Vibrio chanodichtyis sp. nov., isolated from the intestine of swordfish Chanodichthys dabryi

A Gram-stain-negative, facultatively anaerobic, motile, curved-rod-shaped flagellated bacterium, designated DSL-7T, was isolated from the intestine of Chanodichthys dabryi in the Yangtze river, PR China. The strain grew optimally in tryptone soy broth medium at 37 °C, pH 7.0 and with 1 % (w/v) NaCl. Strain DSL-7T showed less than 96.2 % 16S rRNA gene sequence similarity to type strains of the genus Vibrio. Phylogenetic analysis based on genomes indicated that strain DSL-7T belonged to the genus Vibrio and formed a subclade with Vibrio mimicus NCTC 11435T, Vibrio metoecus OP3HT, Vibrio cholerae ATCC 14035T, Vibrio albensis ATCC14547T, Vibrio paracholerae OP3HEDC-792T and Vibrio tarriae 2521-89T. The average nucleotide identity (ANI) and in digital DNA-DNA hybridization (dDDH) values between DSL-7T and closely related type strains were below the accepted threshold to delineate a new species of 95 and 70 %, respectively. The major cellular fatty acids were summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c), C16 : 0, summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c) and C14 : 0. The genomic DNA G+C content was 47.6 mol%. Based on the phenotypic, chemotaxonomic, phylogenetic and genomic data, strain DSL-7T represents a novel species of the genus Vibrio, for which the name Vibrio chanodichtyis sp. nov. is proposed, with strain DSL-7T (=KCTC 92851T=CCTCC AB 2022396T) as the type strain.

Isolation and characterization of Pinibacter soli sp. nov., and in silico genome mining of Pinibacter for biosynthetic gene cluster prediction

A Gram-stain-negative, aerobic, rod-shaped, non-motile and non-flagellated novel bacterial strain, designated MAH-24T, was isolated from the rhizospheric soil of a pine garden. The colonies were observed to be orange-coloured, smooth, spherical and 0.4-0.8 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAH-24T was found to be able to grow at 10-35 °C, at pH 6.0-9.0 and in the presence of 0-1.0 % NaCl (w/v). The strain was found to be positive for the catalase and oxidase tests. The strain was positive for hydrolysis of aesculin and l-tyrosine. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Pinibacter and to be closely related to Pinibacter aurantiacus MAH-26T (99.2 % sequence similarity). The novel strain MAH-24T has a draft genome size of 5 918 133 bp (13 contigs), annotated with 4613 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-24T and the closest type strain P. aurantiacus MAH-26T were in the range of 85.3 and 29.9 %, respectively. In silico genome mining revealed that both novel strain MAH-24T and P. aurantiacus MAH-26T have a significant potential for the production of novel natural products in the future. The genomic DNA G+C content was determined to be 41.0 mol%. The predominant isoprenoid quinone was menaquinone-7. The major fatty acids were identified as C15:0 iso, C15:1 iso G and C17:0 iso 3OH. On the basis of dDDH, ANI, genotypic, chemotaxonomic and physiological data, strain MAH-24T represents a novel species within the genus Pinibacter, for which the name Pinibacter soli sp. nov. is proposed, with MAH-24T (=KACC 19747T=CGMCC 1.13659T) as the type strain.

