemotaxonomic properties were consistent with its classification in the genus Streptomyces . On the basis of 16S rRNA gene sequence analysis, strain RS10V-4T belongs to the genus Streptomyces and had the highest sequence similarity to Streptomyces noursei NBRC 15452T (98.3 %). The G+C content of the genomic DNA was 73.8 %. Digital DNA–DNA hybridization and average nucleotide identity values between the genome sequences of strain RS10V-4T and S.noursei ATCC 11455T were lower than the recommendation threshold values for the recognition of species within the same genus. The whole-cell hydrolysates of strain RS10V-4 T contained ll -diaminopimelic acid as the diagnostic diamino acid and the whole-cell sugars were glucose and ribose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The predominant cellular fatty acids (>10 %) were iso-C16 : 0, anteiso-C15 : 0, iso-C14 : 0 and iso-C15 : 0. The polar lipids of strain RS10V-4T contained diphosphatidylglycerol, hydroxyphosphatidylethanolamine, phosphatidylethanolamine, phosphatidylinositol, an unidentified aminolipid, two unidentified lipids and an unidentified phospholipid. On the basis of these phenotypic and genotypic characteristics, it is supported that strain RS10V-4T represents a novel species of the genus Streptomyces , for which the name Streptomyces rhizoryzae sp. nov. is proposed. The type strain is RS10V-4T (=TBRC 15167T=NBRC 115345T). In addition, the comparison of the whole genome sequences and phenotypic features suggested that S. noursei and S. albulus belong to the same species. Therefore, it is proposed that S. albulus is reclassified as a later heterotypic synonym of S. noursei .
-
-
-
Frankia colletiae sp. nov., a nitrogen-fixing actinobacterium isolated from Colletia cruciata
More LessA nitrogen-fixing actinobacterium strain (Cc1.17T) isolated from a root nodule of Colletia cruciata was subjected to polyphasic taxonomic studies. The strain was characterized by the presence of meso-diaminopimelic acid in its peptidoglycan, galactose, glucose, mannose, rhamnose, ribose and xylose as cell-wall sugars, phosphatidylinositol, diphosphatidylglycerol, glycophospholipids, phosphatidylglycerol, glycophospholipid and uncharacterized lipids as its polar lipids, and C16 : 0, iso-C16 : 0, C17 : 1 ω9 and C18 : 1 ω9 as major fatty acids (>10 %). Strain Cc1.17T showed 16S rRNA gene sequence similarities of 97.4–99.8 % to validly named Frankia species. Phylogenetic trees based on 16S rRNA gene and genome sequences placed strain Cc1.17T in a new lineage within the genus Frankia . Digital DNA–DNA hybridization and average nucleotide identity values between strain Cc1.17T and its closest phylogenomic neighbours were well below the thresholds recommended for prokaryotic species delineation. Therefore, strain Cc1.17T (=DSM 43829T=CECT 9313T) merits recognition as the type strain of a new species for which the name Frankia colletiae sp. nov. is proposed.
-
-
-
Description of Jidongwangia harbinensis gen. nov. sp. nov
More LessDuring our previous study, strain NEAU-J3T was classified as representing a novel genus ‘ Wangella ’ within the family Micromonosporaceae . Nevertheless, it is a great pity the name cannot be validated as the proposed genus name is illegitimate (Principle 2 of the ICNP). In this study, we describe Jidongwangia as a novel genus within the family Micromonosporaceae and a polyphasic approach was used to provide evidence to support the classification. The G+C content of the genomic DNA of the type strain is 71.6 %. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values could be used to differentiate NEAU-J3T from its related type strains. The phenotypic, genetic and chemotaxonomic data also indicated that NEAU-J3T occupies a branch separated from those of known genera in the family Micromonosporaceae . Therefore, NEAU-J3T represents a novel species of a novel genus in the family Micromonosporaceae , for which the name Jidongwangia harbinensis gen. nov., sp. nov. is proposed. The type strain of Jidongwangia harbinensis is NEAU-J3T (= CGMCC 4.7039T = DSM 45747T).
-
-
-
Pseudarthrobacter humi sp. nov., an actinobacterium isolated from soil
Inhyup Kim and Taegun SeoA Gram-stain-positive, facultatively aerobic, rod-shaped and non-motile bacterial strain designated RMG13T was isolated from the soil near Gaetgol Eco Park and collected in Siheung-si, Republic of Korea. It was taxonomically characterized through polyphasic analysis. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel isolate was most closely related to the type strains of species of the genus Pseudarthrobacter . RMG13T shared the highest similarities with Pseudarthrobacter sulfonivorans ALLT (99.2 %) and Pseudarthrobacter psychrotolerans YJ56T (99.0 %). In silico DNA–DNA hybridization values of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 28.1 and 41.8 %, respectively. The average nucleotide identities of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 84.2 and 70.3 %, respectively, whilst the average amino acid identities of RMG13T with P. sulfonivorans ALLT and P. psychrotolerans YJ56T were 90.5 and 74.6 %, respectively. Two-dimensional thin-layer chromatography showed that the major polar lipids of RMG13T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9 (H2) was the sole menaquinone. Cells grew at 4–37 °C (optimum 30 °C) and pH 5.0–12.0 (optimum pH 8.0) in Reasoner’s 2A (MB cell). The cells tolerated 0–5% NaCl (w/v) but not 6 % NaCl. The DNA G+C content of RMG13T was 65.0 %. The results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses indicated that RMG13T represents a novel member of the genus Pseudarthrobacter , and the proposed name is P. humi sp. nov. The type strain of P. humi is RMG13T (= KACC 22359T = TBRC 15115T).
-
-
-
Solicola gregarius gen. nov., sp. nov., a soil actinobacterium isolated after enhanced cultivation with Micrococcus luteus culture supernatant
An actinobacterial strain, designated A5X3R13T, was isolated from a compost soil suspension supplemented with extracellular material from a Micrococcus luteus -culture supernatant. The strain was cultured on tenfold-diluted reasoner’s 2A agar. The cells were ovoid-to-rod shaped, non-motile, Gram-stain-positive, oxidase-negative, catalase-positive and had a width of 0.5 µm and a length of 0.8–1.2 µm. The results of both 16S rRNA-based phylogenetic and whole-genome analyses indicate that A5X3R13T forms a distinct lineage within the family Nocardioidaceae (order Propionibacteriales ). On the basis of the 16S rRNA gene sequence, A5X3R13T was closely related to Aeromicrobium terrae CC-CFT486T (96.2 %), Nocardioides iriomotensis IR27-S3T (96.2 %), Nocardioides guangzhouensis 130T (95.6 %), Marmoricola caldifontis YIM 730233T (95.5 %), Aeromicrobium alkaliterrae KSL-107T (95.4 %), Aeromicrobium choanae 9H-4T (95.4 %), Aeromicrobium panaciterrae Gsoil 161T (95.3 %), and Nocardioides jensenii NBRC 14755T (95.2 %). The genome had a length of 4 915 757 bp, and its DNA G+C content was 68.5 mol %. The main fatty acids were 10-methyl C17 : 0, C16 : 0, C15 : 0, C18 : 0, C17 : 0 and iso-C16 : 0. The main polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and two unidentified phospholipids. MK-9(H4) was the predominant respiratory quinone. The peptidoglycan type was A3γ (A41.1) and contained alanine, glycine, glutamic acid and ll-diaminopimelic acid in a molar ratio of 1.2 : 0.9 : 1.0 : 0.8. On the basis of the results of the phylogenetic and phenotypic analyses and comparisons with other members of the family Nocardioidaceae , strain A5X3R13T is proposed to represent a novel species within a novel genus, for which the name Solicola gregarius gen. nov., sp. nov. is proposed. The type strain is A5X3R13T (=DSM 112953T=NCCB 100840T).
