Department of Forage Plants and Agrometeorology, Faculty of Agronomy, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
Sci Rep. 2023 Apr 11;13(1):5854. doi: 10.1038/s41598-023-33067-5.
Less invasive rumen sampling methods, such as oro-esophageal tubing, became widely popular for exploring the rumen microbiome and metabolome. However, it remains unclear if such methods represent well the rumen contents from the rumen cannula technique. Herein, we characterized the microbiome and metabolome in the rumen content collected by an oro-esophageal tube and by rumen cannula in ten multiparous lactating Holstein cows. The 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Untargeted metabolome was characterized using gas chromatography of a time-of-flight mass spectrometer. Bacteroidetes, Firmicutes, and Proteobacteria were the top three most abundant phyla representing ~ 90% of all samples. Although the pH of oro-esophageal samples was greater than rumen cannula, we found no difference in alpha and beta-diversity among their microbiomes. The overall metabolome of oro-esophageal samples was slightly different from rumen cannula samples yet more closely related to the rumen cannula content as a whole, including its fluid and particulate fractions. Enrichment pathway analysis revealed a few differences between sampling methods, such as when evaluating unsaturated fatty acid pathways in the rumen. The results of the current study suggest that oro-esophageal sampling can be a proxy to screen the 16S rRNA rumen microbiome compared to the rumen cannula technique. The variation introduced by the 16S rRNA methodology may be mitigated by oro-esophageal sampling and the possibility of increasing experimental units for a more consistent representation of the overall microbial population. Studies should consider an under or over-representation of metabolites and specific metabolic pathways depending on the sampling method.
微创瘤胃液取样方法，如口咽管法，因其能够用于探索瘤胃微生物组和代谢组而被广泛应用。然而，目前仍不清楚这些方法是否能很好地代表瘤胃套管技术采集的瘤胃内容物。在此，我们对 10 头经产荷斯坦奶牛使用口咽管和瘤胃套管采集的瘤胃内容物中的微生物组和代谢组进行了研究。使用 Illumina MiSeq 平台对 16S rRNA 基因进行扩增和测序。采用飞行时间质谱仪的气相色谱法对非靶向代谢组进行了表征。拟杆菌门、厚壁菌门和变形菌门是最丰富的三个门，约占所有样本的 90%。尽管口咽管样本的 pH 值大于瘤胃套管，但我们发现它们的微生物组在 alpha 和 beta 多样性方面没有差异。口咽管样本的整体代谢组与瘤胃套管样本略有不同，但与整个瘤胃套管内容物（包括其液体和颗粒部分）更相关。富集途径分析显示，两种采样方法之间存在一些差异，例如在评估瘤胃中不饱和脂肪酸途径时。本研究结果表明，与瘤胃套管技术相比，口咽管采样可以作为筛选 16S rRNA 瘤胃微生物组的替代方法。口咽管采样可能会减轻 16S rRNA 方法带来的变异，并通过增加实验单位来更一致地代表整个微生物种群。研究应根据采样方法考虑代谢物和特定代谢途径的代表性不足或过度的问题。