Sphingobium agri sp. nov., isolated from rhizospheric soil of eggplant

A Gram-stain-negative, aerobic, short rod-shaped and motile bacterial strain, designated MAH-33T, was isolated from rhizospheric soil of eggplant. The colonies were observed to be yellow-coloured, smooth, spherical and 0.1-0.3 mm in diameter when grown on TSA agar medium for 2 days. Strain MAH-33T was found to be able to grow at 10-40 °C, at pH 5.0-10.0 and at 0-3.0 % NaCl (w/v). The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of tyrosine and aesculin. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingobium and to be closely related to Sphingobium quisquiliarum P25T (98.4 % similarity), Sphingobium mellinum WI4T (97.8 %), Sphingobium fuliginis TKPT (97.3 %) and Sphingobium herbicidovorans NBRC 16415T (96.9 %). The novel strain MAH-33T has a draft genome size of 3 908 768 bp (28 contigs), annotated with 3689 protein-coding genes, 45 tRNA and three rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-33T and closely related type strains were in the range of 79.8-81.6 % and 23.2-24.5 %, respectively. The genomic DNA G+C content was determined to be 62.2 %. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as C16 : 0 and summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c). The polar lipids identified in strain MAH-33T were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, sphingoglycolipid, phosphatidylcholine; one unknown phospholipid and one unknown lipid. On the basis of digital DNA-DNA hybridization, ANI value, genotypic analysis, chemotaxonomic and physiological data, strain MAH-33T represents a novel species within the genus Sphingobium, for which the name Sphingobium agri sp. nov. is proposed, with MAH-33T (=KACC 19973T = CGMCC 1.16609T) as the type strain.

Roseateles albus sp. nov., Roseateles koreensis sp. nov. and Janthinobacterium fluminis sp. nov., isolated from freshwater at Jucheon River, and emended description of Roseateles aquaticus comb. nov

Three Gram-stain-negative, facultatively anaerobic, rod-shaped, catalase-positive, oxidase-negative bacterial strains were designated as hw1T, hw8T and hw3T. Strains hw1T, hw8T and hw3T grew at 15-28 °C (optimum, 25 °C), 15-35 °C (optimum, 30 °C) and 4-28 °C (optimum, 20 °C), respectively, and at pH 7.0-12.0 (optimum, pH 9.0), pH 6.0-11.0 (optimum, pH 9.0) and 5.0-12.0 (optimum, pH 7.0), respectively. Additionally, strains hw1T and hw8T only grew when the NaCl concentration was 0 %, while strain hw3T grew at between 0 and 0.5 % (w/v; optimum, 0 %). The average nucleotide identity (ANI) values between strains hw1T, hw8T and the Roseateles type strains ranged from 73.8 to 84.2 %, while the digital DNA-DNA hybridization (dDDH) values ranged from 19.7 to 27.5 %. The ANI values between strain hw3T and the Janthinobacterium type strains ranged from 78.7 to 80.7 %, while dDDH values ranged from 22.3 to 23.0 %. The draft genomes of strains hw1T, hw8T and hw3T consisted of 5.5, 4.4 and 5.9 Mbp, with DNA G+C contents of 61.7, 61.8 and 66.0 mol%, respectively. The results of the dDDH, ANI, phylogenetic, biochemical and physiological analyses indicated that the novel strains were distinct from other members of their genera. Thus, we proposed the names Roseateles albus sp. nov. (type strain hw1T= KACC 22887T= TBRC 16613T), Roseateles koreensis sp. nov. (type strain hw8T= KACC 22885T= TBRC 16614T) and Janthinobacterium fluminis sp. nov. (type strain hw3T= KACC 22886T= TBRC 16615T).

Sphingomonas oryzagri sp. nov., isolated from a rice field

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-71T, was isolated from the soil of a rice field. The colonies were observed to be milky yellow-coloured, smooth, spherical and 0.1-0.4 mm in diameter when grown on Reasoner's 2A agar medium for 2 days. Strain MAHUQ-71T was found to be able to grow at 15-37 °C, pH 5.0-10.0 and with 0-3.0 % NaCl (w/v). The strain was found to be positive for the catalase test, but negative for the oxidase test. The strain was positive for hydrolysis of aesculin and Tween 20. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Sphingomonas and to be closely related to Sphingomonas chungangi MAH-6T (98.5 % sequence similarity), Sphingomonas polyaromaticivorans B2-7T (98.4 %) and Sphingomonas oligoaromativorans SY-6T (96.6 %). Strain MAHUQ-71T has a draft genome size of 4 255 278 bp (10 contigs), annotated with 4098 protein-coding genes, 47 tRNA and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-71T and the closest type strain S. chungangi MAH-6T were in the range of 85.6 and 30.6 %, respectively. The genomic DNA G+C content was determined to be 66.7 mol%. The predominant isoprenoid quinone was ubiquinone 10. The major fatty acids were identified as summed feature 8 (C18 : 1  ω7c and/or C18 : 1  ω6c), C16 : 0 and C14 : 0 2OH. The main polar lipids were phosphatidylcholine, phosphatidylethanolamine, diphosphatidylglycerol and sphingoglycolipid. On the basis of dDDH and ANI values, as well as the results of genotypic, chemotaxonomic and physiological analyses, strain MAHUQ-71T represents a novel species within the genus Sphingomonas, for which the name Sphingomonas oryzagri sp. nov. is proposed, with MAHUQ-71T (=KACC 22252T=CGMCC 1.19065T) as the type strain.

