Data_Sheet_5_PacBio and Illumina MiSeq Amplicon Sequencing Confirm Full Recovery of the Bacterial Community After Subacute Ruminal Acidosis Challenge in the RUSITEC System.PDF

The impact of subacute rumen acidosis (SARA) on the rumen bacterial community has been frequently studied in in vivo trials. Here we investigated whether these alterations can be mirrored by using the rumen simulation technique (RUSITEC) as an in vitro model for this disease. We hypothezised that the bacterial community fully recovers after a subacute ruminal acidosis challenge. We combined a PacBio nearly full-length 16S rRNA gene analysis with 16S rRNA gene Illumina MiSeq sequencing of the V4 hypervariable region. With this hybrid approach, we aimed to get an increased taxonomic resolution of the most abundant bacterial groups and an overview of the total bacterial diversity. The experiment consisted of a control period I and a SARA challenge and ended after a control period II, of which each period lasted 5 d. Subacute acidosis was induced by applying two buffer solutions, which were reduced in their buffering capacity (SARA buffers) during the SARA challenge. Two control groups were constantly infused with the standard buffer solution. Furthermore, the two SARA buffers were combined with three different feeding variations, which differed in their concentrate-to-hay ratio. The induction of SARA led to a decrease in pH below 5.8, which then turned into a steady-state SARA. Decreasing pH values led to a reduction in bacterial diversity and richness. Moreover, the diversity of solid-associated bacteria was lower for high concentrate groups throughout all experimental periods. Generally, Firmicutes and Bacteroidetes were the predominant phyla in the solid and the liquid phase. During the SARA period, we observed a decrease in fibrolytic bacteria although lactate-producing and -utilizing families increased in certain treatment groups. The genera Lactobacillus and Prevotella dominated during the SARA period. With induction of the second control period, most bacterial groups regained their initial abundance. In conclusion, this in vitro model displayed typical bacterial alterations related to SARA and is capable of recovery from bouts of SARA. Therefore, this model can be used to mimic SARA under laboratory conditions and may contribute to a reduction in animal experiments.

亚急性瘤胃酸中毒（SARA）对瘤胃细菌群落的影响已在体内试验中得到了广泛研究。本研究旨在探讨利用瘤胃模拟技术（RUSITEC）作为该疾病的体外模型，是否能够反映这些变化。我们假设在亚急性瘤胃酸中毒挑战后，细菌群落能够完全恢复。本研究结合了PacBio近乎全长的16S rRNA基因分析和16S rRNA基因Illumina MiSeq测序的V4高度可变区，旨在通过这种混合方法，提高最丰富细菌类群的分类分辨率，并对总细菌多样性进行概述。实验包括一个对照组I和一个SARA挑战期，并在一个持续5天的对照组II后结束。亚急性酸中毒通过应用两种缓冲溶液诱导，这两种缓冲溶液在SARA挑战期间其缓冲能力降低（SARA缓冲液）。两个对照组持续灌注标准缓冲溶液。此外，两种SARA缓冲液与三种不同的饲料变化相结合，这些变化在浓缩料与干草的比例上有所不同。SARA的诱导导致pH值下降至5.8以下，随后转变为稳态SARA。pH值的下降导致细菌多样性和丰富度的减少。此外，在整个实验期间，高浓缩料组的固着细菌多样性较低。总的来说，厚壁菌门和拟杆菌门在固体和液体相中占主导地位。在SARA期间，我们观察到纤维分解细菌数量减少，尽管在特定处理组中，乳酸产生和利用的家族数量增加。在SARA期间，乳杆菌属和普雷沃氏菌属占主导地位。在诱导第二个对照组期间，大多数细菌类群恢复了其初始丰度。总之，该体外模型展示了与SARA相关的典型细菌变化，并且能够从SARA的发作中恢复。因此，该模型可用于在实验室条件下模拟SARA，并可能有助于减少动物实验。