Li Meng M, White Robin R, Guan Le Luo, Harthan Laura, Hanigan Mark D
Deptartment of Dairy Science, Virginia Polytechnic Institute and State University, Litton-Reaves Hall, 175 West Campus Drive, Blacksburg, VA, 24061, USA.
State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P. R. China.
Anim Microbiome. 2021 Apr 23;3(1):32. doi: 10.1186/s42523-021-00092-6.
Volatile fatty acids (VFA) generated from ruminal fermentation by microorganisms provide up to 75% of total metabolizable energy in ruminants. Ruminal pH is an important factor affecting the profile and production of VFA by shifting the microbial community. However, how ruminal pH affects the microbial community and its relationship with expression of genes encoding carbohydrate-active enzyme (CAZyme) for fiber degradation and fermentation are not well investigated. To fill in this knowledge gap, six cannulated Holstein heifers were subjected to a continuous 10-day intraruminal infusion of distilled water or a dilute blend of hydrochloric and phosphoric acids to achieve a pH reduction of 0.5 units in a cross-over design. RNA-seq based transcriptome profiling was performed using total RNA extracted from ruminal liquid and solid fractions collected on day 9 of each period, respectively.
Metatranscriptomic analyses identified 19 bacterial phyla with 156 genera, 3 archaeal genera, 11 protozoal genera, and 97 CAZyme transcripts in sampled ruminal contents. Within these, 4 bacteria phyla (Proteobacteria, Firmicutes, Bacteroidetes, and Spirochaetes), 2 archaeal genera (Candidatus methanomethylophilus and Methanobrevibacter), and 5 protozoal genera (Entodinium, Polyplastron, Isotricha, Eudiplodinium, and Eremoplastron) were considered as the core active microbes, and genes encoding for cellulase, endo-1,4-beta- xylanase, amylase, and alpha-N-arabinofuranosidase were the most abundant CAZyme transcripts distributed in the rumen. Rumen microbiota is not equally distributed throughout the liquid and solid phases of rumen contents, and ruminal pH significantly affect microbial ecosystem, especially for the liquid fraction. In total, 21 bacterial genera, 4 protozoal genera, and 6 genes encoding CAZyme were regulated by ruminal pH. Metabolic pathways participated in glycolysis, pyruvate fermentation to acetate, lactate, and propanoate were downregulated by low pH in the liquid fraction.
The ruminal microbiome changed the expression of transcripts for biochemical pathways of fiber degradation and VFA production in response to reduced pH, and at least a portion of the shifts in transcripts was associated with altered microbial community structure.
微生物在瘤胃发酵过程中产生的挥发性脂肪酸（VFA）为反刍动物提供了高达75%的总可代谢能量。瘤胃pH值是通过改变微生物群落来影响VFA的组成和产生的一个重要因素。然而，瘤胃pH值如何影响微生物群落以及它与编码用于纤维降解和发酵的碳水化合物活性酶（CAZyme）的基因表达之间的关系尚未得到充分研究。为了填补这一知识空白，采用交叉设计，对6头安装有瘤胃瘘管的荷斯坦小母牛进行了为期10天的瘤胃内持续输注蒸馏水或盐酸和磷酸的稀释混合物，以使pH值降低0.5个单位。分别使用从每个时期第9天收集的瘤胃液和固体部分中提取的总RNA进行基于RNA测序的转录组分析。
宏转录组分析在瘤胃内容物样本中鉴定出19个细菌门、156个属、3个古菌属、11个原生动物属和97个CAZyme转录本。其中，4个细菌门（变形菌门、厚壁菌门、拟杆菌门和螺旋体门）、2个古菌属（嗜甲基甲烷杆菌属和短甲烷杆菌属）和5个原生动物属（内毛虫属、多泡胃虫属、等毛虫属、真双毛虫属和空泡虫属）被认为是核心活性微生物，编码纤维素酶、内切-1,4-β-木聚糖酶、淀粉酶和α-N-阿拉伯呋喃糖苷酶的基因是瘤胃中分布最丰富的CAZyme转录本。瘤胃微生物群在瘤胃内容物的液相和固相中分布不均，瘤胃pH值显著影响微生物生态系统，尤其是液相部分。总共有21个细菌属、4个原生动物属和6个编码CAZyme的基因受瘤胃pH值调节。液相部分低pH值下调了参与糖酵解、丙酮酸发酵生成乙酸、乳酸和丙酸的代谢途径。
瘤胃微生物组响应pH值降低改变了纤维降解和VFA产生生化途径的转录本表达，并且转录本的至少一部分变化与微生物群落结构的改变有关。
