Bronze Age coprolites unveil the buffering role of the gut microbiota in the dietary adaptation of dogs to domestication. Solarolo

Dog evolution has long been debated, particularly with regards to the origin of domestication and its effects on the genome, but little is known about the role of the gut microbiome during the recent canine evolutionary history. We sequenced the metagenome of 13 canine coprolites dated ca. 3,600-3,450 y ago from the Bronze Age archaeological site of Solarolo (Italy), which housed a complex farming community. The microbiome structure of Solarolo dogs revealed continuity with that of modern dogs, but it also shared some features with the wild wolf microbiome, as a kind of transitional state between them. The dietary niche, as inferred from the microbiome composition, was omnivorous, with evidence of consumption of starchy agricultural foods. Interestingly, the gut microbiome from Solarolo was particularly enriched in sequences encoding alpha-amylases and complemented a low copy number of the host amylase (AMY2B) gene. These findings suggest that Neolithic dogs could have responded to the transition to a starch-rich diet by expanding microbial functionalities devoted to starch catabolism. Such a microbiome adaptive mechanism would have compensated for delayed host response to the new primarily abundant plant food resources, available from companionship with Bronze Age agriculturalists.

犬类的演化长期以来备受争议，尤其是在驯化起源及其对基因组的影响方面，但学界对近期犬类演化历程中肠道微生物组（gut microbiome）所扮演的角色仍知之甚少。我们对来自意大利索拉罗洛（Solarolo）青铜时代考古遗址的13份距今约3600至3450年的犬类粪化石（coprolite）开展了宏基因组（metagenome）测序，该遗址曾孕育复杂的农耕社群。索拉罗洛犬类的肠道微生物组结构显示，其与现代犬类存在演化延续性，但同时也与野生狼群的微生物组共享若干特征，呈现出介于二者之间的过渡状态。从微生物组组成可推断，其生态位为杂食性，且存在食用淀粉类农耕食物的相关证据。值得注意的是，索拉罗洛犬类的肠道微生物组中编码α-淀粉酶（alpha-amylases）的序列显著富集，同时弥补了宿主淀粉酶（AMY2B）基因较低的拷贝数。上述研究结果表明，新石器时代犬类或许通过扩增负责淀粉分解的微生物功能，以应对向高淀粉饮食的转型。此类微生物组适应性机制，可弥补宿主对青铜时代农耕者伴生关系下出现的新型、以植物为主的丰富食物资源所产生的应答滞后。