Wegmann Udo, MacKenzie Donald A, Zheng Jinshui, Goesmann Alexander, Roos Stefan, Swarbreck David, Walter Jens, Crossman Lisa C, Juge Nathalie
The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK.
State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
BMC Genomics. 2015 Dec 1;16:1023. doi: 10.1186/s12864-015-2216-7.
Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.
To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.
This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.
罗伊氏乳杆菌是多种脊椎动物物种的肠道共生菌，已分化为不同的系统发育分支，在很大程度上具有宿主特异性。先前的研究证明了其在小鼠中的宿主特异性，并开始确定实现肠道定植和宿主限制的机制。然而，罗伊氏乳杆菌菌株如何在猪的胃肠道中定植尚不清楚。
为深入了解罗伊氏乳杆菌在猪肠道中的生态学，完成了猪小肠分离株罗伊氏乳杆菌ATCC 53608的基因组序列测定，其由一条1.94 Mbp的染色体和两条分别为138.5 kbp和9.09 kbp的质粒组成。此外，我们还生成了从猪粪便或下胃肠道分离的另外四株罗伊氏乳杆菌菌株lp167 - 67、pg - 3b、20 - 2和3c6的基因组草图，并将这五个基因组与之前完成的I5007菌株基因组一起进行了比较基因组分析。基于全基因组的系统发育分析表明，猪源罗伊氏乳杆菌菌株可分为两个不同的分支，这与之前多位点序列分析的结果一致。通过OrthoMCL分析确定，这六个猪源罗伊氏乳杆菌基因组包含一组1364个直系同源基因簇的核心集，这些基因簇构成了一个总计3373个基因簇的泛基因组。将这六个猪源罗伊氏乳杆菌菌株与来自其他宿主来源 的14株罗伊氏乳杆菌菌株进行基因组比较，得到一个总计5225个基因簇的泛基因组，其中包括一个851个基因簇的核心基因组，但结果显示不存在猪特异性基因。然而，检测到了两个猪系统发育谱系菌株特有的且保守的基因，其中一些基因编码细胞表面蛋白，这些蛋白可能导致两个谱系的分化及其观察到的宿主特异性。
本研究在全基因组水平上扩展了罗伊氏乳杆菌菌株的系统发育分析，指出了猪源罗伊氏乳杆菌谱系不同的进化轨迹，并为罗伊氏乳杆菌在适应宿主过程中发生的基因组事件提供了新的见解。两个不同的猪源分支的出现可能反映了宿主基因型的差异、饮食成分等环境因素，或者是与猪群接触后源自人类和啮齿动物祖先菌株的进化。
