Fiedler Gregor, Herbstmann Anna-Delia, Doll Etienne, Wenning Mareike, Brinks Erik, Kabisch Jan, Breitenwieser Franziska, Lappann Martin, Böhnlein Christina, Franz Charles M A P
Department of Microbiology and Biotechnology, Max Rubner-Institut (MRI), Federal Research Institute of Nutrition and Food, Hermann-Weigmann-Straße 1, 24103 Kiel, Germany.
Chair of Microbial Ecology, ZIEL-Institute for Food & Health, Technical University of Munich, Weihenstephaner Berg 3, 85354 Freising, Germany.
Microorganisms. 2021 Jan 26;9(2):246. doi: 10.3390/microorganisms9020246.
The genetic heterogeneity of (formerly was evaluated using whole genome sequencing. The genomes of 29 previously identified and two strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two strains could be reclassified as . In addition, the genomes of the type strain (DSM 10599) and the closest phylogenetic neighbors (DSM 9356) and (JCM 19841) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that is highly related to . When examining the genome sequences of all strains from this study, together with 4 genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.
使用全基因组测序对（以前的）的遗传异质性进行了评估。对29株先前鉴定的以及从超高温（UHT）处理的牛奶中分离出的两株菌株的基因组进行了短读长（Illumina）测序。经过序列分析，这两株菌株可重新分类为。此外，还使用长读长（MinION）和短读长（Illumina）测序对型菌株（DSM 10599）以及最接近的系统发育邻居（DSM 9356）和（JCM 19841）的基因组进行了测序。通过混合序列组装，型菌株的基因组相对于短读长组装扩大了15%。这种显著的增加可能是由于基因组中大量的移动元件，推测这些元件与孢子耐热性有关。基于16S rDNA基因序列、核心基因组、单核苷酸多态性和ANI/dDDH的系统发育研究表明，与高度相关。在检查本研究中所有菌株的基因组序列以及GenBank数据库中可用的4个基因组时，所检查的36株菌株中的大多数出现在一个克隆谱系中，单核苷酸多态性少于100个。这些数据证实了先前关于遗传高度同质且耐热的孢子克隆即HRS克隆的存在和传播的报道。
