Therapeutic Phage Candidates for Targeting Prevalent Sequence Types of Carbapenem-Resistant Escherichia coli.

Carbapenem-resistant Escherichia coli (CREC) is a global threat to public health; therefore, alternative treatment options are urgently needed. Bacteriophages have emerged as promising candidates for combating CREC infections. This study aimed to investigate the genetic basis of phage sensitivity in CREC by evaluating carbapenem resistance among multidrug-resistant (MDR) E. coli isolated in Daegu, South Korea and analyzing their sequence types (STs) with phage susceptibility spectra. Among the 60 MDR E. coli isolates, 80.4% were identified as CREC, with 77.0% demonstrating resistance to imipenem and 66.6% to meropenem. Moreover, 70 lytic E. coli bacteriophages were isolated from hospital sewage water and evaluated against those 60 E. coli isolates. The phages exhibited lytic activity of 33%-60%, with average titers ranging from 5.6 × 1012 to 2.4 × 1013 PFU/mL (Plaque-Forming Unit). Furthermore, multilocus sequence typing (MLST) analysis of the bacterial isolates revealed 14 distinct STs, mostly belonging to ST131, ST410, and ST648. Notably, the phage susceptibility spectra of ST73, ST13003, ST648, ST2311, ST167, ST405, ST607, ST7962, and ST131 were significantly different. Thus, the isolated phages can effectively lyse CREC isolates, particularly those with clinically dominant STs. Conversely, ST410 exhibited a 14.2%-87.14% susceptibility spectrum, whereas ST1139, ST1487, ST10, and ST206 did not lyse, suggesting the presence of more resistant STs. Future studies are warranted to identify the reasons behind this resistance and address it. Ultimately, this study will aid in developing focused treatments to address these pressing global health issues.

Kaistella soli sp. nov., isolated from oil-contaminated experimental soil.

A light yellow-coloured, non-motile, aerobic, Gram-stain-negative, and rod-shaped bacterial strain DKR-2T was isolated from oil-contaminated experimental soil. The strain was catalase and oxidase positive, and grew at 0-1.5% (w/v) NaCl concentration, at temperature 10-35 °C, and at pH 6.0-9.5. The phylogenetic analysis suggested that the strain DKR-2T was affiliated to the genus Kaistella, with the closest species being Kaistella haifensis DSM 19056T (97.6% 16S rRNA gene sequence similarity). The principle fatty acids were iso-C15:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), and antiso-C15:0. The sole menaquinone was MK-6 and major polar lipid was phosphatidylethanolamin. The DNA G+C content was 39.5%. The dDDH (in silico DNA-DNA hybridization) and ANI (average nucleotide identity) values between strain DKR-2T and K. haifensis DSM 19056T were 22.4% and 79.3%, respectively. In addition, both dDDH and ANI values between strain DKR-2T and other phylogenetically related neighbours were < 25.0% and < 77.0%, respectively. In overall, the polyphasic taxonomic data presented in this study clearly indicated that strain DKR-2T represents a novel species in the genus Kaistella, for which the name Kaistella soli sp. nov. is proposed. The type strain is DKR-2T (=KACC 22070T=NBRC 114725T).

Cellulomonas fulva sp. nov., isolated from oil-contaminated soil.

