Gluconobacter aidae sp. nov., an acetic acid bacterium isolated from tropical fruits in Thailand

Two bacterial strains, isolates AC10^T and AC20, which were reported in a previous study on the diversity of acetic acid bacteria in Thailand, were subjected to a taxonomic study. The phylogenetic analysis based on the 16S rRNA gene sequences showed that the two isolates were located closely to the type strains of Gluconobacter oxydans and Gluconobacter roseus. However, the two isolates formed a separate cluster from the type strains of the two species. The genomic DNA of isolate AC10^T was sequenced. The assembled genomes of the isolate were analysed for average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). The results showed that the highest ANI and dDDH values between isolate AC10^T and G. oxydans DSM 3503^T were 91.15 and 68.2 %, which are lower than the suggested values for species delineation. The genome-based tree was reconstructed and the phylogenetic lineage based on genome sequences showed that the lineage of isolate AC10^T was distinct from G. oxydans DSM 3503^T and its related species. The two isolates were distinguished from G. oxydans and their relatives by their phenotypic characteristics and MALDI-TOF profiles. Therefore, the two isolates, AC10^T (=BCC 15749^T=TBRC 11329^T=NBRC 103576^T) and AC20 (=BCC 15759=TBRC 11330=NBRC 103579), can be assigned to an independent species within the genus Gluconobacter, and the name Gluconobacter aidae sp. nov. is proposed for the two isolates.

Terrilactibacillus tamarindi sp. nov., isolated from bark of Tamarindus indica

A Gram-stain-positive, catalase-positive, facultatively anaerobic, terminal-spore-forming rod, designated strain BCM23-1^T, was isolated from bark of Tamarindus indica collected from Chiang Mai Province, Thailand. This strain produced d-lactic acid from glucose. It grew at 20-45 °C (optimum, 30 °C), pH 3.5-9 (optimum, pH 7.0) and in the presence of 1-4 % (w/v) NaCl. The cell-wall peptidoglycan contained meso-diaminopimelic acid (A1γ). The major isoprenoid quinone was menaquinone 7 (MK-7). Polar lipids analysis revealed the presence of diphosphatidylglycerol, phosphatidylglycerol, an unidentified aminophospholipid, an unidentified phospholipid and an unidentified lipid. The predominant cellular fatty acids were anteiso-C_17 : 0, anteiso-C_15:0, and iso-C_16 : 0 when cultivated on GYP agar plates. The 16S rRNA gene sequence similarity between strain BCM23-1^T and Terrilactibacillus laevilacticus NK26-11^T was 98.3 %. The draft genome of BCM23-1^T was 3.24 Mb in size and contained 3088 coding sequences with an in silico DNA G+C content of 37.1 mol%. The values of ANIb, ANIm and digital DNA-DNA hybridization between strain BCM23-1^T and T. laevilacticus NK26-11^T were 89.9, 90.8 and 40.4 %, respectively. The results of phenotypic and chemotaxonomic, 16S rRNA gene sequence similarity, and whole genome analyses support strain BCM23-1^T as representing a novel species of Terrilactibacillus for which the name Terrilactibacillus tamarindi sp. nov. is proposed. The type strain is BCM23-1^T (=LMG 31662^T=JCM 33748^T=TISTR 2841^T).

Streptomyces mimosae sp. nov., an endophytic actinomycete isolated from the root of Mimosa pudica in Thailand

An endophytic actinomycete, strain 3MP-10T, isolated from the root of Mimosa pudica was taxonomically studied based upon polyphasic approaches. This strain formed spiral spore chains on aerial mycelia. ll-Diaminopimelic acid, glucose and ribose were found in the whole-cell hydrolysates. It belonged to the genus Streptomyces and was closely related to Streptomyces zhaozhouensis DSM 42101T (98.9 %) and Streptomyces sedi JCM 16909T (98.6 %) based on 16S rRNA gene sequence analysis results. The major menaquinones were MK-10(H8), MK-10(H6) and MK-9(H8). The predominant cellular fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The detected phospholipids were diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylinositol, phosphatidylethanolamine and phosphatidylglycerol. Strain 3MP-10T had a genome size of 7.2 Mb with a genome G+C content of 73.4 mol%. Results of in silico genome-based similarity analysis revealed ANIb values of 84.94 and 84.77 %, ANIm values of 88.01 and 87.92 %, and dDDH values of 29.9 and 29.6 % when compared with S. zhaozhouensis DSM 42101T and S. sedi JCM 16909T, respectively. Based on the polyphasic approach, digital DNA–DNA relatedness and average nucleotide identity, we propose that the novel actinomycete represents a novel species, Streptomyces mimosae, with type strain 3MP-10T (=JCM 33328T=TISTR 2646T).

