• Title/Summary/Keyword: base-isolated

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Complete genome sequence of candidate probiotic Limosilactobacillus fermentum KUFM407

  • Bogun Kim;Ji yu Heo;Xiaoyue Xu;Hyunju Lee;Duleepa Pathiraja;Jae-Young Kim;Yi Hyun Choi;In-Geol Choi;Sae Hun Kim
    • Journal of Animal Science and Technology
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    • v.66 no.4
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    • pp.859-862
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    • 2024
  • It has been reported that the administration of Limosilactobacillus fermentum alleviates diseases such as osteoporosis and colitis. In this study, we report the complete genome sequence of Limosilactobacillus fermentum KUFM407, a probiotic strain of LAB isolated from Korean traditional fermented food, Kimchi. Whole genome sequencing of L. fermentum KUFM407 was performed on the Illumina MiSeq and Oxford Nanopore MinION platform. The genome consisted of one circular chromosome (2,077,616 base pair [bp]) with a guanine cytosine (GC) content of 51.5% and one circular plasmid sequence (13,931 bp). Genome annotation identified 1,932 protein-coding genes, 15 rRNAs, and 58 tRNAs in the assembly. The function annotation of the predicted proteins revealed genes involved in the biosynthesis of bacteriocin and fatty acids. The complete genome of L. fermentum KUFM407 could provide valuable information for the development of new probiotic food and health supplements.

Complete Genome Sequence of Massilia sp. KACC 81254BP Reveals a Potential for Degrading Polyhydroxyalkanoates

  • Sihyun An;Gyeongjun Cho;Jae-Hyung Ahn;Hang-Yeon Weon;Dayeon Kim;Young-Joon Ko;Jehyeong Yeon;Joon-hui Chung;Han Suk Choi;Jun Heo
    • Microbiology and Biotechnology Letters
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    • v.52 no.1
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    • pp.102-104
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    • 2024
  • Massilia sp. KACC 81254BP, isolated from a landfill on Jeju Island, Republic of Korea, possesses the capability to degrade polyhydroxyalkanoates (PHAs). The genomic analysis of strain KACC 81254BP consists of a circular chromosome comprising 5,028,452 base pairs with a DNA G+C content of 64.6%. This complete genome consists of a total of 4,513 genes, including those encoding the PHA degradation enzyme (PhaZ). This study offers valuable genomic insights into the enzymes responsible for degrading polyester plastics.

Microbial Population Diversity of the Mud Flat in Suncheon Bay Based on 16S rDNA Sequences and Extracellular Enzyme Activities (남해안 갯벌 미생물의 세포외효소 활성 및 16S rDNA 분석에 의한 다양성 조사)

  • Kim, Yu-Jeong;Kim, Sung-Kyum;Kwon, Eun-Ju;Baik, Keun-Sik;Kim, Jung-Ho;Kim, Hoon
    • Applied Biological Chemistry
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    • v.50 no.4
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    • pp.268-275
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    • 2007
  • Diversity of the mud flat microbial population in Suncheon Bay was investigated by studying extracellular enzyme activities and 16S rDNA sequences. Four culturable bacterial strains with CMCase, xylanase and protease activities were isolated from the wetland and the mud flat. All the strains produced more xylanase activity than CMCase or protease activity, and the properties of the isolate enzymes from the wetland were similar to those from the mud flat. About 2,000 clones were obtained with the 16S rDNA amplified from the metagenomic DNA isolated from the mud samples. Based on the restriction pattern(s), seventeen clones were selected for base sequence analysis. Of the 17 clones, only 35% (6 clones) were found to be cultured strains and 65% (11 clones) to be uncultured strains. The similarities in the base sequences of the clones ranged from 91.0% to 99.9% with an average similarity of 97.3%. The clones could be divided into 7 groups, Proteobacteria (9 clones, 52.9%), Firmicutes (3 clones, 17.6%), Bacteroidetes (1 clone), Flavobacteria (1 clone), Verrucomicrobia (1 clone), Acidobacteria (1 clone), and Chloroflexi (1 clone). Most of the Proteobacteria clones were gamma Proteobacteria associated with oxidation-reduction of sulfur.

