• Microbiology and Biotechnology Letters
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• v.21 no.2
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• pp.144-149
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• 1993

We have identified a T cell-activating material in the culture supernatant of Streptomyces species. The factor in microbial culture supernatant (MCS) induced thymocyte proliferation in a does dependent fashion and it could be detected by immunoblot analysis using anti-interleukin-1(IL-1) antibody. The factor in MCS was slightly larger(about 21 kd) in its molecular weight than IL-1 on SDS-PAGE. When 125I-MCS was covalently coupled with homo-bifunctional cross-linking agent, disuccinimidyl-propionate to IL-1 receptor(IL-1R) on mouse thymoma cell(EL-4) and immunoprecipitated with anti-IL-1R antibody the molecular weight of this complex of 110 kd was observed.

• Journal of Digestive Cancer Research
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• v.12 no.1
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• pp.6-14
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• 2024

Gastric cancer is the 4th leading cause of death worldwide. The primary cause of gastric cancer is known to be Helicobacter pylori (H. pylori). The advancement of molecular biology has enabled the identification of microbiomes that could not be confirmed through cultivation, and it has been revealed that the microbial communities vary among normal mucosa, atrophic gastritis, intestinal metaplasia, and gastric cancer. It has also been confirmed that the composition of the microbial community differs depending on the presence or absence of H. pylori. Whether changes in the microbiome are causative factors in the carcinogenesis process is not yet clear. Experiments using animal models and in vitro studies on the role of microbes other than H. pylori in the carcinogenic process are underway, but the data is still insufficient.

• Journal of Microbiology and Biotechnology
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• v.29 no.4
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• pp.548-557
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• 2019

Staphylococcus species have a ubiquitous habitat in a wide range of foods, thus the ability to identify staphylococci at the species level is critical in the food industry. In this study, we performed rapid identification of Staphylococcus species using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS). MALDI-TOF MS was evaluated for the identification of Staphylococcus reference strains (n = 19) and isolates (n = 96) from various foods with consideration for the impact of sample preparation methods and incubation period. Additionally, the spectra of isolated Staphylococcus strains were analyzed using principal component analysis (PCA) and a main spectra profile (MSP)-based dendrogram. MALDI-TOF MS accurately identified Staphylococcus reference strains and isolated strains: the highest performance was by the EX method (83.3~89.5% accuracy) at species level identification (EDT, 70.3~78.9% accuracy; DT, less than 46.3~63.2% accuracy) of 24-h cultured colonies. Identification results at the genus level were 100% accurate at EDT, EX sample preparation and 24-h incubation time. On the other hand, the DT method showed relatively low identification accuracy in all extraction methods and incubation times. The analyzed spectra and MSP-based dendrogram showed that the isolated Staphylococcus strains were characterized at the species level. The performance analysis of MALDI-TOF MS shows the method has the potential ability to discriminate between Staphylococcus species from foods in Korea. This study provides valuable information that MALDI-TOF MS can be applied to monitor microbial populations and pathogenic bacteria in the food industry thereby contributing to food safety.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.6
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• pp.880-884
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• 2001

