Riddle Misty R, Nguyen Nguyen K, Nave Maeve, Peuß Robert, Maldonado Ernesto, Rohner Nicolas, Tabin Clifford J
University of Nevada, Reno Reno Nevada USA.
Microbiome Insights Inc Vancouver British Columbia Canada.
Ecol Evol. 2024 Apr 1;14(4):e11192. doi: 10.1002/ece3.11192. eCollection 2024 Apr.
The ecological and genetic changes that underlie the evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics, and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, , in their natural environments and under controlled laboratory conditions. Field-collected samples were dominated by very few taxa and showed considerable interindividual variation. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish evolution shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrated that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.
宿主与微生物相互作用进化背后的生态和遗传变化仍然难以捉摸，主要是因为在厘清改变微生物组组成的变量方面存在挑战。为了了解宿主栖息地、宿主遗传学和进化历史对微生物群落结构的影响，我们在自然环境和受控实验室条件下，研究了墨西哥丽脂鲤的河流型和三种洞穴适应形态型的肠道微生物组。野外采集的样本中优势分类群很少，且个体间差异很大。我们发现，与野生同类相比，实验室饲养的鱼类微生物组丰富度增加且组成不同，这突出了栖息地的重大影响。然而，最值得注意的是，我们发现终生以相同饮食饲养的形态型形成了不同的微生物组，这表明洞穴鱼进化产生的基因座塑造了微生物组组成。我们观察到不同形态型之间梭杆菌门丰度存在稳定差异，并证明这可作为数量性状基因座定位的一个性状，以揭示微生物群落结构的遗传基础。