Massilia agrisoli sp. nov., isolated from rhizospheric soil of banana

A Gram-stain-negative, aerobic, short rod-shaped and motile novel bacterial strain, designated MAHUQ-52^T, was isolated from the rhizospheric soil of a banana plant. Colonies grew at 10-35 °C (optimum, 28 °C), pH 6.0-9.5 (optimum, pH 7.0-7.5), and in the presence of 0-1.0 % NaCl (optimum 0 %). The strain was positive for catalase and oxidase tests, as well as hydrolysis of gelatin, casein, starch and Tween 20. Based on the results of phylogenetic analysis using 16S rRNA gene and genome sequences, strain MAHUQ-52^T clustered together within the genus Massilia. Strain MAHUQ-52^T was closely related to Massilia soli R798^T (98.6 %) and Massilia polaris RP-1-19^T (98.3 %). The novel strain MAHUQ-52^T has a draft genome size of 4 677 454 bp (25 contigs), annotated with 4193 protein-coding genes, 64 tRNA and 19 rRNA genes. The genomic DNA G+C content was 63.0 %. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAHUQ-52^T and closely related type strains were ≤88.4 and 35.8 %, respectively. The only respiratory quinone was ubiquinone-8. The major fatty acids were identified as C_16 : 0 and summed feature 3 (C_15 : 0 iso 2-OH and/or C_16 : 1  ω7c). Strain MAHUQ-52^T contained phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol as the major polar lipids. On the basis of dDDH and ANI values, as well as genotypic, chemotaxonomic and physiological data, strain MAHUQ-52^T represents a novel species within the genus Massilia, for which the name Massilia agrisoli sp. nov. is proposed, with MAHUQ-52^T (=KACC 21999^T=CGMCC 1.18577^T) as the type strain.

Streptomyces longhuiensis sp. nov, a novel species isolated from soil of Lilium brownii in Hunan Province, PR China

An actinobacterium strain, designated BH-MK-02^T, was isolated from the soil of Lilium brownii. The taxonomic position was determined using a polyphasic approach. Strain BH-MK-02^T grew well on International Streptomyces Project series media and formed well-developed, branched substrate hyphae and aerial mycelium that differentiated into straight spore chains with a wrinkled surface. The diagnostic diamino acid was ll-diaminopimelic acid. The major menaquinones were MK-9(H₄), MK-9(H₆) and MK-9(H₈). The polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannosides, phosphatidylglycerol and unidentified lipid spots. The predominant fatty acids were anteiso-C_15 : 0, iso-C_16 : 0, C_16 : 0 and C_16 : 1  ω7c/C_16 : 1  ω6c. The phenotypic characteristics of strain BH-MK-02^T indicated that it belonged to the genus Streptomyces. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain BH-MK-02^T was most closely related to Streptomyces aureus CGMCC 4.1833^T (99.7 %). However, the average nucleotide identity and digital DNA-DNA hybridization values between the whole-genome sequences of strain BH-MK-02^T and S. aureus CGMCC 4.1833^T were 78.1 and 23.2 %, respectively, below the 96.7 and 70 % cut-off points respectively recommended for delineating Streptomyces species. Furthermore, the novel isolate could be distinguished from S. aureus CGMCC 4.1833^T by morphological, physiological and biochemical characteristics. Based on all these data, strain BH-MK-02^T (=MCCC 1K06237^T=JCM 34789^T) clearly represents a novel species within the genus Streptomyces, for which the name Streptomyces longhuiensis sp. nov. is proposed.

