Updated on 2022/07/02

写真a

 
NISHIKAWA, Yohei
 
Affiliation
Research Council (Research Organization), Research Organization for Nano & Life Innovation
Job title
Junior Researcher(Assistant Professor)

Research Institute

  • 2021
    -
    2022

    リサーチイノベ オープンイノベーション推進セクション   兼任センター員

Degree

  • 2019.03   早稲田大学   工学 (Engineering)

Research Experience

  • 2021.04
    -
    Now

    Waseda University   Research Organization for Nano & Life Innovation

  • 2019.04
    -
    2021.03

    National Institute of Advanced Industrial Science and Technology   AIST-Waseda University Comptational Bio Big-Data Open Innovation Laboratory

  • 2016.04
    -
    2019.03

    Japan Society for the Promotion of Science

 

Research Areas

  • Applied microbiology

Papers

  • Strain-level profiling of viable microbial community by selective single-cell genome sequencing

    Masahito Hosokawa, Taruho Endoh, Kazuma Kamata, Koji Arikawa, Yohei Nishikawa, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Haruko Takeyama

    Scientific Reports   12 ( 1 )  2022.12  [Refereed]

     View Summary

    <title>Abstract</title>Culture-independent analysis with high-throughput sequencing has been widely used to characterize bacterial communities. However, signals derived from non-viable bacteria and non-cell DNA may inhibit its characterization. Here, we present a method for viable bacteria-targeted single-cell genome sequencing, called PMA-SAG-gel, to obtain comprehensive whole-genome sequences of surviving uncultured bacteria from microbial communities. PMA-SAG-gel uses gel matrixes that enable sequential enzymatic reactions for cell lysis and genome amplification of viable single cells from the microbial communities. PMA-SAG-gel removed the single-amplified genomes (SAGs) derived from dead bacteria and enabled selective sequencing of viable bacteria in the model samples of <italic>Escherichia coli</italic> and <italic>Bacillus subtilis</italic>. Next, we demonstrated the recovery of near-complete SAGs of eight oxygen-tolerant bacteria, including <italic>Bacteroides</italic> spp. and <italic>Phocaeicola</italic> spp., from 1331 human feces SAGs. We found the presence of two different strains in each species and identified their specific genes to investigate the metabolic functions. The survival profile of an entire population at the strain level will provide the information for understanding the characteristics of the surviving bacteria under the specific environments or sample processing and insights for quality assessment of live bacterial products or fecal microbiota transplantation and for understanding the effect of antimicrobial treatments.

    DOI

  • Male-killing-associated bacteriophage WO identified from comparisons of Wolbachia endosymbionts of Homona magnanima

    Hiroshi Arai, Hisashi Anbutsu, Yohei Nishikawa, Masato Kogawa, Kazuo Ishii, Masahito Hosokawa, Shiou-Ruei Lin, Masatoshi Ueda, Madoka Nakai, Yasuhisa Kunimi, Toshiyuki Harumoto, Daisuke Kageyama, Haruko Takeyama, Maki N. Inoue

       2022.06

    Authorship:Lead author

     View Summary

    Abstract

    The origin and mechanism of male-killing, an advantageous strategy employed by maternally transmitted symbionts such as Wolbachia, remain unclear. We compared genomes of four Wolbachia strains derived from Homona magnanima, a male-killing strain wHm-t (1.5 Mb), and three non-male-killing strains, wHm-a (1.1 Mb), wHm-b (1.3 Mb), and wHm-c (1.4 Mb). A wHm-t-specific 76-kbp prophage region harboured two tandemly arrayed WO-mediated killing (wmk) gene homologs (wmk-1/wmk-2 and wmk-3/wmk-4). Of these, wmk-1 or wmk-3 killed almost all Drosophila melanogaster individuals when transgenically overexpressed. Dual expression of wmk-3 and wmk-4 killed all males and rescued females. We propose a novel hypothesis wherein horizontally transmitted proto-Wolbachia with a single wmk killed both sexes, and tandem duplication of wmk allowed an evolutionary transition to a vertically transmitted symbiont, causing male-killing. Our study highlights the bacteriophage as a critical driver of the evolution of male-killing and argues for a conserved male-killing mechanism in diverse insects.