A yellow-coloured, Gram-stain-positive, motile, aerobic and rod-shaped bacteria, designated DKR-3T, was isolated from oil-contaminated experimental soil. Strain DKR-3T could grow at pH 5.0-10.5 (optimum, pH 7.0-8.5), at 10-40 °C (optimum, 25-32 °C) and tolerated 3.5 % of NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence indicated that strain DKR-3T formed a lineage within the family Cellulomonadaceae and was clustered with members of the genus Cellulomonas. Strain DKR-3T had highest 16S rRNA gene sequence similarities to Cellulomonas gelida DSM 20111T (98.3 %), Cellulomonas persica JCM 18111T (98.2 %) and Cellulomonas uda DSM 20107T (97.8 %). The predominant respiratory quinone was tetrahydrogenated menaquinone with nine isoprene units [MK-9(H4)]. The principal cellular fatty acids were anteiso-C15 : 0, C16 : 0 and anteiso-C17 : 0. The major polar lipids were diphosphatidylglycerol and phosphatidylglycerol. The cell-wall diamino acid was l-ornithine whereas rhamnose and glucose were the cell-wall sugars. The DNA G+C content was 74.2mol %. The genome of strain DKR-3T was 3.74 Mb and contained three putative biosynthetic gene clusters. The average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain DKR-3T and its phylogenetically related members were below the species threshold values. Based on a polyphasic study, strain DKR-3T represents a novel species belonging to the genus Cellulomonas, for which the name Cellulomonas fulva sp. nov. is proposed. The type strain is DKR-3T (=KACC 22071T=NBRC 114730T).

Genome mining revealed polyhydroxybutyrate biosynthesis by Ramlibacter agri sp. nov., isolated from agriculture soil in Korea.

A white-colony-forming, facultative anaerobic, motile and Gram-stain-negative bacterium, designated G-1-2-2 T was isolated from soil of agriculture field near Kyonggi University, Republic of Korea. Strain G-1-2-2 T synthesized the polyhydroxybutyrate and could grow at 10-35 °C. The phylogenetic analysis based on 16S rRNA gene sequence showed that, strain G-1-2-2 T formed a lineage within the family Comamonadaceae and clustered as a member of the genus Ramlibacter. The 16S rRNA gene sequence of strain G-1-2-2 T showed high sequence similarities with Ramlibacter ginsenosidimutans BXN5-27 T (97.9%), Ramlibacter monticola G-3-2 T (97.9%) and Ramlibacter alkalitolerans CJ661T (97.5%). The sole respiratory quinone was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, and an unidentified phospholipid. The principal cellular fatty acids were C16:0, cyclo-C17:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c) and summed feature 8 (C18:1ω7c and/or C18:1ω6c). The genome of strain G-1-2-2 T was 7,200,642 bp long with 13 contigs, 6,647 protein-coding genes, and DNA G + C content of 68.9%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain G-1-2-2 T and close members were ≤ 81.2 and 24.1%, respectively. The genome of strain G-1-2-2 T showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome mining revealed the presence of atoB, atoB2, phaS, phbB, phbC, and bhbD genes in the genome which are responsible for polyhydroxybutyrate biosynthesis. Based on these data, strain G-1-2-2 T represents a novel species in the genus Ramlibacter, for which the name Ramlibacter agri sp. nov. is proposed. The type strain is G-1-2-2 T (= KACC 21616 T = NBRC 114389 T).

Noviherbaspirillum pedocola sp. nov., isolated from oil-contaminated experimental soil.

An orange-coloured, rod-shaped, and aerobic bacterial strain DKR-6 T was isolated from oil-contaminated experimental soil. The strain was Gram-stain-negative, catalase and oxidase positive, and grew at temperature 10-42 °C, at pH 5.5-9.5, and at 0-3.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence analysis suggested that the strain DKR-6 T was affiliated to the genus Noviherbaspirillum, with the closest species being Noviherbaspirillum massiliense JC206T (96.3% sequence similarity). The chemotaxonomic profiles revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine as the principal polar lipids; C16:0, C17:0 cyclo, summed feature 3 (C16:1ω7c and/or C16: 1ω6c), and summed feature 8 (C18:1ω7c/or C18:1ω6c) as the main fatty acids; and Q-8 as a sole ubiquinone. The DNA G + C content was 61.6%. The polyphasic taxonomic features illustrated in this study clearly implied that strain DKR-6 T represents a novel species in the genus Noviherbaspirillum, for which the name Noviherbaspirillum pedocola sp. nov. is proposed with the type strain DKR-6 T (= KACC 22074 T = NBRC 114727 T).

