Chi Cheng

Sphingomonas morindae sp. nov., isolated from Noni (Morinda citrifolia L.) branch

Two yellow bacterial strains, designated NBD5(T) and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6(T) (96.9% similarity), Sphingomonas polyaromaticivorans B2-7(T) (95.8%), Sphingomonas yantingensis 1007(T) (94.9%), Sphingomonas sanguinis IFO 13937(T) (94.7%), Sphingomonas ginsenosidimutans Gsoil 1429(T) (94.6%), Sphingomonas wittichii RW1(T) (94.6%) and Sphingomonas formosensis CC-Nfb-2(T) (94.5%). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5(T) and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5(T) and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5(T) ( = DSM 29151(T) = KCTC 42183(T) = CICC 10879(T)).

Bacteriophage therapy against Enterobacteriaceae.

The Enterobacteriaceae are a class of gram-negative facultative anaerobic rods, which can cause a variety of diseases, such as bacteremia, septic arthritis, endocarditis, osteomyelitis, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, intra-abdominal infections and ophthalmic infections, in humans, poultry, animals and fish. Disease caused by Enterobacteriaceae cause the deaths of millions of people every year, resulting in enormous economic loss. Drug treatment is a useful and efficient way to control Enterobacteriaceae infections. However, with the abuse of antibiotics, drug resistance has been found in growing number of Enterobacteriaceae infections and, as such, there is an urgent need to find new methods of control. Bacteriophage therapy is an efficient alternative to antibiotics as it employs a different antibacterial mechanism. This paper summarizes the history of bacteriophage therapy, its bacterial lytic mechanisms, and the studies that have focused on Enterobacteriaceae and bacteriophage therapy.

Thermoactinomyces daqus sp. nov., a thermophilic bacterium isolated from high-temperature Daqu.

Daqu is a fermentation starter used in the production of Chinese liquors. A thermophilic bacterium, designated strain H-18(T), was isolated from a high-temperature Daqu sample collected from the manufacturing process of a sesame-flavoured liquor in Shandong province, China. It was investigated in a taxonomic study using a polyphasic approach. Strain H-18(T) formed white aerial mycelium and greyish-yellow substrate mycelium, bearing single endospores on aerial and substrate hyphae or on unbranched short sporophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major fatty acids were iso-C15 : 0 and iso-C17 : 0. The predominant menaquinone was MK-7. These chemotaxonomic properties are similar to those of members of the genus Thermoactinomyces. The G+C content of the genomic DNA was 49.1 mol%. 16S rRNA gene sequence comparisons indicated that strain H-18(T) was most closely related to Thermoactinomyces vulgaris KCTC 9076(T) (96.42 % similarity), Thermoactinomyces intermedius KCTC 9646(T) (96.06 %), Laceyella putida KCTC 3666(T) (96.32 %) and Laceyella sacchari KCTC 9790(T) (95.55 %). Strain H-18(T) showed low DNA-DNA relatedness (40.8, 33.4, 20.0 and 14.4 %) with the above strains. Based on morphological and chemotaxonomic characteristics, DNA-DNA hybridization data and physiological properties, strain H-18(T) represents a novel species of the genus Thermoactinomyces, for which the name Thermoactinomyces daqus sp. nov. is proposed. The type strain is H-18(T) ( = DSM 45914(T) = CICC 10681(T)).

Paenibacillus zeae sp. nov., isolated from maize (Zea mays L.) seeds

Four Gram-stain-positive bacterial strains, designated 6R2T, 6R18, 3T2 and 3T10, isolated from seeds of hybrid maize (Zea mays L., Jingke 968) were investigated using a polyphasic taxonomic approach. Cells were aerobic, motile, spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolates may represent a novel species of the genus Paenibacillus, the four closest neighbours being Paenibacillus lautus NRRL NRS-666T (97.1 % similarity), Paenibacillus glucanolyticus DSM 5162T (97.0 %), Paenibacillus lactis MB 1871T (97.0 %) and Paenibacillus chibensis JCM 9905T (96.8 %). The DNA G+C content of strain 6R2T was 51.8 mol%. Its polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was menaquinone 7 (MK-7) and the major fatty acids were anteiso-C15 : 0 and iso-C14 : 0. Strains 6R2T, 6R18, 3T2 and 3T10 were clearly distinguished from the above type strains using phylogenetic analysis, DNA-DNA hybridization, and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains 6R2T, 6R18, 3T2 and 3T10 represent a novel species of the genus Paenibacillus, for which the name Paenibacillus zeae sp. nov. is proposed. The type strain is 6R2T ( = KCTC 33674T = CICC 23860T).

Halomonas alkalicola sp. nov., isolated from a household product plant in China.

