Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE

New insights into the roles of fungi and bacteria in the development of medicinal plant

BACKGROUND

The interaction between microorganisms and medicinal plants is a popular topic. Previous studies consistently reported that microorganisms were mainly considered pathogens or contaminants. However, with the development of microbial detection technology, it has been demonstrated that fungi and bacteria affect beneficially the medicinal plant production chain.

AIM OF REVIEW

Microorganisms greatly affect medicinal plants, with microbial biosynthesis a high regarded topic in medicinal plant-microbial interactions. However, it lacks a systematic review discussing this relationship. Current microbial detection technologies also have certain advantages and disadvantages, it is essential to compare the characteristics of various technologies.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review first illustrates the role of fungi and bacteria in various medicinal plant production procedures, discusses the development of microbial detection and identification technologies in recent years, and concludes with microbial biosynthesis of natural products. The relationship between fungi, bacteria, and medicinal plants is discussed comprehensively. We also propose a future research model and direction for further studies.

Comparison of culture and PCR-DGGE methods to evaluate the airways of cystic fibrosis patients and determination of their antibiotic resistance profile

Background and Objectives

Respiratory infections are the most serious condition in cystic fibrosis (CF) patients; therefore, a thorough comprehension of the diversity and dominant microbial species in CF airways has a crucial role in treatment. Our objective was to determine the antibiotic resistance profile of CF airways microbiota and compare culture methods and PCR-DGGE to evaluate bacterial diversity.

Materials and Methods

Pharyngeal swabs from 121 CF patients were collected. The samples were then cultured, identified and antibiotic resistance testing was performed. Thirty samples were subjected to further molecular surveys. DNA contents of these samples were extracted and amplified using nested-PCR technique and their bacterial diversity was assessed by DGGE. The DGGE patterns were visualized and certain bands were excised and purified. Next, the DNA was amplified by another round of PCR and sent out for sequencing.

Results

Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most prevalent species isolated using culture methods. S. aureus was the most common bacteria among 6 years and younger patients; while, P. aeruginosa had more prevalence among older ones. The PCR-DGGE results showed more diversity than culture methods, particularly in younger patients who exhibited more bacterial diversity than the older groups. Sequencing results unveiled the presence of certain bacterial species including Haemophilus parainfluenzae and Stenotrophomonas maltophilia which were completely missed in culture.

Conclusion

Even though culture-dependent methods are cost-effective, PCR-DGGE appeared to be more efficient to determine bacterial diversity. PCR-DGGE detects less abundant species, though their viability could not be determined using this method.

Enhancement of anti-inflammatory effect of cattle bile by fermentation and its inhibition of neuroinflammation on microglia by inhibiting NLRP3 inflammasome

As a kind of animal medicine, cattle bile has anti-inflammatory, antipyretic and cholagogic effects. The fermentation process of cattle bile is included in the application of many traditional Chinese medicines. In this study, we fermented cattle bile singly and investigated the impact of fermentation on the anti-inflammatory effect of cattle bile, as well as the mechanism of fermented cattle bile on microglia cells. After high temperature sterilization, cattle bile was fermented with Massa Medicata Fermentata (medicated leaven, Shen Qu). We used ultra-high performance liquid chromatography-mass spectrometry/mass spectrometry (UHPLC-MS/MS) to analyze the bile acids of cattle bile and fermented cattle bile. The results showed that 3-dehydrocholic acid, 7-ketolithocholic acid, 12-dehydrocholic acid, 12-Ketolithocholic acid, ursodeoxycholic acid and dehydrolithocholic acid increased more significantly than others; glycocholic acid and glycochenodeoxycholic acid decreased more significantly than others. After fermentation, cattle bile significantly reduced the release of NO and inflammatory factors (TNF-α and IL-1β). Furthermore, the protein expression of TNF-α, IL-1β and iNOS were decreased. In addition, we found that fermented cattle bile could have an anti-inflammatory effect through attenuating the activation of NLRP3 inflammasome. Thus, fermentation can enhance the anti-inflammatory effect of cattle bile. Fermented cattle bile has an anti-inflammatory effect by inhibiting the NLRP3 inflammasome pathway, which can expand the clinical application of cattle bile and provide new thoughts and methods for the application of cattle bile.

