Raw count data of the proximal colon microbiome from parasite resistant and susceptible sheep

Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a 12.8-fold reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P = 1.12 x 10-14; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.

培育宿主抗胃肠道线虫（gastrointestinal nematodes）的抗性，是寄生虫防控的经济高效策略。尽管宿主抗性受中等程度的遗传调控，但参与抗性或易感性形成的肠道微生物组分仍未被广泛探明。本研究基于全长16S rRNA基因测序的微生物组学方法，对经选育获得的抗性与易感型特有绵羊种群的近端结肠微生物组结构及代谢潜能进行了表征。在同一牧场放牧的条件下，抗性羔羊的寄生虫卵排出量显著低于易感羔羊。此外，在受到结肠小杯毛圆线虫（Trichostrongylus colubriformis）攻毒感染后，抗性羔羊的成虫定植量较易感羔羊降低了12.8倍（P=1.12×10^-14；每组n=20）。在抗性组与易感组间相对丰度存在显著差异的32种细菌中，大肠杆菌（E. coli）在易感羔羊体内的丰度更高，同时也是区分宿主抗性与易感状态的核心物种。此外，以大肠杆菌（E. coli）为分子、狄氏副拟杆菌（Parabacteroides distasonis）和多形拟杆菌（Bacteroides thetaiotaomicron）为分母构建的微生物特征或平衡指数，可高精度预测宿主的抗性状态。宏基因组功能预测分析还显示，两种表型组间与传染病相关的多条通路（如志贺菌病（Shigellosis）和致病性大肠杆菌感染）均发生了显著改变。本研究结果表明，具备高抗性状态预测能力的微生物特征可作为生物标志物，用于辅助绵羊宿主抗性的选育工作。