    DOI

  • Identification of Lipolytic Enzymes Using High-Throughput Single-cell Screening and Sorting of a Metagenomic Library

    Amani Alma’abadi, Hayedeh Behzad, Mohammed Alarawi, David Conchouso, Yoshimoto Saito, Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori

    New Biotechnology    2022.05  [Refereed]

    DOI

  • Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral

    Keigo Ide, Yohei Nishikawa, Toru Maruyama, Yuko Tsukada, Masato Kogawa, Hiroki Takeda, Haruka Ito, Ryota Wagatsuma, Rimi Miyaoka, Yoshikatsu Nakano, Koji Kinjo, Michihiro Ito, Masahito Hosokawa, Kei Yura, Shoichiro Suda, Haruko Takeyama

       2022.04

    Authorship:Lead author

     View Summary

    Abstract

    Endozoicomonas bacteria symbiose with various marine organisms and are known to be beneficial for coral health. However, genome analysis of coral-associated Endozoicomonas has been limited owing to the difficulty in cultivation and metagenomic approach by contamination of host-derived sequences. In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genome (SAGs) for coral-associated Endozoicomonas spp. genome. We obtained seven novel Endozoicomonas genomes from Acropora tenuis coral. These genomes revealed that Endozoicomonas bacteria played host-associated functions in host corals and had undergone independent host-adaptive evolution in different clades. These adaptive evolutions were mediated by host-derived eukaryotic-like genes, some of which were speculated to influence host immune mechanisms. These genes are speculated to enhance coral tolerance to environmental stresses. This study suggests the possibility of host adaptation of Endozoicomonas spp. in symbiosis with corals and their contribution to coral bleaching tolerance.

    DOI

  • Revealing within-species diversity in uncultured human gut bacteria with single-cell long-read sequencing

    Masato Kogawa, Yohei Nishikawa, Tatsuya Saeki, Takuya Yoda, Koji Arikawa, Haruko Takeyama, Masahito Hosokawa

       2022.03

     View Summary

    Abstract

    Bacterial genome structure changes dynamically, and structural variants can change bacterial phenotype; However, obtaining the complete genome and analyzing genome structure of uncultured bacteria has been challenging. We aimed to develop a single-cell amplified genome long-read assembly (scALA) workflow to construct circular single-cell amplified genomes (cSAGs) from long-read single-cell sequencing data of targeted uncultured bacteria. In particular, scALA generated cSAGs from nanopore long-read sequencing data of SAGs by producing contiguous sequences with repeated bias reduction and assembly processes. From 12 human fecal samples, scALA generated 16 cSAGs of three specifically targeted bacterial species, Anaerostipes hadrus, Agathobacter rectalis, and Ruminococcus gnavus. A. hadrus cSAGs exhibited large, ten kbp-long, phage insertions, saccharide metabolic capacity, and frequent genomic recombination with related strains from cohabitant hosts. Noteworthy, cSAGs constructed using this method could expand bacterial genome databases and our understanding of within-species diversities in uncultured bacteria.

    DOI

  • Single-cell metabolite detection and genomics reveals uncultivated talented producer

    Masato Kogawa, Rimi Miyaoka, Franziska Hemmerling, Masahiro Ando, Kei Yura, Keigo Ide, Yohei Nishikawa, Masahito Hosokawa, Yuji Ise, Jackson K B Cahn, Kentaro Takada, Shigeki Matsunaga, Tetsushi Mori, Jörn Piel, Haruko Takeyama

    PNAS Nexus   1 ( 1 )  2022.03  [Refereed]

     View Summary

    <title>Abstract</title>
    The production of bioactive metabolites is increasingly recognized as an important function of host-associated bacteria. An example is defensive symbiosis that might account for much of the chemical richness of marine invertebrates including sponges (Porifera), 1 of the oldest metazoans. However, most bacterial members of sponge microbiomes have not been cultivated or sequenced, and therefore, remain unrecognized. Unequivocally linking metabolic functions to a cellular source in sponge microbiomes is, therefore, a challenge. Here, we report an analysis pipeline of microfluidic encapsulation, Raman microscopy, and integrated digital genomics (MERMAID) for an efficient identification of uncultivated producers. We applied this method to the chemically rich bacteriosponge (sponge that hosts a rich bacterial community) Theonella swinhoei, previously shown to contain ‘Entotheonella’ symbionts that produce most of the bioactive substances isolated from the sponge. As an exception, the antifungal aurantosides had remained unassigned to a source. Raman-guided single-bacterial analysis and sequencing revealed a cryptic, distinct multiproducer, ‘Candidatus Poriflexus aureus’ from a new Chloroflexi lineage as the aurantoside producer. Its exceptionally large genome contains numerous biosynthetic loci and suggested an even higher chemical richness of this sponge than previously appreciated. This study highlights the importance of complementary technologies to uncover microbiome functions, reveals remarkable parallels between distantly related symbionts of the same host, and adds functional support for diverse chemically prolific lineages being present in microbial dark matter.