Helicobacter kumamotonensis sp. nov., isolated from human clinical specimens

A Gram-stain-negative, spiral bacterium (PAGU 1991^T) was isolated from the blood of a patient with diffuse large B-cell lymphoma. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate was very closely related to Helicobacter equorum LMG 23362^T (99.1 % similarity), originally isolated from a faecal sample from a healthy horse. PAGU 1991^T was also very closely related to PAGU 1750 in our strain library (=CCUG 41437) with 99.7 % similarity. Additional phylogenetic analyses based on the 23S rRNA gene sequence and GyrA amino acid sequence further supported the close relationship between the two human isolates (PAGU 1991^T and PAGU 1750) and the horse strain. However, a phylogenetic analysis based on 16S rRNA showed that the two human isolates formed a lineage that was distinct from the horse strain (less than 99.2 % similarity). In silico whole-genome comparisons based on digital DNA-DNA hybridization, average nucleotide identity based on blast and orthologous average nucleotide identity using usearch between the two human isolates and the type strain of H. equorum showed values of less than 52.40, 93.47, and 93.50 %, respectively, whereas those between the two human isolates were 75.8, 97.2, and 97.2 %, respectively. These data clearly demonstrated that the two human isolates formed a single species, distinct from H. equorum. Morphologically, the human isolates could be distinguished by the type of flagella; the human isolates showed a bipolar sheathed flagellum, whereas that of H. equorum was monopolar. Biochemically, the human isolate was characterized by growth at 42 °C under microaerobic conditions and nitrate reduction unability. We conclude that the two human isolates, obtained from geographically and temporally distinct sources, were a novel species, for which we propose the name Helicobacter kumamotonensis sp. nov., with the type strain PAGU 1991^T (=GTC 16810^T=CCUG 75774^T).

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-6^T 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-6^T) and the dominant fatty acids were C_16 : 1 ω7c (28.4 % HCPI-6^T, ≈16 % EUR-108), C_16 : 0 iso (≈22.5 % and ≈13 %) and C_15 : 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-6^T (=CCUG 75071^T=CECT 30569^T).

Frateuria flava sp. nov., isolated from soil

A Gram-stain-negative, aerobic, rod-shaped and non-motile novel bacterial strain, designated MAH-13^T, was isolated from a soil sample. The colonies were observed to be yellow-coloured, smooth, spherical and 1.8-3.0 mm in diameter when grown on nutrient agar medium for 2 days. Strain MAH-13^T was found to be able to grow at 20-40 °C, at pH 5.0-10.0 and with 0-1.0% NaCl (w/v). Cell growth occurred on tryptone soya agar, Luria-Bertani agar, nutrient agar and Reasoner's 2A agar. The strain was found to be positive for both oxidase and catalase tests. The strain was positive for hydrolysis of casein, starch, DNA and l-tyrosine. According to 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Frateuria and to be closely related to Frateuria terrea DSM 26515^T (98.2% similarity), Dyella thiooxydans ATSB10^T (98.2 %), Frateuria defendens HyOG^T (97.9 %), Rhodanobacter glycinis MO64^T (97.8 %) and Frateuria aurantia DSM 6220^T (97.8 %). The novel strain MAH-13^T has a draft genome size of 3 682 848 bp (40 contigs), annotated with 3172 protein-coding genes, 49 tRNA genes and three rRNA genes. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain MAH-13^T and five closely related type strains were in the range of 73.7-85.5 % and 20.7-30.1%, respectively. The genomic DNA G+C content was determined to be 68.0 mol%. The predominant isoprenoid quinone was ubiquinone 8. The major fatty acids were identified as iso-C_15:0, iso-C_16:0 and summed feature 9 (iso-C_17 : 1 ω9c and/or C_16:0 10-methyl). On the basis of dDDH and ANI values, genotypic analysis, and chemotaxonomic and physiological data, strain MAH-13^T represents a novel species within the genus Frateuria, for which the name Frateuria flava sp. nov. is proposed, with MAH-13^T (=KACC 19743^T=CGMCC 1.13655^T) as the type strain.

