Transcriptome Analysis Reveals Catabolite Control Protein A Regulatory Mechanisms Underlying Glucose-Excess or -Limited Conditions in a Ruminal Bacterium, Streptococcus bovis

Transcriptomic analysis of Lacticaseibacillus paracasei Zhang in transition to the viable but non-culturable state by RNA sequencing

Background

Some bacteria enter the viable but non-culturable (VBNC) state to survive harsh environmental conditions and external stresses. This alters cell physiology and has implications for the food industry as some bacteria, such as lactobacilli, undergo similar changes during food processing.

Methods

This study aimed to investigate the transcriptomic changes of a probiotic strain, Lacticaseibacillus paracasei Zhang (L. paracasei Zhang), upon transition to the VBNC state using high throughput RNA sequencing (RNA-seq).

Results

Bacteria were inoculated into the de Man, Rogosa, and Sharpe medium and maintained at low temperature and pH to induce cell transition to the VBNC state. Cells were harvested for analysis at five stages of VBNC induction: 0, 3, 30, and 180 days after induction and 210 days when the cells entered the VBNC state. Our results showed that the expression of 2,617, 2,642, 2,577, 2,829, and 2,840 genes was altered at these five different stages. The function of differentially expressed genes (DEGs, compared to healthy cells collected at day 0) and their encoded pathways were analyzed by the Gene Ontology Consortium and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. A total of 10 DEGs were identified in cells that entered the VBNC state: five continuously upregulated (LCAZH_0621, LCAZH_1986, LCAZH_2038, LCAZH_2040, and LCAZH_2174) and five continuously downregulated (LCAZH_0024, LCAZH_0210, LCAZH_0339, LCAZH_0621, and LCAZH_0754).

Conclusions

This study proposes a molecular model of the VBNC mechanism in L. paracasei Zhang, highlighting that changes in cell metabolism improve substrate utilization efficiency, thereby enhancing bacterial survival under adverse conditions. These data may be useful for improving the survival of probiotics in industrial food processing.

Transcriptional control of carbohydrate catabolism by the CcpA protein in the ruminal bacterium Streptococcus bovis

As a potent, pleiotropic regulatory protein in Gram-positive bacteria, catabolite control protein A (CcpA) mediates the transcriptional control of carbohydrate metabolism in Streptococcus bovis, a lactate-producing bacterium that plays an essential role in rumen acidosis in dairy cows. Although the rumen uptake of carbohydrates is multi-substrate, the focus of S. bovis research thus far has been on the glucose. With the aid of gene deletion, whole-genome sequencing, and transcriptomics, we have unraveled the role of CcpA in carbohydrate metabolism, on the one hand, and acidosis, on the other, and we show that the S. bovis strain S1 encodes "Carbohydrate-Active Enzymes" and that ccpA deletion slows the organism's growth rate and modulates the organic acid fermentation pathways toward lower lactate, higher formate, and acetate in the maltose and cellobiose. Furthermore, this study revealed the different regulatory functions of the CcpA protein in rumen metabolism and acidosis.IMPORTANCEThis study is important as it illustrates the varying regulatory role of the Streptococcus bovis catabolite control protein A protein in carbohydrate metabolism and the onset of acidosis in dairy cattle.

In Vitro Gene Expression Responses of Bovine Rumen Epithelial Cells to Different pH Stresses

Ruminal acidosis often occurs in production, which greatly affects animal health and production efficiency. Subacute rumen acidosis (SARA) occurs when rumen pH drops rapidly to 5.5−5.8, and acute rumen acidosis (ARA) occurs when rumen pH drops below 5.0, but the molecular regulation mechanism of the rumen epithelium after the rapid decrease in pH is still unclear. Bovine rumen epithelial cells (BRECs) were cultured at pH = 7.4 (control), 5.5 (SARA), and 4.5 (ARA). Transcriptome and metabolomic methods were used to obtain the molecular-based response of BRECs to different pH treatments; pH = 4.5 can significantly induce apoptosis of BRECs. The RNA-seq experiments revealed 1381 differently expressed genes (DEGs) in the control vs. SARA groups (p < 0.05). Fibroblast growth factor (FGF) and tumor necrosis factor (TNF) were upregulated 4.25 and 6.86 fold, respectively, and TLR4 was downregulated 0.58 fold. In addition, 283 DEGs were identified in the control vs. ARA comparison (p < 0.05), and prostaglandin-endoperoxide synthase 2 (PSTG2) was downregulated 0.54 fold. Our research reveals that the MAPK/TNF signaling pathway regulates the inflammatory response of BRECs. Metabolomics identified 35 biochemical compounds that were significantly affected (p < 0.05) in control vs. SARA and 51 in control vs. ARA. Bioinformatics analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database revealed that drug metabolism-cytochrome P450 metabolic and alpha-linolenic acid metabolism changes occurred. These transcriptional and metabolic changes are related to the adaptation of BRECs to low-pH stresses. In conclusion, the combined data analyses presented a worthy strategy to characterize the cellular, transcriptomic, and metabonomic adaptation of BRECs to pH in vitro. We demonstrated transcriptional expression changes in BRECs under pH stress and activation of the molecular mechanisms controlling inflammation.

Ambient pH regulates lactate catabolism pathway of the ruminal Megasphaera elsdenii BE2-2083 and Selenomonas ruminantium HD4

AIMS

To explore the impact of ambient pH on lactate catabolism by Megasphaera elsdenii BE2-2083 and Selenomonas ruminantium HD4 in both pure culture and in binary mixed culture.

METHODS AND RESULTS

The growth rate, substrate consumption, product formation, enzymatic activity and gene expression of M. elsdenii and S. ruminantium at various pHs were examined. Furthermore, the metabolism of lactate catabolism pathways for M. elsdenii and S. ruminantium in the co-culture system were investigated by chasing the conversion of sodium L-[3-¹³ C]-lactate in nuclear magnetic resonance. In the pure culture systems, ambient pH had significant effects on the growth of M. elsdenii, whereas S. ruminantium was less sensitive to pH changes. In addition, lactate metabolic genes and activities of key enzymes were affected by ambient pH in M. elsdenii and S. ruminantium. In the co-culture system, low ambient pH reduced the contribution lactate catabolism by M. elsdenii.

CONCLUSION

M. elsdenii BE2-2083 and S. ruminantium HD4 lactate degradation affected by ambient pH.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study demonstrates the regulatory mechanisms of lactate decomposing bacteria in lactate catabolism under the condition of subacute ruminal acidosis.