Using fecal microbiota as biomarkers for predictions of performance in the selective breeding process of pedigree broiler breeders

Much work has been dedicated to identifying members of the microbial gut community that have potential to augment the growth rate of agricultural animals including chickens. Here, we assessed any correlations between the fecal microbiome, a proxy for the gut microbiome, and feed efficiency or weight gain at the pedigree chicken level, the highest tier of the production process. Because selective breeding is conducted at the pedigree level, our aim was to determine if microbiome profiles could be used to predict feed conversion or weight gain in order to improve selective breeding. Using 16s rRNA amplicon sequencing, we profiled the microbiomes of high and low weight gain (WG) birds and good and poor feed efficient (FE) birds in two pedigree lineages of broiler chickens. We also aimed to understand the dynamics of the microbiome with respect to maturation. A time series experiment was conducted, where fecal samples of chickens were collected at 6 points of the rearing process and the microbiome of these samples profiled. We identified OTUs differences at different taxonomic levels in the fecal community between high and low performing birds within each genetic line, indicating a specificity of the microbial community profiles correlated to performance factors. Using machine-learning methods, we built a classification model that could predict feed conversion performance from the fecal microbial community. With respect to maturation, we found that the fecal microbiome is dynamic in early life but stabilizes after 3 weeks of age independent of lineage. Our results indicate that the fecal microbiome profile can be used to predict feed conversion, but not weight gain in these pedigree lines. From the time series experiments, it appears that these predictions can be evaluated as early as 20 days of age. Our data also indicates that there is a genetic factor for the microbiome profile.已有诸多研究致力于挖掘可提升畜禽（含肉鸡）生长速率的肠道微生物群落成员。本研究以粪便微生物组作为肠道微生物组的替代标志物，在养殖生产流程最高层级的家系肉鸡层面，评估了其与饲料效率、体重增重的相关性。由于选择性育种正是在家系层级开展，本研究旨在探明微生物组谱能否用于预测饲料转化率或体重增重，以助力选择性育种工作的优化。本研究采用16S核糖体RNA（16S rRNA）扩增子测序技术，对两个肉鸡家系品系中高、低体重增重（WG）组以及饲料效率优良、低劣（FE）组肉鸡的粪便微生物组进行了测序分析。此外，本研究还旨在探究微生物组随肉鸡成熟过程的动态变化规律。本研究设置了时序实验，在肉鸡养殖过程的6个时间节点采集粪便样本，并对这些样本的微生物组进行测序分析。本研究在各遗传品系内的高、低性能肉鸡之间，鉴定出粪便群落不同分类学层级上的操作分类单元（Operational Taxonomic Units，OTU）的差异，表明微生物群落谱与生产性能指标存在特异性关联。本研究采用机器学习方法构建了可通过粪便微生物组预测肉鸡饲料转化性能的分类模型。关于肉鸡成熟过程，本研究发现粪便微生物组在生命早期呈动态变化，但在3周龄后趋于稳定，且该稳定趋势不受家系影响。本研究结果表明，在家系肉鸡群体中，粪便微生物组谱可用于预测饲料转化率，但无法有效预测体重增重。时序实验结果显示，此类性能预测最早可在肉鸡20日龄时进行评估。本研究数据同时表明，微生物组谱存在遗传基础。