Arcobacter vandammei sp. nov., isolated from the rectal mucus of a healthy pig

A study on the polyphasic taxonomic classification of an Arcobacter strain, R-73987^T, isolated from the rectal mucus of a porcine intestinal tract, was performed. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain could be assigned to the genus Arcobacter and suggested that strain R-73987^T belongs to a novel undescribed species. Comparative analysis of the rpoB gene sequence confirmed the findings. Arcobacter faecis LMG 28519^T was identified as its closest neighbour in a multigene analysis based on 107 protein- encoding genes. Further, whole-genome sequence comparisons by means of average nucleotide identity and in silico DNA-DNA hybridization between the genome of strain R-73987^T and the genomes of validly named Arcobacter species resulted in values below 95-96 and 70  %, respectively. In addition, a phenotypic analysis further corroborated the conclusion that strain R-73987^T represents a novel Arcobacter species, for which the name Arcobacter vandammei sp. nov. is proposed. The type strain is R-73987^T (=LMG 31429^T=CCUG 75005^T). This appears to be the first Arcobacter species recovered from porcine intestinal mucus.

Niastella soli sp. nov., isolated from rhizospheric soil of a persimmon tree

A Gram-stain-negative, aerobic, motile and rod-shaped novel bacterial strain, designated MAH-29^T, was isolated from rhizospheric soil of a persimmon tree. The colonies were light pink coloured, smooth, spherical and 0.1-0.8 mm in diameter when grown on Reasoner's 2A (R2A) agar for 2 days. Strain MAH-29^T was able to grow at 20-37 °C, at pH 5.0-8.5 and at 0-2.0 % NaCl. Cell growth occurred on nutrient agar and R2A agar. The strain was positive in both oxidase and catalase tests. According to the 16S rRNA gene sequence comparisons, the isolate was identified as a member of the genus Niastella and was closely related to Niastella vici DJ57^T (97.7 % similarity), Niastella koreensis GR20-10^T (97.1 %) and Niastella yeongjuensis GR20-13^T (97.0 %). Strain MAH-29^T has a draft genome size of 8 876 333 bp (31 contigs), annotated with 6920 protein-coding genes, 61 tRNA and four rRNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain MAH-29^T and three closely related type strains were in the range of 78.2-83.2 % and 22.1-27.0 %, respectively. The genomic DNA G+C content was 43.8 mol%. The predominant isoprenoid quinone was menaquinone 7. The major fatty acids were identified as iso-C_15:0, iso-C_15:1 G and iso-C_17:0 3OH. On the basis of DNA-DNA hybridization results, genotypic analysis and chemotaxonomic and physiological data, strain MAH-29^T represents a novel species within the genus Niastella, for which the name Niastella soli sp. nov. is proposed, with MAH-29^T (=KACC 19969^T=CGMCC 1.16606^T) as the type strain.

Roseobacters in a Sea of Poly- and Paraphyly: Whole Genome-Based Taxonomy of the Family Rhodobacteraceae and the Proposal for the Split of the "Roseobacter Clade" Into a Novel Family, Roseobacteraceae fam. nov

The family Rhodobacteraceae consists of alphaproteobacteria that are metabolically, phenotypically, and ecologically diverse. It includes the roseobacter clade, an informal designation, representing one of the most abundant groups of marine bacteria. The rapid pace of discovery of novel roseobacters in the last three decades meant that the best practice for taxonomic classification, a polyphasic approach utilizing phenotypic, genotypic, and phylogenetic characteristics, was not always followed. Early efforts for classification relied heavily on 16S rRNA gene sequence similarity and resulted in numerous taxonomic inconsistencies, with several poly- and paraphyletic genera within this family. Next-generation sequencing technologies have allowed whole-genome sequences to be obtained for most type strains, making a revision of their taxonomy possible. In this study, we performed whole-genome phylogenetic and genotypic analyses combined with a meta-analysis of phenotypic data to review taxonomic classifications of 331 type strains (under 119 genera) within the Rhodobacteraceae family. Representatives of the roseobacter clade not only have different environmental adaptions from other Rhodobacteraceae isolates but were also found to be distinct based on genomic, phylogenetic, and in silico-predicted phenotypic data. As such, we propose to move this group of bacteria into a new family, Roseobacteraceae fam. nov. In total, reclassifications resulted to 327 species and 128 genera, suggesting that misidentification is more problematic at the genus than species level. By resolving taxonomic inconsistencies of type strains within this family, we have established a set of coherent criteria based on whole-genome-based analyses that will help guide future taxonomic efforts and prevent the propagation of errors.

