Host Specific Diversity in <em>Lactobacillus johnsonii</em> as Evidenced by a Major Chromosomal Inversion and Phage Resistance Mechanisms

Genetic diversity and genomic rearrangements are a driving force in bacterial evolution and niche adaptation. We sequenced and annotated the genome of Lactobacillus johnsonii DPC6026, a strain isolated from the porcine intestinal tract. Although the genome of DPC6026 is similar in size (1.97mbp) and GC content (34.8%) to the sequenced human isolate L. johnsonii NCC 533, a large symmetrical inversion of approximately 750 kb differentiated the two strains. Comparative analysis among 12 other strains of L. johnsonii including 8 porcine, 3 human and 1 poultry isolate indicated that the genome architecture found in DPC6026 is more common within the species than that of NCC 533. Furthermore a number of unique features were annotated in DPC6026, some of which are likely to have been acquired by horizontal gene transfer (HGT) and contribute to protection against phage infection. A putative type III restriction-modification system was identified, as were novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) elements. Interestingly, these particular elements are not widely distributed among L. johnsonii strains. Taken together these data suggest intra-species genomic rearrangements and significant genetic diversity within the L. johnsonii species and indicate towards a host-specific divergence of L. johnsonii strains with respect to genome inversion and phage exposure.遗传多样性与基因组重排是细菌演化与生态位适应的核心驱动力。本研究对分离自猪肠道的约氏乳杆菌（Lactobacillus johnsonii）DPC6026的基因组进行了测序与注释。尽管DPC6026的基因组大小（1.97兆碱基对）与GC含量（34.8%）与已测序的人类来源分离株约氏乳杆菌NCC 533相近，但二者存在约750 kb的大型对称基因组倒位差异。对其余12株约氏乳杆菌（含8株猪源、3株人源及1株禽源分离株）的比较分析表明，DPC6026所具有的基因组结构在该物种内的分布频率高于NCC 533。此外，DPC6026基因组中注释到多个独特特征，其中部分可能通过水平基因转移（HGT）获得，且有助于菌株抵御噬菌体感染。研究还鉴定到一个推定的III型限制性修饰系统，以及新型成簇的规律间隔的短回文重复序列（CRISPR）元件。值得注意的是，这类特殊元件在约氏乳杆菌菌株中的分布并不广泛。综合上述数据可知，约氏乳杆菌物种类内存在基因组重排现象与显著的遗传多样性，且该物种菌株在基因组倒位与噬菌体感染压力层面呈现出宿主特异性的分化趋势。