Analysis of the cow microbiome, as well as host genetic influences on the establishment and colonization of the rumen microbiota, is critical for development of strategies to manipulate ruminal function toward more efficient and environmentally friendly milk production. To this end, the development and validation of noninvasive methods to sample the rumen microbiota at a large scale are required. In this study, we further optimized the analysis of buccal swab samples as a proxy for direct bacterial samples of the rumen of dairy cows. To identify an optimal time for sampling, we collected buccal swab and rumen samples at six different time points relative to animal feeding. We then evaluated several biases in these samples using a machine learning classifier (random forest) to select taxa that discriminate between buccal swab and rumen samples. Differences in the inverse Simpson’s diversity, Shannon’s evenness, and Bray-Curtis dissimilarities between methods were significantly less apparent when sampling was performed prior to morning feeding (P < 0.05), suggesting that this time point was optimal for representative sampling. In addition, the random forest classifier was able to accurately identify nonrumen taxa, including 10 oral and putative feed-associated taxa. Two highly prevalent (>60%) taxa in buccal and rumen samples had significant variance in relative abundances between sampling methods but could be qualitatively assessed via regular buccal swab sampling. This work not only provides new insights into the oral community of ruminants but also further validates and refines buccal swabbing as a method to assess the rumen bacterial in large herds.

中文翻译：

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通过使用时间过程和随机森林分类方法，验证使用牛颊采样作为瘤胃微生物群的代理。

牛微生物组的分析以及宿主对瘤胃微生物群的建立和定植的遗传影响，对于制定操纵瘤胃功能以提高生产效率和环境友好性的策略至关重要。为此，需要开发和验证用于大规模采样瘤胃微生物群的非侵入性方法。在这项研究中，我们进一步优化了口腔拭子样品的分析，以作为奶牛瘤胃直接细菌样品的替代指标。为了确定最佳采样时间，我们在相对于动物喂养的六个不同时间点收集了口腔拭子和瘤胃样品。然后，我们使用机器学习分类器（随机森林）评估了这些样本中的几种偏差，以选择区分颊拭子和瘤胃样本的分类单元。P <0.05），表明该时间点是代表性采样的最佳时间。此外，随机森林分类器能够准确识别非瘤胃类群，包括10种与饲料相关的口服和推定类群。颊和瘤胃样品中的两种高度盛行（> 60％）的分类单元在采样方法之间的相对丰度上有显着差异，但可以通过常规颊拭子采样进行定性评估。这项工作不仅为反刍动物的口腔界提供了新的见解，而且还进一步验证和改进了口腔拭子检查，作为评估大群瘤胃细菌的一种方法。