Gluconacetobacter dulcium sp. nov., a novel Gluconacetobacter species from sugar-rich environments

A phylogenomic analysis based on 107 single-copy core genes revealed that three strains from sugar-rich environments, i.e. LMG 1728^T, LMG 1731 and LMG 22058, represented a single, novel Gluconacetobacter lineage with Gluconacetobacter liquefaciens as nearest validly named neighbour. OrthoANIu and digital DNA-DNA hybridization analyses among these strains and Gluconacetobacter type strains confirmed that the three strains represented a novel Gluconacetobacter species. Biochemical characteristics and MALDI-TOF mass spectra allowed differentiation of this novel species from the type strains of G. liquefaciens and other closely related Gluconacetobacter species. We therefore propose to classify strains LMG 1728^T, LMG 1731 and LMG 22058 in the novel species Gluconacetobacter dulcium sp. nov., with LMG 1728^T (=CECT 30142^T) as the type strain.

Flavobacterium supellecticarium sp. nov., isolated from an abandoned construction timber

A bacterial strain CC-CTC003^T was isolated from a synthetic wooden board. Cells of strain CC-CTC003^T were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003^T belonged to the genus Flavobacterium and was most closely related to Flavobacterium cerinum (95.3 % sequence identity), Flavobacterium maris (94.9 % sequence identity), Flavobacterium qiangtangense (94.8 %) and Flavobacterium subsaxonicum (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003^T and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with F. cerinum was 19.4 %. Strain CC-CTC003^T contained C_15 : 0, iso-C_15 : 0, iso-C_15 : 0 3-OH, iso-C_17 : 0 3-OH, summed feature 3 (C_16 : 1  ω6c / C_16 : 1  ω7c) and summed feature 9 (C_16 : 0 10-methyl / iso-C_17 : 1  ω9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was sym-homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003^T should be classified as a novel species, for which the name Flavobacterium supellecticarium sp. nov. is proposed. The type strain is CC-CTC003^T (=BCRC 81146^T=JCM 32838^T).

Dokdonia sinensis sp. nov., a flavobacterium isolated from surface seawater

A taxonomic study was carried out on strain SH27^T, which was isolated from seawater collected around Xiaoshi Island, PR China. Cells of strain SH27^T were Gram-stain-negative, non-motile, rod-shaped, orange-pigmented and grew at 15-37 °C (optimum, 28 °C), at pH 6.0-8.0 (pH 7.0) and in 1.0-7.0 % (w/v) NaCl (2.0-3.0 %). The isolate was positive for catalase, but negative for nitrate reduction, oxidase, indole production and urease. Carotenoid pigment was produced. Phylogenetic analysis based on the 16S rRNA gene placed strain SH27^T in the genus Dokdonia with the closest relative being Dokdonia donghaensis KCTC 12391^T, exhibiting 96.7 % 16S rRNA gene pairwise similarity. The results of genomic comparisons, including average nucleotide identity and digital DNA-DNA hybridization, showed 72.9 and 19.2 % identity to D. donghaensis KCTC 12391^T, respectively. The major cellular fatty acids were iso-C_15 : 0, iso-C_15 : 1 G and iso-C_17 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and two unidentified lipids. Menaquinone-6 was the only respiratory quinone. The G+C content of the genomic DNA was 32.9 mol%. On the basis of the phenotypic and phylogenetic data, strain SH27^T represents a novel species of the genus Dokdonia, for which the name Dokdonia sinensis sp. nov. is proposed, with the type strain SH27^T (MCCC 1H00358^T=CCTCC AB 2018323^T=KCTC 62962^T).