Identification and lipolytic activity of yeasts isolated from foods and wastes

Thirty-three yeasts were isolated from palm oil industrial wastes and traditional fermented foods in Thailand. Based on the analysis of the sequences of the D1/D2 region of the large subunit ribosomal RNA gene (LSU rDNA) and their phenotypic characteristics, they were identified as Pichia kudriavzevii (11 isolates), Candida ethanolica (1 isolate), Clavispora lusitaniae (2 isolates), Ogataea polymorpha (1 isolate), Hanseniaspora opuntiae (1 isolate), Lodderomyces elongisporus (1 isolate), Saccharomyces cerevisiae (2 isolates), C. tropicalis (5 isolates), Yarrowia lipolytica (2 isolates), Magnusiomyces ingens (1 isolate), and Magnusiomyces capitatus (3 isolates), Trichosporon insectorum (1 isolate), and Trichosporon asteroides (2 isolates). Seven strains, T. insectorum 4E-1D, M. capitatus 5E-1T and 5E-2D, T. asteroides 8E-1T and 8E-1D, and Y. lipolytica Fy-12 and Fy-13, showed high lipolytic activity ranged from 5.21 ± 0.09 to 45.68 ± 2.37 U/mL. Moreover, these seven strains exhibited good lipolytic activity after culturing in the medium containing palm oil (11.79 ± 0.67 to 28.19 ± 4.84 U/mL) and soy oil (9.14 ± 1.08 to 22.97 ± 0.69 U/mL) as lipase inducers. The result of this study suggests that the palm oil industrial wastes and Thai fermented foods could be promised as the invaluable sources of lipolytic yeasts.

Corynebacterium suranareeae sp. nov., a glutamate producing bacterium isolated from soil and its complete genome-based analysis

Strain N24T was isolated from soil contaminated with starling’s feces collected from Roi-Et province, Thailand. Cells of N24T were Gram-stain-positive rods, aerobic and non-spore-forming. N24T was positive for catalase, urease, citrate utilization, nitrate reduction and Methyl Red (MR) test but negative for oxidase, casein, gelatin liquefaction, tyrosine, Voges–Proskauer (VP) reaction and starch hydrolysis. Meso-diaminopimelic acid, rhamnose, ribose, arabinose and galactose were detected in its whole-cell hydrolysates. The results of the 16S rRNA gene sequence analysis indicated that N24T represented a member of the genus Corynebacterium . N24T was closely related to Corynebacterium glutamicum ATCC 13032T, with 99.0 % 16S rRNA gene sequence similarity. According to results obtained using in silico DNA–DNA hybridization approaches, N24T showed highest DNA–DNA relatedness (27.6 %) and average nucleotide identity (84.1 %) to Corynebacterium glutamicum ATCC 13032T. The DNA G+C content of N24T was 51.8 mol% (genome based). The major cellular fatty acids of N24T were C16 : 0, and C18 : 1ω9c. N24T had the nine isoprenes unit, MK-9(H2) as the predominant menaquinone. The predominant polar lipids were phosphatidylglycerol, phosphatidylinositol and diphosphatidylglycerol. Mycolic acids were also present. According to the complete genome sequence data, strain N24T and C. glutamicum ATCC 13032T are close phylogenetic neighbours, but have different genome characteristics. On the basis of the results of the genotypic and genomic studies and phenotypic characteristics including chemotaxonomy, strain N24T should be classified as representing a novel species of the genus Corynebacterium , for which the name Corynebacterium suranareeae sp. nov. is proposed. The type strain is N24T (TBRC 5845T=NBRC 113465T).

Changes in protein patterns of Staphylococcus aureus and Escherichia coli by silver nanoparticles capped with poly (4-styrenesulfonic acid-co-maleic acid) polymer

Background

While silver nanoparticles (AgNPs) are increasingly attractive as an antibacterial agent in many applications, the effect of AgNPs on bacterial protein profiles, especially AgNPs stabilized by polymeric molecules, is not well understood.

