• Parasites, Hosts and Diseases
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• v.61 no.2
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• pp.202-209
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• 2023

Lophomonas blattarum is an anaerobic protozoan living in the intestine of cockroaches and house dust mites, with ultramicroscopic characteristics such as the presence of a parabasal body, axial filament, and absence of mitochondria. More than 200 cases of Lophomonas infection of the respiratory tract have been reported worldwide. However, the current diagnosis of such infection depends only on light microscopic morphological findings from respiratory secretions. In this study, we attempted to provide more robust evidence of protozoal infection in an immunocompromised patient with atypical pneumonia, positive for Lophomonas-like protozoal cell forms. A direct search of bronchoalveolar lavage fluid via polymerase chain reaction (PCR), transmission electron microscopy (TEM), and metagenomic next-generation sequencing did not prove the presence of protozoal infection. PCR results were not validated with sufficient rigor, while de novo assembly and taxonomic classification results did not confirm the presence of an unidentified pathogen. The TEM results implied that such protozoal forms in light microscopy are actually non-detached ciliated epithelial cells. After ruling out infectious causes, the patient's final diagnosis was drug-induced pneumonitis. These findings underscore the lack of validation in the previously utilized diagnostic methods, and more evidence in the presence of L. blattarum is required to further prove its pathogenicity.

• Korean Journal of Organic Agriculture
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• v.25 no.4
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• pp.843-859
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• 2017

The JK-1 isolate which was the best producer of indole-3-acetic acid and carotenoid among the 388 strains isolated from 28 wetlands in Jeju, was identified to be Rhodopseudomonas palustirs belongs to a typical group of non sulfur purple bacteria based on 16S sRNA sequencing. This study investigated the effect of different cultural conditions of pH, temperature, agitation, light and aeration on growth, IAA and carotenoid production of photosynthetic bacterium JK-1 for optimization of IAA and carotenoid production. It was found that growth, IAA, carotenoid, and bacteriochlorophyll production with light (3,000~3,500 Lux) and agitation (100 rpm) showed better results than those with dark/static or dark/agitation (100 rpm) in anaerobic conditions. The optimal pH, temperature and agitation speed for cell growth were 7, $30^{\circ}C$, 150 rpm, for IAA production were 9, $30^{\circ}C$, 150rpm and for carotenoid production were 6, $25^{\circ}C$, 50 rpm, cultured for 72 h under anaerobic light, respectively. The growth and IAA production were high in aerobic culture compared with anaerocic culture, whereas carotenoid and bacteriochlorophyll content were decreased extremely in aerobic condition (0.5~1 vvm). Subsequently, the optimal culture conditions for JK-1 were selected with pH 7, $30^{\circ}C$ and 100 rpm under anaerobic light and the effect on plant growth was tested by pot assay. Inoculation of JK-1 with 3% (v/v) level caused increase in shoot and root dry weigh that varied from 20%~58% to 40%~28% in young radish in camparison to uninoculated treatment at 50 days of growth. The study suggests that the JK-1 isolate may serve as efficient biofertilizer inoculants to promote plant growth.

• Journal of the korean academy of Pediatric Dentistry
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• v.32 no.2
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• pp.344-356
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• 2005