Allorhizobium terrae sp. nov., isolated from paddy soil, and reclassification of Rhizobium oryziradicis (Zhao et al. 2017) as Allorhizobium oryziradicis comb. nov

A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110^T, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110^T were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110^T associated with Rhizobium oryziradicis (98.4 % sequence identity), Allorhizobium vitis (97.8 %), Allorhizobium taibaishanense (97.7 %) and Allorhizobium undicola (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110^T and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110^T contained C_16 : 0 3-OH, C_14 : 0 3-OH/iso C_16 : 1 I and C_18 : 1 ω7c/C_{18  : 1} ω6c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110^T is proposed to represent a novel Allorhizobium species, for which the name Allorhizobium terrae sp. nov. (type strain CC-HIH110^T=BCRC 80932^T=JCM 31228^T). In addition, Rhizobium oryziradicis is reclassified as Allorhizobium oryziradicis (type strain N19^T=ACCC 19962^T=KCTC 52413^T) comb. nov.

Trichococcus shcherbakoviae sp. nov., isolated from a laboratory-scale anaerobic EGSB bioreactor operated at low temperature

A new species of the genus Trichococcus, strain Art1^T, was isolated from a psychrotolerant syntrophic propionate-oxidizing consortium, obtained before from a low-temperature EGSB reactor fed with a mixture of VFAs (acetate, propionate and butyrate). The 16S rRNA gene sequence of strain Art1^T was highly similar to those of other Trichococcus species (99.7-99.9 %) but digital DNA-DNA hybridization values were lower than those recommended for the delineation of a novel species, indicating that strain Art1^T is a novel species of the genus Trichococcus. Cells of strain Art1^T are non-motile cocci with a diameter of 0.5-2.0 µm and were observed singularly, in pairs, short chains and irregular conglomerates. Cells of Art1^T stained Gram-positive and produced extracellular polymeric substances . Growth was optimal at pH 6-7.5 and cells could grow in a temperature range of from -2 to 30 °C (optimum 25-30 °C). Strain Art1^T can degrade several carbohydrates, and the main products from glucose fermentation are lactate, acetate, formate and ethanol. The genomic DNA G+C content of strain Art1^T is 46.7 %. The major components of the cellular fatty acids are C16 : 1 ω9c, C16 : 0 and C18 : 1 ω9c. Based on genomic and physiological characteristics of strain Art1^T, a new species of the genus Trichococcus, Trichococcusshcherbakoviae, is proposed. The type strain of Trichococcusshcherbakoviae is Art1^T (=DSM 107162^T = VKM B-3260^T).

Phylogenomic Analysis of the Gammaproteobacterial Methanotrophs (Order Methylococcales) Calls for the Reclassification of Members at the Genus and Species Levels

