In-Soon Park

Sporolactobacillus vineae sp. nov., a spore-forming lactic acid bacterium isolated from vineyard soil

Two spore-forming, facultatively anaerobic, lactic acid bacteria, strains SL153(T) and SL1153, were isolated from vineyard soil in Korea. Cells of both strains were slightly curved, Gram-positive, motile rods that measured between 1 and 4 mum in length and were approximately 0.5 mum in diameter. Strains SL153(T) and SL1153 fermented glucose, fructose, mannose and sorbitol, but were negative for nitrate reduction, catalase and oxidase. The predominant cellular fatty acids of the two isolates were iso-C(15 : 0), anteiso-C(15 : 0) and anteiso-C(17 : 0). meso-Diaminopimelic acid, glucose, mannose and galactose were determined in their whole-cell hydrolysates. 16S rRNA gene sequences from the two strains were almost identical (99.9 %) and they could be placed in the genus Sporolactobacillus according to phylogenetic analysis. The species most closely related to SL153(T) were Sporolactobacillus inulinus and Sporolactobacillus terrae with 16S rRNA gene similarities of 95.7 and 95.5 %, respectively, with the type strains. Levels of DNA-DNA relatedness between strain SL153(T) and the type strains of S. inulinus, S. terrae and Sporolactobacillus kofuensis were 18.5, 18.0 and 17.0 %, respectively. On the basis of the phylogenetic (16S rRNA gene), chemotaxonomic and phenotypic evidence given in this study, it is proposed that strains SL153(T) and SL1153 should be assigned to the genus Sporolactobacillus as representatives of the novel species Sporolactobacillus vineae sp. nov. The type strain is SL153(T) (=KCTC 5376(T)=JCM 14637(T)).

Description of Lysinibacillus sinduriensis sp. nov., and transfer of Bacillus massiliensis and Bacillus odysseyi to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov. with emended description of the genus Lysinibacillus.

A Gram-positive, rod-shaped, endospore-forming bacterium, designated strain BLB-1(T), was isolated from samples of tidal flat sediment from the Yellow Sea. 16S rRNA gene sequence analysis demonstrated that the isolate belonged to the Bacillus rRNA group 2 and was closely related to Bacillus massiliensis CIP 108446(T) (97.4%), Bacillus odysseyi ATCC PTA-4993(T) (96.7%), Lysinibacillus fusiformis DSM 2898(T) (96.2%) and Lysinibacillus boronitolerans DSM 17140(T) (95.9%). Sequence similarities with related species in other genera, including Caryophanon, Sporosarcina and Solibacillus, were <96.1%. Chemotaxonomic data supported the affiliation of strain BLB-1(T) with the genus Lysinibacillus. The major menaquinone was MK-7, the cell-wall sugars were glucose and xylose, the cell-wall peptidoglycan type was A4α (L-Lys-D-Asp), the major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and several unknown phospholipids, and the major fatty acids were anteiso-C(15:0) (35.6%), iso-C(15:0) (25.6%) and anteiso-C(17:0) (16.5%). The most closely related species, Bacillus massiliensis and Bacillus odysseyi, were also assigned to this genus based on phylogenetic analysis and phenotypic data. The results of DNA-DNA hybridizations and phenotypic tests supported the differentiation of all three taxa from species of the genus Lysinibacillus with validly published names. Thus, strain BLB-1(T) ( = KCTC 13296(T)  = JCM 15800(T)) represents a novel species, for which the name Lysinibacillus sinduriensis sp. nov. is proposed. It is also proposed that Bacillus massiliensis CIP 108446(T) ( =4400831(T) = CCUG49529(T)  =KCTC 13178(T)) and Bacillus odysseyi NBRC 100172(T) ( =34hs-1(T)  =ATCC PTA-4993(T)  =NRRL B-30641(T)  =DSM 18869(T)  =CIP 108263(T)  =KCTC 3961(T)) be transferred to the genus Lysinibacillus as Lysinibacillus massiliensis comb. nov. and Lysinibacillus odysseyi comb. nov., respectively.

Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea.

A Gram-positive, rod-shaped, endospore-forming organism, strain BL3-6T, was isolated from tidal flat sediments of the Yellow Sea in the region of Tae-An. A 16S rRNA gene sequence analysis demonstrated that this isolate belongs to the Bacillus cereus group, and is closely related to Bacillus mycoides (99.0% similarity), Bacillus thuringiensis (99.0%), Bacillus weihenstephanensis (99.0%), Bacillus cereus (98.9%), Bacillus anthracis (98.8%), and Bacillus pseudomycoides (98.1%). The phylogenetic distance from any validly described Bacillus species outside the Bacillus cereus group was less than 95.6%. The DNA G+C content of the strain was 39.4 mol% and the major respiratory quinone was menaquinone-7. The major cellular fatty acids were iso-C14:0 (17.8%), iso-C16:0 (15.8%), and iso-C12:0 (11.3%). The diagnostic amino acid of the cell wall was meso-diaminopimelic acid and the major cell wall sugar was galactose. The results of DNA-DNA hybridization (<55.6%) and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain BL3-6T from the published Bacillus species. BL3-6T therefore represents a new species, for which the name Bacillus gaemokensis sp. nov. is proposed, with the type strain BL3-6T (=KCTC 13318T =JCM 15801T).

