High-Throughput Sequencing and Metagenomic Data Analysis

Metagenomic approaches are a growing branch of science and have many applications in different fields. Metagenomics seems to be the ideal culture-independent technique for unraveling the biodiversity of soils and to study how this biodiversity is affected with continuously changing conditions. In addition, its application in clinical and diagnostic approaches was reported. The emergence of several next-generation sequencing (NGS) strategies enriched the metagenomics. The combination between NGS and metagenomic approaches helped the investigators resolve several issues regarding the microbial diversity and the functions and relationships among different microbial flora. A number of NGS approaches were developed including Roche/454 pyrosequencing, Illumina/Solexa sequencing, and Applied Biosystems/SOLiD sequencing. In this chapter, different NGS platforms are discussed in terms of principle, advantages, and limitations. In addition, third-generation sequencing technologies are also addressed

Tomato RNA-seq Data Mining Reveals the Taxonomic and Functional Diversity of Root-Associated Microbiota

Next-generation approaches have enabled researchers to deeply study the plant microbiota and to reveal how microbiota associated with plant roots has key effects on plant nutrition, disease resistance, and plant development. Although early “omics” experiments focused mainly on the species composition of microbial communities, new “meta-omics” approaches such as meta-transcriptomics provide hints about the functions of the microbes when interacting with their plant host. Here, we used an RNA-seq dataset previously generated for tomato (Solanum lycopersicum) plants growing on different native soils to test the hypothesis that host-targeted transcriptomics can detect the taxonomic and functional diversity of root microbiota. Even though the sequencing throughput for the microbial populations was limited, we were able to reconstruct the microbial communities and obtain an overview of their functional diversity. Comparisons of the host transcriptome and the meta-transcriptome suggested that the composition and the metabolic activities of the microbiota shape plant responses at the molecular level. Despite the limitations, mining available next-generation sequencing datasets can provide unexpected results and potential benefits for microbiota research

Antibacterial Activity of Silver Nanoparticles against Staphylococcus warneri Synthesized Using Endophytic Bacteria by Photo-irradiation

Diseases caused by Staphylococcus warneri have a significant impact on human health. We evaluated the antibacterial activity of silver nanoparticles (synthesized using the endophytic strain SYSU 333150) against S. warneri. The strain SYSU 333150 was isolated from the roots of Borszczowia aralocaspica Bunge. The 16S rRNA sequence results suggest that SYSU 333150 belongs to the genus Isoptericola and is likely a new species. Photo-irradiation was used to synthesize silver nanoparticles, which were characterized using UV-visible spectroscopy, transmission electron microscopy and X-ray diffraction. The nanoparticles were spherical and measured to be11 to 40 nm. X-ray diffraction revealed four peaks corresponding to the 111, 200, 220, and 311 planes of the face-centered cubic lattice, indicating a crystalline nature. Fourier transform infrared spectroscopy suggested that the metabolites in the culture supernatant were likely reducing and capping agents. The silver nanoparticles possessed antimicrobial activity (14 mm zone of inhibition) against S. warneri, which was likely a result of DNA cleavage. The synthesized silver nanoparticles have potent antibacterial activity against S. warneri and can be used to control infection

Straw biochar increases the abundance of inorganic phosphate solubilizing bacterial community for better rape (Brassica napus) growth and phosphate uptake

The direct application of inorganic-phosphate-solubilizing bacteria (iPSBs) for improving the efficiency of phosphorus (P) use leads to a low rate of bacterial survival. Biochar is a good inoculum carrier for microbial survival, and diverse feedstocks can have different effects. We generated an iPSB community using seven selected iPSB strains with various phylogenic taxonomies and P-solubilizing abilities. Biochar was then inoculated with the iPSB community and applied to soil in pots seeded with rape (Brassica napus). Growth of the rape for four weeks and the effects of biochars produced from six raw feedstocks, rice straw, rice husks, soybean straw, peanut shells, corn cobs and wood, were compared. The synthetic iPSB community had a larger capacity to solubilize inorganic P and exude organic anions than any of the individual strains. The structure of the iPSB community was analyzed by high-throughput sequencing four weeks after inoculation. All seven iPSB strains were detected, dominated by Arthrobacter defluvii 06-OD12. The abundance of the iPSB community was significantly correlated with rape biomass, P content and P uptake (P < 0.05). The biochar amendments conferred 6.86-24.24% survival of the iPSB community, with the straw biochars conferring the highest survival. The available-P content of the biochar rather than soil pH was the dominant factor for iPSB community structure, suggesting that the biochar material was critical for the survival and functioning of the iPSB community. Our study demonstrates the feasibility of biochar-assisted iPSB improvement of crop growth and P uptake

