Acknowledgement
This research was supported by the National Research Foundation (NRF) of Korea funded by the Korea government(MSIT)(NRF-2022R1F1A1074305 and RS-2023-00218150).
References
- Dethlefsen L, Huse S, Sogin ML, Relman DA. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6: e280.
- Janssen PH. 2006. Identifying the dominant soil bacterial taxa in libraries of 16S rRNA and 16S rRNA genes. Appl. Environ. Microbiol. 72: 1719-1728. https://doi.org/10.1128/AEM.72.3.1719-1728.2006
- Kim M, Chun J. 2005. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103: 91-96. https://doi.org/10.1016/j.ijfoodmicro.2004.11.030
- Revetta RP, Pemberton A, Lamendella R, Iker B, Santo Domingo JW. 2010. Identification of bacterial populations in drinking water using 16S rRNA-based sequence analyses. Water Res. 44: 1353-1360. https://doi.org/10.1016/j.watres.2009.11.008
- Neefs JM, Van de Peer Y, De Rijk P, Chapelle S, De Wachter R. 1993. Compilation of small ribosomal subunit RNA structures. Nucleic Acids Res. 21: 3025-3049. https://doi.org/10.1093/nar/21.13.3025
- Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. 1985. Rapid determination of 16S rRNA sequences for phylogenetic analyses. Proc. Natl. Acad. Sci. 82: 6955-6959. https://doi.org/10.1073/pnas.82.20.6955
- Martinez-Porchas M, Villalpando-Canchola E, Vargas-Albores F. 2016. Significant loss of sensitivity and specificity in the taxonomic classification occurs when short 16S rRNA gene sequences are used. Heliyon 2: e00170.
- Hakovirta JR, Prezioso S, Hodge D, Pillai SP, Weigel LM. 2016. Identification and analysis of informative single nucleotide polymorphisms in 16S rRNA gene sequences of the Bacillus cereus group. J. Clin. Microbiol. 54: 2749-2756. https://doi.org/10.1128/JCM.01267-16
- King WL, Siboni N, Kahlke T, Green TJ, Labbate M, Seymour JR. 2019. 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: 2907.
- Bassey AP, Chen Y, Zhu Z, Odeyemi OA, Frimpong EB, Ye K, et al. 2021. Assessment of quality characteristics and bacterial community of modified atmosphere packaged chilled pork loins using 16S rRNA amplicon sequencing analysis. Food Res. Int. 145: 110412.
- de Boer P, Caspers M, Sanders J-W, Kemperman R, Wijman J, Lommerse G, et al. 2015. Amplicon sequencing for the quantification of spoilage microbiota in complex foods including bacterial spores. Microbiome 3: 30.
- Shehata HR, Mitterboeck TF, Hanner R. 2020. Characterization of the microbiota of commercially traded finfish fillets. Food Res. Int. 137: 109373.
- Artimova R, Jatiova M, Baumgartnerova J, Lipkova N, Petrova J, Makova J, et al. 2023. Microbial communities on samples of commercially available fresh-consumed leafy vegetables and small berries. Horticulturae 9: 150.
- Choi H, Hwang BK, Kim B-S, Choi SH. 2020. Influence of pathogen contamination on beef microbiota under different storage temperatures. Food Res. Int. 132: 109118.
- Kim TY, Lee JJ, Kim BS, Choi SH. 2017. Whole-body microbiota of sea cucumber (Apostichopus japonicus) from South Korea for improved seafood management. J. Microbiol. Biotechnol. 27: 1753-1762. https://doi.org/10.4014/jmb.1707.07067
- Lee JJ, Kim TY, Choi SH, Kim BS. 2017. 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: 51-60. https://doi.org/10.1016/j.foodres.2017.09.084
- You HJ, Lee JH, Oh M, Hong SY, Kim D, Noh J, et al. 2021. Tackling Vibrio parahaemolyticus in ready-to-eat raw fish flesh slices using lytic phage VPT02 isolated from market oyster. Food Res. Int. 150: 110779.
- Lee JH, Oh M, Kim B-S. 2023. Phage biocontrol of zoonotic food-borne pathogen Vibrio parahaemolyticus for seafood safety. Food Control 144: 109334.
- Su YC, Liu C. 2007. Vibrio parahaemolyticus: a concern of seafood safety. Food Microbiol. 24: 549-558. https://doi.org/10.1016/j.fm.2007.01.005
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
- Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. 2016. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13: 581-583. https://doi.org/10.1038/nmeth.3869
- Pruesse E, Quast C, Knittel K, Fuchs BM, Ludwig W, Peplies J, et al. 2007. SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res. 35: 7188-7196. https://doi.org/10.1093/nar/gkm864
- Kim SY, Ban GH, Hong YW, Jang MJ, Kim SA. 2022. Microbiome shifts in sprouts (alfalfa, radish, and rapeseed) during production from seed to sprout using 16S rRNA microbiome sequencing. Food Res. Int. 152: 110896.
- Bukin YS, Galachyants YP, Morozov I, Bukin S, Zakharenko A, Zemskaya T. 2019. The effect of 16S rRNA region choice on bacterial community metabarcoding results. Sci. Data 6: 190007.
- Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, et al. 2019. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat. Commun. 10: 5029.
- King WL, Kaestli M, Siboni N, Padovan A, Christian K, Mills D, et al. 2021. Pearl oyster bacterial community structure is governed by location and tissue-type, but Vibrio species are shared among oyster tissues. Front. Microbiol. 12: 723649.
- Lee MJ, Lee JJ, Chung HY, Choi SH, Kim BS. 2016. Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management. Int. J. Food Microbiol. 234: 45-52. https://doi.org/10.1016/j.ijfoodmicro.2016.06.032
- Curry KD, Wang Q, Nute MG, Tyshaieva A, Reeves E, Soriano S, et al. 2022. Emu: species-level microbial community profiling of full-length 16S rRNA Oxford Nanopore sequencing data. Nat. Methods 19: 845-853. https://doi.org/10.1038/s41592-022-01520-4
- Callahan BJ, Wong J, Heiner C, Oh S, Theriot CM, Gulati AS, et al. 2019. High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution. Nucleic Acids Res. 47: e103-e103. https://doi.org/10.1093/nar/gkz569
- Karst SM, Ziels RM, Kirkegaard RH, Sorensen EA, McDonald D, Zhu Q, et al. 2021. High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing. Nat. Methods 18: 165-169. https://doi.org/10.1038/s41592-020-01041-y
- Wang H, Shankar V, Jiang X. 2022. Compositional and functional changes in microbial communities of composts due to the composting-related factors and the presence of listeria monocytogenes. Microbiol. Spectr. 10: e01845-01821.