Animal microbiomes are assembled predominantly from environmental microbes, yet the mechanisms by which individual symbionts regulate their transmission into hosts remain underexplored. By tracking the experimental evolution of Aeromonas veronii in gnotobiotic zebrafish, we identify bacterial traits promoting host colonization. Multiple independently evolved isolates with increased immigration harbored mutations in a gene we named sensor of proline diguanylate cyclase enzyme (SpdE) based on structural, biochemical, and phenotypic evidence that SpdE encodes an amino-acid-sensing diguanylate cyclase. SpdE detects free proline and to a lesser extent valine and isoleucine, resulting in reduced production of intracellular c-di-GMP, a second messenger controlling bacterial motility. Indeed, SpdE binding to amino acids increased bacterial motility and host colonization. Hosts serve as sources of SpdE-detected amino acids, with levels varying based on microbial colonization status. Our work demonstrates that bacteria use chemically regulated motility, or chemokinesis, to sense host-emitted cues that trigger active immigration into hosts.

动物微生物组主要由环境微生物组装而成，但个体共生体调节其向宿主传播的机制仍未得到充分探索。通过追踪维罗尼气单胞菌的实验进化在知生斑马鱼中，我们确定了促进宿主定殖的细菌特征。根据结构、生化和表型证据表明，SpdE 编码一种氨基酸感应双鸟苷酸环化酶，多个独立进化的分离株在一个基因中存在突变，我们将其命名为脯氨酸二鸟苷酸环化酶 (SpdE) 传感器。SpdE 检测游离脯氨酸和少量的缬氨酸和异亮氨酸，导致细胞内 c-di-GMP 的产生减少，后者是控制细菌运动的第二信使。事实上，SpdE 与氨基酸的结合增加了细菌的运动性和宿主定植。宿主作为 SpdE 检测到的氨基酸的来源，其水平根据微生物定植状态而变化。我们的工作表明细菌使用化学调节的运动或趋化作用，