-
-
-
Streptomyces guryensis sp. nov. exhibiting antimicrobial activity, isolated from riverside soil
More LessA novel Gram-stain-positive, aerobic actinobacterial strain designated NR30T was isolated from riverside soil. A polyphasic approach was employed for the taxonomic characterization of NR30T. The strain developed extensively branched light brown to light pink substrate mycelia and light grey aerial mycelia, and produced spiny spores in loose spiral spore chains on ISP 3 and 4 agars. NR30T grew at 10–40°C (optimum, 30°C), at pH 6.0–9.0 (optimum, pH 8.0) and in the presence of 0–3 % NaCl (optimum, 0 %). Analysis of 16S rRNA gene sequences indicated that NR30T represents a member of the genus Streptomyces . NR30T shared the highest 16S rRNA gene sequence similarity with Streptomyces cyaneus NRRL B-2296T (98.6 %). On the basis of orthologous average nucleotide identity, NR30T was most closely related to Streptomyces panaciradicis NBRC 109811T with 86.3 % identity. The results of the digital DNA–DNA hybridization analysis also indicated low levels of relatedness with other species, as the highest value was observed with Streptomyces panaciradicis NBRC 109811T (31.1 %). The major fatty acids of the strain were anteiso-C15 : 0, C16 : 0, iso-C16 : 0 and anteiso-C17 : 0. The major respiratory quinones were MK-9(H8) and MK-9(H6). The diagnostic polar lipids were diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol mannoside. The major cell wall diamino acid was ll-diaminopimelic acid, and the characteristic whole-cell sugars were rhamnose, ribose and glucose. The DNA G+C content was 70.3 mol %. NR30T exhibited antimicrobial activity against several Gram-negative bacteria and yeasts. On the basis of the results of both phenotypic and phylogenetic analyses, strain NR30T evidently represents a novel species of the genus Streptomyces , and the name Streptomyces guryensis sp. nov. (type strain=NR30T =KCTC 49653T=LMG 32476T) is proposed accordingly.
-
-
-
Streptomyces macrolidinus sp. nov., a novel soil actinobacterium with potential anticancer and antimalarial activity
A novel actinomycete, strain RY43-2T, belonging to the genus Streptomyces , was isolated from a peat swamp forest soil collected from Rayong Province, Thailand. The strain was characterized by using a polyphasic approach. The cell-wall peptidoglycan contained ll-diaminopimelic. Ribose and glucose were detected in its whole-cell hydrolysates. The strain contained anteiso-C15:0, iso-C14:0 and iso-C16:0 as the predominant fatty acids, and MK-9(H4), MK-9(H6) and MK-9(H8) as the major menaquinones. The phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, three unidentified ninhydrin-positive phospholipids and two unidentified phospholipids. Strain RY43-2T showed the highest 16S rRNA gene similarity to Streptomyces misionensis JCM 4497T (98.9 %) and Streptomyces lichenis LCR6-01T (98.9 %). The draft genome of RY43-2T was 6.7 Mb with 6078 coding sequences with an average G+C content of 70.8 mol%. Genomic analysis revealed that the average nucleotide identity (ANI) values based on blast (ANIb) and MUMmer (ANIm) between strain RY43-2T and S. misionensis JCM 4497T were 80.1 and 86.1%, respectively. The ANIb and ANIm values between strain RY43-2T and S. lichenis LCR6-01T were 77.0 and 85.5%, respectively. The digital DNA–DNA hybridization values were 25.2 and 23.0% in comparison with the draft genomes of S. misionensis JCM 4497T and S. lichenis LCR6-01T, respectively. The results of taxonomic analysis suggested that strain RY43-2T represented a novel species of the genus Streptomyces for which the name Streptomyces macrolidinus sp. nov. is proposed. The type strain is RY43-2T (=TBRC 7286T=NBRC 115640T). Strain RY43-2T exhibited antimicrobial activity against Enterococcus faecium ATCC 51559, Colletotrichum capsici BMGC 106 and Colletotrichum gloeosporioides BMGC 107 with the minimum inhibitory concentration values of 25.0, 12.5, and 6.25 µg ml−1. It also exhibited potent antimalarial activity against Plasmodium falciparum K1 with IC50 of 0.0031 µg ml−1. In addition, it showed cytotoxicity against Vero, KB, MCF-7 and NCI-H187 with IC50 values of 0.0347, 6.15, 3.36 and 0.0352 µg ml−1, respectively.
-
-
-
Actinomadura terrae sp. nov. and Actinomadura litoris OS3-89, isolated from rhizosphere soil of cactus
More LessTwo mycelium-forming actinobacterial strains, designated OS3-83 T and OS3-89, were isolated from rhizosphere soil of a cactus (Opuntia ficus-indica) sampled on Mara Island, Jeju, Republic of Korea. Both of the isolates were found to grow at 20–37 °C, pH 6.0–10.0 and with 0–2 % (w/v) NaCl. Their taxonomic positions were investigated by a polyphasic approach. Strains OS3-83T and OS3-89 were most closely related to the type strain of Actinomadura litoris (99.5 % and 98.9 % 16S rRNA gene sequence similarity, respectively). Both of the isolates shared 99.2 % sequence similarity to each other. Morphological and chemotaxonomic characteristics supported the affiliation of the two isolates to the genus Actinomadura . 16S rRNA gene phylogeny exhibited that strain OS3-83T formed a tight cluster with A. litoris , while strain OS3-89 occupied a position located remotely from A. litoris . Nevertheless, phylogenomic analysis based on 92 core gene sequences showed that both of the isolates formed a tight clade with A. litoris . The values of average nucleotide identity and digital DNA–DNA hybridization between strain OS3-83T and the closest relative, A. litoris , were 92.2 and 46.2 %, respectively, whereas strain OS3-89 shared an average nucleotide identity value of 97.5 % and a digital DNA–DNA hybridization value of 76.9 % with A. litoris . These results strongly suggested that strain OS3-83T (=KACC 19752T=NBRC 114688T) represents a novel species and strain OS3-89 (=KACC 19753=NBRC 114400) is a strain of A. litoris . On the basis of the data obtained here, strain OS3-83T is considered to represent a new species of the genus Actinomadura , for which the name Actinomadura terrae sp. nov. is proposed.
