Project description:YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.
Project description:<p class='ql-align-justify'>Megasphaera hexanoica KCCM 43214T, isolated from cow rumen, is capable of producing medium-chain carboxylic acids such as n-caproate and n-caprylate. In this study, we present a high-quality genome assembly, along with intracellular metabolomic profiling and pangenomic analysis. Illumina sequencing generated 2.3 Mbp from 15,293,634 reads with a GC content of 49.5%, while PacBio HiFi sequencing produced 331.5 Mbp across 45,266 reads, with an average read length of 7,323 bp and a HiFi read N50 of 8,214 bp. Hybrid assembly of short and long reads resulted in a single 2.88 Mbp contig, containing 2,075-2,083 unique genes. A genome-scale metabolic model was constructed, to evaluate its metabolic capabilities under specific growth conditions. Intracellular metabolomic analysis of cells grown in fructose medium and lactate medium revealed key metabolic activities associated with chain elongation. Pangenomic analysis across nine annotated genomes identified 6,721 orthologous gene using OrthoMCL, emphasizing the genetic and functional diversity within the Megasphaera genus. This dataset offers valuable insights into the metabolism and biotechnological potential of M. hexanoica KCCM 43214T.</p>
2026-04-03 | MTBLS14019 | MetaboLights
Project description:bile isolated bacteria Genome sequencing and assembly
| PRJNA763811 | ENA
Project description:Metaviromics for environmentally isolated phage samples
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).