Microbiome and Functional Analysis of a Traditional Food Process: Isolation of a Novel Species (Vibrio hibernica) With Industrial Potential

Genetic analysis of Vibrio alginolyticus challenged by Fructus schisandrae reveals the mechanism of virulence genes

Due to the abusive use of antibiotics, bacterial resistance has become a global problem and poses severe threats to aquaculture. The drug-resistant diseases caused by Vibrio alginolyticus have caused significant economic losses to cultured marine fish. Fructus schisandrae is used to treat inflammatory diseases in China and Japan. There have been no reports of bacterial molecular mechanisms associated with F. schisandrae stress. In this study, the inhibiting effect of F. schisandrae on the growth of V. alginolyticus was detected to understand response mechanisms at the molecular level. The antibacterial tests were analyzed via next-generation deep sequencing technology (RNA sequencing, RNA-seq). Wild V. alginolyticus (CK) was compared with V. alginolyticus, F. schisandrae incubated for 2 h, and V. alginolyticus, F. schisandrae incubated for 4 h. Our results revealed that there were 582 genes (236 upregulated and 346 downregulated) and 1068 genes (376 upregulated and 692 downregulated), respectively. Differentially expressed genes (DEGs) were involved in the following functional categories: metabolic process, single-organism process, catalytic activity, cellular process, binding, membrane, cell part, cell, and localization. FS_2 h was compared with FS_4 h, and 21 genes (14 upregulated and 7 downregulated) were obtained. The RNA-seq results were validated by detecting the expression levels of 13 genes using quantitative real-time polymerase chain reaction (qRT-PCR). The qRT-PCR results matched those of the sequencing, which reinforced the reliability of the RNA-seq. The results revealed the transcriptional response of V. alginolyticus to F. schisandrae, which will provide new ideas for studying V. alginolyticus' complex virulence molecular mechanism and the possibility of developing Schisandra to prevent and treat drug-resistant diseases.

Microbial and Biochemical Profile of Different Types of Greek Table Olives

Analysis of table olives microbiome using next-generation sequencing has enriched the available information about the microbial community composition of this popular fermented food. In this study, 16S and 18S rRNA sequencing was performed on table olives of five Greek popular cultivars, Halkidikis, Thassou, Kalamon, Amfissis, and Konservolia, fermented either by Greek style (in brine or salt-drying) or by Spanish style, in order to evaluate their microbial communities. Moreover, analytical methods were used to evaluate their biochemical properties. The prevailing bacterial species of all olives belonged to Lactobacillaceae, Leuconostocaceae, and Erwiniaceae families, while the most abundant yeasts were of the Pichiaceae family. Principal coordinates analysis showed a clustering of samples cured by salt-drying and of samples stored in brine, regardless of their cultivar. The biochemical evaluation of total phenol content, antioxidant activity, hydroxytyrosol, oleuropein, oleocanthal, and oleacein showed that salt-dried olives had low amounts of hydroxytyrosol, while Spanish-style green olives had the highest amounts of oleocanthal. All the other values exhibited various patterns, implying that more than one factor affects the biochemical identity of the final product. The protocols applied in this study can provide useful insights for the final product, both for the producers and the consumers.

Study on the mechanism of Fufang E'jiao Jiang on precancerous lesions of gastric cancer based on network pharmacology and metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

Fufang E'jiao Jiang (FEJ) is a prominent traditional Chinese medicine prescription, which consists of Asini Corii Colla (Donkey-hide gelatin prepared by stewing and concentrating from the hide of Equus asinus Linnaeus., ACC), Codonopsis Radix (the dried roots of Codonopsis pilosula (Franch.) Nannf., CR), Ginseng Radix et Rhizoma Rubra (the steamed and dried root of Panax ginseng C.A. Mey., GRR), Crataegi Fructus (the mature fruits of Crataegus pinnatifida Bunge., CF), and Rehmanniae Radix Praeparata (the steamed and sun dried tuber of Rehmannia glutinosa (Gaertn.) Libosch. ex Fisch. & C.A. Mey., RRP). It is a popularly used prescription for "nourishing Qi and nourishing blood".

AIM OF THE STUDY

To explore the potential mechanism of FEJ on precancerous lesion of gastric cancer in rats by combining network pharmacology and metabolomics.

METHODS

Traditional Chinese Medicine Systems Pharmacology and Bioinformatics Analysis Tool for Molecular mechanism of Traditional Chinese Medicine were used to identify the ingredients and potential targets of FEJ. GeneCards database was used to define PLGC-associated targets. We built a herb-component-disease-target network and analyzed the protein-protein interaction network. Underlying mechanisms were identified using Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, 40% ethanol, N-methyl-N'-nitro-N-nitroguanidine and irregular eating were used to establish PLGC rats model. We also evaluated the efficacy of FEJ on MNNG-induced PLGC rats by body weight, histopathology, blood routine and cytokine levels, while the predicted pathway was determined by the Western blot. Ultra-performance liquid chromatography-tandem mass spectrometry-based serum non-targeted metabolomics was used to select potential biomarkers and relevant pathways for FEJ in the treatment of PLGC.

RESULTS

Network pharmacology showed that FEJ exhibited anti-PLGC effects through regulating ALB, TNF, VEGFA, TP53, AKT1 and other targets, and the potential pathways mainly involved cancer-related, TNF, PI3K-AKT, HIF-1, and other signaling pathways. Animal experiments illustrated that FEJ could suppress inflammation, regulate gastrointestinal hormones, and inhibit the expression of PI3K/AKT/HIF-1α pathway-related proteins. Based on serum non-targeted metabolomics analysis, 12 differential metabolites responding to FEJ treatment were identified, and metabolic pathway analysis showed that the role of FEJ was concentrated in 6 metabolic pathways.

CONCLUSION

Based on network pharmacology, animal experiments and metabolomics, we found that FEJ might ameliorate gastric mucosal injury in PLGC rats by regulating gastrointestinal hormones and inhibiting inflammation, and its mechanism of action is related to the inhibition of excessive activation of PI3K/AKT/HIF-1α signaling pathway and regulation of disorders of body energy metabolism. This comprehensive strategy also provided a reasonable way for unveiling the pharmacodynamic mechanisms of multi-components, multi-targets, and multi-pathways in Traditional Chinese Medicine.

Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities

Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genus Halomonas was identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernica B1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA, atpA, gyrB, rpoD and secA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated that H. hibernica B1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover, H. hibernica exhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.