• Microbiology and Biotechnology Letters
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• v.42 no.3
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• pp.238-248
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• 2014

The metalloid arsenic (Z = 33) is considered to be a significant potential threat to human health due to its ubiquity and toxicity, even in rural regions. In this study a rural region contaminated with arsenic, located at longitude $85^{\circ}$ 32'E and latitude $25^{\circ}$ 11'N, was initially examined. Arsenic tolerant bacteria from the rhizosphere of Amaranthas viridis were found and identified as Bacillus licheniformis through 16S rRNA gene sequencing. The potential for the uptake and removal of arsenic at 3, 6 and 9 mM [As(V)], and 2, 4 and 6 mM [As(III)], and for the reduction of the above concentrations of As(V) to As(III) by the Bacillus licheniformis were then assessed. The minimal inhibitory concentrations (MIC) for As(V) and As(III) was determined to be 10 and 7 mM, respectively. At 3 mM 100% As(V) was uptaken by the bacteria with the liberation of 42% As(III) into the medium, whereas at 6 mM As(V), 76% AS(V) was removed from the media and 56% was reduced to As(III). At 2 mM As(III), the bacteria consumed 100%, whereas at 6 mM, the As(III) consumption was only 40%. The role of pH was significant for the speciation, availability and toxicity of the arsenic, which was measured as the variation in growth, uptake and content of cell protein. Both As(V) and As(III) were most toxic at around a neutral pH, whereas both acidic and basic pH favored growth, but at variable levels. Contrary to many reports, the total cell protein content in the bacteria was enhanced by both As(V) and As(III) stress.

• Journal of Microbiology and Biotechnology
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• v.23 no.7
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• pp.993-1003
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• 2013

Methanotrophs are the most important sink of $CH_4$, which is a more highly potent greenhouse gas than $CO_2$. Methanotrophic abundance and community diversity in cover soils from two typical semi-aerobic landfills (SALs) in China were detected using real-time polymerase chain reaction (real-time-PCR) and denaturing gradient gel electrophoresis (DGGE) based on 16S rRNA genes, respectively. Real time-PCR showed that Type I methanotrophs ranged from $1.07{\times}10^6$ to $2.34{\times}10^7$ copies/g soil and that of Type II methanotrophs from $1.51{\times}10^7$ to $1.83{\times}10^8$ copies/g soil. The ratio of Type II to Type I methanotrophic copy numbers ranged from 5.61 to 21.89, indicating that Type II methanotrophs dominated in SAL. DGGE revealed that Type I methanotrophs responded more sensitively to the environment, changing as the community structure varied with different soil types and locations. Methylobacter, Methylosarcina, and Methylomicrobium for Type I, and Methylocystis for Type II were most prevalent in the SAL cover layer. Abundant interflow $O_2$ with high $CH_4$ concentration in SALs is the reason for the higher population density of methanotrophs and the higher enrichment of Type II methanotrophs compared with anaerobic landfills and other ecosystems, which proved a conclusion that increasing the oxygen supply in a landfill cover layer would greatly improve $CH_4$ mitigation.

• Journal of Microbiology and Biotechnology
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• v.27 no.2
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• pp.342-349
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• 2017

Polylactic acid (PLA) has been highlighted as an alternative renewable polymer for the replacement of petroleum-based plastic materials, and is considered to be biodegradable. On the other hand, the biodegradation of PLA by terminal degraders, such as microorganisms, requires a lengthy period in the natural environment, and its mechanism is not completely understood. PLA biodegradation studies have been conducted using mainly undefined mixed cultures, but only a few bacterial strains have been isolated and examined. For further characterization of PLA biodegradation, in this study, the PLA-degrading bacteria from digester sludge were isolated and identified using a polymer film-based screening method. The enrichment of sludge on PLA granules was conducted with the serial transference of a subculture into fresh media for 40 days, and the attached biofilm was inoculated on a PLA film on an agar plate. 3D optical microscopy showed that the isolates physically degraded the PLA film due to bacterial degradation. 16S rRNA gene sequencing identified the microbial colonies to be Pseudomonas sp. MYK1 and Bacillus sp. MYK2. The two isolates exhibited significantly higher specific gas production rates from PLA biodegradation compared with that of the initial sludge inoculum.

