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首页> 外文期刊>Applied Microbiology >Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach
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Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach

机译：通过使用时间课程和随机森林分类方法，验证牛颊样品用作瘤胃微生物群的代理

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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 ? 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.IMPORTANCE The gastrointestinal tracts of ruminants harbor a diverse microbial community that coevolved symbiotically with the host, influencing its nutrition, health, and performance. While the influence of environmental factors on rumen microbes is well documented, the process by which host genetics influences the establishment and colonization of the rumen microbiota still needs to be elucidated. This knowledge gap is due largely to our inability to easily sample the rumen microbiota. There are three common methods for rumen sampling but all of them present at least one disadvantage, including animal welfare, sample quality, labor, and scalability. The development and validation of noninvasive methods, such as buccal swabbing, for large-scale rumen sampling is needed to support studies that require large sample sizes to generate reliable results. The validation of buccal swabbing will also support the development of molecular tools for the early diagnosis of metabolic disorders associated with microbial changes in large herds.
机译：牛微生物组的分析以及对瘤胃微生物瘤的建立和定植的宿主遗传影响，对于操纵谣言功能朝着更高效和环保牛奶生产的策略至关重要。为此，需要以大规模对瘤胃微生物瘤瘤瘤微生物进行样本的非侵入性方法的开发和验证。在这项研究中，我们进一步优化了对颊拭子样本的分析作为乳制奶牛瘤胃的直接细菌样本的代理。为了确定采样的最佳时间，我们在相对于动物饲养的六个不同时间点收集了颊拭子和瘤胃样本。然后，我们使用机器学习分类器（随机林）在这些样本中评估多个偏差，以选择区分颊拭子和瘤胃样本之间的分类群。当在早晨喂养之前进行取样（P？60％）在口腔和瘤胃样品中进行抽样之前进行取样时，方法之间的差异，Shannon的多样性，Shannon的均匀性和Bray-Curtis的差异显然明显不那么明显但可以通过常规颊棉签采样进行定性评估。这项工作不仅为反刍动物的口头社区提供了新的洞察力，而且还进一步验证和改进了颊擦拭，作为评估大牧群中瘤胃细菌的方法。分析反刍动物的胃肠道患者与主人共同共同地互化的微生物群体，影响其营养，健康和性能。虽然环境因素对瘤胃微生物的影响有很好的记录，但宿主遗传学影响的过程仍然需要阐明瘤胃微生物瘤的建立和定植。这种知识差距主要是由于我们无法轻易地样瘤胃微生物群。瘤胃抽样有三种常见的方法，但所有这些方法都存在至少一个缺点，包括动物福利，样品质量，劳动力和可扩展性。不需要对大规模瘤胃抽样等非侵入性方法的开发和验证，以支持需要大样本尺寸以产生可靠的结果的研究。颊拭子的验证还将支持在大畜群中早期诊断到与大畜群中微生物变化相关的代谢障碍的分子工具的发展。

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