Production of GABA-rich Tomato Paste by Lactobacillus sp. Fermentation (유산균 발효에 의한 GABA 함유 토마토 페이스트의 생산)

  • Cho, Seok-Cheol;Kim, Dong-Hyun;Park, Chang-Seo;Koh, Jong-Ho;Pyun, Yu-Ryang;Kook, Moo-Chang
    • The Korean Journal of Food And Nutrition
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    • v.25 no.1
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    • pp.26-31
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    • 2012
  • For the purpose of production of GABA-rich tomato paste, this study was carried out to investigate GABA producing lactic acid bacteria from Korean traditional fermented food, Kimchi and optimize the culture conditions. As a result of fermentation, Lactobacillus brevis B3-20 among lactic acid bacteria isolated at the pre-experiments was the best producer of GABA at the tomato paste medium with 50%(wet-base) levels of dionized water. At the result of fermentation on the tomato paste medium with 0.5%(w/w) yeast extract, as a source of nitrogen, 3%(w/w) MSG(monosodium glutamate) and dionized water(the ratio of tomato paste and water was 2:8), Lb. brevis B3-20 produced the maximum GABA concentration, 143.38 mM. GABA-rich tomato paste showed the activity of free radical scavenging. Because GABA-rich tomato paste have functional ingredients such as ascorbic acid, lycopene, carotenoid, as well as GABA by lactic acid bacteria fermentation, GABA-rich tomato paste can be considered high functional materials.

Etiological Properties and Coat Protein Gen Analysis of Potato Virus Y Occuring in Potatoes of Korea (우리나라 감자에 발생하는 PVY의 병원학적 특성 및 외피단백질 유전자 분석)

  • ;Richard M. Bostock
    • Proceedings of the Korean Society of Plant Pathology Conference
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    • 1995.06b
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    • pp.77-96
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    • 1995
  • To obtain basic informations for the improvement of seed potato production in Korea, some etiological properties of potato virus Y(PVY) distributed in the major seed potato production area(Daekwanryeong) were characterized, and the nucleotide and amino acid sequences of the coat protein gene of the PVY strains isolated were analyzed. PVY strains in Daekwonryeong, an alpine area, were identified to be two strains, PVYo and PVYN by symptoms of indicator plants, and their distribution in potato fields was similar. Major symptom on potato varieties by PVY was grouped as either mosaic alone or mosaic accompanied with veinal necrosis in the lower leaves. The symptom occurrence of the two symptoms was similar with Irish Cobbler, but Superior showed a higher rate of mosaic symptom than the other. The PVY strain which was isolated from potato cv. Superior showing typical mosaic symptoms produced symptoms of PVY-O on the indicator plants of Chenopodium amaranticolor, Nicotiana tabacum cv. Xanthi nc and Physalis floridana, but no symptom o Capsicum annum cv. Ace. Moreover, results from the enzyme-linked immunosorbent assay with monoclonal and polyclonal antibodies showed that the isolated PVY reacts strongly with PYV-O antibodies but does not react specifically with PVY-T antibodies. The purified virus particles were flexious with a size of 730$\times$11nm. On the basis of the above characteristics, the strain was identified to be a PVY-O and named as of PVY-K strain. The flight of vector aphids was observed in late May, however, the first occurrence of infected plants was in mid June with the bait plants surrounded with PVY-infected potato plants and early July with the bait plants surrounded with PVY-free potato plants. PVY infection rates by counting symptoms on bait plants (White Burley) were 1.1% with the field surrounded with PVY-free potato plants and 13.7% the fields surrounded with PVY-infected potato plants, showing the effect of infection pressure. The propagated PVY-K strain on tobacco(N. sylvestris) was purified, and the RNA of the virus was extracted by the method of phenol extraction. The size of PVY-K RNA was measured to be 9, 500 nucleotides on agarose gel electrophoresis. The double-stranded cDNAs of PVY-K coat protein(CP) gene derived by the method of polymerase chain reaction were transformed into the competent cells of E. coli JM 109, and 2 clones(pYK6 and pYK17) among 11 clones were confirmed to contain the full-length cDNA. Purified plasmids from pYK17 were cut with Sph I and Xba I were deleted with exonuclease III and were used for sequencing analysis. The PVY-K CP gene was comprised of 801 nucleotides when counted from the clevage site of CAG(Gln)-GCA(Ala) to the stop codon of TGA and encoded 267 amino acids. The molecular weight of the encoded polypeptides was calculated to be 34, 630 daltons. The base composition of the CP gene was 33.3% of adenine, 25.2% of guanine, 20.1% of cytosine and 21.4% of uracil. The polypeptide encoded by PVY-K CP gene was comprised of 22 alanines, 20 threonines, 19 glutamic acids and 18 glycines in order. The homology of nucleotide sequence of PVY-K CP gene with those of PVY-O(Japan), PVY-T(Japan), PVY-TH(Japan), PVYN(the Netherlands), and PVYN(France) was represented as 97.3%, 88.9%, 89.3%, 89.6% and 98.5%, respectively. The amino acid sequence homology of the polypeptide encoded by PVY-K CP gene with those encoded by viruses was represented as 97.4%, 92.5%, 92.9%, 92.9%, and 98.5%, respectively.