Rumen microbiology research has undergone several evolutionary steps: the isolation and nutritional characterization of readily cultivated microbes; followed by the cloning and sequence analysis of individual genes relevant to key digestive processes; through to the use of small subunit ribosomal RNA (SSU rRNA) sequences for a cultivation-independent examination of microbial diversity. Our knowledge of rumen microbiology has expanded as a result, but the translation of this information into productive alterations of ruminal function has been rather limited. For instance, the cloning and characterization of cellulase genes in Escherichia coli has yielded some valuable information about this complex enzyme system in ruminal bacteria. SSU rRNA analyses have also confirmed that a considerable amount of the microbial diversity in the rumen is not represented in existing culture collections. However, we still have little idea of whether the key, and potentially rate-limiting, gene products and (or) microbial interactions have been identified. Technologies allowing high throughput nucleotide and protein sequence analysis have led to the emergence of two new fields of investigation, genomics and proteomics. Both disciplines can be further subdivided into functional and comparative lines of investigation. The massive accumulation of microbial DNA and protein sequence data, including complete genome sequences, is revolutionizing the way we examine microbial physiology and diversity. We describe here some examples of our use of genomics- and proteomics-based methods, to analyze the cellulase system of Ruminococcus flavefaciens FD-1 and explore the genome of Ruminococcus albus 8. At Illinois, we are using bacterial artificial chromosome (BAC) vectors to create libraries containing large (>75 kbases), contiguous segments of DNA from R. flavefaciens FD-1. Considering that every bacterium is not a candidate for whole genome sequencing, BAC libraries offer an attractive, alternative method to perform physical and functional analyses of a bacterium's genome. Our first plan is to use these BAC clones to determine whether or not cellulases and accessory genes in R. flavefaciens exist in clusters of orthologous genes (COGs). Proteomics is also being used to complement the BAC library/DNA sequencing approach. Proteins differentially expressed in response to carbon source are being identified by 2-D SDS-PAGE, followed by in-gel-digests and peptide mass mapping by MALDI-TOF Mass Spectrometry, as well as peptide sequencing by Edman degradation. At Ohio State, we have used a combination of functional proteomics, mutational analysis and differential display RT-PCR to obtain evidence suggesting that in addition to a cellulosome-like mechanism, R. albus 8 possesses other mechanisms for adhesion to plant surfaces. Genome walking on either side of these differentially expressed transcripts has also resulted in two interesting observations: i) a relatively large number of genes with no matches in the current databases and; ii) the identification of genes with a high level of sequence identity to those identified, until now, in the archaebacteria. Genomics and proteomics will also accelerate our understanding of microbial interactions, and allow a greater degree of in situ analyses in the future. The challenge is to utilize genomics and proteomics to improve our fundamental understanding of microbial physiology, diversity and ecology, and overcome constraints to ruminal function.

• Journal of Environmental Health Sciences
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• v.50 no.2
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• pp.102-112
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• 2024

Background: Despite the rise in the number of domestic indoor climbing gyms, there is a lack of specific hygiene standards and research on the holds installed in them. Holds can act as vectors for microbial transmission through the hands, posing a risk of infectious diseases, especially with damaged skin. Objectives: The aim of this study is to investigate the contamination level and species of microorganisms on holds according to the management methods practiced in indoor climbing gyms and identify effective strategies for reducing microbial contamination. Methods: We investigated factors that may influence microbial contamination of holds, including hold management methods, user information, and hygiene management at three climbing gyms in Seoul. A total of 72 holds were sampled, 18 for each management method of brushing, high-pressure washing, and ethanol disinfection. Samples were cultured on LB and blood agar at 37℃ for 48 hours to calculate CFUs. PCR assay targeting 16S rRNA was carried out to identify microorganisms. Dunn-Bonferroni was employed to see the microbial reduction effect of the management method and the difference in microbial contamination by management method and climbing gym. Results: As a result of microbial identification, microorganisms such as Bacillus, Staphylococcus, and Micrococcus, which were derived from various environments such as skin and soil, were discovered on the surface of the climbing hold. Among the discovered microorganisms, some species had potential pathogenic properties that could cause food poisoning, gastrointestinal disease, bacteremia, and sepsis. All hold management methods were effective in reducing microorganisms (p<0.05), with ethanol disinfection being the most effective (p<0.001). Conclusions: Our results indicate that there are potential pathogens on holds that demand thorough management for microbial prevention. Proposed methods include regular brushing and ethanol disinfection in addition to high-pressure washing with long cycles, which are the existing forms of hold management. Further studies on shoe management are advised to curb soil-derived microorganisms.

• Journal of Food Hygiene and Safety
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• v.23 no.3
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• pp.191-197
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• 2008

This work was intended for the identification of markers that are found only in the spoiled red pepper powder. When analyzed by GC/MASS, the spoiled red pepper powder contains characteristic naphthalene derivatives, 1, 2, 3, 5, 6, 7, 8, $8\alpha$-octahydro-1, $8\alpha$-dimethyl-7-(1-methylethenyl)-naphthalene and 2-isopropenyl-$4\alpha$, 8-dimethyl-1, 2, 3, 4, $4\alpha$, 5, 6, $8\alpha$-octahydronaphthalene, which have not found in the normal red pepper powder. In addition, microscopic observation and microbial enumeration of the red pepper powder had been performed. Images by scanning electron microscopy showed that the surfaces of spoiled pepper powder were rough with many kinds of microbes, compared with those of normal red pepper powder. A good correlation between the bacterial and fungal counts in the same sample was observed and could be clearly classified into two groups, the normal and the spoiled group, by difference in the microbial counts. These results suggest that the spoiled red pepper powder can be identified by a combination of GC/MASS, microbial counts, and scanning electron microscopy.

