Flavobacterium edaphi sp. nov., isolated from soil from Jeju Island, Korea

Paenimyroides aestuarii gen. nov. sp. nov., a novel bacterium isolated from sediment in the Pearl River Estuary and reclassification of five Flavobacterium and four Myroides species

An aerobic, Gram-negative, non-motile, yellow-to-orange pigmented and round bacterium, designated strain SCSIO 72103T, was isolated from sediment collected in the Pearl River Estuary, Guangdong Province, PR China and subjected to a polyphasic taxonomic study. Growth occurred at 20-37 °C (optimum, 28 °C), pH 6-8 (optimum, pH 7) and with 1-5.5% NaCl (optimum, 1-3 %). Comparative 16S rRNA gene analysis indicated that strain SCSIO 72103T had the highest similarities to Flavobacterium baculatum SNL9T (94.7 %) and Myroides aquimaris SW105T (94.2 %). Phylogenetic analysis based 16S rRNA gene sequences showed that strain SCSIO 72103T formed a single clade with M. aquimaris SW105T. Strain SCSIO 72103T contained iso-C15 : 0 as the major fatty acid and the predominant respiratory quinone was menaquinone MK-6. These characteristics are consistent with those of F. baculatum SNL9T and M. aquimaris SW105T. Phosphatidylethanolamine, most notably, unidentified aminolipid and unidentified aminophospholipid were major polar lipids. Strain SCSIO 72103T had a single circular chromosome of 2.96 Mb with a DNA G+C content of 35.1 mol%. The average nucleotide identity, average amino acid identity (AAI) and digital DNA-DNA hybridization values showed that the pairwise similarities between SCSIO 72103T and the type strains of F. baculatum SNL9T and M. aquimaris SW105T were 78.5-80.5 %, 79.0-81.4 % and 22.7-22.8 %, respectively. The AAI values between species in this clade and the type species of Flavobacterium and Myroides were below the 65 % threshold, indicating that these species belong to a novel genus. On the basis of phylogenetic, physiological and chemotaxonomic characteristics, strain SCSIO 72103T represents a new species of a novel genus, for which the name Paenimyroides aestuarii gen. nov. sp. nov. is proposed. The type strain is SCSIO 72103T (=KCTC 92043T=MCCC 1K06659T). It is also proposed that nine known species in the genera Flavobacterium and Myroides are reclassified as Paenimyroides species.

Discovery and characterization of a novel α-l-fucosidase from the marine-derived Flavobacterium algicola and its application in 2'-fucosyllactose production

2'-Fucosyllactose (2'-FL) is one of the nutrient ingredients in human milk, which has various beneficial health effects. α-l-fucosidase is a biotechnological tool for 2'-FL preparation. Here, a novel and efficient α-l-fucosidase OUC-Jdch16 from the fucoidan-digesting strain Flavobacterium algicola 12076 was heterologously expressed and applied to produce 2'-FL in vitro. OUC-Jdch16 belongs to glycoside hydrolases (GH) family 29 and exhibits the highest 4-nitrophenyl-α-l-fucopyranoside-hydrolyzing activity at 25 °C and pH 6.0. OUC-Jdch16 could catalyze the synthesis of 2'-FL via transferring the fucosyl residue from pNP-α-fucose to lactose. Under the optimal transfucosylation conditions, the yield of the transfucosylation product reached 84.82% and 92.15% (mol/mol) from pNP-α-fucose within 48 h and 120 h, respectively. Moreover, OUC-Jdch16 was capable of transferring the fucosyl residue to other glycosyl receptors with the generation of novel fucosylated compounds. This study demonstrated that OUC-Jdch16 could be a promising tool to prepare 2'-FL and other novel glycosides.

Pontibacter aquaedesilientis sp. nov., isolated from Jeongbang Waterfall, Jeju Island