Objectives

To investigate the changes in bacterial protein patterns by AgNPs capped with poly (4-styrenesulfonic acid-co-maleic acid) (AgNPs-PSSMA) polymer toward Staphylococcus aureus ATCC 25923 and Escherichia coli ATCC 25922.

Methods

The growth of bacteria after incubated with AgNPs-PSSMA for different time intervals was determined by optical density at 600 nm. Their protein patterns were observed using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), and the proteomic analysis of extracted proteins was determined by liquid chromatography-tandem mass spectrometry (LC–MS/MS).

Results

AgNPs-PSSMA was able to inhibit the growth of both S. aureus and E. coli cells. The treated bacterial cells expressed more proteins than the untreated cells as seen from SDS-PAGE study. Nanosilver (NS) caused the upregulation of metabolic gene, waaA, in S. aureus cells. For E. coli cells, the upregulated proteins were metabolic genes (srlB, fliE, murD) and other genes dealt with DNA replication (dinG), DNA–RNA transcription (yrdD), RNA– protein translation (rplD), molecular transport (sapF), and signal transduction (tdcF).

Conclusions

The antibacterial effect of AgNPs-PSSMA may arise by changing the bacterial proteins and thus interfering with the normal cell function.

Lentibacillus lipolyticus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi)

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9^T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9^T and Lentibacillus juripiscarius TISTR 1535^T and Lentibacillus halophilus TISTR 1549^T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9^T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9^T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9^T (=JCM 32625^T=TISTR 2597^T).

Streptomyces bauhiniae sp. nov., isolated from tree bark of Bauhinia variegata Linn. in Thailand

A novel actinomycete strain, Bv016^T, belonging to the genus Streptomyces, was isolated from the bark of tree, Bauhinia variegata Linn., collected in Thailand. The taxonomic position of the strain was characterized by using a polyphasic approach. ll-Diaminopimelic acid, glucose, mannose, ribose and galactose were detected in its whole-cell hydrolysates. The N-acyl type of muramic acid was acetyl. The strain contained anteiso-C_{15  :  0}, iso-C_{16  :  0}, iso-C_{15  :  0} and iso-C_{14  :  0} as the major fatty acids and MK-9(H₈), MK-9(H₆) and MK-9(H₄) as the major menaquinones. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol and phosphatidylinositol mannoside. The strain was closely related to Streptomyces griseoluteus JCM 4041^T (98.4 %), Streptomyces seoulensis JCM 10116^T (98.4 %) and Streptomyces recifensis JCM 4408^T (98.2 %). The draft genome of Bv016^T was 6.74 Mb with 5949 coding sequences with an average G+C content of 71.7 mol%. The ANIb and ANIm values of strain Bv016^T were 94.1 and 95.2 %, respectively, and the digital DNA-DNA hybridization value was 60.6 % in comparison with the draft genome of S. griseoluteus JCM 4765^T. The results of the taxonomic analysis suggested that strain Bv016^T represented a novel species of the genus Streptomyces for which the name Streptomyces bauhiniae sp. nov. is proposed. The type strain is Bv016^T (=JCM 33208^T=TISTR 2645^T).

Nonomuraea phyllanthi sp. nov., an endophytic actinomycete isolated from the leaf of Phyllanthus amarus

A novel actinomycete, strain PA1-10^T, isolated from the leaf of Phyllanthus amarus collected from Bangkok, Thailand, was characterized taxonomically using a polyphasic approach. This strain contained the characteristics consistent with those of members of the genus Nonomuraea. It formed short rugose spore chain on aerial mycelium. The diamino acid in cell wall peptidoglycan was meso-diaminopimelic acid. Galactose, glucose, madurose, mannose, and ribose were found in whole-cell hydrolysates. Predominant menaquinones were MK-9 (H₂), MK-9 (H₄), and MK-9 (H₆). Major cellular fatty acids were iso-C_16:0 and C_17:0 10-methyl. Phospholipid profiles were composed of phosphatidylinositol mannoside (PIM), lyso-phosphatidylethanolamine (lyso-PE), phosphatidylethanolamine (PE), methylphosphatidylethanolamine (PME), diphosphatidylglycerol (DPG), and phosphatidylglycerol (PG). The G + C content of DNA was 71.2 mol%. Strain PA1-10^T showed the highest 16S rRNA gene sequence similarity with Nonomuraea candida JCM 15928^T (98.35%) and shared the same node with Nonomuraea maritima JCM 18321^T in the phylogenetic tree analysis. Based on the phenotypic characteristics, DNA-DNA relatedness, and average nucleotide identity (ANI), the strain is considered to represent a novel species of the genus Nonomuraea, for which the name Nonomuraea phyllanthi is proposed. The type strain is PA1-10^T (= JCM 33073^T = NBRC 112774^T = TISTR 2497^T).

