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A001 Sphingorhabdus Pulchriflava Sp. Nov., Isolated from a River Gi

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A001 Sphingorhabdus pulchriflava sp. nov., Isolated from a River Gi-Yong Jung1,2 and So-Jeong Kim1* 1Geologic Environment Division, Korea Institute of Geoscience and Mineral Resources, 2Department of Microbiology, Chungbuk National University A facultative anaerobic and Gram-negative bacterium, strain GY_GT, was isolated from a river (Daedeock-cheon) in Daejeon, Republic of Korea. The isolate was catalase-positive and oxidase-positive and formed yellow colonies. The strain GY_GT was phylogenetically classified in the genus Sphingorhabdus and other closely related strains were Sphingorhabdus wooponensis 03SU3-PT (97.30% similarity) and Sphingorhabdus contaminans JC216T (96.75% similarity) based on 16S rRNA gene sequences. The growth conditions for GY_GT were temperatures ranging from T 10°C to 45°C (optimal 25°C), pH 6–10 (optimum pH 7) and 0–6% NaCl (optimum 0.5-1.5%). GY_G could utilize D- turanose, D-fructose-6-phosphate, glucuronamide, α-keto-glutaric acid, and acetoacetic acid. The major fatty acids T of GY_G were summed features 8 (C18:1 ω7c/C18:1 ω6c, 40.0%) and 3 (C16:1 ω6c/C16:1 ω7c, 27.6%). The major quinone required for respiration was Q-10. The polar lipids of GY_GT consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), and sphingolipid (SGL). The G+C content of the genome was 57.7%. The Average nucleotide identity (ANI) and Average amino acid identity (AAI) values between GY_GT and 03SU3-PT were 71.04% and 72.69%. Based on phylogenetic and phenotypic attributes, we suggest that strain GY_GT is a novel species in the genus Sphingorhabdus and is named Sphingorhabdus pulchriflava. The type strain is GY_GT (=KCTC 62791T =JCM 32855T). [Supported by KIGAM (19-3413)] A002 Potential Survival and Pathogenesis of a Novel Strain, Vibrio parahaemolyticus FORC_022, Isolated from a Soy Sauce Marinated Crab by Genome and Transcriptome Analyses Han Young Chung, Eun Jung Na, Han Hyeok Im, and Sang Ho Choi* Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Seoul National University Vibrio parahaemolyticus can cause gastrointestinal illness through consumption of seafood. In this study, a novel strain of V. parahaemolyticus FORC_022, was isolated from soy sauce marinated crabs, and its genome and transcriptome were analyzed. FORC_022 did not include major virulence factors of thermostable direct hemolysin and TDH-related hemolysin. However, FORC_022 showed high cytotoxicity and had several V. parahaemolyticus islands and other virulence factors, such as various secretion systems, in comparative genome analysis with CDC_K4557 and RIMD2210633. FORC_022 harbored additional virulence genes, including accessory cholera enterotoxin, zona occludens toxin, and tight adhesion locus. The expressions levels of genes involved in the virulence factors of type III secretion system, tad locus, and thermolabile hemolysin were overexpressed. Therefore, the risk of foodborne-illness may be high following consumption of FORC_022 contaminated crab. These results provided molecular information regarding the survival and pathogenesis of V. parahaemolyticus FORC_022 strain in contaminated crab and may have application in food safety. [Supported by a grant (14162MFDS972) from Ministry of Food and Drug Safety in 2018, and by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through High Value-added Food Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA)(117064033HD040).] 1 A003 Pelagibacterium sediminicola sp. nov., Isolated from Tidal Flat Sediment Hye-Jin Jang, Jaeho Song, Yochan Joung, and Jang-Cheon Cho* Department of Biological Sciences, Inha University A Gram-stain-negative, aerobic, cream-coloured, non-gliding, motile with a single polar flagellum and rod-shaped bacterium, designated IMCC34151T, was isolated from tidal flat sediment of the Yellow sea, Republic of Korea. Phylogenetic analysis based 16S rRNA gene sequences indicated that strain IMCC34151T was affiliated with the genus Pelagibacterium in the family Hyphomicrobiaceae and shared 94.7-96.8 % sequence similarities with Pelagibacterium species. Whole genome sequencing of strain IMCC34151T revealed genome size of 3.2 Mbp and the G+C content of 62.6 mol%. The ranges of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34151T and other Pelagibacterium species were 75.4-74.0 % and 20.6-19.8 %, respectively. The strain contained summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), C19:0 cyclo ω8c and C16:0 as the major fatty acids and ubiquinone-10 (UQ-10) as the major respiratory quinone. The polar lipids detected in the strain were phosphatidylglycerol, diphosphatidylglycerol, two unidentified glycolipids and twelve unidentified lipids. On the basis of phylogenetic and phenotypic characteristics, strain IMCC34151T is considered to represent a novel species of the genus Pelagibacterium, for which the name Pelagibacterium sediminicola (type strain IMCC34151T = KACC 19595T = NBRC 113420T) sp. nov., is proposed. [Supported by a grant from the Collaborative Genome Program of the KIMST funded by the MOF (No. 20180430), Korea.] A004 Characterization of Probiotic Properties of Lactobacillus plantarum SRCM101502 Isolated from Kimchi Su-Jin Shin1, Ho Yeon Yang2, Jin Won Kim2, Gwangsu Ha2, Su A Im2, Seong-Yeop Jeong2, and Do-Youn Jeong2* 1Korean Culture Center of Microorganisms (KCCM), 2Microbial Institute for Fermentation Industry (MIFI) This study was aimed to isolate lactic acid bacteria having probiotics properties from Korean fermented food, Kimchi. 6 isolates were investigated for safety verification by biogenic amine, antimicrobial and antioxidant activities. Especially, SRCM1502 showed higher antioxidant activity (21.27%) than other strains. SRCM101502 was also evaluated to various antimicrobial spectrum and biogenic amines non-producing microorganisms. Finally, SRCM101502 was selected to confirm probability of probiotics strain, and named as Lactobacillus plantarum SRCM101502 by 16S rRNA sequencing analysis. Additionally, SRCM101502 was analyzed to their hemolytic, harmful substances and enzyme productivity, coagulation of milk protein, bile salt hydrolase, antibiotic resistance and survival ability of acidic and bile condition. As a result, SRCM101502 was confirmed as safe strain because of its non-hemolytic activity and non-production of harmful substances (Phenyl pyruvic acid and indole) and enzymes (β- glucuronidase and urase). And SRCM101502 showed survivability more than 102 CFU/ml in acidic condition at pH 2.0. Also, SRCM101502 has higher survival rate (97%) in 0.5% bile resistance. In addition, SRCM101502 has resistant to various antibiotics. These results suggest that SRCM101502 has potential for application as probiotic lactic acid bacteria. 2 A005 Paracoccus intestinalis sp. nov., from the Gut of a Blood Cockle, Tegillarca granosa June-Young Lee and Jin-Woo Bae* Kyung Hee University A novel bacterial isolate, designated as strain BM15T, was isolated from the gastrointestinal tract of a blood cockle, Tegillarca granosa, which was collected from the foreshore of Beolgyo-eup in Korea. Strain BM15T was Gram-stain- negative, nonmotile, strictly aerobic and coccus-shaped. Optimum growth of the isolate occurred at 20˚C, in the presence of 4% (w/v) NaCl and at pH 6. The 16S rRNA gene sequence analysis showed that strain BM15T belonged to the genus Paracoccus in the family Rhodobacteraceae and had more than 97% 16S rRNA gene sequence similarity with Paracoccus zhejiangensis J6T (97.40% similarity) and P. lutimaris HDM-25T (97.04% similarity). The polar lipid profiles of strain BM15T comprised phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an unidentified glycolipid and an unidentified lipids. The predominant respiratory quinone was ubiquinone-10 (Q-10). The major cellular fatty acids (>20%) was summed feature 8 (C18: 1 ω7c and/or C18:1 ω6c). Complete genome sequence of strain BM15T comprised 3,759,866 bp with 62.2 mol% G+C contents. The results of the phylogenetic, phenotypic and genotypic analyses indicateted that strain BM15T represents a novel species in the genus Paracoccus, for which the name Paracoccus intestinalis is proposed. The type strain is BM15T (= KCTC 72032T = JCM 33289T). A006 Salicibibacter halophilus sp. nov., a Moderately Halophilic Bacterium Isolated from Kimchi Young Joon Oh, Hyo Kyeong Park, Min-Sung Kwon, Seul Ki Lim, Namhee Kim, Misun Yun, and Hak-Jong Choi* Research and Development Division, World Institute of Kimchi A Gram-positive, rod-shaped, motile, and halophilic bacterium, designated strain NKC3-5T, was isolated from kimchi. Comparative phylogenetic analysis based on the 16S rRNA genes showed that the isolated strain was most closely related to the Salicibibacter kimchii NKC1-1T with a similarity of 96.2–97.6%. The isolated strain NKC3-5T was observed to grow at 0.0–20.0% (w/v) NaCl (optimum 10%), pH 6.5–10.0 (optimum pH 9.0), and 25–37C (optimum 35C). The polar lipids of strain NKC3-5T consisted of phosphatidylglycerol and two unidentified lipids. This strain possessed anteiso-C15:0 and anteiso-C17:0 as the major cellular fatty acids and menaquinone-7 as the major isoprenoid quinone. The cell wall peptidoglycan of strain NKC3-5T was determined as meso-diaminopimelic acid. The complete genome of strain NKC3-5T was 3,754,174 bp long with a G+C content of 45.87 mol%. Strain NKC3-5T genome contained 4,103 coding sequences,