-
-
-
Agromyces seonyuensis sp. nov., isolated from island soil
More LessA Gram-positive, non-motile, pale yellow coloured actinobacterial strain designated MMS17-SY077T was isolated from island soil, and its taxonomic position was investigated using a polyphasic approach. Strain MMS17-SY077T grew optimally at 30 °C, at pH 7 and in the absence of NaCl on Reasoner's 2A agar. Based on the 16S rRNA gene sequence analysis, the strain was assigned to the genus Agromyces of the family Microbacteriaceae , and the most related species were Agromyces italicus DSM 16388T (98.8 % sequence similarity), Agromyces allii UMS-62T (98.1 %) and Agromyces terreus DS-10T (97.8 %). Strain MMS17-SY077T formed a distinct cluster within the Agromyces clade in the phylogenetic tree. Genome-based comparative analyses confirmed a clear distinction between the strain and neighbouring species, as the highest orthologous average nucleotide identity and digital DNA–DNA hybridization values with other related species were 77.2 and 21.4% respectively, which were far below the cutoffs for species distinction. The diagnostic polar lipids of MMS17-SY077T were diphosphatidylglycerol and phosphatidylglycerol, and unidentified glycolipids and an unidentified aminolipid were also present. The main isoprenoid quinones were menaquinones with 11 and 12 isoprene units (MK-11 and MK-12), and main fatty acids were anteiso-C15 : 0 (34.4 %) and iso-C16 : 0 (33.2 %). The whole-cell hydrolysates contained rhamnose, ribose and galactose as diagnostic sugars, and l-2,4-diaminobutyric acid as the major diamino acid. The DNA G+C content was 72.1 mol %. Based on phenotypic, chemotaxnomic and phylogenetic characterization, strain MMS17-SY077T should be classified as representing a new species of the genus Agromyces , for which the name Agromyces seonyunensis sp. nov. is proposed (type strain MMS17-SY077T=KCTC 49423T=LMG 31762T).
-
- Archaea
-
-
Methanocaldococcus lauensis sp. nov., a novel deep-sea hydrothermal vent hyperthermophilic methanogen
More LessThree hyperthermophilic methanogens, designated strain SG7T, strain SG1 and strain SLH, were isolated from the ABE and Tu’i Malila deep-sea hydrothermal vent fields along the Eastern Lau Spreading Center. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strains SG7T, SG1 and SLH were affiliated with the genus Methanocaldococcus within the family Methanocaldococcaceae , order Methanococcales . They shared 95.5–99.48 % 16S rRNA gene sequence similarity to other Methanocaldococcus species and were most closely related to Methanocaldococcus bathoardescens . Cells of strains SG7T, SG1 and SLH were cocci, with a diameter of 1.0–2.2 µm. The three strains grew between 45 and 93 °C (optimum, 80–85 °C), at pH 5.0–7.1 (optimum pH 6.2) and with 10–50 g l−1 NaCl (optimum 20–25 g l−1). Genome analysis revealed the presence of a 5.1 kbp plasmid in strain SG7T. Based on the results of average nucleotide identity and digital DNA–DNA hybridization analyses, we propose that strains SG1 and SG7T are representatives of a novel species, for which the name Methanocaldococcus lauensis sp. nov. is proposed; the type strain is SG7T (=DSM 109608T=JCM 39049T).
-
- Bacteroidota
-
-
Flavihumibacter fluminis sp. nov., a novel thermotolerant bacterium isolated from river silt
A yellow, Gram-stain-positive, strictly aerobic, thermotolerant, non-motile and rod-shaped bacterial strain, designated RY-1T, was isolated from a silt sample of Fuyang River, Wuqiang County, Hengshui City, Hebei Province, PR China. Cells showed oxidase- and catalase-positive activities. Growth occurred at 20–45 °C (optimum, 37 °C) and pH 6.0–8.0 (optimum, pH 7.0), and in the presence of 0–1.5 % (w/v) NaCl (optimum, 0%). A phylogenetic tree based on 16S rRNA gene sequences revealed that strain RY-1T formed a phylogenetic lineage with Flavihumibacter members within the family Chitinophagaceae . A comparison of 16S rRNA gene sequences showed that strain RY-1T was most closely related to Flavihumibacter cheonanensis WS16T (98.6 %), Flavihumibacter sediminis CJ663T (97.7 %) and Flavihumibacter solisilvae 3-3T (97.6 %). The genome size of strain RY-1T was 4.71 Mb, and the DNA G+C content was 44.3 %. The average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values between strain RY-1T and reference strains were all lower than the threshold values for species delineation. Strain RY-1T contained menaquinone-7 and iso-C15 : 0, iso-C17 : 0 3-OH and iso-C15 : 1G as the sole respiratory isoprenoid quinone and major cellular fatty acids (≥5 %), respectively. The major polar lipids consisted of phosphatidylethanolamine, three unidentified aminolipids and four unidentified lipids. According to the results of phenotypic, phylogenetic and chemotaxonomic characteristics, strain RY-1T represents a novel species of the genus Flavihumibacter , for which the name Flavihumibacter fluminis sp. nov. is proposed. The type strain is RY-1T (=GDMCC 1.2775T=JCM 34870T).
-
-
-
Bacteroides faecium sp. nov. isolated from human faeces
A novel bacterial strain, CBA7301T, was isolated from human faeces and was characterised using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences revealed that CBA7301T represented a member of the genus Bacteroides , in the family Bacteroidaceae . The similarity between the 16S rRNA gene sequence of CBA7301T and that of its most closely related species, Bacteroides faecichinchillae JCM 17102T, was 96.2 %, and the average nucleotide identity between these two strains was 77.9 %. The genome size was 6 782 182 bp, and the DNA G+C content was 42.5 mol%. Cells of CBA7301T were Gram-stain-negative, strictly anaerobic and rod-shaped. The optimal growth of this organism occurred at 30–35 °C, pH 7.0 and 0.5 % (w/v) NaCl. The respiratory quinone was menaquinone 10. The predominant polar lipids were phosphatidylethanolamine, phospholipids and aminophospholipids. The major cellular fatty acid was anteiso-C15 : 0. According to the results of the polyphasic taxonomic analysis, CBA7301T represents a novel species of the genus Bacteroides , which we named Bacteroides faecium sp. nov. The type strain is CBA7301T (=KCCM 43355T=ATCC TSD-227T).
-
- Bacillota
-
-
Allobaculum mucilyticum sp. nov. and Allobaculum fili sp. nov., isolated from the human intestinal tract
More LessAs part of a culturomics study to identify bacterial species associated with inflammatory bowel disease, a large collection of bacteria was isolated from patients with ulcerative colitis. Two of these isolates were tentatively identified as members of the family Erysipelotrichaceae . Following phylogenetic analysis based on 16S rRNA gene sequence and genome sequences, both strain 128T and 539T were found to be most closely related to Allobaculum stercoricanis , with G+C contents of 48.6 and 50.5 mol%, respectively, and the genome sizes of 2 864 314 and 2 580 362 base pairs, respectively. Strains 128T and 539T were strict anaerobe rods that grew in long chains between 37 and 42 °C. Scanning electron microscopy did not reveal flagella, fimbriae or visible endospores. Biochemical analysis showed nearly identical results for both strains with enzymatic activity of C4 and C8 esterases, acid phosphatase, naphthol-AS-BI-phosphohydrolase, β-glucuronidase, N-acetyl-β-glucosaminidase and arginine arylamidase. In addition, both strains produced indole and reduced nitrate. Major fatty acids were identified as C18:1 ω9c (oleic acid, 64.06% in 128T and 74.35% in 539T), C18:1 ω7c/C18:1 ω9t/C18:1 ω12t/UN17.834 (16.18 % in 128T and 6.22% in 539T) and C16:0 (6.23% in 128T and 7.37% in 538T). Based on these analyses two novel species are proposed, Allobaculum mucilyticum sp. nov. with the type strain 128T (=NCTC 14626T=DSM 112815T) and Allobaculum fili sp. nov. with the type strain 539T (=NCTC 14627T=DSM 112814T).