• Journal of Microbiology and Biotechnology
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• v.27 no.7
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• pp.1216-1222
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• 2017

To develop starters for the production of functional foods or materials, lactic acid bacteria producing ${\gamma}-aminobutyric$ acid (GABA) were screened from jeotgals, Korean fermented seafoods. One isolate producing a high amount of GABA from monosodium $\text\tiny{L}$-glutamate (MSG) was identified as Enterococcus avium by 16S rRNA gene sequencing. E. avium M5 produced $18.47{\pm}1.26mg/ml$ GABA when incubated for 48 h at $37^{\circ}C$ in MRS broth with MSG (3% (w/v)). A gadB gene encoding glutamate decarboxylase (GAD) was cloned and overexpressed in E. coli BL21 (DE3) using the pET26b (+) expression vector. Recombinant GAD was purified through a Ni-NTA column and the size was estimated to be 53 kDa by SDS-PAGE. Maximum GAD activity was observed at pH 4.5 and $55^{\circ}C$and the activity was dependent on pyridoxal 5'-phosphate. The $K_m$ and $V_{max}$ values of GAD were $3.26{\pm}0.21mM$ and $0.0120{\pm}0.0001mM/min$, respectively, when MSG was used as a substrate. Enterococcus avium M5 secretes a lot of GABA when grown on MRS with MSG, and the strain is useful for the production of fermented foods containing a high amount of GABA.

• Journal of Microbiology and Biotechnology
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• v.28 no.6
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• pp.946-956
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• 2018

The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, on the basis of the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp (Macrobrachium nipponense) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38-99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense. In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.

• Journal of Microbiology and Biotechnology
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• v.30 no.11
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• pp.1640-1650
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• 2020

Colorectal cancer (CRC) is the leading cause of common malignant neoplasm worldwide. Many studies have analyzed compositions of gut microbiota associated with various diseases such as inflammatory bowel diseases (IBD) and colon cancer. One of the most representative bacteria involved in CRC is enterotoxigenic Bacteroides fragilis (ETBF), a species belonging to phylum Bacteroidetes. We used ETBF colonized mice with azoxymethane (AOM)/dextran sulphate sodium (DSS) and zerumbone, a compound with anti-bacterial effect, to determine whether zerumbone could restore intestinal microbiota composition. Four experimental groups of mice were used: sham, ETBF colonized AOM/DSS group, ETBF colonized AOM/DSS group zerumbone 60 mg kg-1 (ETBF/AOM/DSS + Z (60)), and only zerumbone (60 mg kg^-1)-treated group. We performed reversible dye terminators-based analysis of 16S rRNA gene region V3-V4 for group comparison. Microbiota compositions of ETBF/AOM/DSS + Z (60) group and ETBF colonized AOM/DSS group not given zerumbone were significantly different. There were more Bacteroides in ETBF/AOM/DSS + Z (60) group than those in ETBF colonized AOM/DSS group, suggesting that B. fragilis could be a normal flora activated by zerumbone. In addition, based on linear discriminant analysis of effect size (LEfSe) analysis, microbial diversity decreased significantly in the ETBF colonized AOM/DSS group. However, after given zerumbone, the taxonomic relative abundance was increased. These findings suggest that zerumbone not only influenced the microbial diversity and richness, but also could be helpful for enhancing the balance of gut microbial composition. In this work, we demonstrate that zerumbone could restore the composition of intestinal microbiota.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.44 no.6
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• pp.605-611
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• 2011

This study examined the suitability of characteristics of potential strains of probiotic bacteria. Among 25 lactic acid bacteria isolated from Korean traditional fermented food, the Hard Clam Meretrix meretrix Shikhae, the SH-10 strain, which exhibited superior resistance to low pH and bile salts, was selected as a potential probiotic bacteria. By examining carbohydrate utilization, morphological properties, and the 16S rRNA gene sequence, the SH-10 strain was identified as Pediococcus pentosaceus (hereafter, P. pentosaceus SH-10). P. pentosaceus SH-10 was resistant to amikacin, cefotetan, ciprofloxacin, gentamicin, kanamycin, nalidixic acid, streptomycin, and vancomycin. Tests of antimicrobial activities against pathogens such as Bacillus cereus, Listeria monocytogenes, Salmonella choleraesuis, and Staphylococcus aureus, indicated that P. pentosaceus SH-10 inhibited the growth of pathogenic bacteria. These results suggest that P. pentosaceus SH-10 can be developed as a probiotic bacteria.