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    Prokaryotes (2006) 4:5–75 DOI: 10.1007/0-387-30744-3_1 CHAPTER 1.2.1 ehT areneG succocolyhpatS dna succocorcMa The Genera Staphylococcus and Macrococcus FRIEDRICH GÖTZ, TAMMY BANNERMAN AND KARL-HEINZ SCHLEIFER Introduction zolidone (Baker, 1984). Comparative immu- nochemical studies of catalases (Schleifer, 1986), The name Staphylococcus (staphyle, bunch of DNA-DNA hybridization studies, DNA-rRNA grapes) was introduced by Ogston (1883) for the hybridization studies (Schleifer et al., 1979; Kilp- group micrococci causing inflammation and per et al., 1980), and comparative oligonucle- suppuration. He was the first to differentiate otide cataloguing of 16S rRNA (Ludwig et al., two kinds of pyogenic cocci: one arranged in 1981) clearly demonstrated the epigenetic and groups or masses was called “Staphylococcus” genetic difference of staphylococci and micro- and another arranged in chains was named cocci. Members of the genus Staphylococcus “Billroth’s Streptococcus.” A formal description form a coherent and well-defined group of of the genus Staphylococcus was provided by related species that is widely divergent from Rosenbach (1884). He divided the genus into the those of the genus Micrococcus. Until the early two species Staphylococcus aureus and S. albus. 1970s, the genus Staphylococcus consisted of Zopf (1885) placed the mass-forming staphylo- three species: the coagulase-positive species S. cocci and tetrad-forming micrococci in the genus aureus and the coagulase-negative species S. epi- Micrococcus. In 1886, the genus Staphylococcus dermidis and S. saprophyticus, but a deeper look was separated from Micrococcus by Flügge into the chemotaxonomic and genotypic proper- (1886). He differentiated the two genera mainly ties of staphylococci led to the description of on the basis of their action on gelatin and on many new staphylococcal species.
  • Supplement of Biogeographical Distribution of Microbial Communities Along the Rajang River–South China Sea Continuum

    Supplement of Biogeographical Distribution of Microbial Communities Along the Rajang River–South China Sea Continuum

    Supplement of Biogeosciences, 16, 4243–4260, 2019 https://doi.org/10.5194/bg-16-4243-2019-supplement © Author(s) 2019. This work is distributed under the Creative Commons Attribution 4.0 License. Supplement of Biogeographical distribution of microbial communities along the Rajang River–South China Sea continuum Edwin Sien Aun Sia et al. Correspondence to: Moritz Müller ([email protected]) The copyright of individual parts of the supplement might differ from the CC BY 4.0 License. Supp. Fig. S1: Monthly Mean Precipitation (mm) from Jan 2016 to Sep 2017. Relevant months are highlighted red (Aug 2016), blue (Mar 2017) and dark blue (Sep 2017). Monthly precipitation for the period in between the cruises (August 2016 to September 2017) were obtained from the Tropical Rainfall Measuring Mission website (NASA 2019) in order to gauge the seasonality (wet or dry). As the rainfall data do not correlate with the monsoonal periods, the seasons in which the sampling cruises coincide with were classified based on the mean rainfall that occurred for each month. The August 2016 cruise (colored red) is classified as the dry season based on the lower mean rainfall value as compared to the other two (March 2017 and September 2017), in which the both are classified as the wet season. Supp. Fig. S2: Non-metric Multi-dimensional Scaling (NMDS) diagram of seasonal (August 2016, March 2017 and September 2017) and particle association (particle-attached or free-living) Seasonality was observed within the three cruises irrespective of the particle association (Supp. Fig. 3). The August 2016 cruise was found to cluster with the September 2017 whereas the March 2017 cruise clustered separately from the other two cruises.