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Itto-Nakama K, Watanabe S, Kondo N, Ohnuki S, Kikuchi R, Nakamura T, Ogasawara W, Kasahara K, Ohya Y. AI-based forecasting of ethanol fermentation using yeast morphological data. Biosci Biotechnol Biochem 2021; 86:125-134. [PMID: 34751736 DOI: 10.1093/bbb/zbab188] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 11/12/2022]
Abstract
Several industries require getting information of products as soon as possible during fermentation. However, the trade-off between sensing speed and data quantity presents challenges for forecasting fermentation product yields. In this study, we tried to develop AI models to forecast ethanol yields in yeast fermentation cultures, using cell morphological data. Our platform involves the quick acquisition of yeast morphological images using a nonstaining protocol, extraction of high-dimensional morphological data using image processing software, and forecasting of ethanol yields via supervised machine learning. We found that the neural network algorithm produced the best performance, which had a coefficient of determination of >0.9 even at 30 and 60 min in the future. The model was validated using test data collected using the CalMorph-PC(10) system, which enables rapid image acquisition within 10 min. AI-based forecasting of product yields based on cell morphology will facilitate the management and stable production of desired biocommodities.
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Affiliation(s)
- Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shun Watanabe
- Chitose Laboratory Corp., Biotechnology Research Center, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ryota Kikuchi
- Chitose Laboratory Corp., Biotechnology Research Center, Miyamae-ku, Kawasaki, Kanagawa, Japan
- Circular Bioeconomy Development, Office of Society Academia Collaboration for Innovation, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, Japan
| | - Toru Nakamura
- NRI System Techno Ltd., Hodogaya-ku, Yokohama, Kanagawa, Japan
| | - Wataru Ogasawara
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata, Japan
| | - Ken Kasahara
- Chitose Laboratory Corp., Biotechnology Research Center, Miyamae-ku, Kawasaki, Kanagawa, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Nakagawa Y, Ohnuki S, Kondo N, Itto-Nakama K, Ghanegolmohammadi F, Isozaki A, Ohya Y, Goda K. Are droplets really suitable for single-cell analysis? A case study on yeast in droplets. LAB ON A CHIP 2021; 21:3793-3803. [PMID: 34581379 DOI: 10.1039/d1lc00469g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Single-cell analysis has become one of the main cornerstones of biotechnology, inspiring the advent of various microfluidic compartments for cell cultivation such as microwells, microtrappers, microcapillaries, and droplets. A fundamental assumption for using such microfluidic compartments is that unintended stress or harm to cells derived from the microenvironments is insignificant, which is a crucial condition for carrying out unbiased single-cell studies. Despite the significance of this assumption, simple viability or growth tests have overwhelmingly been the assay of choice for evaluating culture conditions while empirical studies on the sub-lethal effect on cellular functions have been insufficient in many cases. In this work, we assessed the effect of culturing cells in droplets on the cellular function using yeast morphology as an indicator. Quantitative morphological analysis using CalMorph, an image-analysis program, demonstrated that cells cultured in flasks, large droplets, and small droplets significantly differed morphologically. From these differences, we identified that the cell cycle was delayed in droplets during the G1 phase and during the process of bud growth likely due to the checkpoint mechanism and impaired mitochondrial function, respectively. Furthermore, comparing small and large droplets, cells cultured in large droplets were morphologically more similar to those cultured in a flask, highlighting the advantage of increasing the droplet size. These results highlight a potential source of bias in cell analysis using droplets and reinforce the significance of assessing culture conditions of microfluidic cultivation methods for specific study cases.
