• 한국수산과학회지
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• 제42권5호
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• pp.461-467
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• 2009

A bacterial strain was screened and identified from sea sediments in Tongyeong coastal area in order to obtain proteases or peptidase cleaving C-terminal of glutamic acid. Strain TS0611, which showed the highest activity from 5 isolated protease producing strains, was selected and its properties investigated. Strain TS0611 was a gram-positive rod, $1.2\;{\mu}m$ in cell length, catalase positive, motility-positive, melanin-negative and grew at 15~$50^{\circ}C$, and hydrolyzed gelatin and casein. This strain was identified as Bacillus thuringiensis or Bacillus cereus based on results from the API system(API 50 CHB) which examined saccharides properties, fatty acid composition of cell wall, and 16S rRNA gene sequence.

• Journal of Microbiology and Biotechnology
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• 제20권2호
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• pp.410-414
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• 2010

A bacterial strain, 13-$25^T$ with xylanolytic activity isolated from a single soil sample, was characterized with respect to its phenetic and phylogenetic characteristics. The cells of the isolate are Gram-staining variable rods, but spore formation was not observed. This strain is catalase- and oxidase-positive, and able to degrade starch and xylan. The predominant fatty acids are anteiso-$C_{15:0}$, $C_{16:0}$, and iso-$C_{16:0}$. The major respiratory quinone is menaquinone 7(MK-7), with a polar lipid profile consistent with the genus Cohnella. The DNA G+C content is 54.3 mol%. The 168 rRNA gene sequence analysis indicates that this organism belongs to the genus Cohnella, with Cohnella panacarvi as the closest phylogenetic neighbor. Low levels of 168 rRNA gene sequence similarity (<97.0%) with respect to other taxa with published names and the identification of distinctive phenetic features in the isolate indicate that the strain 13-$25^T$ represents a novel species of the genus Cohnella, for which the name Cohnella damensis sp. novo is proposed. The type strain is 13-$25^T$ (=CCTCC AB $208103^T$=KCTC $13422^T$).

• Journal of Microbiology and Biotechnology
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• 제27권11호
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• pp.2028-2036
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• 2017

The Escherichia coli K-12 and B strains are among the most frequently used bacterial hosts for scientific research and biotechnological applications. However, omics analyses have revealed that E. coli K-12 and B exhibit notably different genotypic and phenotypic attributes, even though they were derived from the same ancestor. In a previous study, we identified a limited number of proteins from the two strains using two-dimensional gel electrophoresis and tandem mass spectrometry (MS/MS). In this study, an in-depth analysis of the physiological behavior of the E. coli K-12 and B strains at the proteomic level was performed using six-plex isobaric tandem mass tag-based quantitative MS. Additionally, the best lysis buffer for increasing the efficiency of protein extraction was selected from three tested buffers prior to the quantitative proteomic analysis. This study identifies the largest number of proteins in the two E. coli strains reported to date and is the first to show the dynamics of these proteins. Notable differences in proteins associated with key cellular properties, including some metabolic pathways, the biosynthesis and degradation of amino acids, membrane integrity, cellular tolerance, and motility, were found between the two representative strains. Compared with previous studies, these proteomic results provide a more holistic view of the overall state of E. coli cells based on a single proteomic study and reveal significant insights into why the two strains show distinct phenotypes. Additionally, the resulting data provide in-depth information that will help fine-tune processes in the future.

