Tamarit Daniel, Ellegaard Kirsten M, Wikander Johan, Olofsson Tobias, Vásquez Alejandra, Andersson Siv G E
Department of Molecular Evolution, Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sweden.
Medical Microbiology, Department of Laboratory Medicine, Lund University, Sweden.
Genome Biol Evol. 2015 May 6;7(6):1455-73. doi: 10.1093/gbe/evv079.
Lactobacillus kunkeei is the most abundant bacterial species in the honey crop and food products of honeybees. The 16 S rRNA genes of strains isolated from different bee species are nearly identical in sequence and therefore inadequate as markers for studies of coevolutionary patterns. Here, we have compared the 1.5 Mb genomes of ten L. kunkeei strains isolated from all recognized Apis species and another two strains from Meliponini species. A gene flux analysis, including previously sequenced Lactobacillus species as outgroups, indicated the influence of reductive evolution. The genome architecture is unique in that vertically inherited core genes are located near the terminus of replication, whereas genes for secreted proteins and putative host-adaptive traits are located near the origin of replication. We suggest that these features have resulted from a genome-wide loss of genes, with integrations of novel genes mostly occurring in regions flanking the origin of replication. The phylogenetic analyses showed that the bacterial topology was incongruent with the host topology, and that strains of the same microcluster have recombined frequently across the host species barriers, arguing against codiversification. Multiple genotypes were recovered in the individual hosts and transfers of mobile elements could be demonstrated for strains isolated from the same host species. Unlike other bacteria with small genomes, short generation times and multiple rRNA operons suggest that L. kunkeei evolves under selection for rapid growth in its natural growth habitat. The results provide an extended framework for reductive genome evolution and functional genome organization in bacteria.
昆氏乳杆菌是蜜蜂蜜囊和食物产品中最为丰富的细菌种类。从不同蜜蜂种类中分离出的菌株的16S rRNA基因在序列上几乎相同，因此不足以作为共进化模式研究的标记。在此，我们比较了从所有已确认的蜜蜂属物种中分离出的10株昆氏乳杆菌菌株以及从无刺蜂属物种中分离出的另外两株菌株的1.5 Mb基因组。一项基因通量分析，包括将先前测序的乳酸杆菌属物种作为外类群，表明了还原进化的影响。基因组结构独特之处在于垂直遗传的核心基因位于复制终点附近，而分泌蛋白基因和假定的宿主适应性特征基因则位于复制起点附近。我们认为这些特征是全基因组基因丢失的结果，新基因的整合大多发生在复制起点两侧的区域。系统发育分析表明，细菌的拓扑结构与宿主的拓扑结构不一致，并且同一微簇的菌株经常跨越宿主物种屏障进行重组，这与共多样化的观点相悖。在个体宿主中发现了多种基因型，并且对于从同一宿主物种中分离出的菌株，可以证明移动元件的转移。与其他基因组较小的细菌不同，较短的世代时间和多个rRNA操纵子表明昆氏乳杆菌在其天然生长栖息地中是在快速生长的选择下进化的。这些结果为细菌中的还原基因组进化和功能基因组组织提供了一个扩展的框架。