Chryseobacterium cheonjiense sp. nov., isolated from forest soil.

A yellow-pigmented, non-motile and rod-shaped bacterium, designated RJ-7-14T was obtained from forest soil sampled at Cheonji-dong, Seogwipo-si, Jeju-do, South Korea. Cells were Gram-stain-negative and produced flexirubin type pigments. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RJ-7-14T formed a lineage within the family Weeksellaceae and clustered as members of the genus Chryseobacterium. The closest members were Chryseobacterium geocarposphaerae DSM 27617T (98.2% sequence similarity), Chryseobacterium hispalense DSM 25574T (98.0%) and Chryseobacterium nepalense KACC 18907T (98.0%). The sequence similarity for other members was < 98.0%. The genome was 4,276,416 bp long with 9 scaffolds and 3779 protein-coding genes. The sole respiratory quinone was MK-6. The major cellular fatty acids were iso-C15:0, summed feature 9 (iso-C17:1 ω9c and/or C16:0 10-methyl), summed feature 3 (iso-C15:0 2-OH and/or C16: 1ω7c) and iso-C17:0 3-OH. The major polar lipid was phosphatidylethanolamine (PE). The DNA G + C content of the type strain was 37.2 mol%. In addition, the average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain RJ-7-14T and phylogenetically closest members were ≤ 88.2% and ≤ 35.0%, respectively, which were below the threshold values of 95-96% (for ANI) and 70% (for dDDH), suggesting the allocation of novel strain to a new species. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RJ-7-14T represents novel species in the genus Chryseobacterium, for which the name Chryseobacterium cheonjiense sp. nov. is proposed. The type strain is RJ-7-14T (= KACC 21625T = NBRC 114362T).

Luteolibacter luteus sp. nov., isolated from stream bank soil.

A non-motile, Gram-stain-negative, rod-shaped and yellow-colored bacterium, designated G-1-1-1T was obtained from soil sampled at Gwanggyo stream bank, Gyeonggi-do, Republic of Korea. Cells were aerobic, catalase positive, grew optimally at 25-30 °C and hydrolysed aesculin and casein. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-1-1-1T formed a lineage within the genus Luteolibacter. The closest members were Luteolibacter flavescens GKXT (97.7% sequence similarity) and Luteolibacter arcticus MC 3726T (97.3%). The sequence similarities with other members of the genus Luteolibacter were ≤ 93.9%. The genome of strain G-1-1-1T was 6,412,079 bp long with 5176 protein-coding genes. The diagnostic amino acid of cell-wall peptidoglycan of strain G-1-1-1T was meso-diaminopimelic acid. The only respiratory quinone was menaquinone-9 and the principal polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and unidentified phospholipids. The predominant cellular fatty acids were iso-C14:0, C16:1 ω9c, C16:0, C14:0 and anteiso-C15:0. The DNA G + C content was 61.0 mol%. The anti-SMASH analysis of whole genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Based on genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain G-1-1-1T represents a novel species in the genus Luteobacter, for which the name Luteolibacter luteus sp. nov. is proposed. The type strain is G-1-1-1T (= KACC 21614T = NBRC 114341T).

Schlegelella koreensis sp. nov., isolated from evaporator core of automobile air conditioning system.

