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Extensive single-cell genomics reveals bacterial diversity and diverse phage host ranges in the area in and around the Red Sea

View ORCID ProfileYohei Nishikawa, Masato Kogawa, View ORCID ProfileMasahito Hosokawa, Ryota Wagatsuma, View ORCID ProfileKatsuhiko Mineta, Kai Takahashi, Keigo Ide, View ORCID ProfileKei Yura, Hayedeh Behzad, View ORCID ProfileTakashi Gojobori, View ORCID ProfileHaruko Takeyama
doi: https://doi.org/10.1101/2020.03.05.962001
Yohei Nishikawa
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
2Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
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Masato Kogawa
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
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Masahito Hosokawa
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
2Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
4Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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  • For correspondence: masahosokawa@aoni.waseda.jp haruko-takeyama@waseda.jp
Ryota Wagatsuma
2Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
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Katsuhiko Mineta
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
5King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
6King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
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Kai Takahashi
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
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Keigo Ide
2Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
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Kei Yura
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
7Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
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Hayedeh Behzad
8King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE) Division, Thuwal 23955-6900, Saudi Arabia
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Takashi Gojobori
6King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Saudi Arabia
8King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE) Division, Thuwal 23955-6900, Saudi Arabia
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Haruko Takeyama
1Research Organization for Nano & Life Innovation, Waseda University, 513 Waseda tsurumaki-cho, Shinjuku-ku, Tokyo, 162–0041, Japan
2Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo, 169–0072, Japan
3Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162–8480, Japan
4Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, Japan
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  • For correspondence: masahosokawa@aoni.waseda.jp haruko-takeyama@waseda.jp
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Abstract

To improve our understanding of the environmental microbiome, we developed a single-cell genome sequencing platform, named SAG-gel, which utilizes gel beads for single-cell isolation, cell lysis, and whole genome amplification (WGA) for sequencing. SAG-gel enables serial, parallel and independent reactions of > 100,000 single cells in a single tube, delivering high-quality genome recovery with storable randomized single-cell genome libraries. From soil and marine environmental sources, we acquired 734 partial genomes that are recapitulated in 231 species, 35% of which were assigned as high-to-medium qualities. We found that each genome to be almost unique and 98.7% of them were newly identified, implying the complex genetic diversities across 44 phyla. The various metabolic capabilities including virulence factors and biosynthetic gene clusters were found across the lineages at single-cell resolution. This technology will accelerate the accumulation of reference genomes of uncharacterized environmental microbes and provide us new insights for their roles.

Competing Interest Statement

M.H. and H.T. are shareholders in bitBiome, to which the patents 849pertaining to SAG-gel workflow were transferred.

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Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Extensive single-cell genomics reveals bacterial diversity and diverse phage host ranges in the area in and around the Red Sea
Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama
bioRxiv 2020.03.05.962001; doi: https://doi.org/10.1101/2020.03.05.962001
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Extensive single-cell genomics reveals bacterial diversity and diverse phage host ranges in the area in and around the Red Sea
Yohei Nishikawa, Masato Kogawa, Masahito Hosokawa, Ryota Wagatsuma, Katsuhiko Mineta, Kai Takahashi, Keigo Ide, Kei Yura, Hayedeh Behzad, Takashi Gojobori, Haruko Takeyama
bioRxiv 2020.03.05.962001; doi: https://doi.org/10.1101/2020.03.05.962001

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