A red-pigmented, aerobic, motile by gliding, pleomorphic to long-rods and divided by budding bacterium, Gram-stain negative bacterium, designated JH31^T, was isolated from stream water of Jeongbang Waterfall, famous feature of Jeju Island, Republic of Korea. The cells grew at 9-40 °C (optimum, 28-30 °C), at pH 5.0-10.0 (pH 6.5-7.5) and with 0-6% NaCl (0% NaCl). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain JH31^T forms a lineage within the family Hymenobacteriaceae and clusters with its closest related species Pontibacter virorsus KCTC 42941^T (98.1%), Pontibacter salisaro KACC 16885^T (98.0%), Pontibacter amylolyticus JCM 19653^T (97.2%), Pontibacter ramchanderi KACC 17384^T (97.2%) and Pontibacter lucknowensis DM9^T (96.4%). Strain JH31^T produced carotenoid-type pigments but no flexirubin-type pigments. The genome was 4117105 bp long with 18 contigs and 3509 protein-coding genes. The DNA G+C content was 49.7 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genome sequence of strain JH31^T and its closely related reference strains were less than 19 and 72%, respectively. The draft genome of strain JH31^T contained vital gene clusters involved in resistance against various metals, antibiotics, toxic compounds and radiation. The respiratory quinone of strain JH31^T was menaquinone 7 and the predominant cellular fatty acids were iso-C_15:0, and summed feature 4 (comprising iso-C_17:1 I and/or anteiso B). The major polar lipids were phosphatidylethanolamine, three unidentified glycolipids, one unidentified phospholipid, one unidentified phosphoglycolipid and one unidentified aminoglycolipid. The phylogenetic, physiochemical and biochemical data showed that strain JH31^T should represent a novel species in the genus Pontibacter, for which the name Pontibacter aquaedesilientis sp. nov. is proposed. The type strain for this novel species is JH31^T (KACC 21705^T=NBRC 114480^T).

Flavobacterium tagetis sp. nov., a novel urea-hydrolysing bacterium isolated from the roots of Tagetes patula

A Gram-stain-negative, rod-shaped, motile by gliding, non-sporulating and strictly aerobic bacterium, designated strain GN10^T, was isolated from the roots of Tagetes patula, collected from the garden of Dongguk University, Goyang, Republic of Korea. The cells could grow at 10-42 °C and at pH 5.5-9.0. Strain GN10^T was sensitive to NaCl and tolerated up to 4 % NaCl (w/v). Comparative analysis of 16S rRNA gene sequences revealed the highest similarities to Flavobacterium tistrianum GB 56.1^T (98.9 %), Flavobacterium sharifuzzamanii A7.6^T (98.6 %), Flavobacterium zhairuonense A5.7^T (98.3 %) and Flavobacterium anhuiense D3^T (98 %). Phylogenetic analysis showed that strain GN10^T clustered within the genus Flavobacterium and formed a monophyletic cluster with its close relative members. The average nucleotide identity and digital DNA-DNA hybridization values between strain GN10^T and related species belonging to the genus Flavobacterium were well below the standard threshold for prokaryotic species delineation. The DNA G+C content of strain GN10^T was 33.6 mol%. The predominant cellular fatty acids (>10 %) were identified as iso-C_15 : 0, C_16 : 0 and summed feature 3 (C_{16  : 1} ω6c and/or C_{16  :  1} ω7c). Strain GN10^T contained menaquinone 6 as the major respiratory quinone. The major polar lipids were phosphatidylethanolamine, three unidentified aminoglycolipids, two unidentified glycolipids, one unidentified phosphoglycolipid and five unidentified lipids. Urease is a nickel-containing enzyme found in archaea, bacteria, plants and unicellular eukaryotes. It serves as a virulence factor and is responsible for pathogenesis in humans and animals. Here, we describe a novel urease-hydrolysing bacterium, strain GN10^T. The urease activity of this strain may serve as an indicator of pathogenic potential and drug resistance, which may facilitate the development of many diseases. The results of physiological and biochemical tests allowed the genotypic and phenotypic differentiation of strain GN10^T from its closely related members and considered to represent novel species in the genus Flavobacterium, for which the name Flavobacterium tagetis (GN10^T=KCTC 82695^T=NBRC 114841^T) is proposed.

