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.
Highlights
Lactobacillus hokkaidonensis is an obligate heterofermentative lactic acid bacterium, which is isolated from Timothy grass silage in Hokkaido, a subarctic region of Japan
Genome features of L. hokkaidonensis LOOC260T Whole-genome sequencing was conducted with the PacBio single-molecule real-time (SMRT) sequencing system to determine the genome sequence of L. hokkaidonensis LOOC260T
In this study, we successfully reconstructed the complete genome of L. hokkaidonensis LOOC260T by whole-genome sequencing using the PacBio SMRT sequencing system and de novo assembly based on the hierarchical genome assembly process (HGAP) method
Summary
Lactobacillus 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. LAB produce lactic acid anaerobically as the major end product of central carbohydrate metabolism, which reduces the pH of the surrounding environment. These anaerobic and acidic conditions prevent the propagation of detrimental microorganisms such as listeria, clostridia, yeasts, and other fungi. L. hokkaidonensis can grow at temperatures as low as 4°C (optimal growth at 25°C), and its type strain LOOC260T was shown to decrease pH even in cold conditions when used to inoculate pilot-scale grass silage.
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