WGA-LP: a pipeline for whole genome assembly of contaminated reads.

SUMMARY: Whole genome assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-the-art programs for microbial analysis and novel scripts to check and improve the quality of both samples and resulting assemblies. WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads. AVAILABILITY AND IMPLEMENTATION: WGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Activity evaluation of pure and doped zinc oxide nanoparticles against bacterial pathogens and Saccharomyces cerevisiae.

AIMS: This work aimed to evaluate the antimicrobial activity of pure (ZnO) and doped (ZnMgO) zinc oxide (ZnO) nanoparticles on bacterial pathogens and Saccharomyces cerevisiae to confirm their applicability as an alternative to antibiotics and to estimate their biocompatibility. METHODS AND RESULTS: Microbial growth inhibition on agar plates, microbial viability and adaptation tests in broth with ZnO nanoparticles, spore germination, random amplified polymorphic DNA and SDS-PAGE analysis were conducted to evaluate the effects of ZnO nanoparticles on cell morphology, viability, DNA damage and protein production. For this purpose, Escherichia coli, Salmonella, Listeria monocytogenes, Staphylococcus aureus, Bacillus subtilis and S. cerevisiae were studied after the addition of ZnO nanoparticles to the growth media. The contact with ZnO nanoparticles produced changes in morphology, shape, viability, DNA arrangement (DNA fingerprints) and protein content (SDS-PAGE) in treated cells. CONCLUSIONS: As reported in this study, ZnO nanoparticles have an antimicrobial effect on both prokaryotic and eukaryotic cells. Before using ZnO nanoparticles as antimicrobial agents, it is important to evaluate the target because their effect depends on their composition, size and dose. SIGNIFICANCE AND IMPACT OF THE STUDY: We believe that the results obtained can help to optimize manufactured metal oxide nanoparticles in terms of their composition, size and working concentration. The parameters obtained directly define the applicability and biocompatibility of ZnO nanoparticles and thus are essential for any utilization in food, medicine and industry where pathogen control is crucial.

Identification of the unculturable bacteria Candidatus arthromitus in the intestinal content of trouts using Dot blot and Southern blot techniques.

The rainbow trout gastroenteritis (RTGE) syndrome is affecting progressively more sites in various European countries causing significant economical losses for the rainbow trout industries. As Candidatus arthromitus, a not yet culturable bacteria, is the microorganism responsible for the RTGE, molecular methods have been identified as an important tool for the identification of this microorganism. An early, fast and specific detection of C. arthromitus using specific primers and probes, are important goals for the aquaculture sector. In the present study were used: a polymerase chain reaction (PCR), using universal primers annealing the 16S rRNA gene, to obtain amplification products representatives of the microbiota present in the intestinal content of trouts, including C. arthromitus when present; a denaturing gradient gel electrophoresis (DGGE) to produce DNA finger printings corresponding to the microbiota present in the intestinal contents of each trout analysed; a specific DNA probe designed within the 16S rDNA that was used both in Dot blot and Southern blot techniques to detect the unculturable bacterium C. arthromitus. Dot blot applied directly onto DNA extracted from the intestinal contents allowed a fast identification of the samples containing C. arthromitus. Southern blotting allowed the identification of the specific DNA band corresponding to C. arthromitus among the various DNA bands obtained by the utilisation of the universal primers and run in DGGE. Molecular methods such as Dot blot and Southern blot are useful methods for a fast identification of the unculturable C. arthromitus.

A molecular method to detect Bacillus cereus from a coffee concentrate sample used in industrial preparations.

AIMS: The aim of this work was to develop specific primers which are able to detect Bacillus cereus in a coffee concentrate sample. METHODS AND RESULTS: A pre-PCR step to clean the DNA, used for PCR, was developed to avoid PCR inhibition by Maillard products. The combination of centrifugation and washing the pellet, employing EDTA and water, before DNA extraction improved the detection of low numbers of B. cereus cells (10 cells ml-1). The development of specific primers enabled to detect low numbers of B. cereus without the need of a pre-enrichment step. CONCLUSIONS: The data obtained demonstrated the specificity and the sensitivity of the primers that could be used to check the presence of B. cereus in different food products, avoiding the need for labourious and time-consuming culture-based techniques. SIGNIFICANCE AND IMPACT OF THE STUDY: The method could help food microbiologists to check food samples quickly for the presence of B. cereus.