    DOI

  • Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics: An Engineering Head Start

    David Conchouso, Amani Al-Ma'abadi, Hayedeh Behzad, Mohammed Alarawi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Katsuhiko Mineta, Takashi Gojobori

    Genomics, Proteomics & Bioinformatics    2021.12  [Refereed]

    DOI

  • MBC2019: Marine Biotechnology Conference 2019.

    Haruko Takeyama, Hiroshi Saito, Yohei Nishikawa

    Marine biotechnology (New York, N.Y.)   22 ( 6 ) 725 - 726  2020.12  [International journal]

    DOI PubMed

  • High-Quality Draft Genome Sequence of a Rickettsiales Bacterium Found in Acropora tenuis Coral from Okinawa, Japan.

    Keigo Ide, Yohei Nishikawa, Masato Kogawa, Eisuke Iwamoto, Ashok Zachariah Samuel, Yoshikatsu Nakano, Haruko Takeyama

    Microbiology resource announcements   9 ( 48 )  2020.11  [International journal]

    Authorship:Lead author

     View Summary

    Rickettsiales-like organisms are important for the survival and functioning of corals, prompting an investigation of their complete genomes. Earlier reports of the genomes of these organisms remain incomplete. Here, we report a novel draft genome of Rickettsiales bacterial strain SESOKO1, found in Acropora tenuis coral, using single-cell genome technology.

    DOI PubMed

  • Draft Genome Sequence of Okeania sp. Strain KiyG1, Assembled from Single-Amplified Genomes Collected from Cape Kiyan, Okinawa, Japan.

    Muhammad Wahyudin Lewaru, Yohei Nishikawa, Keigo Ide, Masato Kogawa, Masahito Hosokawa, Ashok Zachariah Samuel, Shinpei Sumimoto, Handung Nuryadi, Shoichiro Suda, Haruko Takeyama

    Microbiology resource announcements   9 ( 46 )  2020.11  [International journal]

    Authorship:Lead author

     View Summary

    The genus Okeania is a globally distributed group of microorganisms that live in shallow seabed regions. These organisms play several environmentally important roles and are also known producers of several active secondary metabolites with potential human applications. Here, we present a draft genome of Okeania sp. strain KiyG1 (92.7% completeness) that was assembled from four single-amplified genomes.

    DOI PubMed

  • Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota.

    Rieka Chijiiwa, Masahito Hosokawa, Masato Kogawa, Yohei Nishikawa, Keigo Ide, Chikako Sakanashi, Kai Takahashi, Haruko Takeyama

    Microbiome   8 ( 1 ) 5 - 5  2020.01  [Refereed]  [International journal]

     View Summary

    BACKGROUND: The gut microbiota can have dramatic effects on host metabolism; however, current genomic strategies for uncultured bacteria have several limitations that hinder their ability to identify responders to metabolic changes in the microbiota. In this study, we describe a novel single-cell genomic sequencing technique that can identify metabolic responders at the species level without the need for reference genomes, and apply this method to identify bacterial responders to an inulin-based diet in the mouse gut microbiota. RESULTS: Inulin-feeding changed the mouse fecal microbiome composition to increase Bacteroides spp., resulting in the production of abundant succinate in the mouse intestine. Using our massively parallel single-cell genome sequencing technique, named SAG-gel platform, we obtained 346 single-amplified genomes (SAGs) from mouse gut microbes before and after dietary inulin supplementation. After quality control, the SAGs were classified as 267 bacteria, spanning 2 phyla, 4 classes, 7 orders, and 14 families, and 31 different strains of SAGs were graded as high- and medium-quality draft genomes. From these, we have successfully obtained the genomes of the dominant inulin-responders, Bacteroides spp., and identified their polysaccharide utilization loci and their specific metabolic pathways for succinate production. CONCLUSIONS: Our single-cell genomics approach generated a massive amount of SAGs, enabling a functional analysis of uncultured bacteria in the intestinal microbiome. This enabled us to estimate metabolic lineages involved in the bacterial fermentation of dietary fiber and metabolic outcomes such as short-chain fatty acid production in the intestinal environment based on the fibers ingested. The technique allows the in-depth isolation and characterization of uncultured bacteria with specific functions in the microbiota and could be exploited to improve human and animal health. Video abstract.

