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  • Benchmarking and improvement of the BaseClear 16S rRNA gene profiling pipeline.

    Benchmarking and improvement of the BaseClear 16S rRNA gene profiling pipeline.

    16S rRNA gene based microbial profiling remains an important tool to determine the composition of micro-organisms in a myriad of environmental samples, including faeces, soil, water as well as samples derived from food products. Though the technological methodology by itself is reproducible, the influence of DNA extraction, primer specificity, PCR protocol, sequencing and data analysis may affect the outcome of the microbial profiles. As a result, the profiles may not accurately represent the true bacterial composition in the original sample. Here, DNA extraction and 16S rRNA gene profiling was evaluated by characterization of so-called a mock community consisting of 8 bacterial strains.

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  • Genomics and bioinformatics tools unlocking the secrets of microorganism communities

    Genomics and bioinformatics tools unlocking the secrets of microorganism communities

    Your body hosts as many bacterial cells as it does your own cells and microbial communities are the dominant life form on our planet. Genomics and bioinformatics can unlock this hidden world and explore the diversity, composition and functional capacity of these communities.

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  • Innovative methods for GMO traceability

    Innovative methods for GMO traceability

    BaseClear, together with RIKILT (Wageningen UR) has recently developed innovative methods for GMO traceability within the context of the FP7 European Decathlon project.

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  • MinION simplifies the analysis of genetic material

    MinION simplifies the analysis of genetic material

    Since the introduction of the MinION of Oxford Nanopore Technologies, it is possible to read DNA very quickly and relatively easily. And the device fits your pocket too. “This could just be the iPod of the DNA world."

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  • Pharmacogenetics: Concerns of healthcare providers biggest hurdle for implementing DNA-test

    Pharmacogenetics: Concerns of healthcare providers biggest hurdle for implementing DNA-test

    The application of pharmacogenetic screening in first line patient care has great potential, but also raises concerns. The potential, the interests of stakeholders and the objections are identified in discussions with experts, doctors, pharmacists, health insurers and representatives of the Ministry of Public Health.

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  • Towards single contig high quality genomes

    Towards single contig high quality genomes

    Microbial genomics is an essential instrument for understanding microorganisms. BaseClear offers different sequencing technologies in order to produce high-quality microbial genomes, and our aim is to deliver completely closed genomes. With the addition of the latest platform from Pacific Biosciences, the Sequel system, we can now offer a new and improved approach for your microbial genome sequencing project.

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  • E. colonizer: gardening on Mars!

    E. colonizer: gardening on Mars!

    Have you ever thought of starting a garden on Mars? Perchlorate (ClO4-) contamination is a widely spread hazard for the environment and our health on Earth, but poses even a larger challenge when colonizing our neighbouring red planet Mars. The worrying fact is that Martian soil of toxic perchlorate consists for about 0.5 to 1%, which makes everything grown on it toxic as well. It thus needs to be remediated before we can cultivate our own edible crops on Mars. But how on Earth – or Mars – do you manage that?

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  • Insight into gut bacteria may help understanding of intestinal complaints

    Insight into gut bacteria may help understanding of intestinal complaints

    Flatulence, constipation and diarrhea are some of the many intestinal problems that we have to deal with. These can be annoying and the cause is often unclear. BaseClear spin-off MyMicroZoo now intends to change this by mapping the inhabitants of the intestines (the bacteria) so that bacterial population unbalance can be identified and addressed.

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  • The value of PacBio methylation data

    The value of PacBio methylation data

    PacBio sequencing is often used for sequencing complete microbial genomes. The long reads offer a clear added value to the shorter Illumina reads. Since the sequencing errors on the PacBio platform are basically unbiased, high quality assemblies can be made when coverage is high enough or when combining this with Illumina data in a hybrid strategy. However, in many projects not the full potential of the PacBio data is used. One of the great advantages of PacBio sequencing is that it permits the detection of methylated bases (m4C and m6A) which are quite common in bacterial and archaeal genomes.

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  • How to use Next Generation sequencing in microbial diagnostics?

    How to use Next Generation sequencing in microbial diagnostics?

    The number of applications for NGS in microbiological diagnostics is increasing rapidly. The possibilities are almost endless, but there are also many pitfalls. It is difficult for busy professionals working in clinical and diagnostics laboratories to keep up with the latest developments on NGS and so implementation is hindered by an inability to decide what the best technology to use is. So, how can this powerful, data-rich technology be used to provide clinically relevant information for diagnosis and treatment?

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  • How to overcome complex NCBI-compliant genome submissions & the importance of data standardization

    How to overcome complex NCBI-compliant genome submissions & the importance of data standardization

    As the costs for sequencing have significantly decreased over the last couple of years the number of whole genome sequencing (WGS) is vastly increasing. Often the end result consists of assembly (and annotated) draft genomes and researchers are required to submit these to the National Center for Biotechnology Information (NCBI) archive prior to publication of the manuscript. Although this seems a small step of the research process, it may become quite a complex task to share sequence data with the scientific community through these databases as many validation criteria apply.

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  • Nucleid acid extraction is an essential part of your sequencing project

    Nucleid acid extraction is an essential part of your sequencing project

    Microbial profiling studies depend heavily on obtaining high-molecular weight, sufficient concentration, and adequate quality DNA. As different extraction methods differ in their principle of obtaining nucleic acids and the outcome in terms of quantity as well as quality, this post describes basic considerations that help microbial ecologists select an appropriate extraction method for their sequencing project.

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  • DNA/RNA Sequencing Platforms: A Short Overview

    DNA/RNA Sequencing Platforms: A Short Overview

    With this blog Björn te Boekhorst provides a short overview of the history of DNA and RNA sequencing, the market leading sequencing platforms and a brief selection of emerging technologies.

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  • Oxford Nanopore is here to stay: ready for the challenges?

    Oxford Nanopore is here to stay: ready for the challenges?

    “A rollercoaster with many ups”, this is how Hans Jansen, Senior scientist at ZF-screens, describes their experiences with the MinION Nanopore sequencer so far. About a year ago ZF-screens decided to take part to the early access program of Oxford Nanopore Technologies (ONT) to experience first-hand the promises of this new technology.

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  • Close your bacterial genome using Oxford Nanopore sequencing technology!

    Close your bacterial genome using Oxford Nanopore sequencing technology!

    The latest long read sequencing technologies, in particular that of Oxford Nanopore Technologies, have the potential to further ease the process of bacterial genomic research and breakdown the analysis costs. So-called USB-stick DNA sequencing is promised to have an enormous strong impact on genomic research as the library preparation and sequencing steps will gradually become only a fraction of the costs of current long read sequencing technologies. But there are still some hurdles to take, also at the bioinformatics side.

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  • The potential of the DNA barcoding of Life project

    The potential of the DNA barcoding of Life project

    DNA barcoding is in very short the method used to identify species based on (a small part of) their DNA and to use these DNA sequences to build the tree of life. Why would you like to embark on such a project? There are many scientific reasons why the DNA barcoding of life project is very interesting.

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