Foodomics is an emerging research field in food science that applies advanced omics technologies to assess relevant aspects related to food and nutrition, with the ultimate goal to improve human ...health and well-being. Many studies have already shown the tremendous potential of this approach to boost food science research regarding food authentication and traceability, safety issues, improved quality, bioactivity and the action of specific bioactive compounds in diverse biological systems. Honey bees provide high-quality products and a wide range of benefits to humans. Honey is certainly the most widespread edible bee product. However, nowadays other edible bee products (royal jelly, propolis, pollen and naturally fermented pollen (bee bread) are considered superfoods due to their high nutritional value and their beneficial effects on human health. This review aims to present current omics implementations in honey bee product research related to authentication (e.g. botanical origin, biomarker identification), adulteration detection, bioactivity (e.g. anti-microbial, antioxidant), microbiome characterization and their effects on human health. Conclusively, many studies have proven the tremendous potential of -omics technologies in bee product research. This approach will be further implemented in the future: (i) for the comprehensive assessment of bee product authentication, quality, safety and traceability; (ii) to elucidate the role of bioactive compounds in bee products, (iii) to identify novel molecular biomarkers for disease prevention; (iv) to establish the effect of bee products on gut microbiome; (v) to elucidate biological processes of agronomic interest and economic relevance to bee products.
Bees are important pollinators worldwide, promoting sustainability in agriculture and natural ecosystems. Moreover, honey bees produce a variety of honey bee products (beehive products). Honey is the ...main edible bee product. The consumption of pollen, bee bread, royal jelly, and propolis is becoming more popular nowadays. All these products are characterized by high nutritional value and/or bioactivity. A high microbial diversity has been reported in bees and beehive products, forming distinct microbial communities. The honey bee gut microbiome actively promotes good health and nutrient availability for the host. Furthermore, it prevents food spoilage and contributes to the maintenance of good hygiene conditions in the hive. Pseudomonads are often reported in investigations on bee and bee product microbiomes. Diverse Pseudomonas species demonstrate high metabolic adaptability, producing a wide range of bioactive enzymes and secondary metabolites. Several studies have provided evidence that Pseudomonads might play a role in bee well-being and the bioactivity exerted by honey bee products, though further research is warranted to fully understand the effects and mechanisms. The aim of this narrative review is to highlight the importance of Pseudomonads in the context of up-to-date knowledge regarding the bee and bee product microbiomes.
Considering that 70% of our planet's surface is covered by oceans, it is likely that undiscovered biodiversity is still enormous. A large portion of marine biodiversity consists of microbiomes. They ...are very attractive targets of bioprospecting because they are able to produce a vast repertoire of secondary metabolites in order to adapt in diverse environments. In many cases secondary metabolites of pharmaceutical and biotechnological interest such as nonribosomal peptides (NRPs) and polyketides (PKs) are synthesized by multimodular enzymes named nonribosomal peptide synthetases (NRPSes) and type-I polyketide synthases (PKSes-I), respectively. Novel findings regarding the mechanisms underlying NRPS and PKS evolution demonstrate how microorganisms could leverage their metabolic potential. Moreover, these findings could facilitate synthetic biology approaches leading to novel bioactive compounds. Ongoing advances in bioinformatics and next-generation sequencing (NGS) technologies are driving the discovery of NRPs and PKs derived from marine microbiomes mainly through two strategies: genome-mining and metagenomics. Microbial genomes are now sequenced at an unprecedented rate and this vast quantity of biological information can be analyzed through genome mining in order to identify gene clusters encoding NRPSes and PKSes of interest. On the other hand, metagenomics is a fast-growing research field which directly studies microbial genomes and their products present in marine environments using culture-independent approaches. The aim of this review is to examine recent developments regarding discovery strategies of bioactive compounds synthesized by NRPS and type-I PKS derived from marine microbiomes and to highlight the vast diversity of NRPSes and PKSes present in marine environments by giving examples of recently discovered bioactive compounds.
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our ...large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes. In the course of this analysis, highly conserved protein motifs and domains within each of the AARS loci were identified and used to build a web-based computational tool for the genome-wide detection of AARS coding sequences. This is based on hidden Markov models (HMMs) and is available together with a cognate database that may be used for specific analyses. The bioinformatics tools that we have developed may also help to identify new antibiotic agents and targets using these essential enzymes. These tools also may help to identify organisms with alternative pathways that are involved in maintaining the fidelity of the genetic code.
The antibacterial activity of 31 Greek and Cypriot honeys against Staphylococcus aureus and Pseudomonas aeruginosa was initially screened using an agar-well diffusion assay in comparison with manuka ...honey. The minimum inhibitory concentration (MIC) was determined in broth using a spectrophotometric-based assay. The MIC of treated honeys with catalase or proteinase K was determined and compared with those of untreated honeys. All tested honeys demonstrated antibacterial activity against S. aureus on agar-well diffusion assay. MICs of tested honeys were determined as 3.125-25% (v/v), compared with manuka honey at 6.25% (v/v). Similarly, 21 of 31 tested honeys demonstrated antibacterial activity on agar-well diffusion assay against P. aeruginosa. Their MICs ranged from 6.25% to 25% (v/v) compared with 12.5% (v/v) for manuka honey. Antibacterial activity of tested honeys could be largely attributed to hydrogen peroxide formation and in some cases to unidentified proteinaceous compounds. In conclusion, Greek and Cypriot honeys demonstrated significant but variable antibacterial activity against P. aeruginosa and especially S. aureus. To the best of our knowledge this is the first study that has thoroughly examined the antibacterial activity of Greek and Cypriot honeys compared with manuka honey. The high antibacterial activity exerted by some tested honeys warrants further investigation.
The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic ...components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers.