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Identification of Novel Bacillus subtilis IDCC 9204 Producing a High-Level Fibrinolytic Enzyme and Properties of NK-IL9204 (고농도 혈전용해효소를 생산하는 신규 Bacillus subtilis IDCC 9204의 분리 및 NK-IL9204의 효소학적 특성)

  • Lee, Seung-Hun;An, Gwangmin;Kim, Heu-Hang;Kang, Jae-Hoon;Kang, Dae-Jung
    • Korean Journal of Food Science and Technology
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    • v.44 no.5
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    • pp.600-606
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    • 2012
  • A Bacillus sp. that produces fibrinolytic enzyme was isolated from Cheonggukjang, a traditional Korean soybean-fermented food. According to 16S rRNA gene base sequencing, the bacillus was identified as a variety of Bacillus subtilis, and named Bacillus subtilis IDCC 9204. Fibrinolytic enzyme NK-IL9204 was stable up to $60^{\circ}C$ and within pH range of 5-10. Purified NK-IL9204 was detected through fibrin zymography. The molecular weight and isoelectric point of the enzyme were estimated to be 27.7 kDa and 6.7 by SDS-PAGE and 2D electrophoresis, respectively. Its amino acid sequence was similar to that of nattokinase (identities 99.5%) and different from that of nattokinase BPN (identities 86.4%). The plasma fibrinolytic activity of NK-IL9204 was measured by euglobulin clot lysis times (ECLT). The NK-IL9204 was orally administered to SD rats for 3 weeks (1,000 FU/rat/day). The ECLT was significantly shortened by supplementation of NK-IL9204.

Transformation of Rice Embryogenic Cells by Electroporation Mediated Plasmid Uptake into Protoplasts 1. Plant Regeneration from Electroporated Protoplasts of Rice (원형질체 내 Plasmid Electroporation에 의한 벼 배발생세포의 형질전환 1. 벼의 Electroporation 원형질체로부터 식물체 재분화)

  • 김명덕;최성진김준철
    • KSBB Journal
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    • v.10 no.1
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    • pp.23-29
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    • 1995
  • Calli were induced from leaf base region of germinated rice(Oryza sativa L. cv. Nakdong) with high frequency of up to 65% on LS medium supplemented with $2.5mg/{\ell}2$, 4-D in the dark at $27^{\circ}C$. Embryogenic calli of pale yellow, globular type were selected and used for the initiation of cell suspension cultures in AA2 liquid medium with $2mg/\ell$ 2,4-D, 0.2mg/$\ell$ kinetin arid $0.1mg/\ell$ GA3. Protoplasts were isolated from the embryogenic cell suspensions after 4 months of culture and then were electroporated with 400V/cm for 1 msec. Electroporated protoplasts divided with plating efficiency of 1.1% on PCM liquid medium supplemented with $2.5mg/\ell$ 2, 4-D, $0.1mg/\ell$ kinetin and 10mM proline. The protoplasts-derived microcalli were cultured on $0.2{\mu}m$ membrane fitter placed onto LS2.5 solid medium containing fine suspension cells as a feeder cells, for 2 weeks in the dark at $27^{\circ}C$. After an additional 2 weeks of culture under fluorescent light of $30{\pm}/3{\mu}E$.m^{-2}S^{-1}, yellow calli of 2mm diameter were transferred to regeneration medium. Shoots were produced from the green spot of protoplasts-derived calli and plants were regenerated form protoplast-derived green calli with frequencies of 11∼33%.

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Dermatophytosis of the Four-toed Hedgehog Caused by Trichophyton erinacei

