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Kim, Eiseul,Cho, Youngjae,Lee, Yoonju,Han, Sun-Kyung,Kim, Chang-Gyeom,Choo, Dong-Won,Kim, Young-Rok,Kim, Hae-Yeong Elsevier 2017 International journal of food microbiology Vol.243 No.-
<P>Weissella are obligate heterofermentative lactic acid bacteria belonging to the Leuconostocaceae family. Some Weissella can be found in salted and fermented foods, such as kimchi and jeotgal, and plays an important role in the fermentation process. In the present study, for the first time, a rapid and accurate identification method for Weissella species from kimchi and jeotgal was developed based on MALDI-TOF MS, supplemented with an in-house database. Of the 135 Weissella spectra aligned with the MALDI bioTyper database, 56 isolates (41.5%) yielded no reliable identification results with low log scores (<1.7). After registering the spectra of six Weissella reference strains, all of the isolates were correctly identified, of which 113 (83.7%) and 22 (163%) were identified at the species and genus level, respectively. Moreover, a dendrogram generated by protein profiles of the different Weissella species clearly presented distinctive clusters, and PCA analysis separated the spectra of Weissella species into four clusters. In comparing food origins, different Weissella species were identified from two fermented foods. W. soli and W. cibaria were isolated from kimchi, while W. thailandensis and W. halotolerans were isolated from jeotgal. The results of our proteomic approach confirm that the MALDI bioTyper database, with our in-house Weissella database, is sufficient for Weissella identification. The MALDI-TOF MS method provides fast and reliable discrimination between different species in the genus Weissella and, therefore, will be useful for safety control in fish farms or in the production of fermented foods. This method can also be applied to the control of opportunistic pathogenic Weissella in human clinical infections. (C) 2016 Elsevier B.V. All rights reserved.</P>
Kim Eiseul,Lee Shin-Young,Gwak Yoon-Soo,Kim Hyun-Jae,Kim Ik-Seon,Kwak Hyo-Sun,김해영 한국미생물·생명공학회 2023 한국미생물·생명공학회지 Vol.51 No.1
Dairy products are extensively used as carriers of probiotic strains that have potential health benefits. Assessment of the viability of probiotic strains during manufacturing is important to ensure that products meet recommended levels. Hence, the method for accurately quantifying lactic acid bacteria (LAB) in probiotic or dairy products is required. The present study aims to examine the performance of de-Man Rogosa Sharpe (MRS), plate count agar with bromocresol purple (PCA with BCP), and glucose blood liver (BL) agars recommended in the Korea Food Code guidelines for counting LAB. Analysis of the performance of culture media containing 19 lactic acid bacterial species commonly encountered in probiotic and dairy products showed no statistically significant difference between 18 reference strains and three culture media (p > 0.01). Furthermore, the suitability of three culture media was verified for the quantitative assessment of LAB in 25 probiotic and dairy products. The number of LAB in three culture media was determined to be more than 107 colony-forming unit (CFU)/ml for fermented milk products and 108 CFU/ml for condensed fermented milk and probiotic products, indicating that they all satisfied the Korea Food Code guidelines. Moreover, there was no statistically significant difference in the amount of LAB counted in all three culture media, suggesting that they can be used to isolate or enumerate LAB in commercial products. Finally, three culture media will be useful for isolating and enumerating LAB from fermented foods as well as gut microflora.
( Eiseul Kim ),( Hyun-joong Kim ),( Seung-min Yang ),( Chang-gyeom Kim ),( Dong-won Choo ),( Hae-yeong Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2019 Journal of microbiology and biotechnology Vol.29 No.4
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.
