Wageningen Bioveterinary Research (WBVR) has a bioinformatics group dedicated to multi-omics analyses of different sample types. Bioinformatics and multi-omics applications are mostly applied for basic research to study pathogens in interaction with their hosts.
Using multi-omics techniques, virulence mechanisms of Coxiella burnetti isolates involved in the Dutch Q-fever outbreak were unravelled. In addition, these multi-omics techniques are used to study the interplay of bacteria and viruses within complex microbial communities, like the intestinal microbiota. Microbiomics is a rapidly developing field that studies how complex microbial communities develop and change under the influence of external interventions.
Data-driven approaches using multi-omics, support detection and prevention of infectious diseases by identifying novel targets for diagnostics as well as vaccines. By comparing sequences of many members of a certain pathogen, differences or similarities within populations can be identified. Deep sequencing can support the pathogen characterization. This can be applied to diagnostic samples, but also in an epidemiological context or as part of microbiome interactions.
Our NGS services include bacterial and viral genome (re)sequencing, reconstruction, annotation and differential analysis. Sequencing applications include a variety of short- and long-read sequencing technologies that can be applied on pathogens up to BSL level 3. Additional bioinformatics analysis can include genome-derived in silico serotyping, multiple locus sequence typing (MLST), multiple-locus variable-number tandem repeat analysis (MLVA) using a variety of available or provided schemes. Alternatively, whole genome comparisons and clustering using machine-learning algorithms allows the identification of group-specific genotypic/phenotypic signatures.
We offer services at an academic and CRO level that include:
- Tailored microbiota characterization in a variety of matrices like ingesta, milk, dust or faeces (16S and ITS-based)
- Metagenomic and meta-transcriptomic functional and epidemiological characterization of microbial communities (including quantifying the antibiotic resistance gene repertoire (resistome))
- High-throughput (brute-force) in silico or serological screening of diagnostic bacterial protein candidates (bacterial proteome) based on genomic sequencing information
- RNA sequencing to characterize host-microbe interactions
- Customized and tailor made bioinformatics solutions to characterize pathogens and their environment.
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Please feel free to contact the expert of our contract research organization (CRO) to discuss tailormade solutions or request a sharp quote.