Vermicompost Supply Modifies Chemical Composition and Improves Nutritive and Medicinal Properties of Date Palm Fruits From Saudi Arabia

To meet the increased demand for phytochemicals, plant cultivation in soil amended with biofertilizers has been developed. Here, we aimed to use vermicompost as an environmentally safe biofertilizer to enhance the nutritive and medicinal value of five common cultivars of Saudi date palm; namely Phoenix dactylifera L. var. Ajwa, Hulwa, Ruthana, Sefri, and Luban. To determine changes in the fruit nutritive composition, primary metabolites, antioxidants, phenolic compounds and mineral profiles were analyzed in the fruits from non-fertilized and vermicompost-fertilized date palms. We also tested how changes in the fruit chemical compositions due to vermicompost fertilization affected their medicinal potentials. Applying vermicomposts generally increased primary metabolites, vitamins, and mineral content as well as the medicinal potential of the date palm fruits. This positive effect is possibly explained by the role of vermicomposts in improving soil health and fertility. Furthermore, clustering analyses and principal component analysis (PCA) indicated cultivar-specific responses. PCA analysis also revealed that the bioactivities of the date palm fruit extracts and their antioxidants tended to display correlated output values. One of the highly accumulated phenolic compounds, β-D-glucogallin, was extracted and purified from P. dactylifera L. var. Ajwa fruits and showed significant antioxidant, anticancer, antibacterial, antimutagenic, and antiprotozoal activities. Overall, applying vermicompost is an innovative approach to increase the nutritive quality and medicinal potential of date palm fruits

PROPOLIS AND BEE VENOM IN DIABETIC WOUNDS; A POTENTIAL APPROACH THAT WARRANTS CLINICAL INVESTIGATION

Background: Wound healing in diabetes mellitus is a complex multi-stage process that requires the proper function of multiple systems. The mechanisms of impaired wound healing of diabetic wounds are still poorly understood. Therefore, various interventions are being used for wound management without great success. Bee products have various properties that make them an important addition to the diabetic wound management. Methods: This review summarized previous and recently published papers of the effects of two bee products, propolis and bee venom, on the wound healing. The main results were obtained from preclinical experimentation. Results: Diabetes mellitus compromises immune system, increases infections, impairs wound healing, and affects cells and factors involved in the wound healing. There is an increasing interest in natural products in modern medicine as part of disease management. Bee products are natural substances that others and we have explored some of their biological activities and applications in the treatment of various diseases. Some of these products are bee venom and propolis. These products have analgesic, antioxidant, antimicrobial, and anti-inflammatory properties. In addition, both propolis and bee venom contain considerable amounts of antioxidants that have a great role in accelerating wound healing. Conclusion: There is sound rationality and scientific data for using propolis and bee venom in diabetic wound healing. We believe that topical application of propolis in addition to bee venom might have a place in repairing damaged tissues and accelerating the healing of diabetic wounds

Enhancement and Identification of Microbial Secondary Metabolites

Screening for microbial secondary metabolites (SMs) has attracted the attention of the scientific community since 1940s. In fact, since the discovery of penicillin, intensive researches have been conducted worldwide in order to detect and identify novel microbial secondary metabolites. As a result, the discovery of novel SMs has been decreased significantly by using traditional experiments. Therefore, searching for new techniques to discover novel SMs was one of the most priority objectives. However, the development and advances of omics-based techniques such as metabolomics and genomics have revealed the potential of discovering novel SMs which were coded in the microorganisms’ DNA but not expressed in the lab media or might be produced in undetectable amount by detecting the biosynthesis gene clusters (BGCs) that are associated with the biosynthesis of secondary metabolites. Nowadays, the development and integration of gene editing tools such as CRISPR-Cas9 in metabolomics provide a successful platform for the identification and detection of known and novel SMs and also to increase the production of SMs