Flavobacterium agrisoli sp. nov., a novel bacterium isolated from soil

A Gram-stain negative, rod shaped, motile by gliding, yellow-pigmented, aerobic bacterium, designated SE-1-e^T, was isolated from a soil sample collected on Dokdo Island, South Korea. The isolate was characterized taxonomically using a polyphasic approach based on the phenotypic and genomic analyses. The phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SE-1-e^T belonged to the genus Flavobacterium in the family Flavobacteriaceae and had the highest sequence similarity with Flavobacterium cheongpyeongense IMCC34759^T (97.5%), Flavobacterium arsenitoxidans S2-3H^T (97.4%), Flavobacterium resistens BD-b365^T (97.4%), and Flavobacterium chungangense CJ7^T (97.4%). The predominant respiratory quinone of the isolate was found to be MK-6; the main polar lipid was phosphatidylethanolamine; and the major fatty acids were identified as summed feature 3 (C_16:1 ω7c/C_16:1 ω6c), C_15:0 iso, and C_16:0. The draft genome of strain SE-1-e^T had a length of 3,715,609 bp and a DNA G + C content of 34.8 mol%. The nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the novel isolate and F. cheongpyeongense IMCC34759^T, F. resistens BD-b365^T, and Flavobacterium chungangense CJ7^T ranged from 74.9 to 75.3% and from 20.2 to 20.9%, respectively. On the basis of its phenotypic properties, genotypic distinctiveness, and chemotaxonomic features, strain SE-1-e^T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium agrisoli sp. nov. is proposed. The type strain is SE-1-e^T (= KCTC 82352 ^T = JCM 34302 ^T).

Taibaiella lutea sp. nov., Isolated from Ubiquitous Weedy Grass

An aerobic, Gram-stain-negative, non-motile and rod-shaped bacterial strain, designated as KVB11^T was isolated from the root of plant Setaria viridis near Dongguk University. Phylogenetic analysis indicated that strain KVB11^T belonged to the genus Taibaiella of the family Chitinophagaceae. Comparative 16S rRNA gene analysis indicated that the strain KVB11^T has closest similarities to Taibaiella smilacinae PTJT-5 ^T (96.6%) and Taibaiella yonginensis THG-SC4^T (96.4%). Strain KVB11^T grew optimally at 25-28°C, at pH 7.0 and tolerates NaCl upto 1% (w/v) NaCl. Flexirubin-type pigments were present. Phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and genomic sequences demonstrated that strain KVB11^T formed a distinct branch with all seven type strains of genus Taibaiella. MK-7 was identified as the predominant isoprenoid quinone. The polar lipid were phosphatidylethanolamine, one unidentified aminophosphoglycolipid, one unidentified aminoglycolipid and two unidentified phosphoglycolipids. C_15:0 (28.3%), iso-C_15:1 G (28.5%) and iso-C_17:0 3-OH (10.5%) were the major fatty acids of the strain KVB11^T. The DNA G + C content of the genomic DNA of novel isolate was determined to be 38.9%. The above results clearly confirmed that strain KVB11^T represents a novel species of the genus Taibaiella, for which the name Taibaiella lutea sp. nov. is proposed. The type strain is KVB11^T (= KACC 19904 ^T = NBRC 113690 ^T).

Flavobacterium baculatum sp. nov., a carotenoid and flexirubin-type pigment producing species isolated from flooded paddy field

A Gram-stain-negative, aerobic, asporogenous, motile by gliding, dull-yellow, long rod-shaped bacterial strain, designated SNL9^T, was isolated from a flooded paddy field near Dongguk University, Republic of Korea. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that SNL9^T represents a member of the genus Flavobacterium and is most closely related to Flavobacterium ummariense DS-12^T (96.2%) and Flavobacterium viscosum YIM 102796^T (96.3%). The average nucleotide identity and in silico DNA-DNA hybridization (DDH) values with F. ummariense DS-12^T and F. viscosum YIM 102796^T were 89.3/39.1 and 87.1/33 %, respectively. The major fatty acids of SNL9^T were identified as iso-C_15 : 0, summed feature 3 (comprising C_{16  :  1}ω6c and/or C_{16  :  1}ω7c) and summed feature 9 (comprising iso-C_17 : 1ω9c and/or 10 methyl C_16 : 0). SNL9^T contained MK-6 as the major respiratory quinone. The polar lipids were phoshatidylethanolamine, one unidentified aminophosphoglycolipid, three unidentified aminoglycolipids, two unidentified glycolipids and one unidentified phosphoglycolipid. The DNA G+C content was 34.2 mol%. SNL9^T produces carotenoid and flexirubin-type pigments. Among them, carotenoids are particularly valuable for the biotechnological and pharmaceutical industries due to their antioxidant activity. Aryl polyenes (APE) pigments were also found in SNL9^T which are responsible for yellow pigment in bacteria. They are stored in the bacterial membrane and protect the bacteria from oxidative stress, particularly from reactive oxygen species. In this paper, we describe a novel isolate, SNL9^T, which protect itself from the attack of free radicals using specific natural products in the membrane. Because of their anti-oxidation properties, aryl polyenes may also be of interest to the cosmetic industry. On the basis of the results of phenotypic, genotypic and chemotaxonomic analyses, SNL9^T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium baculatum sp. nov. is proposed. The type is SNL9^T (=KACC 21170^T=NBRC 113746^T).

