• Journal of Microbiology and Biotechnology
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• v.18 no.12
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• pp.1966-1974
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• 2008

A typical tropical soil from the northeast of Brazil, where an important terrestrial oil field is located, was accidentally contaminated with a mixture of oil and saline production water. To study the bioremediation potential in this area, molecular methods based on PCR-DGGE were used to determine the diversity of the bacterial communities in bulk and in contaminated soils. Bacterial fingerprints revealed that the bacterial communities were affected by the presence of the mixture of oil and production water, and different profiles were observed when the contaminated soils were compared with the control. Halotolerant strains capable of degrading crude oil were also isolated from enrichment cultures obtained from the contaminated soil samples. Twenty-two strains showing these features were characterized genetically by amplified ribosomal DNA restriction analysis (ARDRA) and phenotypically by their colonial morphology and tolerance to high NaCl concentrations. Fifteen ARDRA groups were formed. Selected strains were analyzed by 16S rDNA sequencing, and Actinobacteria was identified as the main group found. Strains were also tested for their growth capability in the presence of different oil derivatives (hexane, dodecane, hexadecane, diesel, gasoline, toluene, naphthalene, o-xylene, and p-xylene) and different degradation profiles were observed. PCR products were obtained from 12 of the 15 ARDRA representatives when they were screened for the presence of the alkane hydroxylase gene (alkB). Members of the genera Rhodococcus and Gordonia were identified as predominant in the soil studied. These genera are usually implicated in oil degradation processes and, as such, the potential for bioremediation in this area can be considered as feasible.

• Journal of Microbiology and Biotechnology
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• v.18 no.11
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• pp.1741-1746
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• 2008

This study was conducted to select endophytic actinomycetes as biocontrol agents against Chinese cabbage clubroot caused by Plasmodiophora brassicae. A total of 81 endophytic actinomycetes were isolated from surface-sterilized roots of Chinese cabbage that was grown on paddy field and upland soils collected from various locations in Korea. By using 16S ribosomal DNA (rDNA) gene sequencing, they were classified to 8 actinobacterial genera. The genus Microbispora (67%) was most frequently isolated, followed by Streptomyces (12%) and Micromonospora (11%). Three of the 81 isolates, when inoculated in germinated Chinese cabbage seeds and then transplanted to pots, effectively suppressed the occurrence of a post-inoculated strain of P. brassicae in the pots. They showed control values of 58% for strain A004, 33% for strain A011, and 42% for strain A018. Based on cell wall components, morphological characteristics, and phylogenetic analyses, the three antagonistic isolates were identified as Microbispora rosea subsp. rosea (A004 and A011) and Streptomyces olivochromogenes (A018). Further researches on the field efficacy and action modes of the three actinomycetes are in progress.

• Food Science and Preservation
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• v.20 no.5
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• pp.705-711
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• 2013

Gamma amino butyric acid (GABA), known as a non-protein amino acid and major inhibitory neurotransmitter in the brain, has several functional properties such as neurotransmission, induction of hypotension, tranquilizer, and diuretic effects. The purpose of this study was to isolate and identify lactic acid bacteria, producing high GABA in fermented soy curd. Thirty-two strains of tofu-forming lactic acid bacteria were isolated from kimchi which a traditional Korean food fermented with many kind of microorganism. Among 32 strains, four strains (strain No. 10, 104, 214, 249) formed firm soycurd. In order to select lactic acid bacteria having high GABA producing potential, the isolated strains were cultured in the soymilk and fermented for 48 hr at $37^{\circ}C$. A strain No. 383, which showed highest GABA contents in fermented soycurd, was identified as L. sakei by 16S rDNA sequencing and API analysis, and named as L. sakei 383. L. sakei 383 showed optimal growth up to 24 hr at $35^{\circ}C$ in MRS broth. The optimal time and temperature for GABA production were 18 hr and $35^{\circ}C$ in soymilk. In the optimal condition time and temperature, GABA content of fermented soycurd by L. sakei 383 was 8.65 mg/100 g.

• Parasites, Hosts and Diseases
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• v.53 no.1
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• pp.95-99
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• 2015

Strongyloides stercoralis can cause systemic infection, termed strongyloidiasis, and gastrointestinal ulcer disease in immunocompromised patients. However, to our knowledge, there are no reported cases of comorbid gastric adenocarcinoma and S. stercoralis infection. Here, we report a case of an 81-year-old Korean man who presented with S. stercoralis infection coexisting with early gastric adenocarcinoma (T1aN0M0). S. stercoralis eggs, rhabditiform larvae, and adult females were observed in normal gastric and duodenal crypts. They were also observed in atypical glands representative of adenocarcinoma and adenoma. Preliminary laboratory tests revealed mild neutrophilic and eosinophilic leukocytosis. A routine stool test failed to detect rhabditiform larvae in the patient's fecal sample; however, S. stercoralis was identified by PCR amplification and 18S rRNA sequencing using genomic DNA extracted from formalin-fixed paraffin-embedded tissues. Postoperatively, the patient had a persistent fever and was treated with albendazole for 7 days, which alleviated the fever. The patient was followed-up by monitoring and laboratory testing for 4 months postoperatively, and no abnormalities were observed thus far. The fact that S. stercoralis infection may be fatal in immunocompromised patients should be kept in mind when assessing high-risk patients.