-
-
-
Terrisporobacter hibernicus sp. nov., isolated from bovine faeces in Northern Ireland
A new species of Terrisporobacter , a Gram-positive, spore-forming anaerobic group, proposed name Terrisporobacter hibernicus sp. nov., was isolated in Northern Ireland from bovine faeces collected in 2016. Designated as MCA3T, cells of T. hibernicus sp. nov. are rod shaped and motile. Cells tolerate NaCl from 0.5 to 5.5 % (w/v), with a pH tolerance between pH 6 and 9. The optimal temperature for growth is 35–40 °C, and temperatures from 20 to 30 °C are tolerated. The polar lipid profile displays diphosphatidylglycerol, phosphatidylglycerol, two aminoglycolipids, one glycophospholipid, one aminolipid, three glycolipids, five phospholipids and one lipid. No respiratory quinones are detected. The predominant fatty acid profile includes C16 : 0 at 22.8 %. Strain MCA3T is positive for glucose and maltose acidification, as well as glycerol and sorbitol. The biochemical results from a VITEK2 assay of strain MCA3T, Terrisporobacter petrolearius LAM0A37T and Terrisporobacter mayombei DSM 6539T are also included for the first time. The closed and complete genome of strain MCA3T from a hybrid Oxford Nanopore Technology MinION/Illumina assembly reveals no evidence for known virulence genes. Draft genome sequencing of T. mayombei DSM 6539T and T. petrolearius LAM0A37T, as performed by Illumina MiSeq, provides reference genomes for these respective species of Terrisporobacter for the first time. DNA–DNA hybridization values (d4) of MCA3T to Terrisporobacter glycolicus ATCC 14880T, T. petrolearius LAM0A37T and T. mayombei DSM 6539T are 48.8, 67.4 and 46.3 %, with cutoff value at 70 %. The type strain for T. hibernicus sp. nov. is MCA3T (=NCTC 14625T=LMG 32430T).
-
-
-
Lutispora saccharofermentans sp. nov., a mesophilic, non-spore-forming bacterium isolated from a lab-scale methanogenic landfill bioreactor digesting anaerobic sludge, and emendation of the genus Lutispora to include species which are non-spore-forming and mesophilic
More LessA novel anaerobic, mesophilic, non-spore-forming bacterium (strain m25T) was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor containing anaerobic digester sludge. Cells were Gram-stain-negative, catalase-positive, oxidase-negative, rod-shaped, and motile by means of a flagellum. The genomic DNA G+C content was 40.11 mol%. The optimal NaCl concentration, temperature and pH for growth were 2.5 g l−1, 35 °C and at pH 7.0, respectively. Strain m25T was able to grow in the absence of yeast extract on glycerol, pyruvate, arginine and cysteine. In the presence of 0.2 % yeast extract, strain m25T grew on carbohydrates and was able to use glucose, cellobiose, fructose, raffinose and galactose. The novel strain could utilize glycerol, urea, pyruvate, peptone and tryptone. The major fatty acids were iso-C15 : 0, C14 : 0, C16 : 0 DMA (dimethyl acetal) and iso-C15 : 0 DMA. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was closely related to Lutispora thermophila EBR46T (95.02 % 16S rRNA gene sequence similarity). Genome relatedness was determined using both average nucleotide identity and amino acid identity analyses, the results of which both strongly supported that strain m25T belongs to the genus Lutispora . Based on its unique phylogenetic features, strain m25T is considered to represent a novel species within the genus Lutispora . Moreover, based on its unique physiologic features, mainly the lack of spore formation, a proposal to amend the genus Lutispora is also provided to include the non-spore-forming and mesophilic species. Lutispora saccharofermentans sp. nov. is proposed. The type strain of the species is m25T (=DSM 112749T=ATCC TSD-268T).
-
-
-
Clostridium caldaquaticum sp. nov., a thermophilic bacterium isolated from a hot spring sediment
A novel anaerobic bacterium, designated SYSU GA19001T, was isolated from a hot spring sediment sample. Phylogenetic analysis indicated that the isolate belongs to the genus Clostridium , and showed the highest sequence similarity to Clostridium swellfunianum CICC 10730T (96.63 %) and Clostridium prolinivorans PYR-10T (96.11 %). Cells of strain SYSU GA19001T were Gram-stain-positive, spore-forming, rod-shaped (0.6–0.8×2.6–4.0 µm) and motile. Growth was observed at pH 5.0–9.0 (optimum, pH 7.0), 37–55 °C (optimum, 45 °C) and in NaCl concentrations of 0–2.0 % (optimum, 0 %). The genomic DNA G+C content was 31.62 %. The major cellular fatty acids of strain SYSU GA19001T were C14 : 0, iso-C15 : 0, C16 : 0 and summed feature 8. The prominent polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol. Meso-diaminopimelic acid was the diamino acid in peptidoglycan. Based on the results of phylogenetic, chemotaxonomic and phenotypic analyses, strain SYSU GA19001T represents a novel species of the genus Clostridium , for which the name Clostridium caldaquaticum sp. nov. is proposed. The type strain of the proposed novel species is SYSU GA19001T (=NBRC 115040T= CGMCC 1.17864T).
-
-
-
Reclassification of Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia as Thomasclavelia cocleata gen. nov., comb. nov., Thomasclavelia ramosa comb. nov., gen. nov., Thomasclavelia spiroformis comb. nov. and Thomasclavelia saccharogumia comb. nov
More LessThe genus Clostridium is phenotypically and genotypically diverse, with many species phylogenetically located outside Clostridium sensu stricto. One such group consists of the species Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia (formally clostridial rRNA cluster XVIII) [ 1 ]. Sequencing of the 16S rRNA and, more recently, the results of genomic analyses have demonstrated that these species represent a coherent cluster separated from other closely related genera located in the family Coprobacillaceae within the order Erysipelotrichales [ 2 ]. In addition to phenotypic, phylogenetic and genomic comparisons, chemotaxonomic features were consistent between all four species, the predominant fatty acids were C16 : 0 and C18 : 1ω9c, while glucose and ribose were the whole cell sugars present in the cell walls. Furthermore, he results of peptidoglycan analysis indicated that meso-2,6-diaminopimelic acid was present as the diagnostic diamino acid in all four species. Biochemical profiles were also concordant with them being closely related species. Therefore, on the basis of phylogenetic, genomic, phenotypic and chemotaxonomic information, a novel genus, Thomasclavelia gen. nov., is proposed. It is suggested that Clostridium cocleatum, Clostridium ramosum, Clostridium spiroforme and Clostridium saccharogumia be transferred to this genus as Thomasclavelia cocleata comb. nov., Thomasclavelia ramosa comb. nov., Thomasclavelia saccharogumia comb. nov. and Thomasclavelia spiroformis comb. nov. The type species of the genus is Thomasclavelia ramosa CCUG 24038T (=ATCC 25582T=DSM 1402T).