Sphingomonas xanthus sp. nov., Isolated from Beach Soil

A light yellow-colored, Gram-stain-negative, aerobic, oxidase- and catalase-positive, flagellated bacterium with motility, designated as strain AE3^T was isolated from soil. Cells of strain AE3^T are rod-shaped, and the colonies are round and convex. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain AE3^T forms a lineage within the genus Sphingomonas of the family Sphingomonadaceae and is most closely related to Sphingomonas edaphi KCTC 62107 ^T (98.6%), Sphingomonas oryziterrae KCTC 22476 ^T (97.9%), and Sphingomonas jaspsi DSM 18422 ^T (97.4%). The growth of the strain AE3^T was observed under 18-42 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 6.5-7.0), and in the absence of NaCl. Strain AE3^T contains Q-10 as a predominant respiratory quinone, and the major fatty acids are C_17:1 ω6c, summed feature 8 (C_18:1 ω7c), and summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c). The major polar lipids are sphingoglycolipids, unidentified phospholipids, and phosphatidylethanolamine. The DNA G + C content of strain AE3^T is 63.6 mol%. The nearly complete genome of strain AE3^T consists of 2.2 Mbp, (2,168 total protein-coding genes, 45 tRNAs, 4 ncRNAs, and 3 rRNAs). Genomic taxonomy analysis demonstrates that the novel strain has < 75.9% average nucleotide identity value, and also shows < 24.9% in silico DNA-DNA hybridization value compared to related taxa, which clearly separates strain AE3^T from other species of the genus Sphingomonas with values below the thresholds for species delineation. Based on phenotypic, genotypic, and phylogenetic analyses, strain AE3^T represents a novel species of the genus Sphingomonas, for which the name Sphingomonas xanthus sp. nov. is proposed. The type strain of Sphingomonas xanthus is AE3^T (= KCTC 620106 ^T = JCM 32376 ^T).

Reinekea thalattae sp. nov., a New Species of the Genus Reinekea Isolated from Surface Seawater in Sehwa Beach

A Gram-stain-negative, non-pigmented, curved rod-shaped, single polarly flagellated, facultatively anaerobic bacterium, designated as SSH23^T, was isolated from surface seawater sample collected at the Sehwa Beach in South Korea. The novel isolate required NaCl for growth and grew optimally between 2 and 3% NaCl. Strain SSH23^T showed high 16S rRNA gene sequence similarities with Reinekea marinisedimentorum DSM 15388^T (96.4%), Reinekea marina KACC 17315^T (96.2%), Reinekea blandensis KACC 17315^T (95.9%) and Reinekea aestuarii KCTC 22813^T (95.6%). The major polar lipids of strain SSH23^T were phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylglycerol. The major cellular fatty acids of strain SSH23^T were C_16:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c), and summed feature 8 (C_18:1 ω7c and/or C_18:1 ω6c). The predominant respiratory quinone was found to be ubiquinone-8. The average nucleotide identity values of strain SSH23^T with R. marinisedimentorum DSM 15388^T and R. blandensis MED297^T were determined to be 72.2% and 69.8%, respectively. The G+C content of the genomic DNA was 45.5 mol%. Based on genotypic, phenotypic, chemotaxonomic, and phylogenetic analyses, strain SSH23^T was considered to represent a novel member of the genus Reinekea, for which the name Reinekea thalattae sp. nov. is proposed. The type strain of Reinekea thalattae is SSH23^T (= KACC 21168^T = NBRC 113795^T).

Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil

A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28^T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28^T was phylogenetically related to Methylobacterium currus PR1016A^T (96.8%), Methylobacterium platani PMB02^T (96.2%), Methylobacterium aquaticum DSM 16371^T (96.3%), Methylobacterium tarhaniae N4211^T (96.4%), Methylobacterium frigidaeris IER25-16^T (95.8%), and Methylobacterium organophilum JCM 2833^T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28^T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7-90.4% and 22-39.6%, respectively. The major fatty acids of strain 17Sr1-28^T were summed feature 8 (C_18:1ω7c and/or C_18:1ω6c), and summed feature 3 (C_16:1ω7c and/or C_16:1ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28^T and its close phylogenetic relatives, strain 17Sr1-28^T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904^T = NBRC 112873^T) is proposed.