• Journal of Microbiology and Biotechnology
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• v.18 no.8
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• pp.1459-1469
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• 2008

Using a rotating biological contactor modified with a sequencing bath reactor system (SBRBC) designed and operated to remove phosphate and nitrogen [58], the microbial community structure of the biofilm from the SBRBC system was characterized based on the extracellular polymeric substance (EPS) constituents, electron microscopy, and molecular techniques. Protein and carbohydrate were identified as the major EPS constituents at three different biofilm thicknesses, where the amount of EPS and bacterial cell number were highest in the initial thickness of 0-100${\mu}m$. However, the percent of carbohydrate in the total amount of EPS decreased by about 11.23%, whereas the percent of protein increased by about 11.15% as the biofilm grew. Thus, an abundant quantity of EPS and cell mass, as well as a specific quality of EPS were apparently needed to attach to the substratum in the first step of the biofilm growth. A FISH analysis revealed that the dominant phylogenetic group was $\beta$- and $\gamma$-Proteobacteria, where a significant subclass of Proteobacteria for removing phosphate and/or nitrate was found within a biofilm thickness of 0-250${\mu}m$. In addition, 16S rDNA clone libraries revealed that Klebsiella sp. and Citrobacter sp. were most dominant within the initial biofilm thickness of 0-250${\mu}m$, whereas sulfur-oxidizing bacteria, such as Beggiatoa sp. and Thiothrix sp., were detected in a biofilm thickness over 250${\mu}m$. The results of the bacterial community structure analysis using molecular techniques agreed with the results of the morphological structure based on scanning electron microscopy. Therefore, the overall results indicated that coliform bacteria participated in the nitrate and phosphorus removal when using the SBRBC system. Moreover, the structure of the biofilm was also found to be related to the EPS constituents, as well as the nitrogen and phosphate removal efficiency. Consequently, since this is the first identification of the bacterial community and structure of the biofilm from an RBC simultaneously removing nitrogen and phosphate from domestic wastewater, and it is hoped that the present results may provide a foundation for understanding nitrate and phosphate removal by an RBC system.

• Journal of Microbiology and Biotechnology
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• v.25 no.6
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• pp.910-917
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• 2015

A total of 646 strains, including green algae and diatoms, were isolated from 220 samples to screen microalgae with high lipid productivity (LP). The samples were obtained from nine habitats in Northern Xinjiang, China in June 2013. This study initially identified eight lipidrich strains, namely, Desmodesmus intermedius XJ-498, D. intermedius XJ-145, D. intermedius XJ-99, Monoraphidium pusillum XJ-489, M. dybowskii XJ-435, M. dybowskii XJ-151, Mychonastes homosphaera XJ-488, and Podohedriella falcata XJ-176, based on 18S rDNA sequencing. The strains were cultured in a photobioreactor for the same period. Results showed that the specific growth rate (day^-1) of M. pusillum XJ-489 was the highest (1.14 ± 0.06), and the biomass concentration (g/l) of D. intermedius XJ-99 was the highest (2.84 ± 0.3). Futhermore, the lipid content (%) of M. dybowskii XJ-151 was the highest (33.5 ± 4.38), and the lipid productivity (mg l^-1 day^-1) of My. homosphaera XJ-488 was the highest (86.41 ± 9.04). C16 to C18 accounted for 86% to 98% of the total lipid, and the biodiesel qualities of the selected algae corresponded to international standards. This study suggests that My. homosphaera XJ-488, D. intermedius XJ-99, and M. dybowskii XJ-151 are the most potential strains for biodiesel production among all the isolated strains.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.82-91
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• 2019