There are normal inhabitants doing medically useful functions in the body. There are many kinds of bacteria performing specific functions in the oral cavity. Two strains of lactic acid bacteria were isolated from inhabitants of caries-free children's oral cavity, which inhibited the formation of artificial plaque by Streptococcus mutans and the production of volatile sulfur compounds by anaerobic bacteria. The isolates were identified by the test using API 50 CHL medium kit and 16S rDNA partial sequencing. 1. Two isolates were Gram-positive bacilli and produced hydrogen peroxide. 2. When Streptococcus mutans was cultured in the media, the mean weight of formed artificial plaque on the orthodontic wires was $124.4{\pm}30.4\;mg$, whereas being reduced to $5.2{\pm}2.0mg$ and $10.6{\pm}6.6mg$ in the media cultured with Streptococcus mutans and each isolate, respectively (p<0.05) 3. The number of viable cells of Streptococcus mutans was $3.4{\times}10^9$ per ml in the cultured solution, whereas those of Streptococcus mutans in the combined culture with each of isolates were $4.6{\times}10^8\;and\;2.4{\times}10^8$ per ml. 4. The optical density was 1.286 in the supernatant of Fusobacterium nucleatum after vortexing for 30minutes, whereas in the supernatant of combined Fusobacterium nucleatum and each isolate, they were reduced to 0.628 and 0.497, which the percentages of coaggregation between them were 29.4% and 57.8%, respectively 5. The optical density of Fusobacterium nucleatum precipitate was 1.794 in the culture media containing cysteine and $FeSO_4$, being reduced to 1.144 and 0.915 in the coaggregated precipitates of Fusobacterium nucleatum and each isolate. The optical density of Porphyromonas gingivalis precipitate was 1.932 in the culture media, being reduced to 1.170 and 1.266 in the coaggregated precipitates of Porphyromonas gingivalis and each isolate. 6. When two isolates were tested with API 50 CHL medium kit, those were identified Lactobaciallius salivarius and Lactobaciallius delbrueckii subsp. lactis. 7. The similarity values of 16S rDNA sequence between each of isolates and Lactobaciallius salivarius subsp. salicinius were 99.60% and 99.73%, respectively, meaning that isolates were Lactobaciallius salivarius subsp. salicinius. These results indicated that two strains isolated from caries-free children's saliva, which inhibited the formation of artificial plaque and the production of volatile sulfur compounds, were identified as Lactobaciallius salivarius subsp. salicinius.

• Journal of Life Science
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• v.28 no.3
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• pp.361-368
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• 2018

This study investigated the diversity of communities of intestinal microorganisms, separated from the intestinal organs of Red tilefish (Branchiostegus japonicas), collected on the Jeju Coast. First, in the isolation of 1.5% BHIA, MA, TSA and R2A Agar on the medium, there were most colonies in 1.5% BHIA. The results of aerobic culture and anaerobic culture were $1.7{\times}10^6CFU/g^{-1}$ and $1.1{\times}10^5cfu/g^{-1}$, respectively, on average, and 147 pure colonies were separated in total. In 16S rDNA sequencing, there were 58 genera and 74 species, showing 95-100% similarity with the basic strain. They were divided broadly into 5 phyla, and as the main phyletic group, Proteobacteria phylum comprised 50% with 9 families, 35 genera and 35 species of Moraxellaceae, Rhodobacteraceae, Shewanellae, Halomondaceae, Enterobacteriaceae, Vibrionaceae, Hahellaceae, Pseudomonadaceae, and Erythrobacteraceae, with the highest index of dominance. Actinobacteria phylum comprised 24% with 8 families, 11 genera and 17 species of Microbacteriaceae, Intrasporangiaceae, Dietziaceae, Dermabacteraceae, Dermacoccaceae, Nocardiodaceae, Brevibacteriaceae and Propionobacteriacea; Firmicutes phylum, 16% with 6 families, 8 genera and 17 species of Bacillaceae, Staphylcoccaceae, Planococcaceae, Streptococcaceae, Paenibacillaceae and Clostridiaceae; Bacteroidetes phylum, 6% with 2 families, 3 genera and 4 species of Cyclobacteriaceae and Flavobacteriaceae; and Deinococcus-Thermus phylum, 4% with 1 family, 1 genus and 1 species of Deinococcaceae.

• Journal of Life Science
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• v.15 no.5 s.72
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• pp.749-754
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• 2005

An antioxidant- producing bacterium was isolated from sea water in Jeju island. The isolated strain, SC2-1 was gram-positive, catalase positive, facultatively anaerobic, oxidase negative, motile and small rods. The strain utilized sucrose, dextrose, fructose, mannitol and maltose as a sole carbon and energy source and sodium chloride was required for the bacteria growth. The radical scavenging activity of the culture supernatants was determined by DPPH (1,1-diphenyl-2-picrylhydrazyl) method. This bacterium was identified based on cellular fatty acids analysis and 16S rDNA sequencing, and then named Exiguobacterium sp. SC2-1. The modified optimal medium compositions required the addition of maltose $2.5\%(w/v)$, yeast extract $1.5\%(w/v)$ and $KH_{2} PO_{4} 0.05\%(w/v)$ in marine broth (Difco. Co. USA). Antioxidant activity of under optimal culture conditions were $93\%$.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• v.32 no.5
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• pp.436-446
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• 2006

