Metagenomic Approach to Identifying Foodborne Pathogens on Chinese Cabbage

Kim, Daeho; Hong, Sanghyun; Kim, You‐Tae; Ryu, Sangryeol; Kim, Hyeun Bum; Lee, Ju-Hoon

doi:10.4014/jmb.1710.10021

Cited by 28 publications

(17 citation statements)

References 54 publications

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“…In this regard, metagenomic analysis based on 16S rRNA gene fragments is frequently used as a rapid and reliable method to study biodiversity and population dynamics in fermented foods (Kim et al . ; Naik et al . ).…”

Section: Introductionmentioning

confidence: 99%

The changes in dominant lactic acid bacteria and their metabolites during corn stover ensiling

Zhang

Zhang³

et al. 2018

J Appl Microbiol

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Section: Introductionmentioning

confidence: 99%

The changes in dominant lactic acid bacteria and their metabolites during corn stover ensiling

Zhang

Zhang³

et al. 2018

J Appl Microbiol

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“…pekinensis) as main ingredient. In this context, we would like to propose that the origin of the KM1 stain is most probably the Baechu cabbage itself as P. agglomerans was shown to grow as an epiphyte on vegetables and fruits [68,69]. However, one cannot exclude contamination of kimchi by humans during the preparation process, as P. agglomerans was found in sputum of cystic fibrosis patient.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes inPantoea agglomeransKM1, a potential opportunistic pathogen

Guevarra

Magez

Peeters

et al. 2020

Preprint

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Pantoea agglomerans is a Gram-negative aerobic bacillus causing a wide range of opportunistic infections in humans including septicemia, pneumonia, septic arthritis, wound infections and meningitis. To date, the determinants of virulence, antibiotic resistance, metabolic features conferring survival and host-associated pathogenic potential of this bacterium remain largely underexplored. In this study, we sequenced and assembled the whole-genome of P. agglomerans KM1 isolated from kimchi in South Korea. The genome contained one circular chromosome of 4,039,945 bp, 3 mega plasmids, and 2 prophages. The phage-derived genes encoded integrase, lysozyme and terminase. Six CRISPR loci were identified within the bacterial chromosome. Further in-depth analysis showed that the genome contained 13 antibiotic resistance genes conferring resistance to clinically important antibiotics such as penicillin G, bacitracin, rifampicin, vancomycin, and fosfomycin. Genes involved in adaptations to environmental stress were also identified which included factors providing resistance to osmotic lysis, oxidative stress, as well as heat and cold shock. The genomic analysis of virulence factors led to identification of a type VI secretion system, hemolysin, filamentous hemagglutinin, and genes involved in iron uptake and sequestration. Finally, the data provided here show that, the KM1 isolate exerted strong immunostimulatory properties on RAW 264.7 macrophages in vitro. Stimulated cells produced Nitric Oxide (NO) and pro-inflammatory cytokines TNF-α, IL-6 and the anti-inflammatory cytokine IL-10. The upstream signaling for production of TNF-α, IL-6, IL-10, and NO depended on TLR4 and TLR1/2. While production of TNF-α, IL-6 and NO involved solely activation of the NF-κB, IL-10 secretion was largely dependent on NF-κB and to a lesser extent on MAPK Kinases. Taken together, the analysis of the whole-genome and immunostimulatory properties provided in-depth characterization of the P. agglomerans KM1 isolate shedding a new light on determinants of virulence that drive its interactions with the environment, other microorganisms and eukaryotic hosts.

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“…The genus Sphingomonas generally acts as a plant-protective genus by suppressing disease symptoms and decreasing pathogen growth ( Kim D. et al, 2018 ). Innerebner et al (2011) showed that the inoculation with a Sphingomonas sp.…”

Section: Discussionmentioning

confidence: 99%

Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants

Purahong

Orrù²,

Donati

et al. 2018

Front. Plant Sci.

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Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker, the most devastating disease of kiwifruit vines. Before entering the host tissues, this pathogen has an epiphytic growth phase on kiwifruit flowers and leaves, thus the ecological interactions within epiphytic bacterial community may greatly influence the onset of the infection process. The bacterial community associated to the two most important cultivated kiwifruit species, Actinidia chinensis and Actinidia deliciosa, was described both on flowers and leaves using Illumina massive parallel sequencing of the V3 and V4 variable regions of the 16S rRNA gene. In addition, the effect of plant infection by Psa on the epiphytic bacterial community structure and biodiversity was investigated. Psa infection affected the phyllosphere microbiome structures in both species, however, its impact was more pronounced on A. deliciosa leaves, where a drastic drop in microbial biodiversity was observed. Furthermore, we also showed that Psa was always present in syndemic association with Pseudomonas syringae pv. syringae and Pseudomonas viridiflava, two other kiwifruit pathogens, suggesting the establishment of a pathogenic consortium leading to a higher pathogenesis capacity. Finally, the analyses of the dynamics of bacterial populations provided useful information for the screening and selection of potential biocontrol agents against Psa.

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Metagenomic Approach to Identifying Foodborne Pathogens on Chinese Cabbage

Cited by 28 publications

References 54 publications

The changes in dominant lactic acid bacteria and their metabolites during corn stover ensiling

The changes in dominant lactic acid bacteria and their metabolites during corn stover ensiling

Comprehensive genomic analysis reveals virulence factors and antibiotic resistance genes inPantoea agglomeransKM1, a potential opportunistic pathogen

Plant Microbiome and Its Link to Plant Health: Host Species, Organs and Pseudomonas syringae pv. actinidiae Infection Shaping Bacterial Phyllosphere Communities of Kiwifruit Plants

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