• Mycobiology
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• v.40 no.1
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• pp.42-46
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• 2012

This report describes the isolation and identification of a potent acetylcholinesterase (AChE) inhibitor-producing yeasts. Of 731 species of yeast strain, the S-3 strain was selected as a potent producer of AChE inhibitor. The selected S-3 strain was investigated for its microbiological characteristics. The S-3 strain was found to be short-oval yeast that did not form an ascospore. The strain formed a pseudomycelium and grew in yeast malt medium containing 50% glucose and 10% ethanol. Finally, the S-3 strain was identified by its physiological characteristics and 26S ribosomal DNA sequences as $Yarrowia$ $lipolytica$ S-3.

• Microbiology and Biotechnology Letters
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• v.23 no.4
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• pp.405-410
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• 1995

In order to screen dextranase with high dextranolytic activity from microbial origins, dextranase producing fungal isolates were isolated from soil of the Taeion area. 197 strains with dextranolytic activities were isolated, out of which 3 strains with high dextranolytic activities were selected in the first screening. A strain (GR-98) with a best dextranolytic activity was selected in the second screening. The strain was identified to be similiar Aspergillus ustus by the morphological and cultural characteristics. The optimum culture temperature and initial pH for the dextranase production of the strain was 30$\circ$C and 7.0, respectively. The optimum culture medium was composed of 2% dextran, 0.3% KNO$_{3}$, 0.05% K$_{2}$HPO$_{4}$, 0.02% MgSO$_{4}$-7H$_{2}$O, 0.05% KC1, and 2.5 $\mu$g/ml pyridoxamine, and the enzyme production was maximum when the strain was subcultured at 30$\circ$C for 7 days.

• Microbiology and Biotechnology Letters
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• v.28 no.5
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• pp.243-250
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• 2000

The study was performed to investigated the excellent microbial anticaries substance which is more effective than the chlorohexidine in the dental caries treatment. For the screening of alkaliphilic microorganism, more than 1200 bacterial strains were isolated from sea soil sample. A typ-ical strain which produced the most excellent antimicrobial substance was selected. The strain was identified novel alkalophilic Bacillus sp. through the results of morphological, biochemical and chemotaxonomical characteristics and 16S rDNA sequencing and designated as Bacillus alkalophilshaggy JY-827.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2206-2213
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• 2016

Recently, several studies have revealed that commercial microbial identification systems do not accurately identify the uncommon causative species of candidiasis, including Candida famata, Meyerozyma guilliermondii, and C. auris. We investigated the accuracy of species-level identification in a collection of clinical isolates previously identified as C. famata (N = 38), C. lusitaniae (N = 1 2), and M. guilliermondii (N = 5) by the Vitek 2 system. All 55 isolates were re-analyzed by the Phoenix system (Becton Dickinson Diagnostics), two matrix-assisted laser desorption ionization-time of flight mass spectrometry analyzers (a Vitek MS and a Bruker Biotyper), and by sequencing of internal transcribed spacer (ITS) regions or 26S rRNA gene D1/D2 domains. Among 38 isolates previously identified as C. famata by the Vitek 2 system, the majority (27/38 isolates, 71.1%) were identified as C. tropicalis (20 isolates) or C. albicans (7 isolates) by ITS sequencing, and none was identified as C. famata. Among 20 isolates that were identified as C. tropicalis, 17 (85%) were isolated from urine. The two isolates that were identified as C. auris by ITS sequencing originated from ear discharge. The Phoenix system did not accurately identify C. lusitaniae, C. krusei, or C. auris. The correct identification rate for 55 isolates was 92.7% (51/55 isolates) for the Vitek MS and 94.6% (52/55 isolates) for the Bruker Biotyper, as compared with results from ITS sequencing. These results suggest that C. famata is very rare in Korea, and that the possibility of misidentification should be noted when an uncommon Candida species is identified.