Microbial community succession and toxic alkaloids change during fermentation of Huafeng Dan Yaomu

Fermentation is a traditional processing method that can impact the abundance of relevant components in Chinese herbal medicines. Huafeng Dan Yaomu was processed by fermentation. In this study, we investigated changes in toxic alkaloids using high-performance liquid chromatography and analysed the changes in microbial communities during fermentation of Huafeng Dan Yaomu by Illumina MiSeq platform. The results indicated that highly toxic alkaloid compounds including aconitine, mesaconitine and hypaconitine were decreased, whereas benzoylmesaconine and benzoylhypaconitine were increased during fermentation. The dominant bacterial genera in the raw material (day 0) were Bacillus (58·38%), Enterobacter (16·05%), Enterococcus (4·10%) and others (11·48%). After 7 days of fermentation, Pediococcus predominated, increasing from 98·26 to 99·97%. The dominant fungal genera in the raw material (day 0) were Incertae_Sedis_incertae_sedis (45·36%), Eurotiales_unclassified (20·63%), Millerozyma (15·58%) and Saccharomycopsis (10·64%). After 7 days of fermentation, Saccharomycopsis was increased to 90·84%. After 14 days of fermentation, Pichia became the main fungal genera in the fermentation process. There were 16 bacterial genera and seven fungal genera that displayed significant correlation with toxic alkaloids. The dynamics of the microbiota and chemical compounds during fermentation of Huafeng Dan Yaomu were revealed, providing a foundation for further investigation of the effects of microbes on chemical compounds and insights into the manufacturing of Huafeng Dan Yaomu. SIGNIFICANCE AND IMPACT OF THE STUDY: Huafeng Dan Yaomu is a unique fermentation-based micro-organism product. This study reveals that the change in toxic alkaloids during fermentation was related to micro-organisms. The results of this study can be used to improve the Chinese herb medicine fermentation process, such as the selection of beneficial strains and their composition for modern fermentation. The results of this study may also provide new ideas for the processing of Traditional Chinese Medicine.

Probiotics-fermented Massa Medicata Fermentata ameliorates weaning stress in piglets related to improving intestinal homeostasis

Weaning stress has serious negative effects on piglets' health and the swine industry. Probiotics-fermented Chinese herbal medicines are potential feed additives to ameliorate weaning stress. In this study, the effects of probiotics-fermented Massa Medicata Fermentata (MMFP) on intestinal homeostasis were evaluated in weaning piglets. Dietary supplementation with MMFP promoted the development of the intestinal structure and elevated the concentrations of lactic acid and short-chain fatty acids (SCFAs) in the intestinal contents and antioxidant capacities in serum. MMFP reduced the levels of inflammatory factors in the intestinal mucosa. Microbial community analysis demonstrated that MMFP led to the selective and progressive enrichment of lactic acid- and SCFA-producing bacteria along the gastrointestinal tract, in particular, OTUs corresponding to Lactobacillus, Streptococcus, Acetitomaculum, Roseburia, and Eubacterium xylanophilum group, while MMFP reduced the relative abundance of pathogenic bacteria. On the contrary, antibiotics had negative effects on intestinal histology and increased the relative abundance of pro-inflammatory bacterium, such as Marvinbryantia, Peptococcus, Turicibacter, and Blautia. Correlation analysis reflected that the bacteria enriched in MMFP group were positively correlated with enhanced intestinal homeostasis, which suggested that dietary supplementation with MMFP enhanced host intestinal homeostasis by modulating the composition of gut microbiota and the levels of beneficial SCFAs, thus ameliorating weaning stress in piglets.

Identification of Different Bile Species and Fermentation Times of Bile Arisaema Based on an Intelligent Electronic Nose and Least Squares Support Vector Machine

Fermentation is one of the most traditionally utilized methods to process the raw materials of traditional Chinese medicine (TCM). Bile Arisaema (BA) is produced by the fermentation of the roots of Arisaema heterophyllum with bile. Fermentation time and bile species are the key factors in producing BA. The study was aimed to develop a new and rapid method for the identification of different fermentation times and bile species of BA. The polysaccharide content (PC), protease activity (PA), and amylase activity (AC) of BA were determined. The changes of PC, PA, and AC were significant indicators for the evaluation of different fermentation times. On the basis of the odor data of BA obtained by electronic nose technology (E-nose), the principal component analysis (PCA) was used to identify bile species. The results were further verified by the least squares support vector machine (LS-SVM). The trained LS-SVM was also used to predict the PC, PA, and AC of the samples to identify fermentation time. The present study indicated that E-nose combined with LS-SVM could effectively predict the PC, PA, and AC of the samples and identify the bile species and fermentation time of BA, and it was proved to be a useful strategy for quality control of fermented products of TCMs.