Athletes often consume functional beverages in order to improve performance and reduce oxidative stress caused by high-intensity exercise. The present study aimed to evaluate the antioxidant and ...antibacterial properties of a functional sports beverage formulation. The beverage's antioxidant effects were assessed on human mesenchymal stem cells (MSCs) by determining thiobarbituric acid reactive substances (TBARS; TBARS levels decreased significantly by 52.67% at 2.0 mg/mL), total antioxidant capacity (TAC; TAC levels increased significantly by 80.82% at 2.0 mg/mL) and reduced glutathione (GSH; GSH levels increased significantly by 24.13% at 2.0 mg/mL) levels. Furthermore, the beverage underwent simulated digestion following the INFOGEST protocol to assess its oxidative stability. The analysis of the total phenolic content (TPC) using the Folin-Ciocalteu assay revealed that the beverage contained a TPC of 7.58 ± 0.066 mg GAE/mL, while the phenolics identified by HPLC were catechin (2.149 mg/mL), epicatechin (0.024 mg/mL), protocatechuic acid (0.012 mg/mL), luteolin 7-glucoside (0.001 mg/mL), and kaempferol-3-O-β-rutinoside (0.001 mg/mL). The beverage's TPC was strongly correlated with TAC (R
= 896). Moreover, the beverage showcased inhibitory and bacteriostatic effects against
and
. Lastly, the sensory acceptance test demonstrated that the functional sports beverage was well accepted by the assessors.
Bee-collected pollen (BCP) and bee bread (BB) are honey bee products known for their beneficial biological properties. The main goal of this study was to investigate BB microbiota and its ...contribution to bioactivity exerted by BB. The microbiota of BB samples collected at different maturation stages was investigated via culture-independent (Next Generation Sequencing, NGS) and culture-dependent methods. Microbial communities dynamically fluctuate during BB maturation, ending in a stable microbial community structure in mature BB. Bee bread bacterial isolates were tested for phenotypes and genes implicated in the production and secretion of enzymes as well as antibacterial activity. Out of 309 bacterial isolates, 41 secreted hemicellulases, 13 cellulases, 39 amylases, 132 proteinases, 85 Coomassie brilliant blue G or R dye-degrading enzymes and 72 Malachite Green dye-degrading enzymes. Furthermore, out of 309 bacterial isolates, 42 exhibited antibacterial activity against Staphylococcus aureus, 34 against Pseudomonas aeruginosa, 47 against Salmonella enterica ser. Typhimurium and 43 against Klebsiella pneumoniae. Artificially fermented samples exerted higher antibacterial activity compared to fresh BCP, strongly indicating that BB microbiota contribute to BB antibacterial activity. Our findings suggest that BB microbiota is an underexplored source of novel antimicrobial agents and enzymes that could lead to new applications in medicine and the food industry.
Previous analyses have identified certain but limited evidence of recombination among HPV16 genomes, in accordance with a general perception that DNA viruses do not frequently recombine. In this ...evolutionary/bioinformatics study we have analyzed more than 3600 publicly available complete and partial HPV16 genomes. By studying the phylogenetic incongruence, similarity plots and the distribution patterns of lineage-specific SNPs, we identify several potential recombination events between the two major HPV16 evolutionary clades. These two clades comprise the (widely considered) phenotypically more benign (lower risk) lineage A and the (widely considered) phenotypically more aggressive (higher risk) non-European lineages B, C and D. We observe a frequency of potential recombinant sequences ranging between 0.3 and 1.2% which is low, but nevertheless considerable. Our findings have clinical implications and highlight that HPV16 genotyping and risk assessment based only on certain genomic regions and not the entire genome may provide a false genotype and, therefore, its associated risk estimate. Finally, based on this analysis, we have developed a bioinformatics tool that automates the entire process of HPV16 lineage genotyping, recombination detection and further identifies, within the submitted sequences, SNPs that have been reported in the literature to increase the risk of cancer.
In this study, the chemical composition of essential oils (EOs) extracted from Origanum vulgare ssp. hirtum Lamiaceae, (oregano), Salvia officinalis Lamiaceae (sage), Mentha pulegium Lamiaceae ...(pennyroyal), and respective hydrosols (HSs) has been investigated by Gas Chromatography–Mass Spectrometry (GC-MS). The antimicrobial activity was assessed against two oral pathogens: Gram-positive bacterium Streptococcus mutans and the fungus Candida albicans by determination of Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal/Fungicidal concentration (MBC/MFC). Three-fold diluted solutions were dispensed into each well of a 96-well microtiter plate and, after incubation, MIC was determined by visual monitoring. The MBC/MFC was determined by transferring a small quantity of sample contained in each replicate well of the microtiter plates to appropriate culture media using a microplate replicator. The EOs of the tested herbs showed antimicrobial properties, especially the EO oil of O. vulgare, which exerted the highest antimicrobial activity. HSs of S. officinalis and M. pulegium exerted no antimicrobial activity, in contrast to oregano HS, which displayed strong antimicrobial activity. In all cases, a higher number of compounds were detected in EOs than in the corresponding HSs. The major compounds of sage EO were detected to be α-thujone (25.1%), 1,8-cineole (15.8%) and β-pinene (10.0%), while the HS was characterized by the presence of 1,8-cineole (32.6%), borneol (22.6%) and α-thujone (22.4%). Pennyroyal EO and HS consists mainly of pulegone (62.1 and 50.6%, respectively). Carvacrol was the major component present in EO (63%) and HS (97.3%) of oregano, probably contributing to the antimicrobial activity. Further research is needed in order to elucidate the antimicrobial mechanisms of specific compounds present in essential oils and hydrosols of Lamiaceae grown in Greece against oral pathogens.
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