A white-coloured, aerobic, and rod-shaped bacterium, designated strain ID0723T was isolated from evaporator core of automobile air conditioning system. The strain was Gram-stain-negative, catalase positive, oxidase negative, and grew at pH 5.5-9.5, at temperature 18-37 °C, and at 0-2.0% (w/v) NaCl concentration. The phylogenetic analysis and 16S rRNA gene sequence data revealed that the strain ID0723T was affiliated to the genus Schlegelella, with the closest phylogenetic member being Schlegelella brevitalea DSM 7029 T (98.1% sequence similarity). The chemotaxonomic features of strain ID0723T were diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine as the main polar lipids; Q-8 as an only ubiquinone; and summed feature 3 (C16:1ω7c and/or C16: 1ω6c), C16:0, and summed feature 8 (C18:1ω7c/or C18:1ω6c) as the major fatty acids. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization values between strain ID0723T and S. brevitalea DSM 7029 T were 74.8% and 20.0%, respectively, which were below the cut-off values of 95% and 70%, respectively. The DNA G + C content was 69.9 mol%. The polyphasic taxonomic data clearly indicated that strain ID0723T represents a novel species in the genus Schlegelella for which the name Schlegelella koreensis sp. nov. is proposed, with the type strain ID0723T (= KCTC 72731 T = NBRC 114611 T).

Aquabacterium terrae sp. nov., isolated from soil.

A yellow-colored bacterial strain, designated S2T was isolated from soil in South Korea. Cells of strain S2T were strictly aerobic, Gram-stain-negative, motile with single polar flagellum, rod-shaped, oxidase and catalase-negative. Growth occurs at 10-37 °C (optimum, 28 °C), pH 5.0-9.0 (optimum, pH 6.5-7.0) and 0-3% NaCl (w/v). Strain S2T consisted of summed feature 3 (iso-C15:0 2-OH and/or C16:1 ω7c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c) as major fatty acids. The sole respiratory quinone was Q-8. The polar lipid profile consisted of phosphatidylethanolamine and an unidentified lipid. The 16S rRNA gene sequence analysis showed that strain S2T is phylogenetically closest to Aquabacterium pictum W35T (98.4% sequence similarity). The genome of strain S2T was 8,039,486 bp with 56 scaffolds. The genome consisted of 10 putative biosynthetic gene clusters that are responsible for various secondary metabolites. Genomic DNA G + C content of strain S2T was 69.4%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain S2T and phylogenetically related taxa were ≤ 77.9 and ≤ 21.4%, and respectively. The results of genotypic and phenotypic data showed that strain S2T could be distinguished from its phylogenetically related species and represents a novel species in the genus Aquabacterium, for which the name Aquabacterium terrae sp. nov. is proposed. The type strain is S2T (= KCTC 72741 T = NBRC 114609 T).

Caenimonas soli sp. nov., isolated from soil.

A non-motile, Gram-stain-negative, rod-shaped bacterium, designated strain S4T, was obtained from soil sampled at Wonju, Gyeonggi-do, Republic of Korea. Cells were white-coloured, aerobic, grew optimally at 25-32 °C on R2A agar plate. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain S4T formed a lineage within the family Comamonadaceae. The closest members were Caenimonas terrae SGM1-15T (98.1% sequence similarity), Caenimonas koreensis EMB320T (97.5%) and Ramlibacter solisilvae 5-10T (97.8%). The sequence similarities of strain S4T with other members of the family Comamonadaceae were ≤ 97.5%. The sole respiratory quinone was ubiquinone-8 (Q-8) and the principal polar lipid was phosphatidylethanolamine. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16 :1 ω7c), C16:0 and summed feature 8 (C18:1 ω7c and/or C18:1 ω6c). The DNA G + C content was 65.1 mol%. In addition, the average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain S4T and Caenimonas koreensis were 77.6 and 21%, respectively. Based on genomic, chemotaxonomic, phenotypic, and phylogenetic analyses, strain S4T represents a novel species in the genus Caenimonas, for which the name Caenimonas soli sp. nov. is proposed. The type strain is S4T (= KCTC 72742T = NBRC 114610T).

Chitinophaga fulva sp. nov., isolated from forest soil.

