Actinoplanes pyxinae sp. nov., a new lichen-derived rare actinobacterium exhibiting antimicrobial and anticancer activity.

A novel lichen-derived actinobacterium, designated Pm04-4T, was isolated from Pyxine cocoes (Sw.) Nyl. lichen collected from Chaiyaphum, Thailand. A polyphasic approach was used to describe the taxonomic position of the strain. The strain had morphological and chemotaxonomic properties similar to members of the genus Actinoplanes. It produced sporangia on the substrate mycelia. Meso-diaminopimelic acid, galactose, glucose and mannose were detected in the whole-cell hydrolysate of the strain. The major menaquinone was MK-9(H4). The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The predominant cellular fatty acids were iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0. Strain Pm04-4T showed the highest 16S rRNA gene sequence similarity to Actinoplanes akusuensis TRM 8003T (99.0 %). In the phylogenomic tree, strain Pm04-4T was positioned close to A. aksuensis TRM88003T, A. maris M416T, A. polyasparticus TRM66264T, A. hotanensis TRM88002T, A. abujensis DSM 45518T, A. bogorensis NBRC 110975T, A. brasiliensis DSM 43805T, A. lichenicola LDG1-01T and A. ovalisporus LDG1-06T. The average nucleotide identity and digital DNA-DNA hybridization values between strain Pm04-4T and its closely related neighbours were below the threshold values for describing new species. Moreover, the strain could be distinguished from its closely related type strains by phenotypic properties. Based on genotypic and phenotypic evidence, it can be concluded that strain Pm04-4T is a representative of a new Actinoplanes species for which the name Actinoplanes pyxinae sp. nov. is proposed. The type strain is Pm04-4T (=TBRC 16207T=NBRC 115836T). The type strain exhibited activity against Staphylococcus aureus ATCC 25923 as well as four yeast strains, namely Candida albicans TISTR 5554, Candida glabrata TISTR 5006, Candida krusei TISTR 5351 and Candida parapsilosis TISTR 5007. It also showed cytotoxicity against Caco-2, MNT-1 and MCF-7 cancer cells.

Streptomyces pyxinae sp. nov. and Streptomyces pyxinicus sp. nov. isolated from lichen Pyxine cocoes (Sw.) Nyl.

Two novel actinobacteria, designated as LP05-1T and LP11T, were isolated from the lichen Pyxine cocoes (Sw.) Nyl. collected in Bangkok, Thailand. Genotypic and phenotypic analyses revealed that both strains represented members of the genus Streptomyces. The 16S rRNA gene of LP05-1T showed the highest similarity to the genome of Streptomyces gelaticus (98.41 %), while the 16S rRNA gene of LP11T was most similar to that of Streptomyces cinerochromogenes (98.93 %). The major menaquinones in LP05-1T were MK-9(H8), MK-9(H6), MK-9(H4) and MK-9(H2), and in LP11T, they were MK-9(H8) and MK-9(H6). Both strains exhibited the major fatty acids iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0, with LP05-1T also possessing iso-C17 : 0. The polar lipids of LP05-1T included phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and an unidentified lipid, while those of LP11T consisted of phosphatidylethanolamine, lyso-phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid and an unidentified glycolipid. The digital DNA-DNA hybridisation (dDDH) and average nucleotide identity (ANI) values indicated that both strains are distinct from each other with values below 70 and 95 %, respectively. dDDH, ANI by blast (ANIb) and ANI by MUMmer (ANIm) values between LP05-1T and its closely related type strains were 26.07-26.80 %, 81.24-82.01 % and 86.82-86.96 %, respectively, while those for LP11T and its closely related type strains were 30.70-31.70 %, 84.09-85.31 % and 88.02-88.39 %, respectively. The results of the taxonomic investigation, including dDDH and ANI values, indicate that LP05-1T and LP11T are novel type strains of two novel species within the genus Streptomyces. The names proposed are Streptomyces pyxinae sp. nov. for strain LP05-1T (=TBRC 15494T, =NBRC 115434T) and Streptomyces pyxinicus sp. nov. for strain LP11T (=TBRC 15493T, =NBRC 115421T).