Objective: This experiment was conducted to compare the structure and composition of ruminal microorganisms in goats with high and low neutral detergent fibre (NDF) digestibility. Methods: Nineteen crossbred goats were used as experimental animals and fed the same total mixed rations during the 30-day pre-treatment and 6-day digestion trialperiods. All faeces were collected during the digestion period for measuring the NDF digestibility. Then, high and the low NDF digestibility individuals were chosen for the high NDF digestibility group (HFD) and low NDF digestibility group (LFD), respectively. Rumen contents were collected for total microbial DNA extraction. The V4 region of the bacterial 16S rRNA gene was amplified using universal primers of bacteria and sequenced using high-throughput sequencer. The sequences were mainly analysed by QIIME 1.8.0. Results: A total of 18,694 operational taxonomic units were obtained, within 81.98% belonged to bacteria, 6.64% belonged to archaea and 11.38% was unassigned microorganisms. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant microbial phyla in both groups. At the genus level, the relative abundance of fifteen microorganisms were significantly higher (p<0.05) and six microorganisms were extremely significantly higher (p<0.01) in LFD than HFD. Overall, 176 core shared genera were identified in the two groups. The relative abundance of 2 phyla, 5 classes, 10 orders, 13 families and 15 genera had a negative correlation with NDF digestibility, but only the relative abundance of Pyramidobacter had a positive correlation with NDF digestibility. Conclusion: There were substantial differences in NDF digestibility among the individual goats, and the NDF digestibility had significant correlation with the relative abundance of some ruminal microorganisms.

• Applied Biological Chemistry
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• v.47 no.4
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• pp.373-378
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• 2004

In this study, established soil-borne Bacillus sp. FF-9 with strong antifungal activity was isolated for identification and to determine optimal culture condition. By using 16s rDNA sequencing method, FF-9 of the selected bacteria was identified as genus Bacillus sp., Bacillus sp. FF-9 was cultured at $30^{\circ}C$, for 24 h in the LB medium. Cell growth increased quickly after 6 h and the highest cell growth was indicated at 12 h. The most antifungal activity against Rhizoctoina solani AGII-II appeared at 18 h and the optimal temperature and pH were 30 and pH 8.0, respectively. A testing of carbon and nitrogen sources showed the highest antifungal activity at 1% lactose and 1% yeast extract Furthermore an addition of salt showed the most antibiotic activity in the 0.15% $K_2HPO_4$.

• Journal of Microbiology
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• v.45 no.3
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• pp.246-255
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• 2007

Mutans streptococci have been implicated as cariogenic bacteria in dental caries because they can produce high levels of dental caries-causing lactic acid and extracellular polysaccharide. The aim of this study was to isolate and characterize the mutans streptococci from the dental plaque obtained from Koreans. The dental plaque samples were collected from the anterior and molar teeth of both jaws in 155 subjects (aged 2 to 33.2 years, average age $13.7{\pm}4.7\;years$). The samples were diluted by 100-fold in $1{\times}\;PBS$ and plated on mitis-salivarius bacitracin (MSB) agar plates. The mutans streptococci grown on MSB plates were screened by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) targeting dextranase gene (dex). The mutans streptococci were identified at the species level using a 16S rDNA sequencing comparison method. The biochemical tests were carried out to biotype the mutans streptococci. Ninety-five strains of the mutans streptococci out of 358 colonies, which were derived from 141 subjects, were isolated. Of them, 77 strains and 18 strains were Streptococcus mutans and Streptococcus sobrinus, respectively. The biotyping data showed that 62, 1, 20, 10, and 2 strains were biotypes I, II, IV, V and variant, respectively. Of the two strains of variant biotype, one strains was similar to biotype IV except that it was positive to the arginine hydrolysis test. We considered this one strain a new biotype, and classified it as biotype VII. In conclusion, S. mutans and its biotype I was most frequently isolated in Korean dental plaque. The mutans streptococci strains isolated in this study might be useful for the study of the pathogenesis and the prevention of dental caries.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.516-525
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• 2012

LAB were isolated from makgeolli locally produced around Jinju, Gyeongnam, S. Korea during spring of 2011. Randomly selected 11 isolates from MRS agar plates were identified first by API CHL 50 kits and then 16S rRNA gene sequencing. All 11 isolates were identified as Lactobacillus plantarum. Among them, ST4 grew in MRS broth with ethanol up to 10%, showing the highest alcohol resistance. L. plantarum ST4 was moderately resistant against acid and bile salts. When cellular proteins of L. plantarum ST4 under ethanol stress were analyzed by two-dimensional gel electrophoresis (2DE), the intensities of 6 spots increased, whereas 22 spots decreased at least 2-fold. Those 28 spots were identified by peptide mass fingerprinting (PMF). FusA2 (elongation factor G) increased 18.8-fold (6% ethanol) compared with control. Other proteins were AtpD (ATP synthase subunit beta), DnaK, GroEL, Tuf (elongation factor Tu), and Npr2 (NADH peroxidase), respectively. Among the 22 proteins decreased in intensities, lactate dehydrogenases (LdhD and LdhL1) were included.