Kim, Daeho
(Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University)
,
Hong, Sanghyun
(Department of Animal Resources Science, Dankook University)
,
Na, Hongjun
(Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University)
,
Chun, Jihwan
(Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and Center for Food and Bioconvergence, Seoul National University)
,
Guevarra, Robin B.
(Department of Animal Resources Science, Dankook University)
,
Kim, You-Tae
(Department of Food Science and Biotechnology, Institute of Life Science and Resources, Kyung Hee University)
,
Ryu, Sangryeol
(Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute of Agriculture and Life Sciences, and)
,
Kim, Hyeun Bum
,
Lee, Ju-Hoon
Bellflower root (Platycodon grandiflorum), which belongs to the Campanulaceae family, is a perennial grass that grows naturally in Korea, northeastern China, and Japan. Bellflower is widely consumed as both food and medicine owing to its high nutritional value and potential therapeutic effects. Sinc...
Bellflower root (Platycodon grandiflorum), which belongs to the Campanulaceae family, is a perennial grass that grows naturally in Korea, northeastern China, and Japan. Bellflower is widely consumed as both food and medicine owing to its high nutritional value and potential therapeutic effects. Since foodborne disease outbreaks often come from vegetables, understanding the public health risk of microorganisms on fresh vegetables is pivotal to predict and prevent foodborne disease outbreaks. We investigated the microbial communities on the bellflower root (n = 10). 16S rRNA gene amplicon sequencing targeting the V6-V9 regions of 16S rRNA genes was conducted via the 454-Titanium platform. The sequence quality was checked and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using the weighted Fast UniFrac distance. The average number of sequence reads generated per sample was 67,192 sequences. At the phylum level, bacterial communities from the bellflower root were composed primarily of Proteobacteria, Firmicutes, and Actinobacteria in March and September samples. Genera Serratia, Pseudomonas, and Pantoea comprised more than 54% of the total bellflower root bacteria. Principal coordinate analysis plots demonstrated that the microbial community of bellflower root in March samples was different from those in September samples. Potential pathogenic genera, such as Pantoea, were detected in bellflower root samples. Even though further studies will be required to determine if these species are associated with foodborne illness, our results indicate that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria on fresh vegetables.
Bellflower root (Platycodon grandiflorum), which belongs to the Campanulaceae family, is a perennial grass that grows naturally in Korea, northeastern China, and Japan. Bellflower is widely consumed as both food and medicine owing to its high nutritional value and potential therapeutic effects. Since foodborne disease outbreaks often come from vegetables, understanding the public health risk of microorganisms on fresh vegetables is pivotal to predict and prevent foodborne disease outbreaks. We investigated the microbial communities on the bellflower root (n = 10). 16S rRNA gene amplicon sequencing targeting the V6-V9 regions of 16S rRNA genes was conducted via the 454-Titanium platform. The sequence quality was checked and phylogenetic assessments were performed using the RDP classifier implemented in QIIME with a bootstrap cutoff of 80%. Principal coordinate analysis was performed using the weighted Fast UniFrac distance. The average number of sequence reads generated per sample was 67,192 sequences. At the phylum level, bacterial communities from the bellflower root were composed primarily of Proteobacteria, Firmicutes, and Actinobacteria in March and September samples. Genera Serratia, Pseudomonas, and Pantoea comprised more than 54% of the total bellflower root bacteria. Principal coordinate analysis plots demonstrated that the microbial community of bellflower root in March samples was different from those in September samples. Potential pathogenic genera, such as Pantoea, were detected in bellflower root samples. Even though further studies will be required to determine if these species are associated with foodborne illness, our results indicate that the 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria on fresh vegetables.
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문제 정의
Therefore, the aim of this study was to investigate the bacterial community associated with bellflower roots from five South Korean farms between March and September of 2016. Bacterial communities of each bellflower root sample were analyzed using the 454 GS-FLX Titanium pyrosequencing system.
가설 설정
In this study, we investigated the microbial community structure of bellflower roots. Although further studies will be required to determine whether the identified species are associated with foodborne illness, our results indicate that 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria on fresh vegetables.
제안 방법
The nhe gene has been shown to possess a variety of biological effects, including cytotoxic, dermonecrotic, and vascular permeability activities [27]. In this study, the relative abundance of genus Bacillus was detected using 16S rRNA gene sequencing in all the samples regardless of the sampling time. Moreover, PCR results showed that the type 1 fimbriae (fimH) gene Fig.
To visualize the relative distances between bacterial communities of each sample, a three-dimensional PCoA plot was constructed (Fig. 2). The plot was generated by analyzing the 16S rRNA gene sequencing data of bellflower root (n = 10) harvested in March and September.
대상 데이터
PCR was used to amplify the V6-V9 regions of the 16S rRNA genes using the universal primers 926F (5’- GCACAAGCRGHG GARCATG-3’) and 1505R (5’-ACGGYTACCTTGTTACGACTT-3’) [20]. Multiplex identifier adaptors and 454 adaptors were attached to the primers for the sorting of samples. After amplification, the PCR products were purified using the Wizard SV Gel and PCR Clean-Up System (Promega Corp.
이론/모형
Alpha-diversity measures were calculated on the basis of normalized read counts using QIIME.
Chimeras were removed from the sequences using UCHIME [22]. Operational taxonomic unit (OTU) picking, taxonomic assignment, diversity analysis, and visualization were performed using the Quantitative Insights into Microbial Ecology (QIIME) pipeline [23]. OTUs were defined and clustered using UCLUST at 3% divergence (97% similarity) [24].
OTUs were defined and clustered using UCLUST at 3% divergence (97% similarity) [24]. Phylogenetic assignment and classification were performed using the RDP classifier implemented in QIIME [25]. Before estimating the alpha-diversity measurements, data were normalized by a random selection of the same sequence number per sample.
성능/효과
marcescens is commonly found in soil, water, plants, and animals [2, 43]. Our results detected Serratia in bellflower roots using 16S rRNA gene sequencing, suggesting that plant-associated Serratia may play a possible role in the contamination of humans and animals.
The 13 other genera were significantly higher in September than in March samples (p < 0.05); namely, Rhodoplanes, Kaistobacter, Sphingosinicella, Terrimonas, Solirubrobacter, Blastomonas, Sinorhizobium, Nocardioides, Erythrobacter, Cystobacter, Plesiocystis, Agromyces, and Amycolatopsis (Fig. 3).
후속연구
In this study, we investigated the microbial community structure of bellflower roots. Although further studies will be required to determine whether the identified species are associated with foodborne illness, our results indicate that 16S rRNA gene-based sequencing approach can be used to detect pathogenic bacteria on fresh vegetables.
참고문헌 (54)
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