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Affiliation(s)
- Yuta Nakagawa
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Naoko Kondo
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kaori Itto-Nakama
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Farzan Ghanegolmohammadi
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Akihiro Isozaki
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8654, Japan.
| | - Keisuke Goda
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Department of Bioengineering, Samueli School of Engineering, University of California, Los Angeles, 420 Westwood Plaza, California 90095, USA
- Institute of Technological Sciences, Wuhan University, Wuhan, Hubei 430072, China
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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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Ohnuki S, Ohya Y. High-dimensional single-cell phenotyping reveals extensive haploinsufficiency. PLoS Biol 2018; 16:e2005130. [PMID: 29768403 PMCID: PMC5955526 DOI: 10.1371/journal.pbio.2005130] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/06/2018] [Indexed: 12/17/2022] Open
Abstract
Haploinsufficiency, a dominant phenotype caused by a heterozygous loss-of-function mutation, has been rarely observed. However, high-dimensional single-cell phenotyping of yeast morphological characteristics revealed haploinsufficiency phenotypes for more than half of 1,112 essential genes under optimal growth conditions. Additionally, 40% of the essential genes with no obvious phenotype under optimal growth conditions displayed haploinsufficiency under severe growth conditions. Haploinsufficiency was detected more frequently in essential genes than in nonessential genes. Similar haploinsufficiency phenotypes were observed mostly in mutants with heterozygous deletion of functionally related genes, suggesting that haploinsufficiency phenotypes were caused by functional defects of the genes. A global view of the gene network was presented based on the similarities of the haploinsufficiency phenotypes. Our dataset contains rich information regarding essential gene functions, providing evidence that single-cell phenotyping is a powerful approach, even in the heterozygous condition, for analyzing complex biological systems. Diploid organisms harboring a wild-type gene and a loss-of-function mutation are called heterozygotes. They are expected to have weak or no individual phenotypes because the mutation is compensated for by the intact allele. The dominant inheritance of phenotypes in heterozygotes is an exceptional phenomenon called haploinsufficiency. Haploinsufficiency was thought to be a rare occurrence; however, a sensitive technique called high-dimensional single-cell phenotyping challenges this perspective. Investigations of single-cell phenotypes revealed that a large extent of the essential genes in yeast exhibit haploinsufficiency. Our analyses also provided crucial information on gene functional networks based on haploinsufficiency phenotypes. This work shows that high-dimensional single-cell phenotyping is a useful tool that can be used to better understand complex biological systems.
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Affiliation(s)
- Shinsuke Ohnuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
| | - Yoshikazu Ohya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan
- AIST-UTokyo Advanced Operando-Measurement Technology Open Innovation Laboratory (OPERANDO-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Kashiwa, Chiba, Japan
- * E-mail:
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Abstract
Sake yeast was developed exclusively in Japan. Its diversification during breeding remains largely uncharacterized. To evaluate the breeding processes of the sake lineage, we thoroughly investigated the phenotypes and differentiation of 27 sake yeast strains using high-dimensional, single-cell, morphological phenotyping. Although the genetic diversity of the sake yeast lineage is relatively low, its morphological diversity has expanded substantially compared to that of the Saccharomycescerevisiae species as a whole. Evaluation of the different types of breeding processes showed that the generation of hybrids (crossbreeding) has more profound effects on cell morphology than the isolation of mutants (mutation breeding). Analysis of phenotypic robustness revealed that some sake yeast strains are more morphologically heterogeneous, possibly due to impairment of cellular network hubs. This study provides a new perspective for studying yeast breeding genetics and micro-organism breeding strategies.