The order Methylococcales constitutes the methanotrophs – bacteria that can metabolize methane, a potent greenhouse gas, as their sole source of energy. These bacteria are significant players in the global carbon cycle and can produce value-added products from methane, such as biopolymers, biofuels, and single-cell proteins for animal feed, among others. Previous studies using single-gene phylogenies have shown inconsistencies in the currently established taxonomic structure of this group. This study aimed to determine and resolve these issues by using whole-genome sequence analyses. Phylogenomic analysis and the use of similarity indexes for genomic comparisons – average amino acid identity, digital DNA–DNA hybridization (dDDH), and average nucleotide identity (ANI) – were performed on 91 Methylococcales genomes. Results suggest the reclassification of members at the genus and species levels. Firstly, to resolve polyphyly of the genus Methylomicrobium, Methylomicrobium alcaliphilum, “Methylomicrobium buryatense,” Methylomicrobium japanense, Methylomicrobium kenyense, and Methylomicrobium pelagicum are reclassified to a newly proposed genus, Methylotuvimicrobium gen. nov.; they are therefore renamed to Methylotuvimicrobium alcaliphilum comb. nov., “Methylotuvimicrobium buryatense” comb. nov., Methylotuvimicrobium japanense comb. nov., Methylotuvimicrobium kenyense comb. nov., and Methylotuvimicrobium pelagicum comb. nov., respectively. Secondly, due to the phylogenetic affinity and phenotypic similarities of Methylosarcina lacus with Methylomicrobium agile and Methylomicrobium album, the reclassification of the former species to Methylomicrobium lacus comb. nov. is proposed. Thirdly, using established same-species delineation thresholds (70% dDDH and 95% ANI), Methylobacter whittenburyi is proposed to be a later heterotypic synonym of Methylobacter marinus (89% dDDH and 99% ANI). Also, the effectively but not validly published “Methylomonas denitrificans” was identified as Methylomonas methanica (92% dDDH and 100% ANI), indicating that the former is a later heterotypic synonym of the latter. Lastly, strains MC09, R-45363, and R-45371, currently identified as M. methanica, each represent a putative novel species of the genus Methylomonas (21–35% dDDH and 74–88% ANI against M. methanica) and were reclassified as Methylomonas sp. strains. It is imperative to resolve taxonomic inconsistencies within this group, first and foremost, to avoid confusion with ecological and evolutionary interpretations in subsequent studies.

Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis

The species within the Mycobacterium tuberculosis Complex (MTBC) have undergone numerous taxonomic and nomenclatural changes, leaving the true structure of the MTBC in doubt. We used next-generation sequencing (NGS), digital DNA-DNA hybridization (dDDH), and average nucleotide identity (ANI) to investigate the relationship between these species. The type strains of Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii were sequenced via NGS. Pairwise dDDH and ANI comparisons between these, previously sequenced MTBC type strain genomes (including 'Mycobacterium canettii', 'Mycobacterium mungi' and 'Mycobacterium orygis') and M. tuberculosis H37Rv^T were performed. Further, all available genome sequences in GenBank for species in or putatively in the MTBC were compared to H37Rv^T. Pairwise results indicated that all of the type strains of the species are extremely closely related to each other (dDDH: 91.2-99.2 %, ANI: 99.21-99.92 %), greatly exceeding the respective species delineation thresholds, thus indicating that they belong to the same species. Results from the GenBank genomes indicate that all the strains examined are within the circumscription of H37Rv^T (dDDH: 83.5-100 %). We, therefore, formally propose a union of the species of the MTBC as M. tuberculosis. M. africanum, M. bovis, M. caprae, M. microti and M. pinnipedii are reclassified as later heterotypic synonyms of M. tuberculosis. 'M. canettii', 'M. mungi', and 'M. orygis' are classified as strains of the species M. tuberculosis. We further recommend use of the infrasubspecific term 'variant' ('var.') and infrasubspecific designations that generally retain the historical nomenclature associated with the groups or otherwise convey such characteristics, e.g. M. tuberculosis var. bovis.

Bacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an "Operational Group B. amyloliquefaciens" within the B. subtilis Species Complex

The plant growth promoting model bacterium FZB42^T was proposed as the type strain of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been recently recognized as being synonymous to Bacillus velezensis due to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as "B. amyloliquefaciens." Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7^T, the type strain of B. amyloliquefaciens. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7^T. Dendrograms based on complete rpoB nucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) B. amyloliquefaciens, (2) Bacillus siamensis, and (3) a conspecific group containing the type strains of B. velezensis, Bacillus methylotrophicus, and B. amyloliquefaciens subsp. plantarum. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related to Bacillus subtilis (0.1 substitutions per nucleotide position). The tight relatedness of the three clusters was corroborated by TETRA, dDDH, ANI, and AAI analysis of the core genomes, but dDDH and ANI values were found slightly below species level thresholds when B. amyloliquefaciens DSM7^T genome sequence was used as query sequence. Due to these results, we propose that the B. amyloliquefaciens clade should be considered as a taxonomic unit above of species level, designated here as "operational group B. amyloliquefaciens" consisting of the soil borne B. amyloliquefaciens, and plant associated B. siamensis and B. velezensis, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.