-
-
-
Anaeromicropila herbilytica gen. nov., sp. nov., a plant polysaccharide-decomposing anaerobic bacterium isolated from anoxic soil subjected to reductive soil disinfestation, and reclassification of Clostridium populeti as Anaeromicropila populeti comb. nov.
More LessAn obligately anaerobic bacterial strain (TB5T) was isolated from a soil sample subjected to reductive or biological soil disinfestation. Cells of the strain were Gram-stain-positive, spore-forming and motile rods. The strain grew at 15–40 °C (optimum, 37 °C) and pH 5.4–7.5 (optimum, pH 7.3). Strain TB5Tutilized a wide variety of carbohydrates including polysaccharides (cellulose, xylan, starch, inulin, glucomannan and laminarin) and organic acids. Acetate, ethanol, H2 and CO2 were products from the substrates utilized. The major components of the cellular fatty acids were C16 : 1 ω7c DMA, C16 : 0 DMA and C18 : 1 ω7c DMA. The diagnostic amino acid of the cell-wall peptidoglycan was meso-diaminopimelic acid. The closest related species to strain TB5T based on 16S rRNA gene sequences was Clostridium populeti 743AT (95.4 % sequence similarity). The genome size of strain TB5T was 5.09 Mb and the genomic DNA G+C content was 32.7 mol%. Strain TB5T had genes encoding polysaccharide-decomposing enzymes such as cellulase, xylanase, β-glucosidase and β-mannosidase in the genome. Based on the phylogenetic, genomic and phenotypic data, a novel species of a novel genus in the family Lachnospiraceae , Anaeromicropila herbilytica gen. nov., sp. nov., is proposed to accommodate the strain. The type species is Anaeromicropila herbilytica with strain TB5T (=NBRC 112093T=DSM 110037T) as the type strain. For the closest related species C. populeti , Anaeromicropila populeti comb. nov. is proposed with an emended description of the species.
-
-
-
Paenibacillus rhizolycopersici sp. nov., an oligotrophic bacterium isolated from a tomato plant in China
More LessA Gram-positive, rod-shaped, motile, endospore-forming strain, DXFW5T, was isolated from the rhizosphere soil of tomato. Strain DXFW5T grew at 20–50 °C (optimum, 25–37 °C), pH 5–8 (optimum, pH 7) and in the presence of 3 % NaCl. It was positive for catalase and oxidase. Phylogenetic analysis using 16S rRNA gene sequences showed this strain was most closely related to Paenibacillus timonensis DSM 16943T (98.0 %) and Paenibacillus barengoltzii DSM 22255T (97.4 %). The DNA G+C content was 52.9 mol%. The digital DNA–DNA hybridization values between strain DXFW5T and P. timonensis DSM 16943T, P. barengoltzii DSM 22255T and P. macerans DSM 24T were 33.1, 24.9 and 21.2 %, respectively. The average nucleotide identity values between strain DXFW5T and P. timonensis DSM 16943T , P. barengoltzii DSM 22255T and P. macerans DSM 24T were 86.93, 81.77 and 75.98 %, respectively. The major fatty acids were anteiso-C15 : 0 (55.1 %), iso-C16 : 0 (13.2 %) and C16 : 0 (10 %). The polar lipids of strain DXFW5T consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine two unidentified phospholipids and three unidentified lipids. MK-7 was the major isoprenoid quinone. Based on these results, it was concluded that the isolate represents a novel species of the genus Paenibacillus, for which the name Paenibacillus rhizolycopersici sp. nov. is proposed, with DXFW5T (=ACCC 61751T=JCM 34488T) as the type strain.
-
- Other Bacteria
-
-
Thermospira aquatica gen. nov., sp. nov., a novel thermophilic spirochete isolated from a Tunisian hot spring, and description of the novel family Thermospiraceae.
A novel thermophilic, anaerobic bacterium, strain F1F22T, was isolated from hot spring water collected in northern Tunisia. The cells were non-motile, Gram-negative and helical with hooked ends, 0.5×10–32 µm in size. Growth of the strain was observed at 45–70 °C (optimum, 55 °C), in 0.0–1.0 % (w/v) NaCl (optimum without NaCl) and at pH 6.5–8.5 (optimum, pH 7.5). Yeast extract was required for growth, and the strain grew on glucose, sucrose and maltose. The major fatty acids were C16:0 (40.2 %), iso-C16: 0 (30.2 %) and C16 :0 DMA (14.5 %). The genome consisted of a circular chromosome (2.5 Mb) containing 2672 predicted protein-encoding genes with a G+C content of 43.15 mol %. Based on a comparative 16S rRNA gene sequence analysis, strain F1F22T formed a deeply branching lineage within the phylum Spirochaetota , class Spirochaetia , order Brevinematales , and had only low sequence similarity to other species of the phylum (lower than 83 %). Genome-based analysis of average nucleotide identity and digital DNA–DNA hybridization of strain F1F22T with Treponema caldarium DSM 7334T, Brevinema andersonii ATCC 43811T and Spirochaeta thermophila DSM 6578T showed values between 63.26 and 63.52 %, and between 20 and 25 %. Hence, we propose strain F1F22T as a representative of a novel family (Thermospiraceae fam. nov.), genus and species of Brevinematales : Thermospira aquatica gen. nov., sp. nov. (type strain F1F22T=JCM 31314T=DSM 101182T).
-
-
-
Akkermansia biwaensis sp. nov., an anaerobic mucin-degrading bacterium isolated from human faeces
More LessA bacterial strain, WON2089T, was isolated from the faeces of healthy Japanese adults and is able to use mucin as the sole carbon and nitrogen source. Sequencing of its 16S rRNA gene showed that WON2089T has 98.0 and 94.4% similarity to Akkermansia muciniphila MucT and Akkermansia glycaniphila PytT, respectively, while phylogenetic tree analysis confirmed that it belongs to the genus Akkermansia . The whole genome of WON2089T was sequenced, which showed that it shares 84.5 % average nucleotide identity (ANI) and 24.9 % digital DNA–DNA hybridization (dDDH) with its closest relative, A. muciniphila MucT. Cells of WON2089T are non-motile, anaerobic and oval-shaped (0.4–0.5×0.5–1.0 µm). The strain is Gram-stain-negative and grows in the temperature range of 25–45 °C (optimum, 30–37 °C) and pH range of pH 5.5–9.5 (optimum, pH 6.5–8.0). WON2089T can utilize d-glucose, d-mannitol, lactose and d-mannose, as assessed by API20A strips. The major cellular fatty acids are C15 : 0 anteiso, C15 : 0 3OH and C18 : 1 ω9c (55.5, 7.5 and 5.8 % of total fatty acids, respectively). Based on 16S rRNA sequencing, ANI, dDDH and acid formation from d-mannitol, WON2089T is distinct from previously reported species of the genus Akkermansia . Based on phenotypic, phylogenetic and genetic characteristics, WON2089T represents a novel species of the genus Akkermansia and the name Akkermansia biwaensis sp. nov. is proposed. The type strain is WON2089T (= NBRC 115679T= DSM 114407T).
