BaseClear BiaNomics offers complete solutions to help determine the effect of probiotics, antibiotics, cosmetics or other interventions on the gut microbiome and/or skin microbiome. The effect can be analysed via microbial community analysis and related approaches (e.g. metagenomics). This can be done during preclinical research on laboratory models or in a later stage during clinical research on patients or healthy volunteers. BaseClear BiaNomics offers a complete microbiome analysis solution. We can facilitate the entire process, including:

Experts meeting on microbiome analysis for clinical tirals

seClear has years of experience in microbiome analysis, including the analysis of interactions between drugs and the microbiota in clinical trials. We routinely organise expert meetings wherein scientists and researchers meet, share and discuss microbiome projects, challenges and opportunities.Topics include multi-omics analysis approaches, study designing and planning to clinical trials, strain-specific studies, microbiome in pharma, studies for health claims and consumer education-branding.

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The first step of your clinical microbiome analysis project is the collection, storage and transport of all the samples. BaseClear BiaNomics offers complete solutions to help you with the logistics of your microbiome analysis project.

  1. We offer sample collection boxes that contain all the necessary materials to, for example, collect a faecal or skin sample.
  2. The kit contents enable the study participants to collect samples themselves according to specific instructions.
  3. The samples are sent directly back to us for analysis in a standardized way.
  4. Besides offering our standard sample collection kit, we can also customize the branding of the kit itself and its contents to suit the needs of your specific project.
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Sampling box BiaNomics


A microbiome analysis has no value if the DNA and/or molecules of the different organisms do not represent the microbial community in the faecal or skin samples from which they were extracted. The method of extraction can have a strong influence on the quantification of the total bacteria and the abundance estimations of specific groups. BaseClear BiaNomics has invested in optimization and validation of our extraction procedures and offers specific solutions to extract DNA as well as RNA from complex samples, such as faeces. However, in case you prefer a certain isolation protocol this is no problem for us. Experts from BaseClear BiaNomics can help you select the most appropriate extraction method for your microbiome analysis project.

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DNA extraction wutg the microbiomics products from Zymo Research


With our microbiome analysis service BaseClear BiaNomics offers the possibility to give participants insight into their personal microbial profiles. They can compare their personal results with those in the same study, or with other groups such as vegetarians or athletes. Of course, BaseClear BiaNomics guarantees complete data confidentiality.

Online microbiome analysis


BaseClear BiaNomics can analyse the complete microbiome that is present in your samples. Usually we do this based on PCR amplification and sequencing of taxonomic (e.g., 16S/18S/23S rRNA genes or ITS) or functional marker genes. We compare the generated data to microbial sequencing databases and analyse the data with our in-house developed tool, the BaseClear Genome Explorer. In this way we can identify thousands of microorganisms in one analysis, including non-cultivable ones, and determine their relative abundance.

Instead of analysing only the specific genes of the microbiome, BaseClear BiaNomics also offers the possibility to analyse the complete collective genomes of the microorganisms present in a sample. This is referred to as metagenomics or community genomics. In addition, we can analyse the total extracted RNA from a sample, showing which genes are predominantly expressed in the present microbiome.

Clinical microbial profiling


For your clinical microbiome analysis project we can digitally record metadata from the participant with an online questionnaire. The questionnaire can be customized exactly to your wishes. With this you can, for example, identify responders and non-responders.

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Using multivariate analyses BaseClear can mine data to stratify individuals in, for example, responders and non-responders based on the abundances of different microbial groups or functional identifiers as well as indicate if the different sample group are significantly different. Furthermore, this microbiota analysis facilitates identification of microbial groups or function identifiers that are important drivers of the difference between sample groups.

Redundancy analysis based on bacterial abundance data stratifying samples coming from non-responder and responders. The horizontal axis is chosen in a way that explains the most variation between sample groups. Each arrow (representing a taxonomic group) points in the direction of the steepest increase of that predictor value. The double lined icons are the centroids of the sample groups. Other symbols represent individual samples. Colored lines connect the outermost samples in a sample group, in such a way that all sample share in the envelope. Arrows (indicating specific taxa) pointing in the direction of a sample or centroid can be considered important for that sample or centroid.

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Multivariate analysis

Meet Tom van den Bogert!

Tom is our metagenomics and microbiome specialist. He is responsible for the development of new and improved metagenomics and microbial profiling services, which are based on Next-Generation sequencing and related technologies. Tom completed his PhD research at the Laboratory for Microbiology at Wageningen University. He studied community and genomic analysis of the human small intestine microbiota in a project funded by TI Food and Nutrition entitled "Complex fermentations."

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