• Journal of the Korean Chemical Society
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• v.47 no.2
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• pp.127-132
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• 2003

We have developed a direct polymerase chain reaction (PCR) and electrophoresis method for the diagnosis of bovine theileriosis from whole blood DNA analysis without DNA extraction. The technique empolyed a FoLT (formamide, low temp.) technique and was utilized in the diagnosis of bovine theileriosis. Formamide solubilize the blood cells, and the lowered incubation temperatures reduced protein coagulation. 100-200 nL of whole blood and PCR reagents were introduced directly into a PCR tube. After the amplification, the PCR product (816-bp DNA) was introduced into the electrophoresis system. The results of this analysis were consist with those obtained using purified DNA.

• Korean Journal of Veterinary Service
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• v.35 no.2
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• pp.99-104
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• 2012

Otitis externa (OE) is a frequent disease in the ear canals of dogs. To identify the pathogens causing OE in dogs and to determine their antimicrobial resistances, specimens were collected from animal hospitals in Daejeon. The isolates were examined by morphological and biochemical tests, 16S rRNA analysis and antimicrobial susceptibility tests. We analyzed correlation between the isolated pathogens and external factors of dogs such as breed, age, gender, ear mite, hair in ears and experience with antibiotic therapy. Thirty three strains of bacteria were isolated from 26 of the 68 heads of dogs with OE. The most isolated bacteria were Enterococcus faecalis (E. faecalis) followed by Staphylococcus aureus (Sta. aureus), Sta. pseudointermedius, E. faecium, E. avium and Streptococcus canis (Strep. canis) in order of frequency of occurrence. Isolation frequency of Enterococcus spp. and Staphylococcus spp. were 51.5% and 45.5%, respectively. E. faecalis and E. faecium isolates showed VanB phenotype, which is resistant to vancomycin but sensitive to teicoplanin were 58% and 25%, respectively. Nine isolates among total twelve isolates of E. faecalis were isolated from the dogs treated with antibiotics. There was no methicillin-resistant Sta. aureus (MRSA), but were MR-Sta. pseudointermedius (MRSP) (57.1%) and vancomycin-resistant (VR)-Sta. pseudointermedius (14.3%) (VRSP) showing VanB phenotype. However, vanA, vanB and vanC genes were not detected in VR isolates from the dogs. Taken together, VR-Enterococcus spp. (VRE) is one of the major pathogens in domestic animals, as well as community-and hospital-acquired infection.

• KSBB Journal
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• v.28 no.1
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• pp.18-23
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• 2013

The purpose of this work was to investigate the several functional characteristics of Lactobacillus sakei JK-17 isolated from long-term fermented kimchi, Muk Eun Ji. Initially, phylogenetic analysis using 16S rRNA sequencing was performed to identify the isolate JK-17, and the strain could be assigned to Lactobacillus sakei and designated as L. sakei JK-17. The strain was registered in GenBank as [JX841311]. The changes of bacterial growth and residual organic acids were monitored and HPLC was used to measure quantitatively two organic acids, lactic acid and acetic acid, produced in the culture during 84 hours of incubation. During the incubation period, several functional characteristics of L. sakei JK-17 were examined. L. sakei JK-17 culture depleted nitrite concentration 94.75%. Antioxidant activity of cultural supernatants of L. sakei JK-17 was approx. 53.8%, and ${\beta}$-galactosidase activities were 0.243 units/mL at pH 7.0 and 0.387 units/mL at pH 4.1, respectively. The antibacterial activities against food-poisoning causing bacteria were examined with 20-fold concentrated culture supernatants from L. sakei JK-17 and the antibacterial effects were clearly observed against all bacteria tested in this work.