Homologous overexpression of omcZ, a gene for an outer surface c-type cytochrome of Geobacter sulfurreducens by single-step gene replacement

The electron transfer pathway of Geobacter sulfurreducens has been intensively studied because of its ability of electron transfer to extracellular electron acceptors, such as Fe(III) and on electrode. However, the absence of overexpression system of G. sulfurreducens is one of the main obstacles for studying the physiology of G. sulfurreducens. OmcZ, an outer membrane-related c-type cytochrome of G. sulfurrducens, was homologously overexpressed via genomic integration. Quantitative RT-PCR analysis showed that the omcZ transcript in the knock-in strain was sixfold more abundant than in the wild type. Notably, omcZ expression appears to downregulate the expression level of OmcS, another outer membrane-related c-type cytochrome of G. sulfurreducens, based on the comparisons of total protein and transcript levels. This is the first report of the successful genetic overexpression system for studying functional genomics of G. sulfurreducens.

Clostridium arbusti sp. nov., an anaerobic bacterium isolated from pear orchard soil.

An obligately anaerobic, Gram-positive, spore-forming bacterial strain, designated SL206(T), was isolated from pear orchard soils. Strain SL206(T) cells were straight or slightly curved rods, with motility by peritrichate flagella. Cell walls contained meso-diaminopimelic acid; wall sugars were glucose, rhamnose and mannose. The major fatty acids were C(16 : 0), C(18 : 1)omega9c and summed feature 10 (containing C(18 : 1)omega11c/9t/6t). API 20A reactions were negative for oxidase, catalase and acid production from l-rhamnose, sucrose, trehalose, d-xylose, melezitose, salicin and d-sorbitol, and positive for acid production from d-glucose, sucrose, maltose, d-mannose and raffinose. Glucose was fermented to acetate, butyrate, CO(2), H(2) and ethanol in culture. The G+C content of the genomic DNA was 31.1 mol%. Based on comparative 16S rRNA gene sequence analysis, the isolate belonged to the genus Clostridium and formed a clade with Clostridium pasteurianum. The species most closely related to strain SL206(T) were C. pasteurianum (98.6 % similarity) and Clostridium acidisoli (97.8 % similarity). In DNA-DNA relatedness studies, the isolate had 59.5 % relatedness with C. pasteurianum and thus represented a unique species. On the basis of these studies, strain SL206(T) (=KCTC 5449(T) =JCM 14858(T)) is proposed to represent the type strain of a novel species, Clostridium arbusti sp. nov.

Genome Sequence of the Probiotic Bacterium Sporolactobacillus vineae SL153T

The novel Sporolactobacillus vineae SL153(T) strain has excellent intestinal adherence and growth inhibitory effect on pathogenic microorganisms, including Vibrio genus microorganisms, and therefore can be effectively used for the prevention and treatment of disease caused by pathogenic microorganisms. Here, we first report the draft genome sequence of a novel species in the genus Sporolactobacillus.

Peptoniphilus rhinitidis sp. nov., isolated from specimens of chronic rhinosinusitis

Chronic rhinosinusitis (CRS) is an inflammatory disorder of the nasal cavity and paranasal sinus related to bacterial infection. A previous study suggested that a specific bacterial group may have an important role in the course of CRS. In this study, bacteria isolated from CRS patients were characterized. A total of 15 strains were identified as Gram-positive anaerobic cocci (GPAC), which were able to utilize peptone as a sole carbon source. Sequencing of the 16S ribosomal RNA gene revealed that the isolates were closely related to members of the genus Peptoniphilus (>97% similarity) within the Clostridiales Family XI. Incertae Sedis. Genotypic and phenotypic characterization suggests that these isolates represent a novel species of the genus Peptoniphilus associated with CRS. The type strain of Peptoniphilus rhinitidis is 1-13T (=KCTC 5985T=JCM 17448T).

Paenibacillus cathormii sp. nov., isolated from tree bark.

A Gram-stain-positive, facultatively anaerobic, rod-shaped and endospore-forming bacterium, strain BK114-2T isolated from tree bark in Thailand was characterized taxonomically using a polyphasic approach. Analysis based on comparison of 16S rRNA gene sequences indicated that strain BK114-2T was affiliated to the genus Paenibacillus, and was closely related to Paenibacillus timonensis 2301032T (96.7 % 16S rRNA gene sequence similarity), Paenibacillus phoenicis 3PO2SAT (96.6 %) and Paenibacillus barengoltzii SAFN-016T (96.4 %). Strain BK114-2T contained meso-diaminopimelic acid in its cell-wall peptidoglycan. The polar lipids were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unknown phospholipids, five unknown aminophospholipids and six unknown lipids. The only menaquinone detected was MK-7 and the dominant cellular fatty acids were C16 : 0 (22.9 %), anteiso-C15 : 0 (22.6 %), iso-C16 : 0 (19.4 %) and anteiso-C17 : 0 (14.7 %). The DNA G+C content was 52.0 mol%. Based on these results, strain BK114-2T repreesents a novel species of the genus Paenibacillus, for which the name Paenibacillus cathormii sp. nov. is proposed. The type strain is BK114-2T ( = KCTC 33251T = TISTR 2282T).

Genome Sequence of the Anaerobic Bacterium Clostridium arbusti SL206T

A new Clostridium species has been isolated from pear orchard soil in Daejeon, Republic of Korea. The isolate, Clostridium arbusti SL206(T) (KCTC 5449(T)), showed a nitrogenase activity as well as an organic acid production. Here we first report the draft genome sequence of a novel species in the genus Clostridium within the largest Gram-positive group.

Erratum to: Bacillus gaemokensis sp. nov., Isolated from Foreshore Tidal Flat Sediment from the Yellow Sea

Korean Collection for Type Cultures, Biological Resource Center, KRIBB, Daejeon 305-806, Republic of Korea National Science Museum, Daejeon 305-705, Republic of Korea R&D Division, Vitabio Inc., Daejeon 300-824, Republic of Korea R&D Division, Korea Gas Corporation, Ansan 426-790, Republic of Korea Department of Microbiology, College of Medicine, Chung-Ang University, Seoul 156-756, Republic of Korea (Received April 16, 2010 / Accepted August 16, 2010)