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Large-Scale Survey of Intraspecific Fitness and Cell Morphology Variation in a Protoploid Yeast Species. G3-GENES GENOMES GENETICS 2016; 6:1063-71. [PMID: 26888866 PMCID: PMC4825641 DOI: 10.1534/g3.115.026682] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
It is now clear that the exploration of the genetic and phenotypic diversity of nonmodel species greatly improves our knowledge in biology. In this context, we recently launched a population genomic analysis of the protoploid yeast Lachancea kluyveri (formerly Saccharomyces kluyveri), highlighting a broad genetic diversity (π = 17 × 10−3) compared to the yeast model organism, S. cerevisiae (π = 4 × 10−3). Here, we sought to generate a comprehensive view of the phenotypic diversity in this species. In total, 27 natural L. kluyveri isolates were subjected to trait profiling using the following independent approaches: (i) analyzing growth in 55 growth conditions and (ii) investigating 501 morphological changes at the cellular level. Despite higher genetic diversity, the fitness variance observed in L. kluyveri is lower than that in S. cerevisiae. However, morphological features show an opposite trend. In addition, there is no correlation between the origins (ecological or geographical) of the isolate and the phenotypic patterns, demonstrating that trait variation follows neither population history nor source environment in L. kluyveri. Finally, pairwise comparisons between growth rate correlation and genetic diversity show a clear decrease in phenotypic variability linked to genome variation increase, whereas no such a trend was identified for morphological changes. Overall, this study reveals for the first time the phenotypic diversity of a distantly related species to S. cerevisiae. Given its genetic properties, L. kluyveri might be useful in further linkage mapping analyses of complex traits, and could ultimately provide a better insight into the evolution of the genotype–phenotype relationship across yeast species.
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Tamura H, Okada H, Kume K, Koyano T, Goshima T, Nakamura R, Akao T, Shimoi H, Mizunuma M, Ohya Y, Hirata D. Isolation of a spontaneous cerulenin-resistant sake yeast with both high ethyl caproate-producing ability and normal checkpoint integrity. Biosci Biotechnol Biochem 2015; 79:1191-9. [PMID: 25787154 DOI: 10.1080/09168451.2015.1020756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In the brewing of high-quality sake such as Daiginjo-shu, the cerulenin-resistant sake yeast strains with high producing ability to the flavor component ethyl caproate have been used widely. Genetic stability of sake yeast would be important for the maintenance of both fermentation properties of yeast and quality of sake. In eukaryotes, checkpoint mechanisms ensure genetic stability. However, the integrity of these mechanisms in sake yeast has not been examined yet. Here, we investigated the checkpoint integrity of sake yeasts, and the results suggested that a currently used cerulenin-resistant sake yeast had a defect in spindle assembly checkpoint (SAC). We also isolated a spontaneous cerulenin-resistant sake yeast FAS2-G1250S mutant, G9CR, which showed both high ethyl caproate-producing ability and integrity/intactness of the checkpoint mechanisms. Further, morphological phenotypic robustness analysis by use of CalMorph supported the genetic stability of G9CR. Finally, we confirmed the high quality of sake from G9CR in an industrial sake brewing setting.
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Affiliation(s)
- Hiroyasu Tamura
- a Research and Development Department , Asahi Sake Brewing Co., Ltd. , Nagaoka , Japan
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Unveiling nonessential gene deletions that confer significant morphological phenotypes beyond natural yeast strains. BMC Genomics 2014; 15:932. [PMID: 25344683 PMCID: PMC4221665 DOI: 10.1186/1471-2164-15-932] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/15/2014] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Phenotypes are variable within species, with high phenotypic variation in the fitness and cell morphology of natural yeast strains due to genetic variation. A gene deletion collection of yeast laboratory strains also contains phenotypic variations, demonstrating the involvement of each gene and its specific function. However, to date, no study has compared the phenotypic variations between natural strains and gene deletion mutants in yeast. RESULTS The morphological variance was compared between 110 most distinct gene deletion strains and 36 typical natural yeast strains using a generalized linear model. The gene deletion strains had higher morphological variance than the natural strains. Thirty-six gene deletion mutants conferred significant morphological changes beyond that of the natural strains, revealing the importance of the genes with high genetic interaction and specific cellular functions for species conservation. CONCLUSION Based on the morphological analysis, we discovered gene deletion mutants whose morphologies were not seen in nature. Our multivariate approach to the morphological diversity provided a new insight into the evolution and species conservation of yeast.
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