• Fisheries and Aquatic Sciences
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• 제15권1호
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• pp.83-89
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• 2012

Flavobacterium johnsoniae was isolated from farmed rainbow trout Oncorhynchus mykiss in Korea, and its biochemical and molecular characterization was determined. Yellow-pigmented bacterial colonies were isolated from 18 of 64 fish samples (28.1%) on trypticase soy agar plates, and their biochemical profiles were characterized by API 20E and API 20NE test kits. F. johnsoniae was identified by biochemical phenotyping of factors including rapid gliding motility, Gram-negative condition, oxidase- and catalase-positive status, Congo red absorption, nitrate reduction, ${\beta}$-galactosidase production, acid production from glucose, and gelatin and casein hydrolysis. PCR and subsequent sequencing of 16S rRNA confirmed that the yellow-pigmented colonies were most similar to F. johnsoniae. The alignment analysis of 16S rRNA sequences also showed that all 18 rainbow trout isolates had highly similar homologies (97-99% identity). One isolate was selected and named FjRt09. This isolate showed 98% homology with previously reported F. johnsoniae isolates, and in phylogenetic analysis was more closely grouped with F. johnsoniae than with F. psychrophilum, F. columnare, or F. branchiophilum. This is the first report on the occurrence and biochemical characterization of F. johnsoniae isolated from rainbow trout in Korea.

• The Plant Pathology Journal
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• 제38권2호
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• pp.102-114
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• 2022

Pectobacterium carotovorum subsp. carotovorum (Pcc) is a gram-negative, broad host range bacterial pathogen which causes soft rot disease in potatoes as well as other vegetables worldwide. While Pectobacterium infection relies on the production of major cell wall degrading enzymes, other virulence factors and the mechanism of genetic adaptation of this pathogen is not yet clear. In the present study, we have performed an in-depth genome-wide characterization of Pcc strain ICMP5702 isolated from potato and compared it with other pathogenic bacteria from the Pectobacterium genus to identify key virulent determinants. The draft genome of Pcc ICMP5702 contains 4,774,457 bp with a G + C content of 51.90% and 4,520 open reading frames. Genome annotation revealed prominent genes encoding key virulence factors such as plant cell wall degrading enzymes, flagella-based motility, phage proteins, cell membrane structures, and secretion systems. Whereas, a majority of determinants were conserved among the Pectobacterium strains, few notable genes encoding AvrE-family type III secretion system effectors, pectate lyase and metalloprotease in addition to the CRISPR-Cas based adaptive immune system were uniquely represented. Overall, the information generated through this study will contribute to decipher the mechanism of infection and adaptive immunity in Pcc.

• The Plant Pathology Journal
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• 제39권1호
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• pp.62-74
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• 2023

Plant pathogenic Pectobacterium species cause severe soft rot/blackleg diseases in many economically important crops worldwide. Pectobacterium utilizes plant cell wall degrading enzymes (PCWDEs) as the main virulence determinants for its pathogenicity. In this study, we screened a random mutant, M29 is a transposon insertion mutation in the metC gene encoding cystathionine β-lyase that catalyzes cystathionine to homocysteine at the penultimate step in methionine biosynthesis. M29 became a methionine auxotroph and resulted in growth defects in methionine-limited conditions. Impaired growth was restored with exogenous methionine or homocysteine rather than cystathionine. The mutant exhibited reduced soft rot symptoms in Chinese cabbages and potato tubers, maintaining activities of PCWDEs and swimming motility. The mutant was unable to proliferate in both Chinese cabbages and potato tubers. The reduced virulence was partially restored by a complemented strain or 100 µM of methionine, whereas it was fully restored by the extremely high concentration (1 mM). Our transcriptomic analysis showed that genes involved in methionine biosynthesis or transporter were downregulated in the mutant. Our results demonstrate that MetC is important for methionine biosynthesis and transporter and influences its virulence through Pcc21 multiplication in plant hosts.

