Project description:In this study we used Illumina RNA-seq to identify genes expressed by A. veronii in mid-log phase growth in a rich medium and within the digestive tract of the medicinal leech. Our results shed light on the physiology of A. veronii during colonization of the leech gut.
Project description:Direct, untargeted sequencing of environmental samples (metagenomics) and de novo genome assembly enable the study of uncultured and phylogenetically divergent organisms. However, separating individual genomes from a mixed community has often relied on the differential-coverage analysis of multiple, deeply sequenced samples. In the metagenomic investigation of the marine bryozoan Bugula neritina, we uncovered seven bacterial genomes associated with a single B. neritina individual that appeared to be transient associates, two of which were unique to one individual and undetectable using certain "universal" 16S rRNA primers and probes. We recovered high quality genome assemblies for several rare instances of "microbial dark matter," or phylogenetically divergent bacteria lacking genomes in reference databases, from a single tissue sample that was not subjected to any physical or chemical pre-treatment. One of these rare, divergent organisms has a small (593 kbp), poorly annotated genome with low GC content (20.9%) and a 16S rRNA gene with just 65% sequence similarity to the closest reference sequence. Our findings illustrate the importance of sampling strategy and de novo assembly of metagenomic reads to understand the extent and function of bacterial biodiversity.
Project description:In this study we used Illumina RNA-seq to identify genes expressed by A. veronii in mid-log phase growth in a rich medium and within the digestive tract of the medicinal leech. Our results shed light on the physiology of A. veronii during colonization of the leech gut. A comparison of Illumina RNA-seq of A. veronii in vivo versus in vitro.
Project description:Biological adhesion (bioadhesion) is referred to attachment of organisms to either biotic or abiotic surfaces. The differentiated ectodermal basal disc cells of the freshwater cnidarian Hydra secrete proteinaceous glue to temporarily attach themselves to surfaces underwater. In this study, we investigate for the first time the protein content of adhesive secretions from the freshwater cnidarian Hydra magnipapillata strain 105. This secretome were analysed using mass spectrometry and resulting MS/MS data were searched against in silico translated H. magnipapillata transcriptome and results from gene expression.
Project description:The microbiome associated with an animal's gut and other organs is considered an integral part of its ecological functions and adaptive capacity. To better understand how microbial communities influence activities and capacities of the host, we need more information on the functions that are encoded in a microbiome. Until now, the information about soil invertebrate microbiomes is mostly based on taxonomic characterization, achieved through culturing and amplicon sequencing. Using shotgun sequencing and various bioinformatics approaches we explored functions in the bacterial metagenome associated with the soil invertebrate Folsomia candida, an established model organism in soil ecology with a fully sequenced, high-quality genome assembly. Our metagenome analysis revealed a remarkable diversity of genes associated with antimicrobial activity and carbohydrate metabolism. The microbiome also contains several homologs to F. candida genes that were previously identified as candidates for horizontal gene transfer (HGT). We suggest that the carbohydrate- and antimicrobial-related functions encoded by Folsomia's metagenome play a role in the digestion of recalcitrant soil-born polysaccharides and the defense against pathogens, thereby significantly contributing to the adaptation of these animals to life in the soil. Furthermore, the transfer of genes from the microbiome may constitute an important source of new functions for the springtail.
Project description:The purpose of this study is to evaluate the gene expression patterns from colorectal mucosal cells collected through the use of a standard anoscope and cytology brush. Patients will include those scheduled for routine colonoscopy procedures and those with confirmed colorectal cancer.
