Phenotypic parallelism during experimental adaptation of a free-living bacterium to the zebrafish gut

Abstract

31Despite the fact that animals encounter a plethora of bacterial species throughout their lives, only 32 a subset are capable of colonizing vertebrate digestive tracts, and these bacteria can profoundly 33 influence the health and development of their animal hosts. However, it is still unknown how 34 bacteria evolve symbioses with animal hosts, and this process is central to both the assembly and 35 function of gut bacterial communities. Therefore, we used experimental evolution to study a 36 free-living bacterium as it adapts to a novel vertebrate host. We serially passaged replicate 37 populations of Shewanella oneidensis, through the digestive tracts of larval zebrafish (Danio 38 rerio). After only 20 passages, representing approximately 200 bacterial generations, isolates 39 from replicate evolved populations displayed an improved ability to colonize larval zebrafish 40 digestive tracts during competition against their unpassaged ancestor. Upon sequencing the 41 genomes of these evolved isolates, we discovered that the two isolates with the highest mean 42 competitive fitness accumulated unique sets of mutations. We characterized the swimming 43 motility and aggregation behavior of these isolates, as these phenotypes have previously been 44 shown to alter host-microbe interactions. Despite exhibiting different biofilm characteristics, 45 both isolates evolved augmented swimming motility. These enhancements are consistent with 46 expectations based on the behavior of a closely related Shewanella strain previously isolated 47 Introduction: 54 Bacterial lineages have radiated into practically every imaginable niche on Earth [1, 2]. 55In particular, the vertebrate digestive tract houses bacterial communities whose composition is 56 distinct from those found in surrounding environments [3, 4], and this suggests that host-57 associated bacteria maintain certain traits that enable them to colonize animal hosts. In order to 58 establish and maintain host-association, bacteria must surmount a multitude of complex 59 challenges, including traversing diverse physical landscapes, harvesting energy from dynamic 60 nutrient sources, and protecting themselves from antimicrobial compounds. Thus, the number of 61 traits involved in host-association is likely enormous [5, 6]. Despite this complexity, previous 62 analyses indicate that novel host-microbe symbioses have arisen multiple times throughout 63 evolutionary history [7]. However, it is unknown which suites of traits enable bacteria to 64 transition to host association, or how likely they are to evolve. 65It is well established that bacteria residing in vertebrate digestive tracts have substantial 66 impacts on the health and development of their animal hosts [8][9][10][11]. Consequently, many 67 researchers have sought to understand which traits provide bacteria the capacity to colonize the 68 vertebrate gut [12][13][14][15][16][17], but this body of work has relied almost exclusively on snapshots of host-69 microbe relationships after they have evolved. Because...