( Youngjae Cho ),( Eiseul Kim ),( Sun-kyung Han ),( Seung-min Yang ),( Mi-ju Kim ),( Hyun-joong Kim ),( Chang-gyeom Kim ),( Dong-won Choo ),( Young-rok Kim ),( Hae-yeong Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2017 Journal of microbiology and biotechnology Vol.27 No.9
Vibrio species are generally recognized as pathogens predominant in seafood along coastal areas. The food industry has sought to develop efficient microbial detection methods. Owing to the limits of conventional methods, this study aimed to establish a rapid identification method for Vibrio isolated from Korea, based on matrix-assisted laser-desorption/ionization timeof- flight mass spectrometry (MALDI-TOF MS). Four different preparation procedures were compared to determine the appropriate means to pretreat Vibrio species, using 17 isolates and five reference strains. Extended direct transfer and full formic acid extraction methods using bacterial colonies on agar plates revealed very low identification rates. Formic acid and trifluoroacetic acid (TFA) extractions using bacterial broth cultures were also performed. All Vibrio isolates and reference strains prepared by TFA extraction were successfully identified to the species level (17/22, 77.3%) and to the genus level (5/22, 22.7%). Thus, TFA extraction was considered the most appropriate method to pretreat Vibrio species for MALDI-TOF MS. The remaining 33 isolates and two reference strains were prepared by TFA extraction and analyzed by MALDI-TOF MS. Overall, 50 isolates were identified to the species level (40/50, 80%) and to the genus level (10/50, 20%). All isolates were identified as 43 V. alginolyticus, six V. parahaemolyticus, and one V. vulnificus species. V. alginolyticus and V. parahaemolyticus were isolated from fish offal (87.5% and 12.5%, respectively), seawater (91.3%, 8.7%), and shellfish (62.5%, 37.5%), whereas V. alginolyticus and V. vulnificus were isolated from sediment (90.9% and 9.1%, respectively). This study established a reliable system of MALDI-TOF MS preparation and analysis for Vibrio identification.
Lee Woojung,Kim Min-Hee,Park Juyeon,Kim You Jin,Kim Eiseul,Heo Eun Jeong,Kim Seung Hwan,Kim Gyungcheon,신학동,Kim Soon Han,김해영 한국미생물·생명공학회 2023 Journal of microbiology and biotechnology Vol.33 No.2
Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.
Eiseul Kim,Hae-Yeong Kim 한국식품영양과학회 2021 한국식품영양과학회 학술대회발표집 Vol.2021 No.10
Accurate investigation of microbial community provides the essential information required to improve fermented food quality and to understand their role in this process. This was the first study to compare two methods for accuracy in the identification of microbial community in kimchi by comparing a culture-independent (high-throughput sequencing) and a culture-dependent method (MALDI-TOF MS). Both methods showed similar results, finding that Latilactobacillus, Leuconostoc, and Weissella, which played an important role in kimchi fermentation, were identified as predominant bacteria. However, the microbial communities observed via high-throughput sequencing exhibited higher diversity than the MALDI-TOF MS. Unlike the high-throughput sequencing, MALDI-TOF MS enabled accurate detection of bacteria at the species level as well as analysis of the viable cell communities by only identifying the live cells. The overall community profiling using both methods provided complementary information by producing a more comprehensive view of the microbial ecology in kimchi. Our data suggest that both methods could be used to obtain reliable data for identifying the microbial community in kimchi.
( Eiseul Kim ),( Eun-ji Cho ),( Seung-min Yang ),( Hae-yeong Kim ) 한국미생물생명공학회(구 한국산업미생물학회) 2021 Journal of microbiology and biotechnology Vol.31 No.2
Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.
Eiseul Kim,Hae-Yeong Kim 한국식품영양과학회 2021 한국식품영양과학회 학술대회발표집 Vol.2021 No.10
Lacticaseibacillus zeae, mainly found in raw milk and fermented dairy products, are closely related to Lacticaseibacillus species that has beneficial probiotic properties. However, it is difficult to distinguish those using conventional identification methods. The objective of this study was to mine a novel genetic marker for discriminating L. zeae from other strains of the Lacticaseibacillus species by pangenome analysis and to develop a real-time PCR assay for detecting a marker with high accuracy and high throughput. The analysis of 141 genomes yielded 17,978 pangenome and 13,563 accessory-genome. The glycosyltransferase family 8 was identified as a novel genetic marker present only in L. zeae and not in 72,899,005 other bacterial genomes. A primer targeting genetic marker accurately distinguished L. zeae in pure and mixed DNA and showed 100% specificity for 61 reference strains. The quantitative curve revealed good linearity in the range of 10<SUP>9</SUP> to 10³ colony- forming units per reaction. Furthermore, a novel genetic marker was proven to be superior to the 16S rRNA gene. Our assay could be further applied to screen L. zeae in complex microbial communities in food samples.