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Kurniawan YN, Shinohara Y, Suzuki K. Applications of the Third-Generation DNA Sequencing Technology to the Identification of Spoilage Microorganisms in the Brewing Industry. Methods Mol Biol 2024; 2851:75-85. [PMID: 39210172 DOI: 10.1007/978-1-0716-4096-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A new nanopore sequencing-based method has been developed for the detection and identification of a wider range of microorganisms. This method uses universal primers to identify virtually all the bacterial or yeast/fungal species via the amplification and nucleotide sequencing of common ribosomal DNA regions. The simplicity of its protocol makes the method suitable for both small and large breweries.
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Affiliation(s)
| | | | - Koji Suzuki
- Asahi Quality & Innovations, LTD, Ibaraki, Japan
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The Current State of Nanopore Sequencing. Methods Mol Biol 2023; 2632:3-14. [PMID: 36781717 DOI: 10.1007/978-1-0716-2996-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Nanopore sensing is a disruptive, revolutionary way in which to sequence nucleic acids, including both native DNA and RNA molecules. First commercialized with the MinIONTM sequencer from Oxford Nanopore TechnologiesTM in 2015, this review article looks at the current state of nanopore sequencing as of June 2022. Covering the unique characteristics of the technology and how it functions, we then go on to look at the ability of the platform to deliver sequencing at all scales-from personal to high-throughput devices-before looking at how the scientific community is applying the technology around the world to answer their biological questions.
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Conti A, Casagrande Pierantoni D, Robert V, Corte L, Cardinali G. MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis. Microbiol Spectr 2023; 11:e0105222. [PMID: 36519933 PMCID: PMC9927109 DOI: 10.1128/spectrum.01052-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.
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Affiliation(s)
- Angela Conti
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | - Vincent Robert
- Westerdjik Institute for Biodiversity, Utrecht, Netherlands
| | - Laura Corte
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
| | - Gianluigi Cardinali
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
- CEMIN Excellence Research Centre, Perugia, Italy
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Yokota K, Takeo A, Abe H, Kurokawa Y, Hashimoto M, Kajimoto K, Tanaka M, Murayama S, Nakajima Y, Taniguchi M, Kataoka M. Application of Micropore Device for Accurate, Easy, and Rapid Discrimination of Saccharomyces pastorianus from Dekkera spp. BIOSENSORS-BASEL 2021; 11:bios11080272. [PMID: 34436074 PMCID: PMC8393547 DOI: 10.3390/bios11080272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 11/25/2022]
Abstract
Traceability analysis, such as identification and discrimination of yeasts used for fermentation, is important for ensuring manufacturing efficiency and product safety during brewing. However, conventional methods based on morphological and physiological properties have disadvantages such as time consumption and low sensitivity. In this study, the resistive pulse method (RPM) was employed to discriminate between Saccharomyces pastorianus and Dekkera anomala and S. pastorianus and D. bruxellensis by measuring the ionic current response of cells flowing through a microsized pore. The height and shape of the pulse signal were used for the simultaneous measurement of the size, shape, and surface charge of individual cells. Accurate discrimination of S. pastorianus from Dekkera spp. was observed with a recall rate of 96.3 ± 0.8%. Furthermore, budding S. pastorianus was quantitatively detected by evaluating the shape of the waveform of the current ionic blockade. We showed a proof-of-concept demonstration of RPM for the detection of contamination of Dekkera spp. in S. pastorianus and for monitoring the fermentation of S. pastorianus through the quantitative detection of budding cells.
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Affiliation(s)
- Kazumichi Yokota
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Asae Takeo
- Institute for Future Beverages, Research & Development Division, Kirin Holdings Company, Limited. 1-17-1, Namamugi, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan; (A.T.); (Y.K.)
| | - Hiroko Abe
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Yuji Kurokawa
- Institute for Future Beverages, Research & Development Division, Kirin Holdings Company, Limited. 1-17-1, Namamugi, Tsurumi-ku, Yokohama, Kanagawa 230-8628, Japan; (A.T.); (Y.K.)
| | - Muneaki Hashimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Kazuaki Kajimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Masato Tanaka
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Sanae Murayama
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan; (S.M.); (M.T.)
| | - Yoshihiro Nakajima
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
| | - Masateru Taniguchi
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan; (S.M.); (M.T.)
| | - Masatoshi Kataoka
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14 Hayashi-cho, Takamatsu, Kagawa 761-0395, Japan; (K.Y.); (H.A.); (M.H.); (K.K.); (M.T.); (Y.N.)
- Correspondence: ; Tel.: +81-87-869-3576
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