Utilizing of Nanopore Technology for Species Identification and Safety Evaluation of Probiotics

Main Article Content

Worarat Kruasuwan
Nipa Chokesajjawatee
Jaruwan Sitdhipol
Punnathorn Thaveetheptaikul
Thidathip Wongsurawat

Article Details

How to Cite
Kruasuwan W, Chokesajjawatee N, Sitdhipol J, Thaveetheptaikul P, Wongsurawat T. Utilizing of Nanopore Technology for Species Identification and Safety Evaluation of Probiotics. Thai Food and Drug J [Internet]. 2024 Apr. 25 [cited 2024 Jun. 22];31(1):5-21. Available from: https://he01.tci-thaijo.org/index.php/fdajournal/article/view/270684
Review Article


กระทรวงสาธารณสุข. ประกาศกระทรวงสาธารณสุข. (คัดลอกจากราชกิจจานุเบกษา ฉบับที่ 346) พ.ศ. 2554 เรื่อง การใช้จุลินทรีย์โพรไบโอติกในอาหาร. ราชกิจจานุเบกษา เล่ม 128, ตอนพิเศษ 86ง (ลงวันที่ 3 สิงหาคม 2554).

Hamilton-Miller JMT, Shah S. Deficiencies in microbiological quality and labelling of probiotic supplements. Int J Food Microbiol 2002;72:175–76.

Chen T, Wu Q, Li S, Xiong S, Jiang S, Tan Q, et al. Microbiological quality and characteristics of probiotic products in China. J Sci Food Agric 2014;94:131–38.

Temmerman R, Pot B, Huys G. Identification and antibiotic susceptibility of bacterial isolates from probiotic products. Int J Food Microbiol 2003;81:1–10.

Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sørensen EA, Wollenberg RD, et al. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat Methods 2022;19:823–26.

Roe AL, Boyte ME, Elkins CA, Goldman VS, Heimbach J, Madden E, et al. Considerations for determining safety of probiotics: A USP perspective. Regul Toxicol Pharmacol 2022;136:105266. doi:10.1016/j.yrtph. 2022.105266

Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B, et al. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014;11:506–14.

กระทรวงสาธารณสุข. ประกาศกระทรวงสาธารณสุข. (คัดลอกจากราชกิจจานุเบกษา ฉบับที่ 346) พ.ศ. 2555 เรื่อง การใช้จุลินทรีย์โพรไบโอติกในอาหาร (ฉบับที่ 2). ราชกิจจานุเบกษา เล่ม 128, ตอนพิเศษ 86ง (ลงวันที่ 25 ตุลาคม 2555).

สิรินดา ยุ่นฉลาด, สุจิตรา ทนสูงเนิน. การผลิต D-lactic acid โดยแบคทีเรียกรดแลคติคเพื่อผลิตพลาสติกย่อยสลายได้ทางชีวภาพ. วารสารศูนย์บริการวิชาการ 2552;17(1-4):16–23.

Sivamaruthi BS, Kesika P, Chaiyasut CA. Mini-review of human studies on cholesterol-lowering properties of probiotics. Sci Pharm 2019;87:26. https://doi.org/10.3390/scip harm87040026

Latif A, Shehzad A, Niazi S, Zahid A, Ashraf W, Iqbal MW, et al. Probiotics: mechanism of action, health benefits and their application in food industries. Front Microbiol 2023;14:1216674. doi:10.3389/fmicb. 2023.1216674.

Mazziotta C, Tognon M, Martini F, Torreggiani E, Rotondo JC. Probiotics mechanism of action on immune cells and beneficial effects on human health. Cells 2023;12:184. doi:10.3390/cells12010184.

Grand View Research, Probiotics market size, share & trends analysis report by product (food & beverages, dietary supplements), by ingredient (bacteria, yeast), by distribution channel, by end-use, by region, and segment forecasts, 2023–2030 [Internet]. 2023 [cited 2023 Jan 21]. Available from: https://www.grandviewresearch.com/industry-analysis/probiotics-market

InsightAce Analytic. Human microbiome-based gut health test and nutrition market size, share & trends analysis report by product (D2C gut health test, probiotic supplements, personalized nutrition, microbiome modulators), by end-user, by region, and segment forecasts, 2023–2030 [Internet]. 2023 [cited 2023 May 18]. Available from: https://www. insightaceanalytic.com/report/global-human-microbiome-based-gut-health-test-and-nutrition-market/1221

Research and Markets. Thailand probiotics market - forecasts from 2021 to 2028. Report No. 5350974 [Internet]. 2023 [cited 2023 Jun 10]. Available from: https://www.research andmarkets.com/reports/5350974/thailand-probiotics-market-forecasts-from-2023

Mater DD, Bretigny L, Firmesse O, Flores MJ, Mogenet A, Bresson JL, et al. Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus survive gastrointestinal transit of healthy volunteers consuming yogurt. FEMS Microbiol Lett 2005;250:185–87.

Mättö J, Fondén R, Tolvanen T, von Wright A, Vilpponen-Salmela T, Satokari R, et al. Intestinal survival and persistence of probiotic Lactobacillus and Bifidobacterium strains administered in triple-strain yoghurt. Int Dairy J 2006;16:1174–180.

