Exploring the Feasibility of 16S rRNA Short Amplicon Sequencing-Based Microbiota Analysis for Microbiological Safety Assessment of Raw Oyster
1
조회
0
다운로드
0
인용
0
참고문헌
키워드
초록
16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treatedgroups even when the bacterial composition was compared at the possible lowest-rank taxa, family/ genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.
Abstract
16S rRNA short amplicon sequencing-based microbiota profiling has been thought of and suggested as a feasible method to assess food safety. However, even if a comprehensive microbial information can be obtained by microbiota profiling, it would not be necessarily sufficient for all circumstances. To prove this, the feasibility of the most widely used V3-V4 amplicon sequencing method for food safety assessment was examined here. We designed a pathogen (Vibrio parahaemolyticus) contamination and/or V. parahaemolyticus-specific phage treatment model of raw oysters under improper storage temperature and monitored their microbial structure changes. The samples stored at refrigerator temperature (negative control, NC) and those that were stored at room temperature without any treatment (no treatment, NT) were included as control groups. The profiling results revealed that no statistical difference exists between the NT group and the pathogen spiked- and/or phage treatedgroups even when the bacterial composition was compared at the possible lowest-rank taxa, family/ genus level. In the beta-diversity analysis, all the samples except the NC group formed one distinct cluster. Notably, the samples with pathogen and/or phage addition did not form each cluster even though the enumerated number of V. parahaemolyticus in those samples were extremely different. These discrepant results indicate that the feasibility of 16S rRNA short amplicon sequencing should not be overgeneralized in microbiological safety assessment of food samples, such as raw oyster.
참고문헌 (31)
- Dethlefsen L, "The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing", PLoS Biol, 6, pp.e280~ (2008)
- Janssen PH, "Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes", Appl. Environ. Microbiol, 72, pp.1719~1728 (2006)
- Kim M, "Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis", Int. J. Food Microbiol, 103, pp.91~96 (2005)
- Revetta RP, "Identification of bacterial populations in drinking water using 16S rRNA-based sequence analyses", Water Res, 44, pp.1353~1360 (2010)
- Neefs JM, "Compilation of small ribosomal subunit RNA structures", Nucleic Acids Res, 21, pp.3025~3049 (1993)
- Lane DJ, "Rapid determination of 16S rRNA sequences for phylogenetic analyses", Proc. Natl. Acad. Sci, 82, pp.6955~6959 (1985)
- Martínez-Porchas M, "Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used", Heliyon, 2, pp.e00170~ (2016)
- Hakovirta JR, "Identification and analysis of informative single nucleotide polymorphisms in 16S rRNA gene sequences of the Bacillus cereus group", J. Clin. Microbiol, 54, pp.2749~2756 (2016)
- King WL, "A new high throughput sequencing assay for characterizing the diversity of natural Vibrio communities and its application to a pacific oyster mortality event", Front. Microbiol, 10, pp.2907~ (2019)
- Bassey AP, "Assessment of quality characteristics and bacterial community of modified atmosphere packaged chilled pork loins using 16S rRNA amplicon sequencing analysis", Food Res. Int, 145, pp.110412~ (2021)
- de Boer P, "Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores", Microbiome, 3, pp.30~ (2015)
- Shehata HR, "Characterization of the microbiota of commercially traded finfish fillets", Food Res. Int, 137, pp.109373~ (2020)
- Artimová R, "Microbial communities on samples of commercially available fresh-consumed leafy vegetables and small berries", Horticulturae, 9, pp.150~ (2023)
- Choi H, "Influence of pathogen contamination on beef microbiota under different storage temperatures", Food Res. Int, 132, pp.109118~ (2020)
- 김태윤, "Whole-Body Microbiota of Sea Cucumber (Apostichopus japonicus) from South Korea for Improved Seafood Management", Journal of Microbiology and Biotechnology, 27(10), pp.1753~1762 (2017), 한국미생물·생명공학회
- Lee JJ, "Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management", Food Res. Int, 102, pp.51~60 (2017)
- You HJ, "Tackling Vibrio parahaemolyticus in ready-to-eat raw fish flesh slices using lytic phage VPT02 isolated from market oyster", Food Res. Int, 150, pp.110779~ (2021)
- Lee JH, "Phage biocontrol of zoonotic food-borne pathogen Vibrio parahaemolyticus for seafood safety", Food Control, 144, pp.109334~ (2023)
- Su YC, "Vibrio parahaemolyticus: a concern of seafood safety", Food Microbiol, 24, pp.549~558 (2007)
- Bolger AM, "Trimmomatic: a flexible trimmer for Illumina sequence data", Bioinformatics, 30, pp.2114~2120 (2014)
- Callahan BJ, "DADA2: High-resolution sample inference from Illumina amplicon data", Nat. Methods, 13, pp.581~583 (2016)
- Pruesse E, "SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB", Nucleic Acids Res, 35, pp.7188~7196 (2007)
- Kim SY, "Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing", Food Res. Int, 152, pp.110896~ (2022)
- Bukin YS, "The effect of 16S rRNA region choice on bacterial community metabarcoding results", Sci. Data, 6, pp.190007~ (2019)
- Johnson JS, "Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis", Nat. Commun, 10, pp.5029~ (2019)
- King WL, "Pearl oyster bacterial community structure is governed by location and tissue-type, but Vibrio species are shared among oyster tissues", Front. Microbiol, 12, pp.723649~ (2021)
- Lee MJ, "Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management", Int. J. Food Microbiol, 234, pp.45~52 (2016)
- Curry KD, "Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data", Nat. Methods, 19, pp.845~853 (2022)
- Callahan BJ, "High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution", Nucleic Acids Res, 47, pp.e103~ (2019)
- Karst SM, "High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing", Nat. Methods, 18, pp.165~169 (2021)
- Wang H, "Compositional and functional changes in microbial communities of composts due to the composting-related factors and the presence of listeria monocytogenes", Microbiol. Spectr, 10, pp.e01845-01821~ (2022)