Complete genome sequence and analysis of Lactobacillus hokkaidonensis LOOC260T,a psychrotrophic lactic acid bacterium isolated from silage |
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Authors: | Yasuhiro Tanizawa Masanori Tohno Eli Kaminuma Yasukazu Nakamura Masanori Arita |
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Affiliation: | .Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8561 Japan ;.Center for Information Biology, National Institute of Genetics, Shizuoka, 411-8540 Japan ;.National Agriculture and Food Research Organization, National Institute of Livestock and Grassland Science, Tochigi, 329-2793 Japan ;.RIKEN Center for Sustainable Resource Science, Kanagawa, 230-0045 Japan |
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Abstract: | BackgroundLactobacillus hokkaidonensis is an obligate heterofermentative lactic acid bacterium, which is isolated from Timothy grass silage in Hokkaido, a subarctic region of Japan. This bacterium is expected to be useful as a silage starter culture in cold regions because of its remarkable psychrotolerance; it can grow at temperatures as low as 4°C. To elucidate its genetic background, particularly in relation to the source of psychrotolerance, we constructed the complete genome sequence of L. hokkaidonensis LOOC260T using PacBio single-molecule real-time sequencing technology.ResultsThe genome of LOOC260T comprises one circular chromosome (2.28 Mbp) and two circular plasmids: pLOOC260-1 (81.6 kbp) and pLOOC260-2 (41.0 kbp). We identified diverse mobile genetic elements, such as prophages, integrated and conjugative elements, and conjugative plasmids, which may reflect adaptation to plant-associated niches. Comparative genome analysis also detected unique genomic features, such as genes involved in pentose assimilation and NADPH generation.ConclusionsThis is the first complete genome in the L. vaccinostercus group, which is poorly characterized, so the genomic information obtained in this study provides insight into the genetics and evolution of this group. We also found several factors that may contribute to the ability of L. hokkaidonensis to grow at cold temperatures. The results of this study will facilitate further investigation for the cold-tolerance mechanism of L. hokkaidonensis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1435-2) contains supplementary material, which is available to authorized users. |
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Keywords: | Lactic acid bacteria Silage fermentation Cold adaptation Pentose metabolism Mobile genetic element Integrative and conjugative element |
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