Genome sequences and functional analysis of Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 from fermented fish cake (Som-fak) with gamma-aminobutyric acid (GABA) production.

Gamma-aminobutyric acid (GABA) is a crucial inhibitory neurotransmitter in the sympathetic nervous system that exerts regulatory effects on the blood, immune, and nervous systems. GABA production in som-fak, a traditional fermented fish of Thailand, has been attributed to the activity of lactic acid bacteria (LAB). The present study aims to characterize the LAB isolates and compare the genomes and GABA synthesis genes of selected isolates capable of GABA production. Thirteen isolates demonstrating GABA synthesis capability were identified based on their phenotypic and genotypic characteristics. Seven isolates (group I: LSF3-3, LSF8-3, LSF9-1, LSF9-3, LSF9-6, LSF9-7, and LSF10-14) were identified as Levilactobacillus brevis with 99.78-100% similarity. LSF2-1, LSF3-2, LSF5-4, and LSF6-5 (group II) were identified as Lactiplantibacillus pentosus with 99.86-100% similarity. Strain LSF1-1 (group III) was identified as Pediococcus acidilactici (99.47%), and LSF10-4 (group IV) was identified as Pediococcus pentosaceus with 99.93% similarity. The GABA production of isolates ranged from 0.087 to 16.935 g/L. The maximum production of 16.935 g/L from 3% monosodium glutamate was obtained from strain LSF9-1. Gene and genome analysis revealed that L. brevis LSF9-1 has multiple gad genes in the genome, such as gadB1, gadB2, gadC1, and gadC2, making it the potential strain for GABA production. Additionally, the genome analysis of P. acidilactici LSF1-1 consists of gadA, gadB, and gadC, which respond to controlling GABA production and export. Furthermore, strain LSF1-1 was considered safe, containing no virulence factors. Thus, Levilactobacillus brevis LSF9-1 and Pediococcus acidilactici LSF1-1 have the potential for GABA production and probiotic use in future studies.

Micromonospora thermarum sp. nov., an actinobacterium isolated from hot spring soil.

An actinomycete, designated strain HSS6-12T, was isolated from hot spring sediment collected from Ranong province, Thailand. The strain showed taxonomic characteristics consistent with those of members of the genus Micromonospora. HSS6-12T produced a single spore directly on the substrate mycelium, and no aerial mycelium was detected. The isomer of diamino acid presented in cell wall peptidoglycan was meso-diaminopimelic acid. Arabinose, xylose, glucose, and ribose were detected in whole-cell hydrolysates. MK-10(H4), MK-9(H4), and MK-10(H6) were major menaquinones. Major cellular fatty acids were iso-C16:0, iso-C15:0, and iso-C17:0. Phospholipid profile was composed of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, and phosphatidylinositolmannosides. 16S rRNA gene analysis revealed that HSS6-12T shared the highest 16S rRNA gene sequence similarity with Micromonospora inositola DSM 43819T (99.3%). In contrast, the genome analysis showed that HSS6-12T formed a tight taxonomic position in a phylogenomic tree with Micromonospora endolithica DSM 44398T. Moreover, the average nucleotide identity-blast, the digital DNA-DNA hybridization, and the average amino acid identity values between HSS6-12T and M. inositola DSM 43819T and M. endolithica DSM 44398T were 83.1-84.0%, 27.5-28.7%, and 80.4-82.2%, respectively, indicating that HSS6-12T was different species with both closely related Micromonospora-type strains. In addition, HSS6-12T could be discriminated from its closely related type strains by many physiological and biochemical characteristics. Thus, HSS6-12T could be considered a novel species of the genus Micromonospora, and the name Micromonospora thermarum is proposed for the strain. The type strain is HSS6-12T (= BCC 41915T = JCM 17127T).