The purpose of this study was to isolate and identify the bacteria in chronic maxillary sinusitis (CMS) lesions from 3 patients and to determine the antimicrobial susceptibility of them against 10 antibiotics. One of them was odontogenic origin and the others were non-odontogenic origin. Pus samples were collected by needle aspiration from the lesions and examined by culture method. Bacterial culture was performed in three culture systems (anaerobic, CO2, and aerobic incubator). Identification of the bacteria was performed by 16S rRNA gene (16S rDNA) nucleotide sequencing method. To test the sensitivity of the bacteria isolated from the maxillary sinusitis lesions against seven antibiotics, penicillin G, amoxicillin, tetracycline, ciprofloxacin, cefuroxime, erythromycin, clindamycin, and vancomycin, minimum inhibitory concentration (MIC) was performed using broth dilution assay. Our data showed that enterobacteria such as Enterobacter aerogenes (30%), Klebsiella pneumoniae (25%), and Serratia marcescens (15%) were predominately isolated from the lesion of non-odontogenic CMS of senile patient (70 year old). Streptococcus spp. (40.3%), Actinomyces spp. (27.4%), P. nigrescens, M. micros, and P. anaerobius strains were isolated in the lesion of odontogenic CMS. In the lesion of non-odontogenic CMS, Streptococcus spp. (68.4%), Rothia spp. (13.2%), and Actinomyces sp. (10.5%) were isolated. The susceptibility pattern of 10 antibiotics was determined according to the host of the bacteria strains ratter than the kinds of bacterial species. Even though the number of CMS was limited as three, these results indicate that antibiotic susceptibility test must be accompanied with treatment of CMS. The combined treatment of two or more antibiotics is better than single antibiotic treatment in the presence of multidrug-resistant bacteria in the CMS lesions.

• Journal of Korean Society of Environmental Engineers
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• v.35 no.12
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• pp.973-977
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• 2013

These studies were attempted to investigate the change of microbial community of anode of microbial fuel cell using swine wastewater in the enrichment step with the lapse of time. Microbial fuel cells enriched by a 1 : 1 mixture of anaerobic digestive juices of the sewage treatment plant and livestock wastewater. Enrichment culture step was divided into three stages to indentify the microorganisms. It was separated by each lag phase, exponential phase, and stationary phase. These steps were determined by the change of the current value. The current after enrichment was generated about $0.84{\pm}0.06mA$. We were cut out the different 17 bands in the DGGE fingerprint gel to do sequencing. The bands which the concentration was increasing or newly appearing with the lapse of time were included for this study. In the lag and exponential phase, Clostridium, Rhodocyclaceae, Bacteriodetes, and Uncultured bacterium etc. were detected. There were in the stationary phase Geobacter sp., Rhodocyclaceae, Candidatus, Nitrospira, Flavobactriaceae and uncultured bacterium etc. Geobactor among microorganisms detected in this study is known as the Electrochemically active microorganisms. It may include electrochemically active microorganisms to be considered as electrical activity microorganisms.

• Restorative Dentistry and Endodontics
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• v.23 no.1
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• pp.328-338
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• 1998

Porphyromonas endodontalis, an anaerobic Gram negative cocobacillus which was known to be associated with the infected root canals and periapical lesions, is very difficult to culture and to detect by the traditional method in that it requires much time to induce the specific black pigmentation, and it is very sensitive to oxygen and the antibiotics added in the culture medium. In this study, the nucleotide sequences of the 'probe h' (0.73kb), one of the specific DNA probes top. endodontalis (ATCC 35406) which had been developed by our department, was determined and then a pair of primers for PCR amplification was fabricated to identify P. endodontalis. The plasmids containing 'probe h' were purified by $Wizard^{TM}$ Midipreps DNA Purification System (Promega Corp.), and the nucleotide sequences of the 'probe h' were determined by the dideoxy chain termination method using TaqTrack Sequencing System (Promega Corp.) and detected by fluorescent labelling method. The sense/antisense PCR primers were designed with computer software (Lasergene, DNASTAR Ind. PCR was done with a programmable GeneAmp PCR System 2400 (Perkin Elmer-Cetus Co.). Each sample containing the whole genomic DNA of P. endodontalis and other black-pigmented Bacteroides was itailly denatured at $94^{\circ}C$ for 5 min and then subjected to 30 cycles, each of them consisting of 60s at $94^{\circ}C$, 60s at $60^{\circ}C$, and 90s. at $72^{\circ}C$. The amplified DNA was resolved electrophoretically in a 1.0 % agarose gel in 1X TAE buffer, stained with EtBr, and photographed on a UV transilluminator. The results were as follows : 1. The nucleotide sequences of 'probe h' (743 base pairs) were obtained by dideoxy chain termination method, and from that results the specific primers to P. endodontalis (ATCC 35406), 'Primer H1/ Primer H2', were designed. 2. It has been found that 'Primer H1/H2' could detect P. endodontalis (ATCC 35406) using PCR. 3. The PCR system with this primers may be a powerful technique to amplify the specific sequences of 'probe h' of P. endodontalis (ATCC 35406) that produce distinct identification of it from other black-pigmented Bacteroides, and this could help us to determine the nature of periapical disease.

