Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses

Lee, Hae-Won; Yoon, So‐Ra; Kim, Su-Ji; Lee, Hee Min; Lee, Jae Yong; Lee, Ji‐Hyun; Kim, Sung Hyun; Ha, Ji‐Hyoung

doi:10.1016/j.lwt.2017.04.001

Cited by 30 publications

(34 citation statements)

References 35 publications

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“…Another disadvantage is related to the fact that the phenotypic characteristics of certain micro‐organisms which would be used for their identification in the culture media may not be expressed (Farber ; Fusco and Quero ; Lee et al . ).…”

Section: Pathogen Identification By Traditional Microbiologymentioning

confidence: 97%

“…It is also worth noting that traditional methodologies are still considered the gold standard for the identification of pathogenic micro‐organisms, and it is only through these techniques that the morpho‐phenotypic characteristics of the bacteria can be evaluated (Fusco and Quero ; Lee et al . ).…”

Section: Pathogen Identification By Traditional Microbiologymentioning

confidence: 97%

“…Lee et al . () performed the identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing through 16S RNA sequencing with Illumina MiSeq. Lee et al .…”

Section: Molecular Biology Identification Techniques and Their Applicmentioning

confidence: 99%

“…; Chahorm and Prakitchaiwattana, ; Kim and Lee ; Lee et al . ). Thus, independent cultivation techniques have emerged as a solution to such limitations (Zhou et al .…”

Section: Introductionmentioning

confidence: 97%

“…; Lee et al . ), and present several advantages, such as high sensitivity, specificity and speed in obtaining results (Janda and Abbott ; Ceuppens et al . ).…”

Section: Introductionmentioning

confidence: 99%

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Application of molecular tools to elucidate the microbiota of seafood

2018

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The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.

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Section: Pathogen Identification By Traditional Microbiologymentioning

confidence: 97%

Section: Pathogen Identification By Traditional Microbiologymentioning

confidence: 97%

Section: Molecular Biology Identification Techniques and Their Applicmentioning

confidence: 99%

“…; Chahorm and Prakitchaiwattana, ; Kim and Lee ; Lee et al . ). Thus, independent cultivation techniques have emerged as a solution to such limitations (Zhou et al .…”

Section: Introductionmentioning

confidence: 97%

“…; Lee et al . ), and present several advantages, such as high sensitivity, specificity and speed in obtaining results (Janda and Abbott ; Ceuppens et al . ).…”

Section: Introductionmentioning

confidence: 99%

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Application of molecular tools to elucidate the microbiota of seafood

2018

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Quantitative microbial risk assessment for Clostridium perfringens foodborne illness following consumption of kimchi in South Korea

Choi

Kang

Lee

et al. 2020

Food Sci Biotechnol

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Microbiological quality and characteristics of isolated Escherichia coli in irrigation water used in Napa cabbage cultivation

et al. 2018

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To ensure the safety of Kimchi, the safety of Napa cabbage is the most important. Contaminated irrigation water can be a major cause of pathogens during growth of Napa cabbage. The purpose of this study was to investigate the microbial quality of irrigation water used in the cultivation of Napa cabbage. A total of 111 samples including surface water (n = 75) and groundwater (n = 36) collected from four different regions in Korea where Napa cabbage is intensively cultivated were analyzed for a fecal indicator (Escherichia coli) Moreover, 164 E. coli isolates from irrigation water were investigated for pathogenic characteristics including antibiotic resistance, pathogenic genes, serotype, and toxicity using Caenorhabditis elegans. E. coli was detected in 96% of surface water samples and 25% of groundwater samples. The level of E. coli in surface water (0.2-3.2 log MPN/100 mL) was higher than that in groundwater (0-2.0 log MPN/100 mL). When the 164 E. coli isolates were investigated concerning antibiotic resistance, resistance rates were 11.0%, 2.4%, 3.0%, 1.8%, 2.4%, 4.3%, and 3.0% for ampicillin, ampicillin/sulbactam, cefazolin, cefoxitin, gentamicin, levofloxacin, and trimethoprim/sulfamethoxazole, respectively. In addition, 10 (6.1%) of the isolates were positive for the eaeA gene, indicative of enteropathogenic E. coli. Eight of these 10 isolates were obtained from the surface water of the mountainous region II and were toxic to C. elegans. The results indicate the need to manage the microbial risk of irrigation water to enhance the safety of cultivated Napa cabbage.

show abstract

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses

Cited by 30 publications

References 35 publications

Application of molecular tools to elucidate the microbiota of seafood

Application of molecular tools to elucidate the microbiota of seafood

Quantitative microbial risk assessment for Clostridium perfringens foodborne illness following consumption of kimchi in South Korea

Microbiological quality and characteristics of isolated Escherichia coli in irrigation water used in Napa cabbage cultivation

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