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http://dx.doi.org/10.23093/FSI.2019.52.3.220

Recent next-generation sequencing and bioinformatic analysis methods for food microbiome research  

Kwon, Joon-Gi (Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University)
Kim, Seon-Kyun (Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University)
Lee, Ju-Hoon (Department of Food Science and Biotechnology, Graduate School of Biotechnology, Kyung Hee University)
Publication Information
Food Science and Industry / v.52, no.3, 2019 , pp. 220-228 More about this Journal
Abstract
Rapid development of next-generation sequencing (NGS) technology is available to study microbes in genomic level. This NGS has been widely used in DNA/RNA sequencing for genome sequencing, metagenomics, and transcriptomics. The food microbiology area could be categorized into three groups. Food microbes including probiotics and food-borne pathogens are studied in genomic level using NGS for microbial genomics. While food fermentation or food spoilage are more complicated, their genomic study needs to be done with metagenomics using NGS for compositional analysis. Furthermore, because microbial response in food environments are also important to understand their roles in food fermentation or spoilage, pattern analysis of RNA expression in the specific food microbe is conducted using RNA-Seq. These microbial genomics, metagenomics, and transcriptomics for food fermentation and spoilage would extend our knowledge on effective utilization of fermenting bacteria for health promotion as well as efficient control of food-borne pathogens for food safety.
Keywords
microbiome; next-generation sequencing; metagenomics; genomics; bioinformatics;
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1 Bokulich NA, Collins TS, Masarweh C, Allen G, Heymann H, Ebeler SE, Mills DA. Associations among wine grape microbiome, metabolome, and fermentation behavior suggest microbial contribution to regional wine characteristics. mBio 7: e00631-16 (2016)
2 Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat. Nanotechnol. 4: 265-270 (2009)   DOI
3 Diener C, Hoge AC, Kearney SM, Edman SE, Gibbons SM. Nonresponder phenotype reveals microbiome-wide antibiotic resistance in the murine gut. bioRxiv. doi: https://doi.org/10.1101/566190 (2019)   DOI
4 Frost&Sullivan. US Next-generation Sequencing Services Market. (2006)
5 Malla MA, Dubey A, Kumar A, Yadav S, Hashem A, Abd_Allah EF. Exploring the human microbiome: The potential future role of next-generation sequencing in disease diagnosis and treatment. Front. Immunol. 9: 2868 (2019)   DOI
6 McCarthy A. Third generation DNA sequencing: pacific biosciences' single molecule real time technology. Chem. Biol. 17: 675-676 (2010)   DOI
7 Morgan XC, Huttenhower C. Human microbiome analysis. PLoS Comp. Biol. 8: e1002808 (2012)   DOI
8 Plummer E, Twin J, Bulach DM, Garland SM, Tabrizi SN. A comparison of three bioinformatics pipelines for the analysis of preterm gut microbiota using 16S rRNA gene sequencing data. J. Proteomics Bioinform. 8: 283 (2015)
9 Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 11: 3-11 (2001)   DOI
10 Timme RE, Rand H, Leon MS, Hoffmann M, Strain E, Allard M, Roberson D, Baugher JD. GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015. Microb. Genom. 4 (2018)
11 Wang Z, Gerstein M, Snyder M. 2009. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10: 57 (2009)   DOI
12 Weimer BC. 100K Pathogen genome project. Genome Announc. 5:e00594-17 (2017)   DOI
13 식품의약품안전처. 식중독 통계 자료 Available from: https://www.foodsafetykorea.go.kr/portal/healthyfoodlife/foodPoisoningStat.do?menu_no=3724&menu_grp=MENU_NEW02. Assesed Jul. 31, 2019.
14 Sanger F, Nicklen S, Coulson. DNA sequencing with chain-terminating inhibitors. Proc. Acad. Sci. USA 74: 5463-5467 (1977)   DOI