Micromonospora radicis sp. nov., isolated from roots of Azadirachta indica var. siamensis Valenton, and reclassification of Jishengella zingiberis as Micromonospora zingiberis comb. nov

A novel endophytic actinomycete strain AZ1-13^T was isolated from roots of Azadirachta indica, and its taxonomic position was investigated using a polyphasic approach. Pairwise 16S rRNA gene sequence similarities of strain AZ1-13^T and its closest species, Jishegella zingiberis PLAI1-1^T and Micromonospora endophytica 202201^T, were 99.7 and 99.2 %, respectively. Phylogenetic analyses of the family Micromonosporaceae based on 16S rRNA gene sequences indicated strains AZ1-13^T and J. zingiberis PLAI1-1^Tare located within the genus Micromonospora. The approximate genome size of the strain was 5.96 Mb with 71.9 mol% of G+C content. The strain AZ1-13^T exhibited ANIb values of 87.4 % with J. zingiberis PLAI1-1^T and 85.1 % with M. endophytica 202201^T. Chemotaxonomic characteristics of strain AZ1-13^T were consistent within the genus Micromonospora: cell-wall peptidoglycan of the strain contained meso-diaminopimelic acid; glucose, mannose, ribose and xylose are presented as the whole-cell sugars; the predominant menaquinones were MK-9(H₄) and MK-9(H₆); major cellular fatty acids were iso-C_15 : 0, 10-methyl C_17 : 0, C_17 : 0, anteiso-C_17 : 0 and iso-C_17 : 1ω8c; diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol were detected as distinguished phospholipids. Based on phenotypic properties, phylogeny and genomic data, the strain AZ1-13^T could be distinguished from its closest neighbours, representing a novel species of the genus Micromonospora, for which the name Micromonospora radicis sp. nov. is proposed. The type strain is AZ1-13^T (=KCTC 39786^T=NBRC 112324^T=JCM 32147^T = TISTR 2404^T). This study also proposed that J. zingiberisis transferred to the genus Micromonospora as Micromonospora zingiberis comb. nov. (type strain PLAI1-1^T=TBRC 7644^T=NBRC 113144^T=JCM 32592^T).

Enterococcus florum sp. nov., isolated from a cotton flower (Gossypium hirsutum L.)

A Gram-stain-positive and catalase negative coccus, designated strain Gos25-1^T, isolated from a cotton flower (Gossypium hirsutum L.) collected from Khao Wong district, Kalasin province, Thailand. The taxonomic position of this strain was systematically studied based upon polyphasic taxonomic methods. The strain was facultatively anaerobic and produced l-lactic acid from glucose. The predominant cellular fatty acids were the straight-chain fatty acids C18 : 1ω9c and C16 : 0. According to 16S rRNA and phenylalanyl-tRNA synthase alpha subunit (pheS) gene sequence similarity, this strain was closely related to Enterococcus pallens NBRC 100697^T, E. hermanniensis CIP 108559^T, E. avium NBRC 100477^T and E. raffinosus NBRC 100492^T with 98.9-99.1 % and 77.0-82.0 % sequence similarities, respectively. Phylogenetic analysis indicated that strain Gos25-1^T was clearly distinguished from closely related species of the genus Enterococcus. Draft genome of Gos25-1^T had a size of 3.99 Mb which was contained 3788 coding sequences with in silico G+C content of 42.4 mol%. The ANIb and a digital DNA-DNA hybridisation (dDDH) values between strain Gos25-1^T and the closest related species, E. pallens NBRC 100697^T were 73.65 and 21.10 %, respectively. According to polyphasic characterisation, this strain represents a novel species of the genus Enterococcus, for which the name Enterococcus florum sp. nov. is proposed. The type strain is Gos25-1^T (=CIP 110956^T=LMG 29007^T=NBRC 111461^T=TISTR 2382^T).