Streptomyces telluris sp. nov., a promising terrestrial actinobacterium with antioxidative potentials.

An actinomycete strain, AA8T, which produced a long straight chain of spores (verticillati type), was isolated from the rhizosphere soil of Mangifera indica in Bangkok, Thailand. A polyphasic taxonomic study was carried out to establish the taxonomic position of the strain. Strain AA8T formed a tight taxonomic position in the 16S rRNA gene tree with Streptomyces roseifaciens MBT76T. In contrast, the genome-based taxonomic analysis showed that strain AA8T shared low average nucleotide identity-BLAST (94.1%), the digital DNA-DNA hybridization (58.2%), and the average amino acid identity (93.6%) values with S. roseifaciens MBT76T. Moreover, a combination of physiological and biochemical properties indicated that strain AA8T was distinguished from all Streptomyces species with effectively published names. Strain AA8T, therefore, represents a novel species of Streptomyces, and the name Streptomyces telluris is proposed for the strain. The type strain is AA8T (= TBRC 8483T = NBRC 113461T). The chemical investigation led to the isolation of nine known compounds (compounds 1-9). Among these compounds, compound 7 (3,4-dihydroxybenzaldehyde) possesses strong antioxidant activity equal to ascorbic acid, a powerful antioxidative agent.

Selenomonas caprae sp. nov., an obligately anaerobic and volatile fatty acid producing bacterium from ruminal fluid of domestic goat (Capra hircus L.).

A novel Gram-stain-negative, motile, obligately anaerobic bacterium strain mPRGC8T was isolated from the ruminal fluid of a domestic goat (Capra hircus L.) in Nakhon Pathom province, Thailand. The strain grew at 20-45 °C (optimum, 37 °C), pH 6.0-9.0 (optimum, pH 7.5) and 3 % (w/v) NaCl. It produced acetate, propionate, valerate, caproate and heptanoate from glucose. The 16S rRNA gene sequence analysis indicated that strain mPRGC8T belonged to the genus Selenomonas and was closely related to Selenomonas ruminantium subsp. ruminantium DSM 2150T (98.0 %) and Selenomonas ruminantium subsp. lactilytica JCM 6582T (97.9 %). The in silico DNA G+C content was 53.0 mol %. Strain mPRGC8T showed average nucleotide identity, digital DNA-DNA hybridization and average animo acid identity values with Selenomonas montiformis JCM 34373T, S. ruminantium subsp. lactilytica JCM 6582T and S. ruminantium subsp. ruminantium DSM 2150T ranging from 84.9 to 86.0 %, 21.3 to 21.8 % and 73.8 to 76.1 %, respectively. The predominant cellular fatty acids were C16 : 1 ω9c and C18 : 1 ω9c. Phosphatidylethanolamine, three unidentified aminophospholipids, two unidentified ninhydrin positive glycolipids, an unidentified phospholipid and an unidentified lipid were detected as polar lipids. The genomic and phenotypic characteristics of strain mPRGC8T strongly support its classification as representative of new species of the genus Selenomonas for which the name Selenomonas caprae sp. nov. is proposed. The type strain is mPRGC8T (=JCM 33725T=KCTC 25178T).

Streptomyces cylindrosporus sp. nov. and Streptomyces spinosisporus sp. nov.: two new endophytic actinobacteria isolated from the roots of Barleria lupulina Lindl.

