Progressive genome-wide introgression in agricultural Campylobacter coli

Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10–11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.

远缘生物间的杂交可促进物种对新环境的快速适应，但可能会受到细胞组分间上位性适合度互作的约束。人畜共患病病原体结肠弯曲杆菌（Campylobacter coli）与空肠弯曲杆菌（C. jejuni）在核苷酸水平上的差异约为15%，对应每个蛋白编码基因平均近40个氨基酸的序列差异。本研究通过全基因组测序（whole genome sequencing）技术发现：一个已成功定殖于农业生态位的结肠弯曲杆菌谱系，正逐步累积获取空肠弯曲杆菌的DNA片段。该谱系可分为两个克隆群，即ST-828与ST-1150克隆复合体（clonal complexes）。其中ST-1150复合体的分离检出率较低，但其基因渐渗（introgression）程度显著更高：不仅置换了高达23%的结肠弯曲杆菌核心基因组（core genome），还导入了新型外源DNA。相较而言，分离检出率更高的ST-828复合体菌株的渐渗DNA占比为10%~11%，而空肠弯曲杆菌及非农业定殖的结肠弯曲杆菌谱系的渐渗DNA占比均低于2%。综上，那些定殖于农业环境、进而引发绝大多数人类感染病例的结肠弯曲杆菌菌株具有杂交起源，但截至目前，这种跨物种基因交换并未对空肠弯曲杆菌或非农业定殖结肠弯曲杆菌的基因库（gene pools）造成显著影响。本研究结果同时表明，在经历长期独立演化后，基本细胞功能组件仍具备显著的可互换性。