Data from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Background: Propionibacterium freudenreichii is an industrially important bacterium granted the Generally Recognized as Safe (the GRAS) status, due to its long safe use in food bioprocesses. Despite the recognized role in the food industry and in the production of vitamin B12, as well as its documented health-promoting potential, P. freudenreichii remained poorly characterised at the genomic level. At present, only three complete genome sequences are available for the species.

Results: We used the PacBio RS II sequencing platform to generate complete genomes of 20 P. freudenreichii strains and compared them in detail. Comparative analyses revealed both sequence conservation and genome organisational diversity among the strains. Assembly from long reads resulted in the discovery of additional circular elements: two putative conjugative plasmids and three active, lysogenic bacteriophages. It also permitted characterisation of the CRISPR-Cas systems. The use of the PacBio sequencing platform allowed identification of DNA modifications, which in turn allowed characterisation of the restriction-modification systems together with their recognition motifs. The observed genomic differences suggested strain variation in surface piliation and specific mucus binding, which were validated by experimental studies. The phenotypic characterisation displayed large diversity between the strains in ability to utilise a range of carbohydrates, to grow at unfavourable conditions and to form a biofilm.

Conclusion: The complete genome sequencing allowed detailed characterisation of the industrially important species, P. freudenreichii by facilitating the discovery of previously unknown features. The results presented here lay a solid foundation for future genetic and functional genomic investigations of this actinobacterial species.

背景：费氏丙酸杆菌（Propionibacterium freudenreichii）是一种工业应用价值突出的细菌，因其在食品生物加工过程中的长期安全使用，被授予一般公认安全（Generally Recognized as Safe，GRAS）资质。尽管该菌在食品工业与维生素B12生产中具有公认的重要作用，且已有研究证实其具备促进健康的潜力，但学界对其基因组层面的特征仍缺乏深入解析。截至目前，该物种仅公开3条完整基因组序列。

结果：本研究采用PacBio RS II测序平台，完成了20株费氏丙酸杆菌的完整基因组测序，并开展了细致的比较分析。比较基因组分析揭示，该类菌株既存在序列保守性，也存在基因组组织层面的多样性。基于长读长序列的组装工作，我们发现了额外的环状遗传元件：2条推定的接合性质粒，以及3条具有活性的溶原性噬菌体。同时，本研究还完成了CRISPR-Cas系统的特征解析。PacBio测序平台的应用使得我们能够鉴定DNA修饰情况，进而解析了限制-修饰系统及其识别基序。观察到的基因组差异提示，不同菌株在表面菌毛形成与特定黏液结合能力上存在差异，该结论后续通过实验研究得到了验证。表型特征分析显示，各菌株在利用多种碳水化合物、在不利条件下生长以及形成生物膜的能力上存在显著差异。

结论：完整基因组测序助力我们发现了此前未被报道的特征，实现了对这一工业重要放线菌物种的精细特征解析。本研究结果为该放线菌物种后续的遗传学与功能基因组学研究奠定了坚实基础。