    DOI PubMed

  • High-throughput identification of peptide agonists against GPCRs by co-culture of mammalian reporter cells and peptide-secreting yeast cells using droplet microfluidics.

    Kenshi Yaginuma, Wataru Aoki, Natsuko Miura, Yuta Ohtani, Shunsuke Aburaya, Masato Kogawa, Yohei Nishikawa, Masahito Hosokawa, Haruko Takeyama, Mitsuyoshi Ueda

    Scientific reports   9 ( 1 ) 10920 - 10920  2019.07  [Refereed]  [International journal]

     View Summary

    Since G-protein coupled receptors (GPCRs) are linked to various diseases, screening of functional ligands against GPCRs is vital for drug discovery. In the present study, we developed a high-throughput functional cell-based assay by combining human culture cells producing a GPCR, yeast cells secreting randomized peptide ligands, and a droplet microfluidic device. We constructed a reporter human cell line that emits fluorescence in response to the activation of human glucagon-like peptide-1 receptor (hGLP1R). We then constructed a yeast library secreting an agonist of hGLP1R or randomized peptide ligands. We demonstrated that high-throughput identification of functional ligands against hGLP1R could be performed by co-culturing the reporter cells and the yeast cells in droplets. We identified functional ligands, one of which had higher activity than that of an original sequence. The result suggests that our system could facilitate the discovery of functional peptide ligands of GPCRs.

    DOI PubMed

  • Correction to: A CCR5+ memory subset within HIV-1-infected primary resting CD4+ T cells is permissive for replication-competent, latently infected viruses in vitro.

    Kazutaka Terahara, Ryutaro Iwabuchi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Yoshimasa Takahashi, Yasuko Tsunetsugu-Yokota

    BMC research notes   12 ( 1 ) 322 - 322  2019.06  [Refereed]  [International journal]

     View Summary

    After publication of the original article [1], the authors became aware of a miscalculation in the original Fig. 2d.

    DOI PubMed

  • A CCR5+ memory subset within HIV-1-infected primary resting CD4+ T cells is permissive for replication-competent, latently infected viruses in vitro.

    Kazutaka Terahara, Ryutaro Iwabuchi, Masahito Hosokawa, Yohei Nishikawa, Haruko Takeyama, Yoshimasa Takahashi, Yasuko Tsunetsugu-Yokota

    BMC research notes   12 ( 1 ) 242 - 242  2019.04  [Refereed]  [International journal]

     View Summary

    OBJECTIVE: Resting CD4+ T cells are major reservoirs of latent HIV-1 infection, and may be formed during the early phase of the infection. Although CCR5-tropic (R5) HIV-1 is highly transmissible during the early phase, newly infected individuals have usually been exposed to a mixture of R5 and CXCR4-tropic (X4) viruses, and X4 viral DNA is also detectable in the host. Our aim was to identify which subsets of resting CD4+ T cells contribute to forming the latent reservoir in the presence of both X4 and R5 viruses. RESULTS: Primary resting CD4+ naïve T (TN) cells, CCR5- memory T (TM) cells, and CCR5+ TM cells isolated by flow cytometry were infected simultaneously with X4 and R5 HIV-1, which harbored different reporter genes, and were cultured in the resting condition. Flow cytometry at 3 days post-infection demonstrated that X4 HIV-1+ cells were present in all three subsets of cells, whereas R5 HIV-1+ cells were present preferentially in CCR5+ TM cells, but not in TN cells. Following CD3/CD28-mediated activation at 3 days post-infection, numbers of R5 HIV-1+ cells and X4 HIV-1+ cells increased significantly only in the CCR5+ TM subset, suggesting that it provides a major reservoir of replication-competent, latently infected viruses.

    DOI PubMed

  • Obtaining high-quality draft genomes from uncultured microbes by cleaning and co-assembly of single-cell amplified genomes.