An aerobic, Gram-stain-negative, oxidase- and catalase-positive, non-motile, non-spore-forming, rod-shaped and yellow-coloured bacterium designated strain G-6-1-13T was isolated from Gwanggyo mountain forest soil. Strain G-6-1-13T could grow at 15-40 °C (optimum, 20-32 °C), pH 4.5-10.5 (optimum, pH 6.0-9.0), at 2 % (w/v) NaCl concentration, and produced flexirubin-type pigments. Phylogenetic analysis based on its 16S rRNA gene sequence showed that strain G-6-1-13T formed a lineage within the genus Chitinophaga that was distinct from other species of the genus. Closest member was Chitinophaga varians 10-7 W-9003T (98.6 % sequence similarity) followed by C. eiseniae DSM 22224T (98.4 %), C. qingshengii JN246T (97.6 %) and C. terrae KP01T (97.4%). The major cellular fatty acids were iso-C15 : 0, C16 : 1 ω5c, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1 ω6c). MK-7 was the sole respiratory quinone. The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The DNA G+C content of strain G-6-1-13T was 48.7 mol%. Average nucleotide identity and in silico DNA-DNA hybridization were below the species threshold. On the basis of phenotypic, genotypic, phylogenetic and chemotaxonomic characterization, G-6-1-13T represents a novel species in the genus Chitinophaga, for which the name Chitinophaga fulva sp. nov. is proposed. The type strain is G-6-1-13T (=KACC 21624T=NBRC 114361T).

Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.

Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4T and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4T formed a lineage within the family Erythrobacteraceae and clustered as members of the genus Novosphingobium. The closest members of strain TW-4T were Novosphingobium subterraneum DSM 12447T (97.9 %, sequence similarity), Novosphingobium lubricantis KSS165-70T (97.8 %), Novosphingobium taihuense T3-B9T (97.8 %), Novosphingobium aromaticivorans DSM 12444T (97.7 %), Novosphingobium flavum UCT-28T (97.7 %), and Novosphingobium bradum STM-24T (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4T was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl-n-methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and in silico DNA-DNA hybridization (dDDH) relatedness values between strain TW-4T and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4T represents novel species in the genus Novosphingobium, for which the name Novosphingobium olei sp. nov. is proposed. The type strain is TW-4T (=KACC 21628T=NBRC 114364T) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans.

Description of antibiotic-producing novel bacteria Paraburkholderia antibiotica sp. nov. and Paraburkholderia polaris sp. nov.

Two white colony-forming, Gram-stain-negative, non-sporulating and motile bacteria, designated G-4-1-8T and RP-4-7T, were isolated from forest soil and Arctic soil, respectively. Both strains showed antimicrobial activity against Gram-negative pathogens (Pseudomonas aeruginosa and Escherichia coli) and could grow at a pH range of pH 4.0-11.0 (optimum, pH 7.0-9.0). Phylogenetic analyses based on their 16S rRNA gene sequences indicated that strains G-4-1-8T and RP-4-7T formed a lineage within the family Burkholderiaceae and were clustered as members of the genus Paraburkholderia. Strain G-4-1-8T showed the highest 16S rRNA sequence similarity to Paraburkholderia monticola JC2948T (98.1 %), while strain RP-4-7T showed the highest similarity to Paraburkholderia metrosideri DNBP6-1T (98.8 %). The only respiratory quinone in both strains was ubiquinone Q-8. Their principal cellular fatty acids were C16 : 0, cyclo-C17 : 0, summed feature 3 (iso-C15 :0 2-OH and/or C16 :1 ω7c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). Their major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and an unidentified aminophospholipid. The DNA G+C content of strains G-4-1-8T and RP-4-7T were 63.7 and 61.3 mol%, respectively, while their genome lengths were 7.44 and 9.67 Mb, respectively. The genomes of both strains showed at least 12 putative biosynthetic gene clusters. The average nucleotide identity and in silico DNA-DNA hybridization relatedness values between both strains and most closely related Paraburkholderia species were below the species threshold values. Based on a polyphasic study, these isolated strains represent novel species belonging to the genus Paraburkholderia, for which the names Paraburkholderia antibiotica sp. nov. (G-4-1-8T= KACC 21617T=NBRC 114603T) and Paraburkholderia polaris sp. nov. (RP-4-7T=KACC 21621T=NBRC 114605T) are proposed.

Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation.

A straw coloured, motile and Gram-stain-negative bacterium, designated RP-1-19T was isolated from soil of Arctic station, Svalbard, Norway. Based on the phylogenetic analysis of its 16S rRNA gene sequence, strain RP-1-19T formed a lineage within the family Oxalobacteraceae and clustered together within the genus Massilia. The closest members were M. violaceinigra B2T (98.6% sequence similarity), M. eurypsychrophilia JCM 30074T (98.3%) and M. atriviolacea SODT (98.1%). The only respiratory quinone was ubiquinone-8. The principal cellular fatty acids were summed feature 3 (iso-C15:0 2-OH/C16:1ω7c) and C16:0. The major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The DNA G + C content of the type strain was 63.2%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain RP-1-19T and closest members were ≤ 80 and 23.2%, respectively. The genome was 4,522,469 bp long with 30 scaffolds and 4076 protein-coding genes. The genome showed eight putative biosynthetic gene clusters responsible for various secondary metabolites. Genome analysis revealed the presence of cold-shock proteins CspA and CspC. Presence of cspA and cspC genes in the genome manifest ecophysiology of strain RP-1-19T that may help in cold-adaptation. Based on these data, strain RP-1-19T represents a novel species in the genus Massilia, for which the name Massilia polaris sp. nov. is proposed. The type strain is RP-1-19T (= KACC 21619T = NBRC 114359T).

Flexivirga aerilata sp. nov., Isolated from an Automobile Air Conditioning System.

A novel light-yellow-coloured, Gram-stain-positive, nearly-coccoid, aerobic bacterium, designated strain ID2601ST was isolated from a car evaporator core collected from South Korea. Strain ID2601ST was catalase positive and oxidase negative, able to grow at pH 6.0-8.0, temperature 20-45 °C, and 0-6.0% (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain ID2601ST belonged to the genus Flexivirga, with the nearest phylogenetic neighbour being Flexivirga endophytica YIM 7505T (97.9% sequence similarity). The strain comprised diphosphatidylglycerol as the main polar lipid; MK-8(H4) as a predominant respiratory quinone; serine, alanine, glycine, glutamic acid, and lysine as main components of peptidoglycan and iso-C16:0, summed feature 9 (iso-C17:1ω9c and/or C16:0 10-methyl), anteiso-C17:0, and C17:0 10-methyl as the major fatty acids. The average nucleotide identity (ANI) values between strain ID2601ST and the closest species (Flexivirga endophytica YIM 7505T and Flexivirga caeni BO-16T) were < 78%. The in silico DNA-DNA hybridization (dDDH) values of strain ID2601ST with the closest species were < 22%. These observations were below the threshold values of 95% (for ANI) and 70% (for dDDH) used for species delineation. The DNA G+C content was 69.8 mol%. Based on the polyphasic taxonomic data, the novel species Flexivirga aerilata sp. nov. is proposed with the type strain ID2601ST (=KCTC 49353T =NBRC 114622T).

Nakamurella aerolata sp. Nov., Isolated from an Automobile Air Conditioning System.

A novel white-colored, aerobic, Gram-stain-positive, rod-shaped bacterium, designated strain DB0629T was isolated from a motor car evaporator core collected in South Korea. Strain DB0629T grew at 10-35 °C, pH 6.0-9.0, and 0-5.0% (w/v) NaCl concentration. The 16S rRNA gene sequence analysis showed that strain DB0629T belonged to the genus Nakamurella, with the nearest phylogenetic neighbor being Nakamurella lactea DSM 19367T (97.6% sequence similarity). The strain comprised diphosphatidylglycerol and phosphatidylinositol as the main polar lipids; MK-8(H4) as a sole respiratory quinone; meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan and anteiso-C15:0, anteiso-C17:0, iso-C16:0, iso-C15:0, and C16:0 as the major fatty acids. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization values between strain DB0629T and N. lactea DSM 19367T were 74.9% and 20.8%, respectively, which were below the threshold values of 95% and 70%, respectively. The DNA G + C content was 69.5 mol%. Based on the polyphasic taxonomic data, the novel species Nakamurella aerolata sp. nov. is proposed with the type strain DB0629T (= KCTC 72726T = NBRC 114624T).