Two endophytic actinobacteria, designated as strains 7R015T and 7R016T, were isolated from the roots of Barleria lupulina collected in Thailand. The morphological characteristics and results of chemotaxonomic studies and 16S rRNA gene analysis indicated that both strains represented members of the genus Streptomyces. They contained ll-diaminopimelic acid in the peptidoglycan. Ribose and glucose were detected as the whole-cell sugars. MK-9(H4), MK-9(H6) and MK-9(H8), were found as the membrane menaquinone. The predominant cellular fatty acids detected were iso-C16 : 0 and anteiso-C15 : 0. The genomes of both strains harboured biosynthetic gene clusters for melanin, terpene, lanthipeptide, polyketides, non-ribosomal peptide synthetase, siderophore and ectoine. The 16S rRNA gene sequence of 7R015T showed the highest similarity to that of Streptomyces pseudovenezuelae DSM 40212T (98.6 %), Streptomyces cyaneus NRRL B2296T (98.6 %) and Streptomyces curacoi DSM 40107T (98.6 %). Strain 7R016T showed the highest 16S rRNA gene sequence similarity to Streptomyces gilvifuscus NBRC 110904T (98.2 %), which is lower than the threshold value for 16S rRNA gene sequence similarity for differentiation at the species level (98.65 %). Comparative genome analysis revealed that the genomes of 7R015T, 7R016T and the closely related type strains had an average nucleotide identity (ANI) of less than 95 % and a digital DNA-DNA hybridisation (dDDH) of less than 70 %, the thresholds for species demarcation. On the basis of the results of the polyphasic study, strains 7R015T and 7R016T represent novel species of the genus Streptomyces and are named herein as Streptomyces cylindrosporus sp. nov. (=NBRC 115200T = TBRC 14542T) for strain 7R015T and Streptomyces spinosisporus sp. nov. (=NBRC 115201T = TBRC 14543T) for strain 7R016T.

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.

Sporolactobacillus mangiferae sp. nov., a spore-forming lactic acid bacterium isolated from tree bark in Thailand.

A Gram-stain-positive, facultatively anaerobic and endospore-forming rod-shaped bacterium, designed strain CPB3-1T, was isolated from tree bark. This homofermentative strain produced dl-lactic acid from glucose. It grew at 20-45 °C, pH 4.0-9.5 and in 0-3.0 % (w/v) NaCl. It contained meso-diaminopimelic acid in cell-wall peptidoglycan and had menaquinone with seven isoprene units (MK-7) as the predominant component. The major fatty acid was anteiso-C17 : 0. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown lipid. Based on the results of 16S rRNA gene sequence analysis, strain CPB3-1T belonged to the genus Sporolactobacillus and was closely related to Sporolactobacillus kofuensis DSM 11701T and Sporolactobacillus spathodeae BK117-1T (both 96.7 % similarity), Sporolactobacillus inulinus NRIC 1133T and Sporolactobacillus terrae DSM 11697T (both 96.6 % similarity), and Sporolactobacillus shoreicorticis MK21-7T, Sporolactobacillus laevolacticus DSM 442T, Sporolactobacillus shoreae BK92T and Sporolactobacillus pectinivorans GD201205T (all 95.8-96.5 % similarity). The draft genome of strain CPB3-1T contained 2 930 919 bps with 3117 coding genes. The DNA G+C content was 45.1 mol%. The digital DNA-DNA hybridization values between strain CPB3-1T and closely related type strains were 19.2-24.0 %. The average nucleotide identity (84.0-87.6 %) and average amino acid identity (66.5-76.3 %) values were lower than the cut-off values for species delineation. Strain CPB3-1T was clearly distinguished from related Sporolactobacillus species based on its phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence similarity and the results of draft genome analysis. Therefore, the strain represents a novel species of the genus Sporolactobacillus, for which the name Sporolactobacillus mangiferae sp. nov. is proposed. The type strain is CPB3-1T (=JCM 35082T=TISTR 10004T).

Streptomyces zingiberis sp. nov., an endophytic actinobacterium isolated from the root tissue of Zingiber montanum.