A Gram-stain-negative, alkaliphilic and moderately halophilic bacterium, designated 56-L4-10aEnT, was isolated from a household product plant in China. Cells of the novel isolate were rod-shaped, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 56-L4-10aEnT belongs to the genus Halomonas, with the six closest neighbours being Halomonas mongoliensis Z-7009T (97.59 % 16S rRNA gene sequence similarity), Halomonas ventosae Al12T (97.35 %), Halomonas campaniensis 5AGT (97.22 %), Halomonas alimentaria YKJ-16T (97.22 %), Halomonas shengliensis SL014B-85T (97.12 %) and Halomonas fontilapidosi 5CRT (97.09 %). The main polar lipids of strain 56-L4-10aEnT contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-9, with Q-8 as a minor component. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0. Strain 56-L4-10aEnT was clearly distinguished from the type strains mentioned above through phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. It is evident from the genotypic and phenotypic data that strain 56-L4-10aEnTcould be classified as a representative of a novel species of the genus Halomonas, for which the name Halomonas alkalicola sp. nov. is proposed. The type strain is 56-L4-10aEnT (=CICC 11012sT=DSM 103354T).

Identification of endophytic bacterial strain RSE1 from seeds of super hybrid rice Shenliangyou 5814 ( Oryza sativa L.,) and evaluation of its antagonistic activity

Endophytes are related with health and growth of plants. In this study, the endophytic bacterial strain RSE1 was isolated from seeds of super hybrid rice Shenliangyou 5814 (Oryza sativa L.,). Strain RSE1 was identified as Paenibacillus polymyxa by polyphasic taxonomy identification. Through the antagonistic test with the pathogenic strain of rice false smut, Ustilaginoidea oryzae CICC 2710, it showed that the strain RSE1 had an effective antagonistic activity against this pathogen. The draft genome of strain RSE1 was sequenced by Illumina HiSeq 2000, and 3 CDSs for glucanase gene were annotated and correlated to antagonistic activity. Using specific primers to amplify the biocontrol gene in glucanase family, β-1,3-1,4-glucanase gene (gluB) was found. This study laid a scientific foundation for developing and utilizing biological bio-control bacteria agent preventing the suffering from rice false smut.

Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch

A Gram-stain-positive bacterial strain, designated as NR2T, isolated from noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a representative of a member of the genus Brachybacterium, to which the most closely related neighbours were Brachybacterium squillarum M-6-3T (97.90 % similarity), Brachybacterium faecium DSM 4810T (97.50 %), Brachybacterium sacelli LMG 20345T (97.41 %), Brachybacterium phenoliresistens phenol-AT (97.36 %), Brachybacterium nesterenkovii DSM 9573T (97.36 %) and Brachybacterium rhamnosum LMG 19848T (97.32 %). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Strain NR2T was clearly distinguishable from the type strains of related species on the basis of phylogenetic analysis, DNA-DNA hybridization, fatty acid composition data analysis and a range of physiological and comparison of biochemical characteristics. It is evident from the genotypic and phenotypic data that strain NR2T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium hainanense sp. nov. is proposed. The type strain is NR2T ( = DSM 29535T = CICC 10874T).

Scopulibacillus daqui sp. nov., a thermophilic bacterium isolated from high temperature daqu.

A Gram-stain-positive, facultatively anaerobic, thermophilic bacterium, designated ZQ18-1T, was isolated from a high temperature daqu sample collected from the sesame-flavour liquor-making process. Oval endospores were formed at the centre of cells with swollen sporangia. The isolate was able to grow at temperatures of 20-60 °C (optimum growth at 50 °C), at pH 4-9 (optimum growth at pH 8) and in the presence of 0-10 % (w/v) NaCl (optimum growth with 2 % NaCl). Glucose and galactose were major cell-wall sugars, and meso-diaminopimelic acid was the diagnostic amino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and three glycolipids. The major cellular fatty acids were anteiso-C17 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ18-1T was most closely related to Scopulibacillus darangshiensis DLS-06T, Pullulanibacillus pueri YN3T, Tuberibacillus calidus 607T, Pullulanibacillus naganoensis ATCC 53909T, Pullulanibacillus uraniitolerans UG-2T, Sporolactobacillus terrae DSM 11697T and Sporolactobacillus inulinus NRIC 1133T. Strain ZQ18-1T showed low DNA-DNA relatedness (40.7, 23.1, 46.5, 27.2, 45.6, 33.7 and 55.1 %) with the strains mentioned above. Based on morphological characteristics, chemotaxonomic characteristics, DNA-DNA hybridization data and physiological properties, strain ZQ18-1T represents a novel species of the genus Scopulibacillus, for which the name Scopulibacillus daqui sp. nov. is proposed. The type strain is Scopulibacillus daqui ZQ18-1T (=DSM 28236T=CICC 10824T). An emended description of the genus Scopulibacillus is provided.

Genome Sequence of Paenibacillus polymyxa Strain CICC 10580, Isolated from the Fruit of Noni (Morinda citrifolia L.) Grown in the Paracel Islands

ABSTRACT Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus polymyxa CICC 10580 is a strain that was isolated from the fruit of noni and showed comprehensive antagonistic activity against many pathogens. Its genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs) correlated with antagonistic activity were annotated.

Genome Sequence of Thermoactinomyces daqus H-18, a Novel Thermophilic Species Isolated from High-Temperature Daqu

ABSTRACT Thermoactinomyces daqus H-18 is a new species of Thermoactinomyces isolated from high-temperature Daqu used in the fermentation of Bandongjing sesame-flavor liquor. Its genome was sequenced and assembled (3.44 Mb). The coding sequences (CDSs) that correlated to high-temperature tolerance were annotated. The metabolic pathways for the compounds responsible for flavor were also found.