-
- Pseudomonadota
-
-
Pseudomonas paralcaligenes sp. nov., isolated from a hospitalized patient
A Gram-stain-negative, aerobic, rod-shaped, non-endospore-forming bacterium, designated as strain MRCP1333T, was isolated from a faecal sample from a hospital patient in Japan. MRCP1333T grew at temperatures of 15–40 °C (optimum 25–35 °C), with 1.0–3.0 % (w/v, 171–513 mM) NaCl [optimum 1–2 % (w/v), 171–342 mM], and at pH 6.0–9.5 (optimum pH 7.0–8.0). The results of phylogenetic analysis based on the sequences of the 16S rRNA gene and the 53 genes encoding the bacterial ribosome protein subunits indicated that MRCP1333T represented a member of the Pseudomonas aeruginosa group, most closely related to Pseudomonas alcaligenes . Whole-genome comparisons, using average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity, confirmed that MRCP1333T represented a distinct species in the P. aeruginosa group. Phenotypic characterization tests demonstrated utilization by this strain of citrate, glycerol, and d-malic acid, the ability to reduce nitrite to nitrogen and the ability of this strain to grow in the presence of minocycline and tetrazolium blue, distinguishing this strain from P. alcaligenes and other closely related species of the P. aeruginosa group. The major fatty acids of MRCP1333T were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c; 38.4 %), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c; 21.1 %) and C16 : 0 (20.6 %). The DNA G+C content of MRCP1333T was 66.5 mol%. Genetic and phenotypic evidence indicated that MRCP1333T should be classified as representing a novel species, for which the name Pseudomonas paralcaligenes sp. nov. is proposed. The type strain is MRCP1333T (=LMG 32254T,=JCM 34250T).
-
-
-
Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov., isolated from a marine red alga and emended description of the genus Octadecabacter
More LessTwo Gram-stain-negative, strictly aerobic, catalase- and oxidase-positive and non-motile rod-shaped bacteria, strains D2-3T and G9-8T, were isolated from a marine red alga. Both strains contained ubiquinone-10 as the sole isoprenoid quinone. As the major cellular fatty acids (>5.0 %), D2-3T contained C16 : 0, 11-methyl-C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c), whereas G9-8T contained C16 : 0, 11-methyl-C18 : 1ω7c, C12 : 1 3-OH, and summed feature 8. The DNA G+C contents of D2-3T and G9-8T were 54.4 % and 56.0 %, respectively. As the major polar lipids, phosphatidylglycerol, diphosphatidylglycerol and unidentified phospholipid, aminolipid and lipid were identified from both strains, and phosphatidylcholine was additionally detected from G9-8T only. The 16S rRNA gene sequence similarity of D2-3T and G9-8T was 98.5 % and their digital DNA–DNA hybridization (DDH) value was 19.1 %. Phylogenetic analyses based on 16S rRNA gene and genome sequences revealed that D2-3T and G9-8T formed respectively distinct phylogenetic lineages within the genus Octadecabacter . D2-3T and G9-8T were most closely related to Octadecabacter ascidiaceicola RA1-3T and Octadecabacter antarcticus 307T, with 98.9 % and 98.5 % 16S rRNA gene sequence similarities, respectively, and digital DDH values between D2-3T and O. ascidiaceicola and between G9-8T and O. antarcticus were 18.3 % and 19.5 %, respectively. Phenotypic, chemotaxonomic and molecular features support the hypothesis that D2-3T and G9-8T represent two novel species of the genus Octadecabacter , for which the names Octadecabacter algicola sp. nov. and Octadecabacter dasysiphoniae sp. nov. are proposed. The type strains of O. algicola and O. dasysiphoniae are D2-3T (=KACC 22493T =JCM 34969T) and G9-8T (=KACC 22488T =JCM 34973T), respectively.
-
-
-
Phylogenomic analysis of the genus Alcanivorax: proposal for division of this genus into the emended genus Alcanivorax and two novel genera Alloalcanivorax gen. nov. and Isoalcanivorax gen. nov.
The members of the genus Alcanivorax are key players in the removal of petroleum hydrocarbons from polluted marine environments. More than half of the species were described in the last decade using 16S rRNA gene phylogeny and genomic-based metrics. However, the 16S rRNA gene identity (<94 %) between some members of the genus Alcanivorax suggested their imprecise taxonomic status. In this study, we examined the taxonomic positions of Alcanivorax species using 16S rRNA phylogeny and further validated them using phylogenomic-related indexes such as digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), average amino acid identity (AAI), percentage of conserved proteins (POCP) and comparative genomic studies. ANI and dDDH values confirmed that all the Alcanivorax species were well described at the species level. The phylotaxogenomic analysis showed that Alcanivorax species formed three clades. The inter-clade values of AAI and POCP were less than 70 %. The pan-genome evaluation depicted that the members shared 1223 core genes and its number increased drastically when analysed clade-wise. Therefore, these results necessitate the transfer of clade II and clade III members into Isoalcanivorax gen. nov. and Alloalcanivorax gen. nov., respectively, along with the emended description of the genus Alcanivorax sensu stricto.
-
-
-
Zeimonas sediminis sp. nov., isolated from mangrove sediment
Jiayi Li, Lirui Liu, Yuhan Huang, Jie Pan and Meng LiA Gram-stain-negative, strictly aerobic, motile, rod-shaped bacterium, FT117T, was isolated from mangrove sediment collected in Shenzhen, Guangdong, PR China. Growth occurred at 20–45 °C (optimum, 40 °C), pH 6–10 (optimum, 8) and in the presence of 0–5 % NaCl (optimum, 0 %). The results of 16S rRNA gene sequence analysis indicated that the identity between FT117T and Zeimonas arvi CC-CFT501T was the highest (98.7 %), followed by Quisquiliibacterium transsilvanicum JCM 31785T (93.6 %), Lautropia mirabilis CCUG 34794T (93.6 %) and Pandoraea eparura LMG 31012T (93.5 %). The main fatty acids (>10 %) were C16 : 0 (35.8 %), cyclo-C17 : 0 (18.5 %) and summed feature 3 (18.1 %). The polar lipids contained phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, two unidentified phospholipids, two unidentified aminophospholipids and one unidentified lipid. The sole respiratory quinone was ubiquinone-8 (Q-8). Its DNA G+C content was 70.6 % (data from the genome sequence) and the estimated genome size was 3.860 Mb. The average nucleotide identity values between the FT117T genome and the genomes of Z. arvi CC-CFT501T, Q. transsilvanicum JCM 31785T, L. mirabilis CCUG 34794T and Paraburkholderia strydomiana LMG 31012T were 85.4 %, 76.4 %, 73.0 % and 71.3 %, and the digital DNA–DNA hybridization values were 29.1 %, 21.0 %, 20.3 % and 19.1 %, respectively. The phylogenetic, phenotypic and chemotaxonomic differences between FT117T and its phylogenetic relatives indicate that FT117T should be regarded as representing a novel species within the genus Zeimonas , for which the name Zeimonas sediminis sp. nov. is proposed. The type strain is FT117T (=KCTC 92314T = MCCC 1K07396T).