    Masato Kogawa, Masahito Hosokawa, Yohei Nishikawa, Kazuki Mori, Haruko Takeyama

    Scientific reports   8 ( 1 ) 2059 - 2059  2018.02  [Refereed]  [International journal]

     View Summary

    Single-cell genomics is a straightforward approach to obtain genomes from uncultured microbes. However, sequence reads from a single-cell amplified genome (SAG) contain significant bias and chimeric sequences. Here, we describe Cleaning and Co-assembly of a Single-Cell Amplified Genome (ccSAG), a novel analytical workflow to obtain composite single-cell genomes with elimination of sequence errors. By the integration of ccSAG with a massively parallel single-cell genome amplification platform based on droplet microfluidics, we can generate multiple SAGs and effectively integrate them into the composite genomes quality equivalent to the data obtained from bulk DNA. We obtained two novel draft genomes from single gut microbial cells with high completeness (>96.6%) and extremely low contamination (<1.25%). Moreover, we revealed the presence of single nucleotide polymorphisms in the specific gene by sequence comparison at the single-cell level. Thus, the workflow yields near-complete genomes from uncultured microbes, and enables analyses of genetic heterogeneity within identical strains.

    DOI PubMed

  • Analysis of environmental bacteria at single-cell level

    Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama

    TRANSDUCERS 2017 - 19th International Conference on Solid-State Sensors, Actuators and Microsystems     634 - 637  2017.07  [Refereed]

     View Summary

    Single-cell genomics has enabled the exploration of cellular diversity in environmental microbes. However, current genome sequencing techniques, which utilizes next-generation sequencing (NGS), typically require nanogram to microgram levels of input DNA sample. Since single bacterial cells contain only a few femtograms of DNA, we have to amplify their genomes to adequate amount for sequencing. We aimed to develop a novel system for precise and high throughput single-cell genomics, to elucidate environmental microbial diversity. In this study, we have developed droplet-based microfluidic system to produce the compartmentalized reaction vessels for single-cell genome sequencing.

    DOI

  • Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics.

    Masahito Hosokawa, Yohei Nishikawa, Masato Kogawa, Haruko Takeyama

    Scientific reports   7 ( 1 ) 5199 - 5199  2017.07  [Refereed]  [International journal]

     View Summary

    Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.

    DOI PubMed

  • Droplet-based microfluidics for high-throughput screening of a metagenomic library for isolation of microbial enzymes.

    Masahito Hosokawa, Yuri Hoshino, Yohei Nishikawa, Tomotada Hirose, Dong Hyun Yoon, Tetsushi Mori, Tetsushi Sekiguchi, Shuichi Shoji, Haruko Takeyama

    Biosensors & bioelectronics   67   379 - 85  2015.05  [Refereed]  [International journal]

     View Summary

    This paper proposes a high-throughput, function-based screening approach of a metagenomic library for isolating novel microbial enzymes by droplet-based microfluidics. We used gel microdroplets (GMDs) dispersed in oil as picoliter-volume reaction vessels for lipolytic enzyme by encapsulating cells in individual GMDs. Using this approach, we monitored the growth of individual cells encapsulated in GMDs and assessed the enzyme reaction activities at the level of an individual GMD. We then applied this method to screen lipolytic enzyme genes from the metagenomic library constructed from soil collected from a quercus serrate forest of Mount Tsukuba, Ibaraki, Japan. In the workflow presented in this study, metagenomic library clones were encapsulated in 100-pL GMDs with a fluorogenic reporter substrate. A total of 67,000 metagenomic library clones can be screened in only 24 h with reduced consumption of reagents (i.e., <10 μL). As a result, we identified a novel lipolytic enzyme, EstT1, belonging to the EstD2 family of esterases and containing a putative signal peptide, which facilitates enzyme export and catalyzation of substrates in the periplasm. Our study demonstrates the potential of microfluidic GMDs as an efficient tool for metagenomic library screening of industrially relevant enzymes with the potential of significantly reducing the cost and time factors involved in successful practical application of microbial enzymes.

    DOI PubMed

  • Monodisperse Picoliter Droplets for Low-Bias and Contamination-Free Reactions in Single-Cell Whole Genome Amplification.