Ganguly NK, Bhattacharya SK, Sesikeran B, Nair GB, Ramakrishna BS, Sachdev HPS, et al. ICMR-DBT guidelines for evaluation of probiotics in food. Indian J Med Res 2011;134:22–25.

Fijan S. Microorganisms with claimed probiotic properties: an overview of recent literature. Int J Environ Res Public Health 2014;11:4745–767.

FAO/WHO. Report of a joint FAO/WHO working group on drafting guidelines for the evaluation of probiotics in food; 2002 [Internet]. [cited 2023 May 18]. Available from: https://www.mhlw.go.jp/file/05-Shingikai-11121000-Iyakushokuhinkyoku-Soumuka/000019 7343.pdf

Fusco V, Fanelli F, Chieffi D. Authenticity of probiotic foods and dietary supplements: A pivotal issue to address. Crit Rev Food Sci Nutr 2022;62:6854–871.

Kruasuwan W, Jenjaroenpun P, Arigul T, Chokesajjawatee N, Leekitcharoenphon P, Foongladda S, et al. Nanopore sequencing discloses compositional quality of commercial probiotic feed supplements. Sci Rep 2003;13:4540. doi:10.1038/s41598-023-31626-4.

Briczinski EP, Roberts RF. Technical note: a rapid pulsed-field gel electrophoresis method for analysis of bifidobacteria. J Dairy Sci 2006;89:2424–27.

Ramachandran P, Lacher DW, Pfeiler EA, Elkins CA. Development of a tiered multilocus sequence typing scheme for members of the Lactobacillus acidophilus complex. Appl Environ Microbiol 2013;79:7220–228.

Tynkkynen S, Satokari R, Saarela M, Mattila-Sandholm T, Saxelin M. Comparison of ribotyping, randomly amplified polymorphic DNA analysis, and pulsed-field gel electrophoresis in typing of Lactobacillus rhamnosus and L. casei strains. Appl Environ Microbiol 1999;65:3908–914.

Merenstein D, Pot B, Leyer G, Ouwehand AC, Preidis GA, Elkins CA, et al. Emerging issues in probiotic safety: 2023 perspectives. Gut Microbes 2023;15:2185034. doi:10.1080/19490976.2023.2185034

EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP), Rychen G, Aquilina G, Bastos ML, Christensen H, Dusemund B, et al. Guidance on the characterisation of microorganisms used as feed additives or as production organisms. EFSA J 2018;16:e05206. doi:10.2903/j.efsa.2018 .5206.

คณะกรรมการประเมินความปลอดภัยของการใช้จุลินทรีย์โพรไบโอติกในอาหาร. ข้อกำหนดขั้นต่ำ (minimum requirement) และ หลักเกณฑ์การประเมินความปลอดภัยของการใช้จุลินทรีย์โพรไบโอติกในอาหาร [อินเทอร์เน็ต]. 2566 [เข้าถึงเมื่อ 30 มิ.ย. 2566]; เข้าถึงได้จาก: https://www.biotec.or.th /biosafety/index.php/guideline

Portik DM, Brown CT, Pierce-Ward NT. Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. BMC Bioinformatics 2022;23:541. doi:10.1186/s12859-022-05103-0

Chokesajjawatee N, Santiyanont P, Chantarasakha K, Kocharin K, Thammarongtham C, Lertampaiporn S, et al. Safety assessment of a nham starter culture Lactobacillus plantarum BCC9546 via whole-genome analysis. Sci Rep 2020;10:10241. doi:10.1038/s41598-020-66857-2

Weirather JL, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang XJ, et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Research 2017;6:100. doi:10.12688/f1000research.10571.2

Umanets A, Surono IS, Venema K. I am better than I look: genome based safety assessment of the probiotic Lactiplantibacillus plantarum IS-10506. BMC Genomics 2023;24:518. doi: 10.1186/s12864-023-09495-y

Wang Y, Liang Q, Lu B, Shen H, Liu S, Shi Y, et al. Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks. BMC Genomics 2021;22:210. doi: 10.1186/ s12864-021-07539-9

Dekham K, Jones SM, Jitrakorn S, Charoonnart P, Thadtapong N, Intuy R, et al. Functional and genomic characterization of a novel probiotic Lactobacillus johnsonii KD1 against shrimp WSSV infection. Sci Rep 2023;13:21610. doi: 10.1038/s41598-023-47897-w

Mollova D, Gozmanova M, Apostolova E, Yahubyan G, Iliev I, Baev V. Illuminating the genomic landscape of Lactiplantibacillus plantarum PU3-A novel probiotic strain isolated from human breast milk, explored through nanopore sequencing. Microorganisms 2023;11:2440. doi: 10.3390/microorganisms11102440

Sudjai A, Suriye K, Kruasuwan W, Jenjaroenpun P, Foongladda S, Wongsurawat T, et al. Long-read 16S rRNA amplicon and metagenomic data of swine feed-additive probiotics product. Microbiol Resour Announc 2022;11: e0039722. doi:10.1128/mra.00397-22

Khongchatee A, Wongsurawat T, Suriye K, Jenjaroenpun P, Leekitcharoenphon P, Kruasuwan W, et al. Full-length 16S rRNA gene amplicon and metagenome taxonomic profiling of beneficial microbes in poultry and swine probiotic product. Microbiol Resour Announc 2022;11:e0069022. doi:10.1128/mra.00690-22