Zoogloea dura sp. nov., a N2-fixing bacterium isolated from forest soil and emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera.

A motile, Gram-stain-negative, rod-shaped bacterium, designated G-4-1-14T, was obtained from forest soil sampled at Gwanggyo mountain, Gyeonggi-do, Republic of Korea. Cells were colourless, aerobic, grew optimally at 28-35 °C and hydrolysed DNA and casein. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain G-4-1-14T formed a lineage within the genus Zoogloea. The closest members were Zoogloea resiniphila ATCC 70068T (98.6 % sequence similarity), Zoogloea caeni EMB43T (98.2 %), Zoogloea oryzae A-7T (97.7 %), Zoogloea ramigera IAM 12136T (96.9 %) and Zoogloea oleivorans BucT (96.2 %). The major respiratory quinone was ubiquinone-8 and the principal polar lipids were phosphatidylethanolamine, phosphatidyl-N-methylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The predominant cellular fatty acids were summed feature 3 (iso-C15 :0 2-OH/C16  : 1 ω7c) and C16 : 0. The DNA G+C content was 65.9 mol%. The average nucleotide identity and digital DNA-DNA hybridization relatedness values between strain G-4-1-14T and other type strains were ≤81.6 and ≤24.9 %, respectively, which are below the species demarcation thresholds. Based on the results of phenotypic, phylogenetic and genomic analyses, strain G-4-1-14T represents a novel species in the genus Zoogloea, for which the name Zoogloea dura sp. nov. is proposed. The type strain is G-4-1-14T (=KACC 21618T=NBRC 114358T). In addition, we propose emendation of the genus Zoogloea and the species Zoogloea oryzae and Zoogloea ramigera.

Hymenobacter polaris sp. nov., a psychrotolerant bacterium isolated from an Arctic station.

A pink-pigmented, non-motile, Gram-stain-negative, rod-shaped bacterium, designated RP-2-7T, was obtained from soil sampled at the Arctic station, Spitsbergen, Svalbard, Norway. Cells were strictly aerobic, psychrotolerant, grew optimally at 15-20 °C and hydrolysed CM-cellulose. Phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain RP-2-7T formed a lineage within the family Hymenobacteraceae and clustered with members of the genus Hymenobacter. Its closest relative was Hymenobacter marinus KJ035T (97.6 % sequence similarity). The sequence similarities to other strains were ≤96.9 %. The principal respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine and an unidentified aminophospholipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), anteiso-C15 : 0, iso-C15 : 0, C16 : 1 ω5c and summed featured 4 (iso-C17 : 1 I and/or anteiso-C17 : 1 B). The DNA G+C content was 62.8 mol%. In addition, the average nucleotide identity and in silico DNA-DNA hybridization relatedness values between strain RP-2-7T and closely related strains were lower than species demarcation thresholds. Based on the resuls of genomic, chemotaxonomic, phenotypic and phylogenetic analyses, strain RP-2-7T represents novel species in the genus Hymenobacter, for which the name Hymenobacter polaris sp. nov. is proposed. The type strain is RP-2-7T (=KACC 21670T=NBRC 114391T).

Nine novel psychrotolerant species of the genus Pedobacter isolated from Arctic soil with potential antioxidant activities.