    Yohei Nishikawa, Masahito Hosokawa, Toru Maruyama, Keisuke Yamagishi, Tetsushi Mori, Haruko Takeyama

    PloS one   10 ( 9 ) e0138733  2015  [Refereed]  [International journal]

     View Summary

    Whole genome amplification (WGA) is essential for obtaining genome sequences from single bacterial cells because the quantity of template DNA contained in a single cell is very low. Multiple displacement amplification (MDA), using Phi29 DNA polymerase and random primers, is the most widely used method for single-cell WGA. However, single-cell MDA usually results in uneven genome coverage because of amplification bias, background amplification of contaminating DNA, and formation of chimeras by linking of non-contiguous chromosomal regions. Here, we present a novel MDA method, termed droplet MDA, that minimizes amplification bias and amplification of contaminants by using picoliter-sized droplets for compartmentalized WGA reactions. Extracted DNA fragments from a lysed cell in MDA mixture are divided into 105 droplets (67 pL) within minutes via flow through simple microfluidic channels. Compartmentalized genome fragments can be individually amplified in these droplets without the risk of encounter with reagent-borne or environmental contaminants. Following quality assessment of WGA products from single Escherichia coli cells, we showed that droplet MDA minimized unexpected amplification and improved the percentage of genome recovery from 59% to 89%. Our results demonstrate that microfluidic-generated droplets show potential as an efficient tool for effective amplification of low-input DNA for single-cell genomics and greatly reduce the cost and labor investment required for determination of nearly complete genome sequences of uncultured bacteria from environmental samples.

    DOI PubMed

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Books and Other Publications

  • Novel insights and possibilities in single cell

    ( Part: Contributor, High-throughput platform for screening of novel bioactive compound producers)

    2021.08

  • -

    ( Part: Joint author)

    2020

  • バイオイノベーションに向けて : バイオテクノロジーの新技術からの新しい視点

    植田, 充美( Part: Contributor)

    シーエムシー出版  2019.03 ISBN: 9784781314112

Awards

  • -

    2016.09   The Society for Biotechnology, Japan  

Research Projects

  • シングルゲノム情報を用いた水圏ファージ-宿主間の相互作用解析

    国立研究開発法人科学技術振興機構(JST)  戦略的創造研究推進事業(ACT-X)

    Project Year :

    2020.12
    -
    2023.03
     

  • 河川水中の薬剤耐性遺伝子の時空間的な伝播・分布を単一細胞全ゲノム情報から解明する

    日本学術振興会  科学研究費助成事業 若手研究

    Project Year :

    2020.04
    -
    2022.03
     

    西川 洋平

  • 育種を加速するパスウェイ型シミュレータの開発とバイオデータ連携基盤構築

    Project Year :

    2019
    -
    2020.03
     

  • マイクロドロップレットを用いた単一微生物からの生合成遺伝子クラスターの超並列解析

    日本学術振興会  科学研究費助成事業 特別研究員奨励費

    Project Year :

    2016.04
    -
    2019.03
     

    西川 洋平

     View Summary

    環境中の微生物は99%以上が難培養性であり、生物界におけるダークマターと例えられる。難培養微生物が有する遺伝子の詳細な解析には、単一細胞レベルでのゲノム解析が有効であるが、従来までの手法では、多様な細胞種に適用可能なスクリーニング量が得られていなかった。そこで本研究では、環境中の微生物がもつ全ゲノムの情報を単一細胞レベルで解析し、標的微生物が有する遺伝子の情報を効率的に取得する技術の開発を目指す。
    本年度の研究では、前年度に開発した微小液滴内での全ゲノム増幅技術を用いて、得られた増幅産物からの次世代シーケンサによる配列解析を行った。この結果、微小液滴を用いた単一細胞のゲノム増幅技術が、従来法に比べより高精度かつ多数の単一細胞に対して応用が可能な技術であることを実証することができた。以上の結果をまとめ、論文発表を行った。
    本年度はまた、開発した手法の環境微生物への応用を行い、土壌細菌やマウスの腸内細菌などを対象としたゲノム解析に取り組んだ。これにより、土壌細菌からは17個、マウス腸内細菌からは72個の単一細胞由来のゲノム情報が獲得され、得られた情報の約65%が国際基準で定められた指標においてHigh-qualityもしくはMedium-qualityに分類されることが明らかとなった。以上の結果から、環境の異なる様々な条件のサンプルを用いた場合においても、開発した手法によって高品質なゲノム情報が取得可能であることが証明された。

Presentations

  • 1細胞・1粒子レベルのゲノム情報から読み解く、環境細菌とファージの相互作用

    西川洋平  [Invited]

    バイオインフォマティクス相談部会 第五回講演会 

    Presentation date: 2022.03

    Event date:
    2022.03
     
     
  • Microfluidic droplet-based single-cell genome sequencing reveals biological diversities of environmental microbiome in the surrounding area of the Red Sea

    Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama

    The 2020 International Chemical Congress of Pacific Basin Societies (Pacifichem 2020) 

    Presentation date: 2021.12

    Event date:
    2021.12
     
     
  • Microfluidic droplet-based single-cell genomics in aquatic and marine environments for revealing microbial and phage diversity.

    Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Keigo Ide, Ryota Wagatsuma, Yuko Tsukada, Haruko Takeyama  [Invited]

    2021 AFOB virtual conference 

    Presentation date: 2021.11

    Event date:
    2021.11
     
     
  • 河川水中の細菌・ウイルスを対象とした1細胞・1粒子レベルでのゲノム解析

    西川 洋平, 我妻 竜太, 塚田 祐子, 井手 圭吾, 小川 雅人, 細川 正人, 竹山 春子

    日本水処理生物学会第57回(神奈川)大会 

    Presentation date: 2021.10

    Event date:
    2021.10
     
     
  • シングルゲノム情報を用いた 水圏ファージ-宿主間の相互作用解析

    西川洋平

    第73回 日本生物工学会大会 

    Presentation date: 2021.10

    Event date:
    2021.10
     
     
  • Single-cell Genomics of River Water Microbiomes for Revealing the Distribution of Mobile Genetic Elements

    Y. Nishikawa, Y. Tsukada, R. Wagatsuma, K. Ide, M Kogawa, M. Hosokawa, H. Takeyama

    World Microbe Forum 2021 

    Presentation date: 2021.06

    Event date:
    2021.06
     
     
  • 水圏環境の細菌・ファージの動態解明に向けたシングルゲノム解析

    西川洋平

    第21回マリンバイオテクノロジー学会大会 

    Presentation date: 2021.05

    Event date:
    2021.05
     
     
  • 多摩川に存在する薬剤耐性菌のゲノム情報をシングルセルレベルで解析する

    西川洋平, 小川雅人, 塚田祐子, 井手圭吾, 細川正人, 竹山春子

    第55回日本水環境学会年会 

    Presentation date: 2021.03

  • 紅海周辺の多様な環境微生物を対象とした大規模かつ高精度なシングルセルゲノム解析

    西川洋平, 小川雅人, 細川正人, 峯田克彦, 高橋海, 坂梨千佳子, 由良敬, 井手圭吾, ベザドハイジ, 五條堀孝, 竹山春子

    第43回日本分子生物学会 

    Presentation date: 2020.12

    Event date:
    2020.12
     
     
  • マイクロ流体デバイスを用いた環境細菌の高精度かつ一細胞選択的な全ゲノム解析

    西川洋平, 細川正人, 小川雅人, 井手圭吾, 竹山春子

    電気化学会第87回大会 

    Presentation date: 2020.03

  • Development of microfluidic droplet-based whole genome amplification method for single-cell genome analysis of coral commensal bacteria; Endozoicomonas

    Yohei Nishikawa, Masahito Hosokawa, Masato Kogawa, Keigo Ide, Haruko Takeyama

    Marine biotechnology conference 2019 

    Presentation date: 2019.09

  • 微小反応場を活用したサンゴ共在微生物の高精度なシングルセルゲノム解析

    西川洋平, 細川正人, 小川雅人, 井手圭吾, 竹山春子

    シングルセルゲノミクス研究会2019 

    Presentation date: 2019.08

  • 微小液滴作製技術を応用したサンゴ共在微生物の高精度な単一細胞ゲノム解析技術の確立

    西川洋平, 細川正人, 小川雅人, 井手圭吾, 竹山春子

    第71回日本生物工学会大会 

    Presentation date: 2019.08

  • マイクロドロップレットを用いた網羅的な単一細胞ゲノム解析技術の開発

    西川洋平, 細川正人, 小川雅人, 竹山春子

    第18回 産総研・産技連LS-BT合同研究発表会 

    Presentation date: 2019.05

  • Microfluidic droplet-based whole genome amplification toward bacteria single-cell genomics

