Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

Metagenomic Analysis of Slovak Bryndza Cheese Using Next-Generation 16S rDNA Amplicon Sequencing

Knowledge about diversity and taxonomic structure of the microbial population present in traditional fermented foods plays a key role in starter culture selection, safety improvement and quality enhancement of the end product. Aim of this study was to investigate microbial consortia composition in Slovak bryndza cheese. For this purpose, we used culture-independent approach based on 16S rDNA amplicon sequencing using next generation sequencing platform. Results obtained by the analysis of three commercial (produced on industrial scale in winter season) and one traditional (artisanal, most valued, produced in May) Slovak bryndza cheese sample were compared. A diverse prokaryotic microflora composed mostly of the genera Lactococcus, Streptococcus, Lactobacillus, and Enterococcus was identified. Lactococcus lactis subsp. lactis and Lactococcus lactis subsp. cremoris were the dominant taxons in all tested samples. Second most abundant species, detected in all bryndza cheeses, were Lactococcus fujiensis and Lactococcus taiwanensis, independently by two different approaches, using different reference 16S rRNA genes databases (Greengenes and NCBI respectively). They have been detected in bryndza cheese samples in substantial amount for the first time. The narrowest microbial diversity was observed in a sample made with a starter culture from pasteurised milk. Metagenomic analysis by high-throughput sequencing using 16S rRNA genes seems to be a powerful tool for studying the structure of the microbial population in cheeses

Identification of Bacterial and Fungal Communities in the Roots of Orchids and Surrounding Soil in Heavy Metal Contaminated Area of Mining Heaps

Orchids represent a unique group of plants that are well adapted to extreme conditions. In our study, we aimed to determine if different soil contamination and pH significantly change fungal and bacterial composition. We identified bacterial and fungal communities from the roots and the surrounding soil of the family Orchidaceae growing on different mining sites in Slovakia. These communities were detected from the samples of Cephalanthera longifolia and Epipactis pontica from Fe deposit Sirk, E. atrorubens from Ni-Co deposit Dobšiná and Pb-Zn deposit Jasenie and Platanthera bifolia by 16S rRNA gene and ITS next-generation sequencing method. A total of 171 species of fungi and 30 species of bacteria were detected from five samples of orchids. In summary, slight differences in pH of the initial soils do not significantly affect the presence of fungi and bacteria and thus the presence of the studied orchids in these localities. Similarly, the toxic elements in the studied localities, do not affect the occurrence of fungi, bacteria, and orchids. Moreover, Cortinarius saturatus, as a dominant fungus, and Candidatus Udaeobacter as a dominant bacterium were present in all soil samples and some root samples. Finally, many of these fungal and bacterial communities have the potential to be used in the bioremediation of the mining areas

Microbiome composition and dynamics while grapes turn to wine

Microbial composition and activity were recorded during preparation of Pinot blanc (“Rulandské biele”) from one vineyard during the years 2018, 2019, and 2020. Both fungi and bacteria are important for primary fermentation and malto-lactic fermentation, therefore total DNA and total RNA were isolated, and genes for 16S and 28S rRNA were amplified to determine both bacterial and yeast profiles. Four phases of wine production were selected for testing. We tested the initial grape juice right after crushing the grapes, must ~2-3 days post inoculation, actively fermenting must and finally – young wine before filtration. We experimented on 3 batches with addition of selected strains of Lachancea thermotolerans, Metschnikowia pulcherrima and commercial strains of Saccharomyces cerevisiae. The most apparent was seasonality and the effect of weather at given year. Naturally occurring yeast Hanseniaspora was detected alongside major players like S. cerevisiae. The most dominant bacterial genera were Gluconobacter, Komagataeibacter and Acetobacter. We were able to detect contaminating coliform bacteria as a result of unexpectedly warm and humid conditions during the harvest in 2018. This method even detected plant pathogens Penicillium, Botrytis, and Alternaria in some samples, and might be indicative of the health of a vineyard

Genetic polymorphisms related to testosterone metabolism in intellectually gifted boys.

Prepubertal testosterone levels are lower in intellectually gifted boys. The aim of this pilot study was to analyze potential genetic factors related to testosterone metabolism in control and gifted boys. Intellectually gifted (IQ>130; n = 95) and control (n = 67) boys were genotyped. Polymorphisms of interests were chosen in genes including androgen and estrogen receptors, 5-alpha reductase, aromatase and sex hormone binding globulin. Significant differences between control and gifted boys in genotype distributions were found for ESR2 (rs928554) and SHBG (rs1799941). A significantly lower number of CAG repeats in the AR gene were found in gifted boys. Our results support the role of genetic factors related to testosterone metabolism in intellectual giftedness. Increased androgen signaling might explain previous results of lower testosterone levels in intellectually gifted boys and add to the understanding of variability in cognitive abilities

Soil Microbiota of Dystric Cambisol in the High Tatra Mountains (Slovakia) after Windthrow

There has been much more damage to forests in the Slovak Republic in the second half of the 20th century than to other European countries. Forested mountain massifs have become a filter of industrial and transportation emissions from abroad, as well as from domestic origins. There are not only acidic deposits of sulphur and heavy metals present in forest soils, but other additional environmental problems, such as climate change, storms, fires, floods, droughts, are worsening the situation. Therefore, forest terrestrial ecosystems are becoming more vulnerable due to changes in natural and environmental conditions. In the High Tatra Mountains in Slovakia, which are protected as a national park, four internationally monitored localities were established after the windthrow disaster in 2004 and fire in 2005: REF, with intact forest; EXT, with extracted wood mass; NEX, with non-extracted wood mass; and FIR, the burnt locality. Soils from these localities were microbiologically analysed with special attention to fungi. Bacterial microbiota detected by high-throughput sequencing showed the prevalence of the genera Acidothermus, Mycobacterium, and Nocardia, and a very low presence of the genera Acidibacter, Burkholderia-Paraburkholderia, Optitus and the uncultured genus Desulfurellaceae H16 in the soil sample from the burnt locality when compared with the unburned sites. Additionally, soil mycocoenoses showed a low similarity between the locality with an intact forest ecosystem and the localities with extracted (REF–EXT) and non-extracted (REF–NEX) wood mass. There was no similarity with the burnt locality (FIR), where heat-resistant fungi dominated. It was shown that the windthrow disaster and subsequent extraction or non-extraction of wood mass did not affect the soil microbial communities or their development. On the other hand, the influence of fire was significant

Novel Arenavirus Isolates from Namaqua Rock Mice, Namibia, Southern Africa

Arenaviruses are feared as agents that cause viral hemorrhagic fevers. We report the identification, isolation, and genetic characterization of 2 novel arenaviruses from Namaqua rock mice in Namibia. These findings extend knowledge of the distribution and diversity of arenaviruses in Africa

Allele frequencies.

<p>Allele frequencies of the single nucleotide polymorphisms that were significantly different distributed in intellectually gifted (black boxes) and control (white boxes) boys. Genotypes of the polymorphisms are shown below the graphs.</p

Androgen receptor gene.

<p>Number of CAG repeats in the first exon of the androgen receptor gene in intellectually gifted (black boxes) and control (white boxes) boys (data are presented as mean+standard deviation).</p