Mining Virulence Genes Using Metagenomics

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enterohaemorragic Escherichia coli against the gut metagenome or in pathogenic Neisseria meningitidis against the oral metagenome) include virulence genes that appear to be absent in related strains or species present in the microbiome of healthy individuals. We propose that this strategy (i.e. recruitment analysis of pathogenic bacteria against the metagenome of healthy subjects) can be used to detect pathogenicity regions in species where the genes involved in virulence are poorly characterized. Using this approach, we detect well-known pathogenicity islands and identify new potential virulence genes in several human pathogens

The Serbian version of the Childhood Health Assessment Questionnaire (CHAQ) and the Child Health Questionnaire (CHQ)

We report herein the results of the cross-cultural adaptation and validation into the Serbian language of the parentis version of two health related quality of life instruments. The Childhood Health Assessment Questionnaire (CHAQ) is a disease specific health instrument that measures functional ability in daily living activities in children with juvenile idiopathic arthritis (JIA). The Child Health Questionnaire (CHQ) is a generic health instrument designed to capture the physical and psychosocial well-being of children independently from the underlying disease. The Serbian CHAQ-CHQ were fully validated with 3 forward and 1 backward translations. A total of 139 subjects were enrolled: 79 patients with JIA (30% systemic onset, 28% polyarticular onset, 6% extended oligoarticular subtype, and 36% persistent oligoarticular subtype) and 60 healthy, children. The CHAQ clinically, discriminated between healthy, subjects and JIA patients, with the systemic, polyarticular and extended oligoarticular subtypes having a higher degree of disability. pain, and a lower overall well-being when compared to their healthy peers. Also the CHQ clinically, discriminated between healthy subjects and JIA patients, with the systemic onset, polyarticular onset and extended oligoarticular subtypes having a lower physical and psychosocial well-being when compared to their healthy peers. In conclusion the Serbian version of the CHAQ-CHQ is a reliable, and valid tool for the functional, physical and psychosocial assessment of children with JIA

Current state and prospects of biotechnology in Central and Eastern European countries. Part II: new and preaccession EU countries(CRO, RO, B&H, SRB)

Innovation holds the potential for economic prosperity. Biotechnology (BT) has proved to be a viable vehicle for the development and utilization of technologies, which has brought not only advances to society, but also career opportunities to nation-states that have enabling conditions. In this review, we assess the current state of BT-related activities within selected new and preaccession EU countries (NPA) of CEE region namely Croatia, Romania, Bosnia and Herzegovina and Serbia, examining educational programs, research activity, enterprises, and the financing systems. The field of BT covers a broad area of activities, including medical, food and agriculture, aquaculture or marine, environmental, biofuels, bioinformatics, and many others. Under the European Commission (EC), member-states are to set their Research and Innovation Strategies for Smart Specialization (RIS3), to identify priorities or strengths in order to develop knowledge intensive economies. As the four countries highlighted in this review are in the early stages of implementing RIS3 or have not yet fully formulated, it presents an opportunity to learn from the successes and failures of those that have already received major structural funds from the EC. A critical point will be the ability of the public and private sectors' actors to align, in the implementation of RIS3 as new investment instruments emerge, and to concentrate efforts on a few select target goals, rather than distribute funding widely without respect to a long-term vision

Culture-independent approaches for studying viruses from hypersaline environments

Hypersaline close-to-saturation environments harbor an extremely high concentration of virus-like particles, but the number of haloviruses isolated so far is still very low. Haloviruses can be directly studied from natural samples by using different culture-independent techniques that include transmission electron microscopy, pulsed-field gel electrophoresis, and different metagenomic approaches. Here, we review the findings of these studies, with a main focus on the metagenomic approaches. The analysis of bulk viral nucleic acids directly retrieved from the environment allows estimations of viral diversity, activity, and dynamics and tentative host assignment. Results point to a diverse and active viral community in constant interplay with its hosts and to a “hypersalineness” quality common to viral assemblages present in hypersaline environments that are thousands of kilometers away from each other.Our work on halophilic viral assemblages has been funded by the projects CGL2006-12714-CO2-01, CGL2006-12714-CO2-02, CGL2009-12651-C02-01, and CGL2009-12651-C02-02 from the Spanish Ministry of Science and Innovation that include funds from the European Community (FEDER funding) and by the project ACOMP/2009/155 from the Generalitat Valenciana

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic bacteroidetes

Hypersaline environments close to saturation harbor the highest density of virus-like particles reported for aquatic systems as well as low microbial diversity. Thus, they offer unique settings for studying virus-host interactions in nature. However, no viruses have been isolated so far infecting the two most abundant inhabitants of these systems (that is, the euryarchaeon Haloquadratum walsbyi and the bacteroidetes Salinibacter ruber). Here, using three different co-occurring strains, we have isolated eight viruses infecting the ubiquitous S. ruber that constitute three new different genera (named as 'Holosalinivirus', 'Kryptosalinivirus' and 'Kairosalinivirus') according to their genomic traits, different host range, virus-host interaction capabilities and abundances in natural systems worldwide. Furthermore, to get a more complete and comprehensive view of S. ruber virus assemblages in nature, a microcosm experiment was set with a mixture of S. ruber strains challenged with a brine virus concentrate, and changes of viral populations were monitored by viral metagenomics. Only viruses closely related to kairosalinivirus (strictly lytic and wide host range) were enriched, despite their low initial abundance in the natural sample. Metagenomic analyses of the mesocosms allowed the complete recovery of kairosalinivirus genomes using an ad hoc assembly strategy as common viral metagenomic assembly tools failed despite their abundance, which underlines the limitations of current approaches. The increase of this type of viruses was accompanied by an increase in the diversity of the group, as shown by contig recruitment. These results are consistent with a scenario in which host range, not only virus and host abundances, is a key factor in determining virus fate in nature.This research was supported by the Spanish Ministry of Economy projects CLG2015_66686-C3-1 (to JA) and CLG2015_66686-C3-3 (to RRM), which were also supported with European Regional Development Fund (FEDER) funds