Microbial community analysis of Korean soybean pastes by next-generation sequencing

Nam, Young-Do; Lee, So‐Young; Lim, Seong-Il

doi:10.1016/j.ijfoodmicro.2012.01.013

Cited by 175 publications

(119 citation statements)

References 29 publications

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“…14,[18][19][20][21] In line with this, many studies regarding the microbial community analysis of traditional Korean foods also implemented pyrosequencing technologies. 3,5,6,12,13,15,22,23) In the present study, we executed pyrosequencingbased metagenomic analysis of the bacterial community resident in gajami-sikhae. We collected eight gajamisikhae samples based on three different regional recipes (Hamgyong-do, Gangwon-do, and Gyeongsang-do).…”

mentioning

confidence: 99%

Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food,gajami-sikhae

Kim

Turner

et al. 2014

Bioscience, Biotechnology, and Biochemistry

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mentioning

confidence: 99%

Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food,gajami-sikhae

Kim

Turner

et al. 2014

Bioscience, Biotechnology, and Biochemistry

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“…Indeed, the more traditional the manufacturing process, the more complex the microbial community in the food. In contrast, industrially obtained foods are characterized by more-simple microbial consortia (16)(17)(18).…”

Section: Hts Applications In Foodmentioning

confidence: 99%

“…However, not all of the studies report a rarefaction analysis and it is not always possible to understand how deep the sample coverage has been. For example, coverage obtained from about 1,000 reads was satisfactory to determine the microbiota of some fermented soybean products (16,17). Most samples of soft, semihard, and hard Irish cheeses were adequately covered with slightly more than 1,000 reads, while cheese rinds, which have a more complex microbiota, required more sequences to be adequately studied (15).…”

Section: Planning Sample Coverage and Taxonomic Resolution To Set Wormentioning

confidence: 99%

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Ercolini

2013

Appl Environ Microbiol

408

229

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Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

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“…In this context, 16S rRNA metagenetics (also called metagenomic analysis targeting 16S ribosomal DNA) has emerged as a powerful tool for exploring the bacterial composition of various ecosystems (Esposito and Kirschberg, 2014). During the last decade, many applications in the field of microbiology have been developed to elucidate the microbiota of different foods such as fermented food, marinated poultry, sausages, cheese, tea, and bottled water (Benson et al, 2014;Delcenserie et al, 2014;Hansen et al, 2013;Jung et al, 2011;Lyu et al, 2013;Nam et al, 2012;Nieminen et al, 2012). With the help of these techniques, researchers can clarify the microfloral distribution of various ecosystems at a higher resolution than had been observed previously (Hanning and Ricke, 2011).…”

Section: Introductionmentioning

confidence: 99%

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis

Korsak

Taminiau

Hupperts

et al. 2017

International Journal of Food Microbiology

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The aim of this study was to investigate the influence of the slaughter technique (Halal vs Classical slaughter) on the superficial contamination of cattle carcasses, by using traditional microbiological procedures and 16S rDNA metagenetics. The purpose was also to investigate the neck area to identify bacteria originating from the digestive or the respiratory tract. Twenty bovine carcasses (10 from each group) were swabbed at the slaughterhouse, where both slaughtering methods are practiced. Two swabbing areas were chosen: one "legal" zone of 1600 cm 2 (composed of zones from rump, flank, brisket and forelimb) and locally on the neck area (200 cm 2 ). Samples were submitted to classical microbiology for aerobic Total Viable Counts (TVC) at 30°C and Enterobacteriaceae counts, while metagenetic analysis was performed on the same samples. The classical microbiological results revealed no significant differences between both slaughtering practices; with values between 3.95 and 4.87 log CFU/100 cm 2 and 0.49 and 1.94 log CFU/100 cm 2 , for TVC and Enterobacteriaceae respectively. Analysis of pyrosequencing data showed that differences in the bacterial population abundance between slaughtering methods were mainly observed in the "legal" swabbing zone compared to the neck area. Bacterial genera belonging to the Actinobacteria phylum were more abundant in the "legal" swabbing zone in "Halal" samples, while Brevibacterium and Corynebacterium were encountered more in "Halal" samples, in all swabbing areas. This was also the case for Firmicutes bacterial populations (families of Aerococcaceae, Planococcaceae). Except for Planococcoceae, the analysis of Operational Taxonomic Unit (OTU) abundances of bacteria from the digestive or respiratory tract revealed no differences between groups. In conclusion, the slaughtering method does not influence the superficial microbiological pattern in terms of specific microbiological markers of the digestive or respiratory tract. However, precise analysis of taxonomy at the genus level taxonomy highlights differences between swabbing areas. Although not clearly proven in this study, differences in hygiene practices used during both slaughtering protocols could explain the differences in contamination between carcasses from both slaughtering groups.

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Microbial community analysis of Korean soybean pastes by next-generation sequencing

Cited by 175 publications

References 29 publications

Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food,gajami-sikhae

Pyrosequencing analysis of microbiota reveals that lactic acid bacteria are dominant in Korean flat fish fermented food,gajami-sikhae

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Assessment of bacterial superficial contamination in classical or ritually slaughtered cattle using metagenetics and microbiological analysis

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