Fifteen isolates of the genus Pedobacter were obtained from Arctic soil samples. All isolates were Gram-stain-negative and rod-shaped. Cells were strictly aerobic, psychrotolerant and grew optimally at 15-20 °C. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all the isolated strains formed a lineage within the family Sphingobacteriaceae and clustered as members of the genus Pedobacter. The sole respiratory quinone was MK-7 and the major polar lipid was phosphatidylethanolamine. The major cellular fatty acids were summed feature 3 (iso-C15 : 02-OH/C16 : 1ω7c/ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. The DNA G+C content of the novel strains was 33.9-41.8 mol%. In addition, the average nucleotide identity and in silico DNA-DNA hybridization relatedness values between the novel type strains and phylogenetically related type strains were below the threshold values used for species delineation. Based on genomic, chemotaxonomic, phenotypic, phylogenetic and phylogenomic analyses, the isolated strains represent novel species in the genus Pedobacter, for which the names Pedobacter cryotolerans sp. nov. (type strain AR-2-6T=KEMB 9005-717T=KACC 19998T=NBRC 113826T), Pedobacter cryophilus sp. nov. (type strain AR-3-17T=KEMB 9005-718T=KACC 19999T=NBRC 113827T), Pedobacter frigiditerrae sp. nov. (type strain RP-1-13T=KEMB 9005-720T=KACC 21147T=NBRC 113829T), Pedobacter psychroterrae sp. nov. (type strain RP-1-14T=KEMB 9005-721T=KACC 21148T=NBRC 113830T), Pedobacter hiemivivus sp. nov. (type strain RP-3-8T=KEMB 9005-724T=KACC 21152T=NBRC 113833T), Pedobacter frigidisoli sp. nov. (type strain RP-3-11T=KEMB 9005-725T=KACC 21153T=NBRC 113927T), Pedobacter frigoris sp. nov. (type strain RP-3-15T=KEMB 9005-726T=KACC 21154T=NBRC 113834T), Pedobacter psychrodurus sp. nov. (type strain RP-3-21T=KEMB 9005-728T=KACC 21156T=NBRC 113835T) and Pedobacter polaris sp. nov. (type strain RP-3-22T=KEMB 9005-729T=KACC 21157T=NBRC 113836T) are proposed.

Flavobacterium sandaracinum sp. nov., Flavobacterium caseinilyticum sp. nov., and Flavobacterium hiemivividum sp. nov., novel psychrophilic bacteria isolated from Arctic soil.

This study presents taxonomic description of strains LB-D12T, AT-3-2T, AT-3-7, and TSA-D2T isolated from Arctic soil. All strains were psychrophilic, Gram-stain-negative, aerobic, non-motile, and rod-shaped. Phylogenetic analysis showed that these strains belonged to the genus Flavobacterium. Strains LB-D12T, AT-3-2T and AT-3-7 were closest to Flavobacterium psychrolimnae LMG 22018T (98.5-98.8% sequence similarity). Strain TSA-D2T was closest to Flavobacterium degerlachei DSM 15718T (98.3 % sequence similarity). These strains shared common chemotaxonomic features comprising MK-6 as a sole quinone, phosphatidylethanolamine as the principal polar lipid, and summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c), iso-C16 : 0 3-OH, C15 : 1ω6c, iso-C16 : 0, and anteiso-C15 : 0 as the main fatty acids. The ANI and dDDH values between these novel isolates and their closest relatives were below the cut-off values of 95 and 70 %, respectively used for species demarcation. The DNA G+C content of all strains ranged from 34.2 to 34.6 mol%. The obtained polyphasic taxonomic data suggested that the isolated strains represent novel species within the genus Flavobacterium, for which the names Flavobacterium sandaracinum sp. nov. (type strain LB-D12T=KEMB 9005-737T=KACC 21180T=NBRC 113784T), Flavobacterium caseinilyticum sp. nov. (type strain AT-3-2T=KEMB 9005-738T=KACC 21176T=NBRC 113785T), and Flavobacterium hiemivividum sp. nov. (type strain TSA-D2T=KEMB 9005-741T=KACC 21179T=NBRC 113788T) are proposed.