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- Evaluation of a bacteriocinogenic Lactobacillus plantarum strain on the microbiological characteristics of “Alheira de Vitela”Publication . Macieira, Ariana; Albano, Helena; Pinto, Miguel; Linheiro, Raquel; Barbosa, Joana; Teixeira, PaulaLactic Acid Bacteria (LAB) and their bacteriocins can be successfully used as natural preservatives in meat products. This work aimed to investigate the effect of fresh and lyophilized starter cultures of an autochthonous bacteriocinogenic LAB strain (Lactobacillus plantarum ST153Ch: bac + culture) on the microbiological characteristics of “Alheira”, a traditional Portuguese smoked product. “Alheira” with the addition of fresh or lyophilized culture (ca. 108 cfu/g) and “Alheira” control (no bacteriocinogenic culture added) were produced by an industrial meat company. The antilisterial activity of this culture in this food matrix was investigated, with some samples being inoculated with Listeria monocytogenes (ca. 105 cfu/g). Detection of L. monocytogenes, Salmonella spp., sulphite reducing clostridia, Yersinia enterocolitica and enumeration of L. monocytogenes, Staphylococcus aureus, Bacillus cereus, Escherichia coli, Enterobacteriaceae, lactic acid bacteria, yeasts and moulds were performed immediately after production and at 3, 7, 15, 21, 28, 60 and 90 days of storage at 4 ℃, according to ISO methodologies. Also, a 16S rRNA Gene Analysis was performed of the microbial communities of “Alheira” with and without the lyophilized bacteriocinogenic culture. Pathogenic and indicator organisms were not detected or were below acceptable levels in all samples. LAB counts increased during storage and reached similar values after 15 days (ca. 1010 cfu/g) in all samples. There was a clear trend for a higher reduction of L. monocytogenes in the presence of the bioprotective culture, more pronounced during the initial 15 days of storage. From the analysis of the microbial communities of samples of “Alheiras” at different stages of fermentation, Leuconostocaceae and Lactobacillaceae predominated in all the samples and Lactobacillus was the genus more prevalent in “Alheiras” after 60 days of storage with the addition of bacteriocinogenic culture.
- McClintock: an integrated pipeline for detecting transposable element insertions in whole-genome shotgun sequencing dataPublication . Nelson, Michael G.; Linheiro, Raquel S.; Bergman, Casey M.Transposable element (TE) insertions are among the most challenging types of variants to detect in genomic data because of their repetitive nature and complex mechanisms of replication. Nevertheless, the recent availability of large resequencing data sets has spurred the development of many new methods to detect TE insertions in whole-genome shotgun sequences. Here we report an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods. We demonstrate the utility of McClintock by evaluating six TE detection methods using simulated and real genome data from the model microbial eukaryote, Saccharomyces cerevisiae. We find substantial variation among McClintock component methods in their ability to detect nonreference TEs in the yeast genome, but show that nonreference TEs at nearly all biologically realistic locations can be detected in simulated data by combining multiple methods that use split-read and read-pair evidence. In general, our results reveal that split-read methods detect fewer nonreference TE insertions than read-pair methods, but generally have much higher positional accuracy. Analysis of a large sample of real yeast genomes reveals that most McClintock component methods can recover known aspects of TE biology in yeast such as the transpositional activity status of families, target preferences, and target site duplication structure, albeit with varying levels of accuracy. Our work provides a general framework for integrating and analyzing results from multiple TE detection methods, as well as useful guidance for researchers studying TEs in yeast resequencing data.
- Genetic variation in the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strainPublication . Ferreira, Catarina; Bogas, Diana; Bikarolla, Santosh K.; Varela, Ana Rita; Frykholm, Karolin; Linheiro, Raquel; Nunes, Olga C.; Westerlund, Fredrik; Manaia, Célia M.Bacteria harboring conjugative plasmids have the potential for spreading antibiotic resistance through horizontal gene transfer. It is described that the selection and dissemination of antibiotic resistance is enhanced by stressors, like metals or antibiotics, which can occur as environmental contaminants. This study aimed at unveiling the composition of the conjugative plasmidome of a hospital effluent multidrug resistant Escherichia coli strain (H1FC54) under different mating conditions. To meet this objective, plasmid pulsed field gel electrophoresis, optical mapping analyses and DNA sequencing were used in combination with phenotype analysis. Strain H1FC54 was observed to harbor five plasmids, three of which were conjugative and two of these, pH1FC54_330 and pH1FC54_140, contained metal and antibiotic resistance genes. Transconjugants obtained in the absence or presence of tellurite (0.5 μM or 5 μM), arsenite (0.5 μM, 5 μM or 15 μM) or ceftazidime (10 mg/L) and selected in the presence of sodium azide (100 mg/L) and tetracycline (16 mg/L) presented distinct phenotypes, associated with the acquisition of different plasmid combinations, including two co-integrate plasmids, of 310 kbp and 517 kbp. The variable composition of the conjugative plasmidome, the formation of co-integrates during conjugation, as well as the transfer of non-transferable plasmids via co-integration, and the possible association between antibiotic, arsenite and tellurite tolerance was demonstrated. These evidences bring interesting insights into the comprehension of the molecular and physiological mechanisms that underlie antibiotic resistance propagation in the environment.