An endophytic actinobacterium, designated strain PLAI 1-29T, was isolated from the root tissue of Zingiber montanum collected from Pathum Thani province, Thailand. Strain PLAI 1-29T was characterized using a polyphasic taxonomic approach. It typically exhibited morphological and chemotaxonomic properties of the genus Streptomyces. Strain PLAI 1-29T produced a spiral spore chain on aerial mycelium and grew at 15-40 °C, pH 6-10 on International Streptomyces Project 2 agar. The maximum NaCl concentration for growth was 9 % (w/v). Cells of strain PLAI 1-29T presented ll-diaminopimelic acid, arabinose, galactose and ribose. The detected phospholipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The major menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The genome-based taxonomic details revealed the assignment of strain PLAI 1-29T to the genus Streptomyces and exhibited low threshold values for the delineation of a novel species by average nucleotide identity-blast (84.0%), average amino acid identity (80.0%) and digital DNA-DNA hybridization (27.6%) with its closest type strain, Streptomyces xinghaiensis S187T. Furthermore, several differential physiological and biochemical characteristics were detected between strain PLAI 1-29T and the closest type strain. Based on the combined phenotypic and genomic features, strain PLAI 1-29T (=TBRC 7645T=NBRC 113170T) is considered to represent a new Streptomyces species, for which we propose the name Streptomyces zingiberis sp. nov.

Gordonia aquimaris sp. nov., a novel marine actinobacterium isolated from seawater in the upper gulf of Thailand.

An actinobacterium strain, SW21T, was isolated from seawater collected in the upper Gulf of Thailand. Cells were Gram-stain-positive, aerobic and rod-shaped. Growth was observed from 15 to 37 °C and at pH 6-8. Maximum NaCl for growth was 14 % (w/v). meso-Diaminopimelic acid, arabinose, galactose, glucose, rhamnose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannoside were detected as the phospholipids in the cells. The major menaquinones were MK-9(H2) and MK-7(H2). The major cellular fatty acids were C16 : 0, C18 : 1 ω9c, C18 : 0 and C18 : 010-methyl (TBSA). The 16S rRNA gene sequence data supported the assignment of strain SW21T to the genus Gordonia and showed that Gordonia mangrovi KCTC 49383T (98.7 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA-DNA hybridization (30.7 %) values between strain SW21T and its closest neighbour were below the threshold values for delineation of a novel species. The combination of genotypic and phenotypic data indicated that strain SW21T is representative of novel species of the genus Gordonia. The name Gordonia aquimaris sp. nov. is proposed for strain SW21T. The type strain is SW21T (=TBRC 15691T=NBRC 115558T).

Micromonospora solifontis sp. nov., an actinobacterium isolated from hot spring soil.

An actinobacterium strain, PPF5-17T, was isolated from hot spring soil collected from Chiang Rai province, Thailand. The strain exhibited morphological and chemotaxonomic properties similar to those of members of the genus Micromonospora. Colonies of PPF5-17T were strong pinkish red and turned black after sporulation in ISP 2 agar medium. Cells formed single spores directly on the substrate mycelium. Growth was observed from 15 to 45 °C and at pH 5-8. Maximum NaCl concentration for growth was 3 % (w/v). PPF5-17T was found to have meso-diaminopimelic acid, xylose, mannose and glucose in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannosides were observed as the membrane phospholipids. MK-10(H6), MK-9(H6), MK-10(H4) and MK-9(H4) were the major menaquinones. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0, anteiso-C17 : 0 and iso-C16 : 0. PPF5-17T shared the highest 16S rRNA gene sequence similarity with Micromonospora fluminis LMG 30467T (99.3 %). A genome-based taxonomic study revealed that PPF5-17T was closely related to Micromonospora aurantinigra DSM 44815T in the phylogenomic tree with an average nucleotide identity by blast (ANIb) of 87.7 % and a digital DNA-DNA hybridization (dDDH) value of, 36.1 % which were below the threshold values for delineation of a novel species. Moreover, PPF5-17T could be distinguished from its closest neighbours, M. fluminis LMG 30467T and M. aurantinigra DSM 44815T, with respect to a broad range of phenotypic properties. Thus, PPF5-17T represents a novel species, for which the name Micromonospora solifontis sp. nov. is proposed. The type strain is PPF5-17T (= TBRC 8478T = NBRC 113441T).