• Asian-Australasian Journal of Animal Sciences
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• 제33권1호
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• pp.166-176
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• 2020

Objective: An experiment was conducted to determine the effects of L-arginine (L-Arg) and N-carbamoylglutamic acid (NCG) on the growth, metabolism, immunity and community of cecal bacterial flora of weanling and young rabbits. Methods: Eighteen normal-grade male weanling Japanese White rabbits (JWR) were selected and randomly divided into 6 groups with or without L-Arg and NCG supplementation. The whole feeding process was divided into weanling stage (day 37 to 65) and young stage (day 66 to 85). The effects of L-Arg and NCG on the growth, metabolism, immunity and development of the ileum and jejunum were compared via nutrient metabolism experiments and histological assessment. The different communities of cecal bacterial flora affected by L-Arg and NCG were assessed using high-throughput sequencing technology and bioinformatics analysis. Results: The addition of L-Arg and NCG enhanced the growth of weanling and young rabbit by increasing the nitrogen metabolism, protein efficiency ratio, and biological value, as well as feed intake and daily weight gain. Both L-Arg and NCG increased the concentration of immunoglobulin A (IgA), IgM, and IgG. NCG was superior to L-Arg in promoting intestinal villus development by increasing villus height, villus height/crypt depth index, and reducing the crypt depth. The effects of L-Arg and NCG on the cecal bacterial flora were mainly concentrated in different genera, including Parabacteroides, Roseburia, dgA-11_gut_group, Alistipes, Bacteroides, and Ruminococcaceae_UCG-005. These bacteria function mainly in amino acid transport and metabolism, energy production and conversion, lipid transport and metabolism, recombination and repair, cell cycle control, cell division, and cell motility. Conclusion: L-Arg and NCG can promote the growth and immunity of weanling and young JWR, as well as effecting the jejunum and ileum villi. L-Arg and NCG have different effects in the promotion of nutrient utilization, relieving inflammation and enhancing adaptability through regulating microbial community.

• 미생물학회지
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• 제46권3호
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• pp.240-247
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• 2010

그람음성 간균인 녹농균(Pseudomonas aeruginosa)은 비뇨기, 결막(conjunctiva), 호흡기(respiratory system), 화상부위 등에 광범위하게 감염하며, 병원성의 발현에 세균의 세포밀도 인식기전인 쿼럼 센싱이 매우 중요하다고 알려진 기회감염성 병원균이다. 국내의 환자들에게 감염하는 녹농균에서 쿼럼 센싱의 중요성을 알아보기 위해 부산 백병원의 환자들로부터 189종의 녹농균을 분리 동정하였다. 이 임상 균주들에서 쿼럼 센싱 신호 물질의 발현을 리포터 균주를 이용한 고체 배지 확산법으로 조사하였다. 전체 임상 균주의 79.4%가 녹농균 야생형균주와 비슷하게 쿼럼 센싱 조절의 가장 상위 신호인식-조절단백질인 LasR을 충분히 활성화 시키는 수준으로 쿼럼 신호물질을 생성하였다. 반면 4.2% 정도는 신호물질을 합성하지 못하는 녹농균 돌연변이주와 비슷하게 LasR을 활성화 시키지 못하는 수준으로 쿼럼 신호물질을 생성하였다. 한편, 전체의 72.5%가 또 다른 쿼럼 신호인식-조절 단백질인 QscR을 충분히 활성화 시킬 수 있는 야생형 수준으로 신호물질을 생성한 반면, 9%가 QscR을 활성화 시키지 못하는 수준으로 신호물질을 생성하였다. 임상 균주들 중 특히 녹농균 감염이 의심되는 환자들에게서 유래한 74종을 선정하여 병독인자로 중요한 프로테아제 활성을 조사한 결과, 44.6%에서 프로테아제 활성이 낮아져 있었으며, 12.2%에서는 프로테아제 활성이 관찰되지 않았다. 같은 균들을 대상으로 만성감염에 중요한 역할을 하는 것으로 알려진 생물막 형성 능력을 확인하였을 때, 대부분이 야생형보다 생물막 형성능력이 떨어져 있었다. 또한 이 균주들의 운동성을 살펴본 결과 많은 균주들이 swarming과 twitching 능력이 저해되어 있었으며(전체의 51.4%가 reduced swarming activity, 전체의 41.9%가 reduced twitching activity), 관찰되지 않는 수준의 균주도 상당부분 있었다(전체의 28.4%가 swarming negative, 전체의 28.4%가 twitching negative). 본 연구결과는 쿼럼 센싱을 정상적으로 하는 임상 균주들 중에서도 상당 부분은 프로테아제 생성, 생물막 형성, 운동성 등의 특징들이 저해될 수 있음을 의미하며, 일부 임상 균주들은 그들의 쿼럼 활성과는 상관관계가 없는 독특한 패턴의 프로테아제 생성능과 생물막 형성능 및 운동성을 보여주고 있음을 확인하였다.

