Project description:Microarray based CGH was conducted over a group of 29 strains of S. Enteritidis spanning different epidemiological periods in Uruguay, plus 6 other S. Enteritidis strains isolated from distant geographical regions. We also included 9 Salmonella enterica strains of other serovars isolated in Uruguay. A S. Enteritidis dispensable genome of 233 chromosomal genes and high extent of variation in virulence plasmid was found. Strains isolated before the epidemic show the highest genomic differences as compared with the PT4 reference strain. Comparison with the gene content of other serovars demonstrate extensive horizontal gene transfer between circulating strains beyond serovar definition. Our results show that the epidemic of S Enteritidis in Uruguay was produced by the introduction of strains closely related to PT4, and corroborate the extensive genetic homogeneity among S. Enteritidis isolates worldwide. Phage SE14 emerges as the only specific region for S. Enteritidis. Genetic differences detected in pre-epidemic strains, mainly associated with the absence of phage SE20, suggest that genetic features encoded in this phage may be related to particular epidemiological behavior.
Project description:Vietnam is one of the top shrimp producing and exporting countries in the world [1]. However, viral and bacterial epidemic diseases cause severe damages to shrimp farming, resulting in millions of US dollars losses annually [2]. Furthermore, inappropriate use of antibiotics in shrimp rearing lead to increased emergence of drug resistant pathogens [3]. Current practices for water quality control, mostly based on chemical and physical parameters; neglected biological criteria necessary for maintaining pond health. Ninh Thuan is a region situated in the South Central Coast of Vietnam. Due to its geographic location, a large part of this region is dedicated to shrimp (Litopenaeus vannamei) post-larvae production and rearing. This article presents a microbiome dataset from two water samples collected in a shrimp rearing pond in Ninh Thuan. We used Oxford Nanopore Technologies (ONT) for metagenomic sequencing of the samples to characterize microbial communities and antibiotic resistance profiles. The metagenome dataset generated will provide an understanding and comparison framework of the microbial diversity and functionality among shrimp ponds with potential application in health management and shrimp rearing industry.
Project description:This dataset includes shotgun metagenomics sequencing of the rhizosphere microbiome of maize infested with Striga hermonthica from Mbuzini, South Africa, and Eruwa, Nigeria. The sequences were used for microbial taxonomic classification and functional categories in the infested maize rhizosphere. High throughput sequencing of the complete microbial community's DNA was performed using the Illumina NovaSeq 6000 technology. The average base pair count of the sequences were 5,353,206 bp with G+C content of 67%. The raw sequence data used for analysis is available in NCBI under the BioProject accession numbers PRJNA888840 and PRJNA889583. The taxonomic analysis was performed using Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST). Bacteria had the highest taxonomic representation (98.8%), followed by eukaryotes (0.56%), and archaea (0.45%). This metagenome dataset provide valuable information on microbial communities associated with Striga-infested maize rhizosphere and their functionality. It can also be used for further studies on application of microbial resources for sustainable crop production in this region.