Novosphingobium kaempferiae sp. nov., a phosphate-solubilizing bacterium isolated from stem of Kaempferia marginata Carey.

A Gram-stain-negative, aerobic, rod-shaped, non-spore-forming and yellow-pigment-producing bacterium, designated as Sx8-5T, was isolated from stem tissue of Kaempferia marginata Carey in Kanchanaburi Province, Thailand. The strain exhibited tricalcium phosphate solubilizing activity. Its taxonomic position was investigated using a polyphasic approach. Sx8-5T grew at 25-37 °C (optimum 30 °C), pH 6-9 (optimum 7) and with 0 and 1% NaCl (optimum 0 %). According to the 16S rRNA gene phylogeny, Sx8-5T represents a member of genus Novosphingobium and shared the highest sequence similarities to Novosphingobium barchaimii LL02T of 99.4 % and shared sequence similarities with other species of the genus Novosphingobium of less than 99.4 %. The whole-genome size was 5.7 Mb, comprised of one contig, with a DNA G+C content of 66 %. The average nucleotide identity using BLASTn (ANIb) or MUMMER (ANIm) values for whole genome comparisons between Sx8-5T and Novosphingobium barchaimii LL02T and six closely related type strains were 72.33-82.14 % and 83.82-87.38 %, respectively, and the digital DNA-DNA hybridization (dDDH) values ranged from 21.0 to 28.6% when compared with the type strains of the members of the genus Novosphingobium. Major fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), respectively. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, unidentified phospholipids and unidentified polar lipids. The major isoprenoid quinone was Q-10. According to results obtained using a polyphasic approach, Sx8-5T represents a novel species of the genus Novosphingobium, the name Novosphingobium kaempferiae sp. nov. is proposed. The type strain is Sx8-5T (=JCM 35076T =TBRC 15600T).

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

Streptomyces barringtoniae sp. nov., isolated from rhizosphere of plant with antioxidative potential.

A novel actinomycete strain, JA03T, belonging to the genus Streptomyces, was isolated from the rhizosphere of Barringtonia racemosa (L.) Spreng. It was characterized taxonomically using a polyphasic approach. It grew at 25-37 °C, at pH 5-10 and with 6 % (w/v) NaCl. It contained ll-diaminopimelic acid in the cell-wall peptidoglycan. Ribose and glucose were detected in its whole-cell hydrolysate. The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0, C16 : 0, iso-C14 : 0 and iso-C15 : 0. Detected polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, unidentified phospholipids and unidentified amino lipids. Based on the results of 16S rRNA gene sequence analyses, strain JA03T showed highest similarity to Streptomyces filipinensis NBRC 12860T (98.76 %), Streptomyces fodineus TW1S1T (98.69 %) and Streptomyces shenzhennensis 172115T (98.68 %). Strain JA03T has a genome size of 9 092 851 bp with DNA G+C content of 71.28 mol%. The average nucleotide identity (ANI)-blast and ANI-MUMmer values of strain JA03T and related type strains were 79.6-89.2 and 86.7-92.5 %, respectively, and the digital DNA-DNA hybridization values were 27.3-46.4 %. Ethyl acetate extract of JA03T exhibited total phenolic content (33.4±0.6 µg mg-1 gallic acid equivalent), ferric reducing power value (70.8±1.8 µg mg-1 ascorbic acid equivalent) and 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity (IC50=67.0±21.1 µg ml-1). Intracellular reactive oxygen species and NO production in RAW264.7 macrophage cells induced by H2O2 and lipopolysaccharide were inhibited with IC50 of 67.40 and 16.95 µg ml-1, respectively. Based on the taxonomic results, it has been concluded that strain JA03T represents a novel species of the genus Streptomyces for which the name Streptomyces barringtoniae sp. nov., is proposed. The type strain is JA03T (=LMG 32415T=TISTR 2999T).