-
-
-
Vibrio amylolyticus sp. nov. and Vibrio gelatinilyticus sp. nov., two marine bacteria isolated from surface seawater of Qingdao
More LessTwo Gram-stain-negative, oxidase-positive, facultative anaerobic and rod-shaped motile bacteria, designated strains ZSDZ34 and ZSDE26, were isolated from offshore surface seawater collected near Qingdao. Phylogenetic analysis based on 16S rRNA gene sequences placed ZSDE26T and ZSDZ34T within the genus Vibrio , family Vibrionaceae , class Gammaproteobacteria . Strain ZSDE26T was most closely related to Vibrio gallaecicus VB 8.9T with 97.3 % sequence similarity, whereas ZSDZ34T was most closely related to Vibrio aestuarianus subsp. cardii DSM 109723T with 97.8 % sequence similarity. Strain ZSDE26T grew with 1–5 % (w/v) NaCl (optimum, 4 %), at 16–28 °C (optimum, 28 °C) and at pH 6.0–9.0 (optimum, pH 7.0). Growth of strain ZSDZ34T occurred with 1–6 % (w/v) NaCl (optimum, 3 %), at 16–37 °C (optimum, 28 °C) and at pH 6.0–9.0 (optimum, pH 7.0). Both strains shared the same major fatty acid components (more than 10 % of total fatty acids) of summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) and C16 : 0. Additionally, strain ZSDZ34T contained a higher proportion of iso-C16 : 0. The DNA G+C contents of strains ZSDE26T and ZSDZ34T were 42.8 and 44.5 mol%, respectively. On the basis of the results of polyphasic analysis, ZSDE26T and ZSDZ34T are considered to represent novel species within the genus Vibrio , for which the names Vibrio amylolyticus sp. nov. (type strain, ZSDE26T=KCTC 82890T=MCCC 1K06290T) and Vibrio gelatinilyticus sp. nov. (type strain, ZSDZ34T=KCTC 82888T=MCCC 1K06292T) are proposed, respectively.
-
-
-
Vibrio sinus sp. nov., a marine bacterium isolated from coastal seawater
A Gram–straining–negative, facultatively anaerobic, motile by means of a polar flagellum and rod-shaped marine bacterium, designated S4M6T, was isolated from surface seawater collected in Dongshan Bay (Fujian, PR China). Phylogenetic analysis based on 16S rRNA genes, phylogenomic analysis of single-copy gene families and whole genome data indicated that S4M6T represented a member of the genus Vibrio . The closest phylogenetic relatives of S4M6T were Vibrio marisflavi CGMCC 1.8994T (97.8 % 16S rRNA gene sequence pairwise similarity), Vibrio variabilis LMG 25438T (96.9 %), Vibrio gangliei SZDIS-1T (96.2 %) and Vibrio aestivus M22T (96.1 %). The growth of S4M6T occurred at 15–35 °C (optimum 28 °C), pH 4.0–9.0 (optimum 5.0–7.0) and in the presence of 2–5 % (w/v) NaCl (optimum 3 %). The predominant fatty acids (>10 %) are C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The DNA G+C content of the assembled genomic sequences was 43.4 % for S4M6T. Average nucleotide identity (ANI) values between S4M6T and the reference species were lower than the threshold for species delineation (95–96 %); in silico DNA–DNA hybridization further indicated that S4M6T had less than 70 % similarity to its relatives. On the basis of the polyphasic evidence, strain S4M6T is proposed to represent a novel species of the genus Vibrio , for which the name Vibrio sinus sp. nov. is proposed. The type strain is S4M6T (= KCTC 92312T= MCCC 1K06167T).
-
-
-
Maritalea mediterranea sp. nov., isolated from marine plastic residues
A novel Gram-reaction-negative, aerobic, motile, rod-shaped, grey bacterium, strain P4.10XT, was isolated from plastic debris sampled from shallow waters in the Mediterranean Sea (Valencia, Spain). P4.10XT was catalase- and oxidase-positive, and grew under mesophilic, neutrophilic and halophilic conditions. The 16S rRNA gene sequences revealed that P4.10XT was closely related to Maritalea myrionectae DSM 19524T and Maritalea mobilis E6T (98.25 and 98.03 % sequence similarity, respectively). The DNA G+C content of the genome sequence of P4.10XT was 53.66 %. The genomic indexes average nucleotide identity by blast (ANIb) and digital DNA–DNA hybridization (dDDH) confirmed its classification as representing a novel species of the genus Maritalea . The predominant fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c) and C18 : 1 ω7c 11-methyl. The results of this polyphasic study confirm that P4.10XT represents a novel species of the genus Maritalea , for which the name Maritalea mediterranea sp. nov. is proposed (type strain P4.10XT=CECT 30306T = DSM 112386T).
-
-
-
Legionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling
Two Legionella -like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, biochemically and genomically in terms of DNA relatedness. Both strains, HCPI-6T and EUR-108, exhibited biochemical phenotypic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYEα agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae , including a requirement for l-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non-fermentative. The major ubiquinone was Q12 (59.4 % HCPI-6T) and the dominant fatty acids were C16 : 1 ω7c (28.4 % HCPI-6T, ≈16 % EUR-108), C16 : 0 iso (≈22.5 % and ≈13 %) and C15 : 0 anteiso (19.5 % and ≈23.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence-based analyses (average nucleotide identity, ANI; digital DNA–DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella . The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8–90.1 % to other members of the genus. The core genome-based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella . ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI-6T (=CCUG 75071T=CECT 30569T).
-
-
-
Sandaracinobacteroides sayramensis sp. nov., a yellow-pigmented bacterium isolated from lake water
More LessA Gram-negative, non-motile, facultatively anaerobic, rod-shaped bacterium, designated strain RS1-74T, was isolated from the surface water of Sayram Lake, Xinjiang Uygur Autonomous Region, China. The strain was able to grow optimally at 30 °C and pH 7.0–7.5, and in the presence of 0–0.5 % (v/w) NaCl. Catalase and oxidase activities were present. H2S was produced. Chemotaxonomic analysis showed Q-10 was the sole respiratory quinone. The polar lipids were composed of phosphatidylethanolamine, diphosphatidylglycerol, two glycolipids, phosphatidylglycerol, sphingoglycolipid and two unidentified lipids. Summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) were the predominant fatty acids. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain RS1-74T was closely related to ‘ Sandaracinobacter neustonicus ’ JCM 30 734 (98.65 %), ‘ Sandaracinobacter sibiricus ’ RB16-17 (98.42 %) and Sandaracinobacteroides hominis SZY PN-1T (97.09%). The genomic DNA G+C content was 66.45 mol%. The average nucleotide identity and DNA–DNA hybridization values among the genomes of strain RS1-74T and ‘ Sandaracinobacter neustonicus ’ JCM 30734 and Sandaracinobacteroides hominis SZY PN-1T were 78.2 and 77.22 %, and 22.2 and 20.40 %, respectively. Based on the physiological, biochemical, phylogenetic and genomic data, strain RS1-74T represents a novel species within the genus Sandaracinobacteroides , for which the name Sandaracinobacteroides sayramensis sp. nov. is proposed, with type strain RS1-74T (=KCTC 82674T=MCCC 1K06282T).