Lumichrome Inhibits Human Lung Cancer Cell Growth and Induces Apoptosis via a p53-Dependent Mechanism

Lumichrome, a major derivative of riboflavin, may exhibit pharmacological activity against cancer cells. Riboflavin is a vitamin found in food, however, certain evidence has suggested its possible potentiating effects on cancer progression. Here, we have shown for the first time that unlike riboflavin, lumichrome can suppress lung cancer cell growth and reduce survival in both normal and anchorage-independent conditions. In addition, lumichrome induced apoptosis in lung cancer cells via a p53-dependent mitochondrial mechanism with substantial selectivity, shown by its lesser toxicity to the normal primary dermal papilla cells. The potency of lumichrome in killing lung cancer cells was found to be comparable to that of cisplatin, a standard chemotherapeutic drug for lung cancer treatment. With regard to the mechanism, lumichrome significantly upregulated p53 and decreased its downstream target BCL-2. Such a shift of BCL-2 family protein balance further activated caspase-9 and -3 and finally executed apoptosis. Furthermore, lumichrome potentially suppressed cancer stem cells (CSCs) in lung cancer by dramatically suppressing CSC markers together with the CSC-maintaining cell signaling namely protein kinase B (AKT) and β-catenin. To conclude, the present study has unraveled a novel role and mechanism of lumichrome against lung cancer that may benefit the development of the compound for management of the disease.

Micromonospora caldifontis sp. nov., isolated from hot spring soil

A single spore forming actinomycete, designated strain HSS6-8^T, was isolated from a sample of hot spring soil. The strain had the chemotaxonomic properties consistent with its classification in the genus Micromonospora. The strain was found to have meso-diaminopimelic acid in the cell-wall peptidoglycan. The acyl type of the cell-wall muramic acid was glycolyl. The reducing sugars in the cell hydrolysates were glucose, arabinose, xylose, ribose, mannose, galactose and rhamnose. The phospholipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphoglycolipid. The major menaquinones were MK-10(H6) and MK-10(H4). The major cellular fatty acids were iso-C16 : 0, anteiso-C17 : 0, C17 : 0 and anteiso-C15 : 0. The G+C content of the genomic DNA was 70.5 mol%. 16S rRNA gene sequence analysis revealed that strain HSS6-8^T was closely related to Micromonospora nigra DSM 43818^T (98.2 %), Micromonospora eburnea DSM 44814^T (98.2 %) and Micromonospora spongicola S3-1^T (98.1 %). The physiological and DNA-DNA hybridization data allowed the differentiation of strain HSS6-8^T from its related species. Thus, the strain represents a novel species of the genus Micromonospora, for which the name Micromonospora caldifontis sp. nov. is proposed. The type strain is HSS6-8^T (=TBRC 8927^T=JCM 17126^T).

Bacillus salacetis sp. nov., a slightly halophilic bacterium from Thai shrimp paste (Ka-pi)

A Gram-stain-positive, slightly halophilic, endospore-forming, strictly aerobic, rod-shaped bacterium, designated SKP7-4^T, was isolated from shrimp paste collected from Samut Sakhon province, Thailand. Strain SKP7-4^T grew at pH 6.0-9.0 (optimum, 7.5), at 20-40 °C (37 °C) and in 0-15 % (w/v) NaCl (1-3 %). The diamino acid found in the cell-wall peptidoglycan was meso-diaminopimelic acid. Menaquinone with seven isoprene units was the major isoprenoid quinone. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unidentified phospholipids were detected as polar lipids. It contained iso-C15 : 0 and anteiso-C15 : 0 as major cellular fatty acids. On the basis of 16S rRNA gene sequence analysis, strain SKP7-4^T belonged to the genus Bacillus and was closely related to Bacillus vietnamensis JCM 11124^T, Bacillus marisflavi JCM 11544^T, Bacillus aquimaris JCM 11545^T and Bacillusoryzaecorticis JCM 19602^T, with 98.7, 97.9, 97.8 and 97.8 % similarity, respectively. The draft genome of SKP7-4^T was 4.68 Mb with 5208 coding sequences with an average G+C content of 43.2 mol%. The ANIb and ANIm values of strain SKP7-4^T were 70.0 and 84.3 %, respectively, and the digital DNA-DNA hybridization value was 20 % in comparison with the draft genome of B. vietnamensis JCM 11124^T. On the basis of the results of phenotypic, chemotaxonomic and phylogenetic analyses, the strain should represent a novel species of the genus Bacillus and the name Bacillus salacetis sp. nov. is proposed. The type strain is SKP7-4^T (=JCM 33205^T=KCTC 43014^T=TISTR 2596^T).