• Restorative Dentistry and Endodontics
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• v.30 no.5
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• pp.409-422
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• 2005

The aim of this study was to identify the bacteria isolated from acute endodontic lesions by cell culture and 16S rDNA sequencing. The necrotic pulpal tissue was collected from 17 infected root canals, which were diagnosed as being either an acute pulpitis or acute periapical abscess. Samples were collected aseptically from the infected pulpal tissue of the infected root canals using a barbed broach and a paper point. The cut barbed broaches and paper points were transferred to an eppendorf tube containing 500 ul of 1 XPBS. The sample solution was briefly mixed and plated onto a BHI-agar plate containing $5\%$ sheep blood. The agar plates were incubated in a $37^{\circ}C$ anaerobic chamber for 7 days. The bacteria growing on the agar plate were identified by 16S rRNA coding gene (rDNA) cloning and sequencing at the species level. Among the 71 colonies grown on the agar plates, 56 strains survived and were identified. In dental caries involving the root canals, Streptococcus spp. were mainly isolated. Actinomyces, Clostridia, Bacteroides and Fusobacteria were isolated in the periapical lesion without dental caries. Interestingly, two new Actinomyces spp. (ChDC B639 and ChDC B631) were isolated in this study. These results showed that there was diversity among the species in endodontic lesions, This suggests that an endodontic infection is a mixed infection with a polymicrobial etiology. These results may offer the bacterial strains for pathogenesis studies related to an endodontic infection.

• Korean Journal of Microbiology
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• v.42 no.3
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• pp.185-194
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• 2006

The aim of this study was to identify the bacteria isolated from endodontic lesions by cell culture and to determine the antimicrobial susceptibility of them against 8 antibiotics. The necrotic pulpal tissues were collected from 27 infected root canals, which were diagnosed as endodontic infection. Samples were collected aseptically from the infected pulpal tissue of the infected root canals using a barbed broach and a paper point. The cut barbed broaches and paper points were transferred to an eppendorf tube containing $500{\mu}l\;of\;1{\times}PBS$. The sample solution was briefly mixed and plated onto a BHI-agar plate containing 5% sheep blood. The agar plates were incubated in a $37^{\circ}C$ anaerobic chamber for 2 to 5 days. The bacteria grown on the agar plates were identified by comparison of 16S rRNA gene (rDNA) sequencing method at the species level. To test the sensitivity of the bacteria isolated from the infected root canals against 8 antibiotics, minimum inhibitory concentrations (MIC) were determined using broth dilution assay. The data showed that 101 bacterial strains were isolated and were identified. Streptococcus spp. (29.7%) and Actinomyces spp. (21.8%) were predominantly isolated. The 9 strains were excluded in antimicrobial susceptibility test because they were lost during the experiment or were not grown in broth culture. The percentage of bacteria susceptible for each antibiotic in this study was clindamycin, 87.0% (80 of 92); tetracycline, 75.0% (69 of 92); cefuroxime axetil, 75.0% (69 of 92); amoxicillin + clavulanic acid (5:1), 71.7% (66 of 92); penicillin G, 66.3% (61 of 92); erythromycin, 66.3% (61 of 92); amoxicillin, 44.6% (41 of 92); and ciprofloxacin, 31.5% (29 of 92). The susceptibility pattern of 8 antibiotics was dependent on the host of the bacteria strains rather than the kinds of bacterial species. These results indicate that antibiotic susceptibility test should be performed when antibiotics are needed for the treatment of infected root canals.