Neokomagataea anthophila sp. nov., an osmotolerant acetic acid bacterium isolated in Thailand and emended description of the genus Neokomagataea.

A novel Gram-stain-negative, rod-shaped, non-motile, aerobic bacterium isolated from a sea bean flower [Canavalia rosea (Sw.) DC.] collected in Surat Thani Province, Thailand, and designated as AH18T was characterized on the basis of polyphasic taxonomy. The phylogenetic analysis of 16S rRNA gene revealed that strain AH18T represented a member of the genus Neokomagataea. In the 16S rRNA gene sequence analysis, the strain's closest phylogenetic neighbour was Neokomagataea thailandica TBRC 376T. The draft genome size of strain AH18T was 2613495 bp, and its DNA G+C content was 52.0 mol%. The strain showed 90.3 and 76.3% pairwise-determined whole-genome average nucleotide identity and 39.8 and 19.6% digital DNA-DNA hybridization values with N. thailandica TBRC 376T and N. tanensis TBRC 7768T, respectively. The 16S rRNA gene sequences and phylogenomic analysis revealed that the strain clustered with the members of the genus Neokomagataea but was located in a distinct branch closely related to N. thailandica TBRC 376T. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), C16:0 and C18:1 2OH (>5%). The major respiratory ubiquinone was Q-10. In addition, strain AH18T was substantiated by differences in several physiological characteristics and by MALDI-TOF profiling. On the basis of the results obtained from phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the strain clearly represented a novel species within the genus Neokomagataea, for which the name Neokomagataea anthophila sp. nov. (AH18T=TBRC 2177T=NBRC 115156T) is proposed. An emended description of the genus Neokomagataea is also given.

Nocardia coffeae sp. nov., an endophytic actinobacterium isolated from the root of Coffea arabica (L.).

The polyphasic taxonomic study of a novel endophytic actinobacterium strain (CA2R105T) was carried out. The strain formed fragmented substrate mycelium and showed chemotaxonomic properties typical of members of the genus Nocardia, i.e. the presence of mycolic acid and MK-8 (H4ω-cycl) in its cells. Strain CA2R105T exhibited the highest 16S rRNA gene sequence similarity to Nocardia jiangxiensis NBRC 101359T (99.2%). The genome-based taxonomic analysis revealed low average nucleotide identity-blast and digital DNA-DNA hybridization values (<93.7, and <65.2%, respectively) to its closest relative. Moreover, many different phenotypic characteristics were observed between strain CA2R105T and all related Nocardia-type strains. This taxonomic evidence suggested that strain CA2R105T should be judged as representing a novel species of the genus Nocardia and the name, Nocardia coffeae sp. nov. is proposed. The type strain is CA2R105T (=TBRC 11247T=NBRC 114292T).

Actinomadura parmotrematis sp. nov., isolated from the foliose lichen, Parmotrema praesorediosum (Nyl.) Hale.