-
-
-
Melaminivora suipulveris sp. nov., isolated from pigpen dust
More LessA bacterial strain designated SC2-9T was isolated from the dust collector of a pigpen located in Wanju-gun, Jeollabuk-do, Republic of Korea. Cells were strictly aerobic, Gram-stain-negative, flagellated and rod-shaped. The strain was catalase- and oxidase-positive, and grew optimally 28–30 °C, pH 8.0 and 0 % NaCl (w/v). Phylogenetic analysis based on 16S rRNA gene sequences showed 99.1 and 98.3 % similarities to Melaminivora jejuensis KBB12T and Melaminivora alkalimesophila CY1T, and revealing less than 97 % similarity to other validly named species. The genomic DNA G+C content of strain SC2-9T was 68.2 %. The orthologous average nucleotide identity and dDDH values of strain SC2-9T with the closest species Melaminivora jejuensis KCTC 32230T were 85.6 and 29.3 %, respectively. The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified aminolipids and one unidentified lipid. The major fatty acids (>10 %) were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c), C16 : 0 and summed feature 8 (C18 : 1 ω6c and/ or C18 : 1 ω7c). The predominant isoprenoid quinone was ubiquinone-8. Based on phenotypic, chemotaxonomic and phylogenetic data, strain SC2-9T should be assigned as a novel species of the genus Melaminivora , for which the name Melaminivora suipulveris sp. nov. is proposed. The type strain is SC2-9T (=KACC 19310T=NBRC 113103T).
-
- Eukaryotic Micro-Organisms
-
-
Morphological and genetic analysis of Ceratomyxa saurida Zhao et al. 2015 and Ceratomyxa mai sp. nov. (Myxozoa: Ceratomyxidae) from the East China Sea
We describe Ceratomyxa saurida Zhao et al. 2015 and Ceratomyxa mai sp. nov. (Myxozoa: Ceratomyxidae) from the East China Sea. C. saurida was found in the gallbladders of 3/13 specimens of its type host, Saurida elongata Temminck and Schlegel 1846 (Aulopiformes). Myxospore characters were consistent with the original description to which we have added small subunit (SSU) rRNA gene data. C. mai sp. nov. was found in gallbladders of 3/13 specimens of S. elongata and 5/13 specimens of Neobythites sivicola Jordan and Snyder 1901 (Ophidiiformes). Mature myxospores of C. mai sp. nov. were crescentic in sutural view, with a deeply concave posterior angle 142.2±8.2° (125.8‒158.2°) and an arched anterior side. Shell valves were smooth and equal, 20.9±1.9 (17.3‒24.7) µm thick and 9.2±0.5 (8.1‒9.9) µm long, and joined at a straight, thin sutural plane passing between two nematocysts (polar capsules). The nematocysts were equal-sized, pyriform, 2.6±0.2 (2.4‒2.9) µm long and 2.7±0.2 (2.4‒3.3) µm wide, with their tapered ends pointed toward each other, located in the anterior third of the spore. Sequences of the SSU rRNA gene and internal transcribed spacer 1 showed that the isolates of C. mai sp. nov. obtained from S. elongata and N. sivicola were identical. The SSU rRNA gene sequence of C. mai sp. nov. was distinct from all known myxosporeans and clustered with C. saurida, and then with Ceratomyxa filamentosi Kalatzis, Kokkari and Katharios 2013, both of which also infect Aulopiformes fishes.
-
- Combined Taxa
-
-
Proposal of Holzapfeliella gen. nov. and Litorivicinus gen. nov. as replacement names for the illegitimate prokaryotic generic names Holzapfelia Zheng et al. 2020 and Litoricola Kim et al. 2007, respectively
More LessThe prokaryotic generic names Holzapfelia Zheng et al. 2020 and Litoricola Kim et al. 2007 are illegitimate because they are later homonyms of the names Holzapfelia Cossmann 1901, an extinct genus of molluscs (Neogastropoda) and Litoricola Woodward 1873, an extinct genus of crustaceans (Arthropoda), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic name Holzapfeliella with type species Holzapfeliella floricola comb. nov. and the replacement generic name Litorivicinus with replacement name Litorivicinus lipolyticus for the type species, the replacement name Litorivicinus marinus, and the family name Litorivicinaceae to replace the illegitimate name Litoricolaceae Kim et al. 2007.
-
- Methods
-
-
-
Collection and curation of prokaryotic genome assemblies from type strains at NCBI
The public sequence databases are entrusted with the dual responsibility of providing an accessible archive to all submitters and supporting data reliability and its re-use to all users. Genomes from type materials can act as an unambiguous reference for a taxonomic name and play an important role in comparative genomics, especially for taxon verification or reclassification. The National Center for Biotechnology Information (NCBI) collects and curates information on prokaryotic type strains and genomes from type strains. The average nucleotide identity (ANI)-based quality control processes introduced at NCBI to verify the genomes from type strains and improve related sequence records are detailed here. Using the curated genomes from type strains as reference, the taxonomy of over 1.1 million GenBank genomes were verified and the taxonomy of over 7000 new submissions before acceptance to GenBank and over 1800 existing genomes in GenBank were reclassified.
-
-
Volumes and issues
-
Volume 74 (2024)
-
Volume 73 (2023)
-
Volume 72 (2022 - 2023)
-
Volume 71 (2020 - 2021)
-
Volume 70 (2020)
-
Volume 69 (2019)
-
Volume 68 (2018)
-
Volume 67 (2017)
-
Volume 66 (2016)
-
Volume 65 (2015)
-
Volume 64 (2014)
-
Volume 63 (2013)
-
Volume 62 (2012)
-
Volume 61 (2011)
-
Volume 60 (2010)
-
Volume 59 (2009)
-
Volume 58 (2008)
-
Volume 57 (2007)
-
Volume 56 (2006)
-
Volume 55 (2005)
-
Volume 54 (2004)
-
Volume 53 (2003)
-
Volume 52 (2002)
-
Volume 51 (2001)
-
Volume 50 (2000)
-
Volume 49 (1999)
-
Volume 48 (1998)
-
Volume 47 (1997)
-
Volume 46 (1996)
-
Volume 45 (1995)
-
Volume 44 (1994)
-
Volume 43 (1993)
-
Volume 42 (1992)
-
Volume 41 (1991)
-
Volume 40 (1990)
-
Volume 39 (1989)
-
Volume 38 (1988)
-
Volume 37 (1987)
-
Volume 36 (1986)
-
Volume 35 (1985)
-
Volume 34 (1984)
-
Volume 33 (1983)
-
Volume 32 (1982)
-
Volume 31 (1981)
-
Volume 30 (1980)
-
Volume 29 (1979)
-
Volume 28 (1978)
-
Volume 27 (1977)
-
Volume 26 (1976)
-
Volume 25 (1975)
-
Volume 24 (1974)
-
Volume 23 (1973)
-
Volume 22 (1972)
-
Volume 21 (1971)
-
Volume 20 (1970)
-
Volume 19 (1969)
-
Volume 18 (1968)
-
Volume 17 (1967)
-
Volume 16 (1966)
-
Volume 15 (1965)
-
Volume 14 (1964)
-
Volume 13 (1963)
-
Volume 12 (1962)
-
Volume 11 (1961)
-
Volume 10 (1960)
-
Volume 9 (1959)
-
Volume 8 (1958)
-
Volume 7 (1957)
-
Volume 6 (1956)
-
Volume 5 (1955)
-
Volume 4 (1954)
-
Volume 3 (1953)
-
Volume 2 (1952)
-
Volume 1 (1951)