Metatranscriptomic analyses reveal ruminal pH regulates fiber degradation and fermentation by shifting the microbial community and gene expression of carbohydrate-active enzymes

Abstract

Background 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. Results 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. Conclusions 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.

Subacute ruminal acidosis phenotypes in periparturient dairy cows differ in ruminal and salivary bacteria and in the in vitro fermentative activity of their ruminal microbiota

“…Ruminal pH is a critical factor affecting and potentially disturbing metabolic activity of rumen microbiota (Chen et al, 2019;Khiaosa-ard et al, 2020). At low pH, in situ fiber degradation and overall rumen fermentation were reduced by alteration of metabolic pathways associated with glycolysis and pyruvate fermentation (Pourazad et al, 2017;Li et al, 2021). In the current study as well as in the study by Khiaosa-ard et al (2020), this reduced fermentation was also observed when exposing rumen inoculum to lower pH conditions in vitro.…”

Methane Mitigation Potential of Foliage of Fodder Trees Mixed at Two Levels with a Tropical Grass

“…The observed pH values of the evaluated treatments are like those reported for tropical diets. Likewise, in the present investigation there is no relation between pH and SCFA variables, as described by Li et al [51]. This observation is perhaps because pH values were not below 6.0, which is a critical value for the activity of the fibrolytic microbial population and, therefore, for fiber degradation.…”

“…However, the methodology used for the quantification of SCFA must be considered since secondary metabolites can affect its production [52]. According to Li et al [51], VFA production in the rumen is directly related to the ME consumed, and this study corroborated this postulate as the BS30-PP70 treatment had a low ME contribution (6.05 MJ kg −1 DM) and resulted in a low content of SCFA (57.88 mMol L −1 ), while with the BA30-PP70 treatment, the opposite occurred (7.2 MJ kg −1 DM and 95.42 mMol L −1 ).…”

In vitro Methane Mitigation Potential of Foliage of Fodder Trees Mixed at Two Levels with a Tropical Grass

“…The observed pH values of the evaluated treatments are like those reported for tropical diets. Likewise, in the present investigation there is no correlation between pH and SCFA variables, as described by Li et al [51]. This observation is perhaps because pH values were not below 6.0, which is a critical value for the activity of the fibrolytic microbial population and, therefore, for fiber degradation.…”