Draft genome sequence of the bacteriophage vB_Eco_slurp01.

Bacteriophage vB_Eco_slurp01 was isolated from porcine feces using Escherichia coli MG1655 as a host. With a genome size of 348 kb, vB_Eco_slurp01 is one of the largest bacteriophages isolated to date

Comparative genomics of bacteriophage of the genus Seuratvirus

Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases

The application of high-throughput sequencing to study the genome composition and transcriptional response of Haemophilus influenzae.

Haemophilus influenzae is an important human pathogen, responsible for respiratory infections, such as otitis media, bronchitis and epiglottitis, as well as invasive disease. Despite being the first free-­‐living organism to have its whole genome sequenced, there have been only a few published studies investigating its transcriptional profile using next-­‐generation sequencing (NGS). The work presented in this thesis aimed to use NGS to improve the understanding of how H. influenzae behaves during natural infection and to identify novel RNA structures with potentially important roles in pathogenesis. The whole transcriptome of H. influenzae during infection-­‐relevant conditions was analysed using high-­‐throughput RNA sequencing. For the first time, the transcriptional profile of H. influenzae during stationary phase and nutritional stress was determined on a whole-­‐genome scale. Differential gene expression analysis of an invasive strain, R2866, and a laboratory strain, Rd KW20, revealed differences in their transcriptional response, particularly during oxidative stress and iron starvation. Importantly, a new systematic and robust bioinformatic tool, "toRNAdo", was developed to identify non-­‐coding RNA elements from the bacterial transcriptomic data. It enabled discovery of a repertoire of novel putative intergenic and antisense non-­‐coding RNAs in H. influenzae. In addition, the first fully sequenced genome of a free-­‐living organism, the Rd KW20 strain of H. influenzae, was re-­‐sequenced and re-­‐ annotated for the first time. This enabled identification of multiple nucleotide-­‐ level differences between original and re-­‐sequenced genomes of Rd KW20. The work presented here facilitates future characterisation of novel RNA elements, with potentially important regulatory roles in pathogenesis in H. influenzae, and has implications for defining a model bacterial strain. Importantly, the findings present significant insight into the pathogenic lifestyle of H. influenzae. They provide the basis for further work, where novel vaccine and antibiotic targets may get developed

Complete Genome Sequence of <i>Lactococcus lactis</i> AH1, Isolated from Viili, a Finnish Dairy Product

Here, we report the complete genome sequence of Lactococcus lactis strain AH1, isolated from viili, a Finnish dairy product. This strain is known for the extreme viscosity it imparts to fermented milk due to its production of exopolysaccharides. The complete sequence was obtained by combining Illumina and Nanopore data, revealing a chromosome with a length of 2,421,519 bp and eight plasmids ranging from 5,773 to 55,958 bp

Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa

Bacterial pathogens evolve during the course of infection as they adapt to the selective pressures that confront them inside the host. Identification of adaptive mutations and their contributions to pathogen fitness remains a central challenge. Although mutations can either target intergenic or coding regions in the pathogen genome, studies of host adaptation have focused predominantly on molecular evolution within coding regions, whereas the role of intergenic mutations remains unclear. Here, we address this issue and investigate the extent to which intergenic mutations contribute to the evolutionary response of a clinically important bacterial pathogen, Pseudomonas aeruginosa, to the host environment, and whether intergenic mutations have distinct roles in host adaptation. We characterize intergenic evolution in 44 clonal lineages of P. aeruginosa and identify 77 intergenic regions in which parallel evolution occurs. At the genetic level, we find that mutations in regions under selection are located primarily within regulatory elements upstream of transcriptional start sites. At the functional level, we show that some of these mutations both increase or decrease transcription of genes and are directly responsible for evolution of important pathogenic phenotypes including antibiotic sensitivity. Importantly, we find that intergenic mutations facilitate essential genes to become targets of evolution. In summary, our results highlight the evolutionary significance of intergenic mutations in creating host-adapted strains, and that intergenic and coding regions have different qualitative contributions to this process