  • Yoon, Ji-Seon;Lee, Jong-Hyun;Yu, Do-Hyeon;Li, Ying-Hua;Lee, Mi-Jin;Iwasaki, T.;Park, Jin-Ho
    • Journal of Veterinary Clinics
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    • v.25 no.3
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    • pp.207-210
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    • 2008
  • Trichophyton erinacei is a dermatophyte pathogen that infects both humans and hedgehogs. A two-month old female four-toed hedgehog presented to the Chonbuk Animal Medical Center with pruritus, excoriation and crust on her face for ten days. The owner of the hedgehog also exhibited the clinical signs of scaly erythema with fine vesicles on her neck. A presumptive diagnosis of dermatophytosis was made based on the results of an acetate tape preparation in which hyphae and chains of arthroconidia were observed. The crusts from the lesions were then cultured on Sabouraud Dextrose Agar for identification. After 10 days of incubation, downy colored colonies that had a central umbo with a white granular surface and a yellow pigment ring in the reverse were observed. Microscopic analysis revealed the presence of numerous teardrop shaped microconidia singly attached to the sides of the hyphae. In addition, 2-6 roomed macroconidia that were somewhat irregular in shape and size were present, and abundant intermediate sized spores were observed between the micro and macro conidia. To confirm that the culture was T. erinacei, the internal transcribed spacer region of the 5.8S phase of the ribosomal RNA gene (ITS1-5.8S-ITS2 rDNA) was amplified by PCR and then sequenced. A 679-base pair fragment of DNA was then compared with sequences in GenBank and found to be 99% homologous with sequences of T. erinacei (Z97997 and Z97996. The clinical signs were resolved after four weeks of treatment with oral and topical ketoconazole and chlorhexidine. To the best of our knowledge, this represents the first case of T. erinacei isolated from a four-toed hedgehog in Korea.

A Commensal Thermophile, Symbiobacterium toebii: Distribution, Characterization, and Genome Analysis

  • Bae Jin-Woo;Kim Kwang;Song Jae Jun;Ha Jae Seok;Kim Joong-Jae;Kang Gwan-Tae;Kim Mi-Hwa;Hong Seung-Pyo;Sung Moon-Hee
    • Proceedings of the Microbiological Society of Korea Conference
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    • 2001.11a
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    • pp.46-53
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    • 2001
  • A commensal thermophile, Symbiobacterium toebii, isolated from hay compost (toebii) in Korea commensally interacted with a thermophilic Geobacillus toebii sp. nov., which was a new species within the genus Geobacillus on the basis of the phenotypic traits and molecular systematic data. S. toebii required the crude extracts and/or culture supernatant of the Geobacillus toebii for axenic growth and could grow on the temperature between 45 and $70^{\circ}C$ (optimum: $60^{\circ}C$; 2.4 h doubling time) and pH 6.0 and 9.0 (optimum: pH 7.5). The G+C content of the genomic DNA was $65 mol\%$, and the major quinones were MK-6 and MK-7. A phylogenetic analysis of its 16S rDNA sequence indicated that Symbiobacterium toebii was closely related with solely reported Symbiobacterium thermophilum. The presence of the commensal thermophile 16S rDNA and accumulation of indole in all the enriched cultures indicate that Symbiobacterium toebii is widely distributed in the various soils. The genome of S. toebii constituted a circular chromosome of 3,280,275 base pairs and there was not an extra-chromosomal element (ECE). It contained about 4,107 predicted coding sequences. Of these protein coding genes, about $45.6\%$ was encoded well-known proteins and annotated the functional assignment of 1,874 open reading frames (ORFs), and the rest predicted to have unknown functions. The genes encoding thermostable tyrosine phenol-lyase and tryptophan indole-lyase were cloned from the genomic DNA of S. toebii and the enzymatic production of L-tyrosine and L-tryptophan was carried out with two thermostable enzymes overexpressed in recombinant E. coli.

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Studies on the Fermentative Production of Inosine-5′-monophosphate by Microorganisms (Part 1) Derivation of 5′-IMP Producing Mutants from Brevibacterium ammoniagenes (미생물에 의한 5′-이노신산의 생산에 관한 연구 (제1보) 5′-이노신산 생산균주의 분리)

  • Bae, Jong-Chan;Gong, Woon-Young;Son, Chung-Hong;Jang, Wook;Yoo, Ju-Hyun
    • Microbiology and Biotechnology Letters
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    • v.7 no.3
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    • pp.119-125
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    • 1979
  • As the first step of domestic developmint of the nucleic acid-related compounds, purine base required auxotrophs from Brevibacterium ammoniagenes ATCC 6872 were derived by the ultraviolet irradiation or the treatment of N-methyl-N'-nitro-N-nitroso guanidine (NTG), diethyl sulfate (DES), and ethylme-thyl sulfate (EMS). The optimum conditions of mutation by means of several mutagens were induced respectively. The yield of mutants was 0.083% by the ultraviolet irradiation, 0.67% by the NTG treatment, 1.1% by the DES treatment, and 0.45% by the EMS treatment. Six strains among 239 auxotrophs were screened out to accumulate 5'-lMP in the culture broth. Cry-stalline 5'-lMP was isolated from the culture broth of Brevifbacterium ammoniagenes adnine-guanine less mutant D-21530 by the use of anion exchange resin, Amberlite IRA-402, and it was identified physically and chemically as 5'-inosinic acid.

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