A novel actinomycete strain PM05-2T was isolated from the lichen Parmotrema praesorediosum (Nyl.) Hale collected from Chaiyaphum Province, Thailand. The taxonomic position of the strain was studied using the polyphasic approach. Based on the morphology and chemotaxonomic properties, strain PM05-2T was identified as a member of the genus Actinomadura. The whole-cell hydrolysate contained meso-diaminopimelic acid, rhamnose, ribose, xylose, madurose, glucose and galactose. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, one unidentified phosphoglycolipid, four unidentified phospholipids and one unidentified lipid. The menaquinones were MK-9(H6), MK-9(H4), MK-9(H2), MK-9(H8) and MK-9(H0). The major cellular fatty acids were C16:0 and C18:1 ω9c. Strain PM05-2T showed the highest 16S rRNA gene similarity to Actinomadura hibisca NBRC 15177T (98.58%), Actinomadura kijaniata NBRC 14229T (98.29 %) and Actinomadura namibiensis DSM 44197T (98.14 %). The phylogenetic tree analysis revealed that strain PM05-2T was related to A. hibisca NBRC 15177T, A. kijaniata NBRC 14229T, A. namibiensis DSM 44197T and Actinomadura macrotermitis RB68T. The genomic analysis revealed that average nucleotide identity values based on both blast and MUMmer between strain PM05-2T and the relative type strains ranged from 77.6 to 86.4%. The digital DNA-DNA hybridization values among the strains were lower than the threshold for assigning to the same species. The taxonomic results suggested that strain PM05-2T represented a novel species of the genus Actinomadura for which the name Actinomadura parmotrematis is proposed. The type strain is PM05-2T (=TBRC 15492T=NBRC 115416T).

Saccharothrix obliqua sp. nov., isolated from soil of Sichang Island, Thailand.

During an investigation of rare actinobacteria, isolate SC076T was isolated from a soil sample collected from Sichang Island, Chonburi Province, Thailand. The strain showed the highest 16S rRNA gene similarity to Saccharothrix australiensis DSM 43800T (98.6%) and Saccharothrix espanaensis DSM 44229T (98.6%). The zigzag morphology of the spore chain was observed on the aerial mycelia. meso-Diaminopimelic acid was detected in the peptidoglycan. Whole-cell sugars contained rhamnose, ribose, mannose glucose and galactose. Polar lipids were phosphatidylethanolamine, hydroxyphosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, unidentified ninhydrin-positive glycolipid, unidentified glycolipid and four unidentified lipids. The menaquinones were MK-9(H8), MK-9(H4), MK-9(H2) and MK-9(H0). The predominant fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C17 : 0. The draft genome of SC076T was 8040245 bp with a G+C content of 72.5 mol%. The results of genomic analysis between strain SC076T and the related type strains showed that the digital DNA-DNA hybridization and average nucleotide identity values among the strains were 23.6-32.8% and 77.7-86.8 %, respectively, which are lower than the thresholds used to distinguish strains from others of the same species. Based on the taxonomic evidence, strain SC076T represents a novel species of the genus Saccharothrix for which the name Saccharothrix obliqua sp. nov. is proposed. The type strain is SC076T (=TBRC 14540T=NBRC 115117T).

Streptomyces acidipaludis sp. nov., an actinobacterium isolated from peat swamp forest soil.

An actinobacterium strain PLK6-54T was isolated from Lankwai peat swamp forest soil collected from Yala province, Thailand. Strain PLK6-54T exhibited morphological and chemotaxonomic properties described for the genus Streptomyces. It formed a spiral spore chain directly on aerial mycelium. Growth was observed between 20 and 40 °C and at pH 5-8. The maximum NaCl for growth was 2 % (w/v). ll-Diaminopimelic acid, arabinose and ribose were detected in the whole-cell hydrolysate. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositolmannoside were detected as the phospholipids. The major menaquinones were MK-10(H2) and MK-9(H6). The major cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and iso-C14 : 0. 16S rRNA gene sequence data supported the assignment of strain PLK6-54T to the genus Streptomyces and showed that Streptomyces rubidus NBRC 102073T (99.0 %) was the closest relative. Moreover, the average nucleotide identity-blast (85.5 %) and digital DNA-DNA hybridization (30.7 %) values reported between strain PLK6-54T and its closest neighbour were below the threshold values for delineation of a novel species. Strain PLK6-54T could be distinguished from related validly described Streptomyces species by several phenotypic properties. The combination of genotypic and phenotypic data indicated that strain PLK6-54T is representative of a novel species of the genus Streptomyces. The name Streptomyces acidipaludis sp. nov. is proposed for strain PLK6-54T. The type strain is PLK6-54T (=TBRC 11250T=NBRC 114297T).