The Notable Achievements and the Prospects of Bacterial Pathogen Genomics

Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short-(Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

Foodomics in bee product research: a systematic literature review

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. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature

Discovery Strategies of bioactive compounds synthesized by nonribosomal peptide synthetases and type-I polyketide synthases derived from marine 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. © 2016 by the authors

Genetic variation of eggplant mottled dwarf virus from annual and perennial plant hosts

The genetic diversity of eggplant mottled dwarf virus (EMDV), a member of the family Rhabdoviridae, was studied using isolates collected from different herbaceous and woody plant species and remote geographic areas. Sequences corresponding to the N, X, P, Y, M and G ORFs as well as the untranslated regions (UTRs) between ORFs were determined from all isolates. Low genetic diversity was found in almost all genomic regions studied except for the X ORF and the UTRs, which were more variable, while interestingly, an EMDV isolate from caper possessed a truncated G gene sequence. Furthermore, low dN/dS ratios, indicative of purifying selection, were calculated for all genes. Phylogenetic analysis showed that the EMDV isolates clustered in three distinct subgroups based on their geographical origin, with the exception of one subgroup that consisted of isolates from northern Greece and Cyprus. Overall, the level of genetic diversity of EMDV differed between seed- and asexually propagated plants in our collection, and this could be related to the mode of transmission. © 2015, Springer-Verlag Wien

Comparative analysis of the core proteomes among the Pseudomonas major evolutionary groups reveals species-specific adaptations for Pseudomonas aeruginosa and Pseudomonas chlororaphis

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. © 2020 by the authors

The challenges of interpreting phosphoproteomics data: A critical view through the bioinformatics lens

During the last decade, there has been great progress in high-throughput (HTP) phosphoproteomics and hundreds or even thousands of phosphorylation sites (p-sites) can now be detected in a single experiment. This success is attributable to a combination of very sensitive Mass Spectrometry instruments, better phosphopeptide enrichment techniques and bioinformatics software that are capable of detecting peptides and localizing p-sites. These new technologies have opened up a whole new level of gene regulation to be studied, with great potential for therapeutics and synthetic biology. Nevertheless, many challenges remain to be resolved; these concern the biases and noise of these proteomic technologies, the biological noise that is present, as well as the incompleteness of the current datasets. Despite these problems, the datasets published so far appear to represent a good sample of a complete phosphoproteome of some organisms and are capable of revealing their major properties. © Springer International Publishing Switzerland 2016

Antimicrobial activity of bee-collected pollen and beebread: State of the art and future perspectives

Bee-collected pollen (BCP) is a well-known functional food. Honey bees process the collected pollen and store it in the hive, inside the comb cells. The processed pollen is called beebread or ambrosia and it is the main source of proteins, lipids, vitamins, macro-and micro-elements in honey bee nutrition. During storage, beebread undergoes solid state fermentation which preserves it and increases the bioavailability of nutrients. Research on beebread has been rather limited until now. In recent years, there is an increasing interest regarding the antimicrobial properties of BCP and beebread, due to emerging antimicrobial resistance by pathogens. Both BCP and beebread exhibit antimicrobial properties against diverse pathogens, like bacteria and fungi. As is the case with other bee products, lack of antimicrobial resistance might be attributed to the synergy of more than one antimicrobial compounds within BCP and beebread. Furthermore, BCP and bee bread exert targeted activity against pathogens and affect the host microbiome in a prebiotic manner. This review aims to present up to date research findings regarding these aspects as well as to discuss current challenges and future perspectives in the field. © 2020 by the authors. Licensee MDPI, Basel, Switzerland

Association of p16 (CDKN2A) polymorphisms with the development of HPV16-related precancerous lesions and cervical cancer in the Greek population

The tumor suppressor protein p16 plays a fundamental role in cell cycle regulation and exerts a protective effect against tumor growth. Two different polymorphisms at positions 540 and 580 at the 3′UTR of exon 3 of p16 gene are implicated in several types of cancer, while their role in cervical cancer development remains rather vague. In the present study, we investigated for the impact of p16 genotypes/haplotypes on patients' vulnerability to cervical disease and examined whether these factors can be used as progression markers in the Greek population. A total of 96 HPV16 positive samples and histologically confirmed as LSIL (42 samples), HSIL (44 samples), and cervical cancer cases (10 samples) along with 50 control cases were tested. The identification of p16 polymorphisms was performed by PCR-RFLP methodology. The present analysis revealed that women with p16 540 CG/GG genotype are at a 2.7-fold higher risk of developing HPV16-associated HSIL (OR = 2.7, 95%CI: 1.01-6.6, P = 0.028). The G allele can be regarded as a risk factor of developing HSIL in the Greek population (OR = 2.7, 95%CI: 1.2-5.9, P = 0.012). Moreover, p16 polymorphism C580T is not associated with the growth of cervical lesion in Greek patients, while 540G/580C haplotype can be regarded as a risk haplotype of developing HSIL (OR = 3.67, 95%CI: 1.56-8.6, P = 0.0019). Our results demonstrated that p16 C540G polymorphism influence patients' susceptibility to more severe dysplasia and consequently this polymorphism could potentially emerge as a valuable biomarker for HSIL development in the Greek population. © 2017 Wiley Periodicals, Inc

The Remarkable Evolutionary Plasticity of Coronaviruses by Mutation and Recombination: Insights for the COVID-19 Pandemic and the Future Evolutionary Paths of SARS-CoV-2

Coronaviruses (CoVs) constitute a large and diverse subfamily of positive-sense sin-gle-stranded RNA viruses. They are found in many mammals and birds and have great importance for the health of humans and farm animals. The current SARS-CoV-2 pandemic, as well as many previous epidemics in humans that were of zoonotic origin, highlights the importance of studying the evolution of the entire CoV subfamily in order to understand how novel strains emerge and which molecular processes affect their adaptation, transmissibility, host/tissue tropism, and patho non-homologous genicity. In this review, we focus on studies over the last two years that reveal the impact of point mutations, insertions/deletions, and intratypic/intertypic homologous and non-homologous recombination events on the evolution of CoVs. We discuss whether the next generations of CoV vaccines should be directed against other CoV proteins in addition to or in-stead of spike. Based on the observed patterns of molecular evolution for the entire subfamily, we discuss five scenarios for the future evolutionary path of SARS-CoV-2 and the COVID-19 pan-demic. Finally, within this evolutionary context, we discuss the recently emerged Omicron (B.1.1.529) VoC. © 2022 by the authors. Licensee MDPI, Basel, Switzerland

Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant of concern (VoC), a study of amino acid substitution (AAS) patterns was performed and compared with those of the other four successful variants of concern (Alpha, Beta, Gamma, Delta) and one closely related variant of interest (VoI—Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but in Omicron this enrichment is significantly higher. The progenitors of each of these VoC/VoI lineages underwent positive selection in the Spike ORF. However, once they were established, their Spike ORFs have been undergoing purifying selection, despite the application of global vaccination schemes from 2021 onwards. Our analyses reject the hypothesis that the heavily mutated receptor binding domain (RBD) of the Omicron Spike was introduced via recombination from another closely related Sarbecovirus. Thus, successive point mutations appear as the most parsimonious scenario. Intriguingly, in each of the six lineages, we observed a significant number of AAS wherein the new residue is not present at any homologous site among the other known Sarbecoviruses. Such AAS should be further investigated as potential adaptations to the human host. By studying the phylogenetic distribution of AAS shared between the six lineages, we observed that the Omicron (BA.1) lineage had the highest number (8/10) of recurrent mutations. © 2022 by the authors. Licensee MDPI, Basel, Switzerland