• Reproductive and Developmental Biology
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• 제38권4호
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• pp.159-163
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• 2014

The objective of this study was to determine the effects of E. coli on boar sperm quality and reproductive performance in sows after artificial insemination. Three different levels of E. coli were artificially inoculated to semen with following concentrations; Control, 500, 5,000 and 50,000 colony forming unit (cfu)/ml. Semen samples were preserved at $17^{\circ}C$ for 5 days. Sperm motility was significantly decreased (p<0.05) on day 3 in the group inoculated with 5,000 cfu/ml compared to control groups. In all treatment groups, sperm motility was gradually decreased as storage time increased, but the decline pattern was more drastic in the groups inoculated with 5,000 and 50,000 cfu/ml groups from day 3 (p<0.05) compared to control group. After 3 day of storage at $17^{\circ}C$, sperm viability in sample inoculated with the highest concentration (50,000 cfu/ml) of bacteria was less (p<0.05) than that of control group. The pH of semen sample pH was maintained 7.2~7.5 in all groups during the experimental period. No differences (p>0.05) were found for both storage time and bacterial concentration. The pregnancy rate and live born piglets tend to decrease by increasing the concentration of E. coli in semen. In particular, the rate of pregnancy was lower in the group inoculated with 50,000 cfu/ml (58.3%) compare to the other groups (81.8, 75.0, 76.5%). These results suggest that the contamination of E. coli in boar semen negatively affects fertilizing ability of boar sperm and the reproductive performance obtained from sows after artificial insemination.

• Journal of Microbiology and Biotechnology
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• 제24권8호
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• pp.1034-1043
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• 2014

This study determined the effect of light intensity and photoperiod on the dry cell weight and total amount of carotenoids in four isolates of purple non-sulfur bacteria obtained from shaded and exposed microhabitats of a mangrove ecosystem in Kota Kinabalu, Sabah, Malaysia. The initial isolation of the bacteria was carried out using synthetic 112 medium under anaerobic conditions (2.5 klx) at $30{\pm}2^{\circ}C$. On the basis of colony appearance, cell morphology, gram staining, motility test, and 16S rRNA gene sequencing analyses, all four bacteria were identified as Afifella marina. One of the bacterial isolates, designated as Af. marina strain ME, which was extracted from an exposed mud habitat within the mangrove ecosystem, showed the highest yield in dry cell weight ($4.32{\pm}0.03g/l$) as well as total carotenoids ($0.783{\pm}0.002mg/g$ dry cell weight). These values were significantly higher than those for dry cell weight ($3.77{\pm}0.02g/l$) and total carotenoid content ($0.706{\pm}0.008mg/g$) produced by the isolates from shaded habitats. Further analysis of the effect of 10 levels of light intensity on the growth characteristics of Af. marina strain ME showed that the optimum production of dry cell weight and total carotenoids was achieved at different light intensities and incubation periods. The bacterium produced the highest dry cell weight of 4.98 g/l at 3 klx in 72 h incubation, but the carotenoid production of 0.783 mg/g was achieved at 2.5 klx in 48 h incubation. Subsequent analysis of the effect of photoperiod on the production of dry cell weight and total carotenoids at optimum light intensities (3 and 2.5 klx, respectively) revealed that 18 and 24 h were the optimum photoperiods for the production of dry cell weight and total carotenoids, respectively. The unique growth characteristics of the Af. marina strain ME can be exploited for biotechnology applications.