Oral samples as non-invasive proxies for assessing the composition of the rumen microbial community. Proxies for rumen samples

Microbial community analysis was carried out on ruminal digesta obtained directly via rumen fistula and buccal fluid, regurgitated digesta (bolus) and faeces of dairy cattle to assess if non- invasive samples could be used as proxies for ruminal digesta. Samples were collected from five cows receiving grass silage based diets containing no additional lipid or four different lipid supplements in a 5 x 5 Latin square design. Extracted DNA was analysed by qPCR and by sequencing 16S and 18S rRNA genes or the fungal ITS1 amplicons. Faeces contained few protozoa, and bacterial, fungal and archaeal communities were substantially different to ruminal digesta. Buccal and bolus samples gave much more similar profiles to ruminal digesta, although fewer archaea were detected in buccal and bolus samples. Bolus samples overall were most similar to ruminal samples. The differences between both buccal and bolus samples and ruminal digesta were consistent across all treatments. It can be concluded that either proxy sample type could be used as a predictor of the rumen microbial community, thereby enabling more convenient large-scale animal sampling for phenotyping and possible use in future animal breeding programs aimed at selecting cattle with a lower environmental footprint.

本研究针对通过瘤胃瘘管（rumen fistula）直接获取的瘤胃内容物（ruminal digesta）、口腔液、反刍食糜（bolus）以及奶牛粪便开展微生物群落分析，以评估非侵入性样本（non-invasive samples）能否作为瘤胃内容物的替代样本（proxies）。本研究采用5×5拉丁方设计（Latin square design），对5头饲喂以青贮牧草为基础日粮的奶牛进行样本采集，日粮分别不添加脂质或添加四种不同的脂质补充剂。通过定量PCR（qPCR）以及16S rRNA基因（16S rRNA gene）、18S rRNA基因（18S rRNA gene）或真菌ITS1扩增子（ITS1 amplicon）测序对提取的DNA进行分析。结果显示，粪便样本中原生动物丰度极低，其细菌、真菌与古菌群落结构与瘤胃内容物存在显著差异。口腔液与食团样本的群落谱与瘤胃内容物更为相似，但二者检测到的古菌丰度均低于瘤胃内容物。总体而言，食团样本与瘤胃样本的相似度最高。口腔液与食团样本和瘤胃内容物之间的群落差异在所有饲喂处理组中均保持一致。据此可得出结论：两类替代样本均可作为瘤胃微生物群落的预测指标，从而实现更便捷的大规模动物采样以开展表型分型，并有望应用于未来以选育低环境足迹奶牛为目标的育种计划。