Transcriptome analysis of Cyclocarya paliurus flavonoids regulation of differently expressed genes in Enterococcus faecalis under low pH stress

The transcriptome response of Enterobacter sp. S-33 is modulated by low pH-stress

BACKGROUND

Acidic environments naturally occur worldwide and uncontrolled use of agricultural practices may also cause acidification of soils. The development of acidic conditions disturbs the establishment of efficient microbial populations in their natural niches. The survival of Enterobacter species under acidic stress remains poorly understood.

OBJECTIVE

This study aimed to investigate the survival of an environmental isolate Enterobacter sp. S-33 under acidic stress and to identify the various genes involved in stress protection at the global gene transcription level. The obtained results provide new targets that will allow understanding the in-depth mechanisms involved in the adaptation of bacteria to environmental pH changes.

METHODS

We used the next-generation sequencing (NGS) method to analyze the expression (up-regulation & down-regulation) of genes under varying pH conditions.

RESULTS

A total of 4214 genes were differentially expressed under acidic conditions (pH 5.0), with 294 up-regulated and 167 down-regulated. At pH 6.0, 50 genes were significantly expressed, of which 34 and 16 were identified as up-regulated and down-regulated, respectively. Many of the up-regulated genes were involved in carbohydrate metabolism, amino acid transport & metabolism, and the most down-regulated genes were related to post-translational modification, lipid transport & metabolism, etc. The observed transcriptomic regulation of genes and pathways identified that Enterobacter reduced its post-translational modification, lipid transport & metabolism, and increased carbohydrate metabolism, amino acid metabolism & transport, energy production & conversion to adapt and grow in acidic stress.

CONCLUSIONS

The present work provides in-depth information on the characterization of genes associated with tolerance or adaptation to acidic stress of Enterobacter bacterium.

Understanding the Effect of Different Glucose Concentrations in the Oligotrophic Bacterium Bacillus subtilis BS-G1 through Transcriptomics Analysis

Glucose is an important carbon source for microbial growth, and its content in infertile soils is essential for the growth of bacteria. Since the mechanism of oligotrophic bacterium adaptation in barren soils is unclear, this research employed RNA-seq technology to examine the impact of glucose concentration on the oligotrophic bacterium B. subtilis BS-G1 in soil affected by desertification. A global transcriptome analysis (RNA-Seq) revealed that the significantly differentially expressed genes (DEGs) histidine metabolism, glutamate synthesis, the HIF-1 signaling pathway, sporulation, and the TCA cycle pathway of B. subtilis BS-G1 were significantly enriched with a 0.015 g/L glucose concentration (L group), compared to a 10 g/L glucose concentration (H group). The DEGs amino acid system, two-component system, metal ion transport, and nitrogen metabolism system of B. subtilis BS-G1 were significantly enriched in the 5 g/L glucose concentration (M group), compared with the H group. In addition, the present study identified the regulation pattern and key genes under a low-glucose environment (7 mRNAs and 16 sRNAs). This study primarily investigates the variances in the regulatory pathways of the oligotrophic B. subtilis BS-G1, which holds substantial importance in comprehending the mechanism underlying the limited sugar tolerance of oligotrophic bacteria.

Dissolved Carbon Dioxide: The Lifespan of Staphylococcus aureus and Enterococcus faecalis in Bottled Carbonated Mineral Water

During the process of mineral water production, many possible contamination settings can influence the quality of bottled water. Microbial contamination can originate from different sources, for example, the ambient air, the bottles, the caps, and from the bottling machine itself. The aim of this study was to investigate the influence of three different carbon dioxide (CO2) concentrations (3.0 g/L, 5.5 g/L, and 7.0 g/L; 20 bottles each) in bottled mineral water on the bacterial growth of Staphylococcus aureus (S. aureus) and Enterococcus faecalis (Ent. faecalis). The examined mineral water was artificially contaminated before capping the bottles inside the factory. After a specific number of days, water samples were taken from freshly opened bottles and after filtration (100 mL), filters were placed on Columbia Agar with 5% Sheep blood to cultivate S. aureus and Slanetz and Bartley Agar to cultivate Ent. faecalis. The respective colony-forming units (CFU) were counted after incubation times ranging from 24 to 120 h. Colony-forming units of S. aureus were not detectable after the 16th and 27th day, whereas Ent. faecalis was not cultivable after the 5th and 13th day when stored inside the bottles. The investigation of the bottles that were stored open for a certain amount of time with CO2 bubbling out showed only single colonies for S. aureus after the 5th day and no CFUs for Ent. faecalis after the 17th day. A reduction in the two investigated bacterial strains during storage in carbonated mineral water bottles means that a proper standardized disinfection and cleaning procedure, according to valid hygiene standards of industrial bottling machines, cannot be replaced by carbonation.

Metabolome and Whole-Transcriptome Analyses Reveal the Molecular Mechanisms Underlying Hypoglycemic Nutrient Metabolites Biosynthesis in Cyclocarya paliurus Leaves During Different Harvest Stages

Cyclocarya paliurus, a well-known nutrient and beverage plant, is under development for use in functional health care products best and natural and organic foods. We hypothesis that the composition and metabolic accumulation of hypoglycemic nutrient metabolites exhibit significant differences depending on harvest time. Therefore, it is of great significance to establish the best harvest time for C. paliurus leaves for the further development of healthy teas and other products. However, the detail compositions and molecular mechanisms of nutrients biosynthesis in C. paliurus leaves during different harvest stages remain largely unclear. Metabolome analysis showed that a suitable leaf-harvesting strategy for C. paliurus could be in September or October each year due to the high content of hypoglycemic nutrient metabolites. We found that two of the seven differentially accumulated phenolic acid metabolites have a relatively good inhibitory effect on α-amylase, indicating that they may play a role in the hypoglycemic function. Combined analysis of coexpression, ceRNA network, and weighted gene correlation network analysis (WGCNA) showed that several genes or transcription factors (TFs) in three modules correlated highly with hypoglycemic nutrient metabolites, including CpPMM, CpMan, CpFK, CpSUS, CpbglX, Cp4CL, CpHCT, and CpWRKY1. These findings help in the understanding of the molecular mechanisms and regulatory networks of the hypoglycemic nutrient metabolites in C. paliurus leaves which are dependent on harvest time and provide theoretical guidance in the development of functional health care products and foods from C. paliurus.

Potential Role of Natural Plant Medicine Cyclocarya paliurus in the Treatment of Type 2 Diabetes Mellitus

Type 2 diabetes mellitus (T2DM) is a common chronic metabolic disease that has become increasingly prevalent worldwide. It poses a serious threat to human health and places a considerable burden on global social medical work. To meet the increasing demand for T2DM treatment, research on hypoglycemic drugs is rapidly developing. Cyclocarya paliurus (Batal.) Iljinskaja is a medicinal plant that grows in China. The leaves of C. paliurus contain polysaccharides, triterpenoids, and other chemical components, which have numerous health benefits. Therefore, the use of this plant has attracted extensive attention in the medical community. Over the past few decades, contemporary pharmacological studies on C. paliurus extracts have revealed that it has abundant biological activities. Multiple in vitro and in vivo experiments have shown that C. paliurus extracts are safe and can play a therapeutic role in T2DM through anti-inflammatory and antioxidation activities, and intestinal flora regulation. Its efficacy is closely related to many factors, such as extraction, separation, purification, and modification. Based on summarizing the existing extraction methods, this article further reviews the potential mechanism of C. paliurus extracts in T2DM treatment, and we aimed to provide a reference for future research on natural plant medicine for the prevention and treatment of T2DM and its related complications.