    ADVANCED TECHNIQUES TO STUDY AND EXPLOIT THE SPONGE AND CORAL MICROBIOMES WORKSHOP 

    Presentation date: 2018.11

  • サンゴ共在微生物の単一細胞ゲノム解析に向けた微小液滴作成技術の応用

    西川 洋平, 細川 正人, 小川 雅人, 竹田 裕貴, 丸山 徹, 竹山春子

    第20回マリンバイオテクノロジー学会 

    Presentation date: 2018.05

  • Droplet microfluidics toward accurate genome sequencing of environmental bacteria at the single-cell level

    NISHIKAWA, Yohei, HOSOKAWA, Masahito, KOGAWA, Masato, TAKAHASHI, Kai, TAKEYAMA, Haruko

    Presentation date: 2018.03

  • Droplet microfluidics for massively parallel and accurate whole genome amplification of single-cells

    International Symposium for Nano-Biotechnology, Chemical & Medical Biology and Robotics, 

    Presentation date: 2018

  • 微小液滴を用いた単一細胞からの超並列ゲノム解析技術の開発

    第69回日本生物工学会大会 

    Presentation date: 2017.09

  • マイクロ流体デバイスによる高精度な超並列1細胞ゲノム増幅技術の開発

    西川 洋平, 細川 正人, 小川 雅人, 竹山 春子

    NGS現場の会第5回研究会 

    Presentation date: 2017

  • マイクロドロップレットを用いた高精度な超並列1細胞ゲノム解析技術の開発

    西川 洋平, 細川 正人, 小川 雅人, 竹山 春子

    第11回バイオ関連化学シンポジウム 

    Presentation date: 2017

  • 単一微生物からの高精度な全ゲノム解析に向けたマイクロ流体デバイスの活用

    西川洋平  [Invited]

    日本生物工学会東日本支部第11回学生発表討論会 

    Presentation date: 2016.11

  • マイクロドロップレットによる単一微生物からの効率的な全ゲノム増幅法の開発

    西川洋平

    第4回日本生物工学会東日本支部コロキウム 

    Presentation date: 2016

  • 微小液滴を用いた単一微生物からの低バイアス全ゲノム増幅法の開発

    西川 洋平, 細川 正人, 竹山 春子

    第10回日本ゲノム微生物学会年会 

    Presentation date: 2016

  • Picoliter-sized droplets for low-bias and contamination-free reactions in whole genome amplification of single bacterial cells

    Yohei Nishikawa, Masahito Hosokawa, Masato Kogawa, Haruko Takeyama

    Biosensors2016 

    Presentation date: 2016

  • ピコリットル容量の微小液滴を用いた単一微生物からの網羅的な全ゲノム増幅

    西川洋平, 細川正人, 小川雅人, 竹山春子

    第68回日本生物工学会大会 

    Presentation date: 2016

  • DROPLET MICROFLUIDICS FOR MASSIVELY PARALLEL AND ACCURATE GENOME AMPLIFICATION OF SINGLE CELLS

    Yohei Nishikawa, Masahito Hosokawa, Masato Kogawa, Haruko Takeyama

    International Confrence on single cell Research 2016 

    Presentation date: 2016

  • 単一細胞ゲノム解析に向けた Droplet-based multiple displacement amplification 法の開発

    西川洋平, 細川正人, 竹山春子

    第17回マリンバイオテクノロジー学会 

    Presentation date: 2015.05

  • マイクロ流体デバイスを用いた単一細胞解析に向けたMultiple displacement amplification (MDA) 法の開発

    西川洋平

    第3回日本生物工学会東日本支部コロキウム 

    Presentation date: 2015

  • Picoliter-sized droplets for low bias whole genome amplification of single cell genome

    2015 International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2015) 

    Presentation date: 2015

  • マイクロドロップレットを用いた微生物の薬剤感受性評価

    西川洋平, 細川正人, 竹山春子

    第2回日本生物工学会東日本支部コロキウム 

    Presentation date: 2014

  • シングルセルゲノミクスに向けた Droplet-based Multiple Displacement Amplification 法の開発

    西川洋平, 細川正人, 竹山春子

    第4回CSJ化学フェスタ2014 

    Presentation date: 2014

  • 単一細胞封入ドロップレットを用いた微生物の薬剤感受性評価

    西川洋平, 細川正人, 竹山春子

    電気化学学会第81回大会 

    Presentation date: 2014

  • Droplet-based multiple displacement amplification method for single-cell genomics using microfluidic device

    10th International Symposium on Electrochemical Micro & Nanosystem Technologies (EMNT 2014) 

    Presentation date: 2014

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