BaseClear offers state-of-the-art microbial community analysis services. This service is based on the latest molecular methods, including PCR and Next-Generation Sequencing (NGS) technology. These technologies have opened a variety of possibilities for microbial identification and microbial diversity studies. We offer a complete microbial community analysis service, including DNA extraction from a range of samples such as gut, skin, probiotics, water or soil samples. By using PCR and NGS technology we can determine the composition of bacteria, Archaea and fungi in your sample.

Why choose our microbial diversity analysis service?

  • BaseClear is specialized in microbial diversity studies for environmental (e.g. food, water and soil) and microbiota samples (e.g. gut microbiome or skin microbiome)
  • With our microbial community analysis service you can identify thousands of microorganisms in one analysis
  • Our microbial profiling service offers the possibility to identify non-cultivable microorganisms
  • Determine the relative abundance of microorganisms
  • Extremely fast method for screening of complex ecosystems
  • Better understanding and control of the microbial flora
  • Experimental design for this kind of projects is crucial, our specialists can help decide which strategy should be used for your project for most reliable results
  • Advanced pipelines for downstream data analysis and interpretation
  • Taxonomic and functional classification performed using specialized software (such as MEGAN)
  • Unique interactive online portal for multilevel taxonomic analysis
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Complete microbiome analysis solutions

The effect of probiotics or biomolecules on the gut or skin microbiome can be analysed via microbial profiling and related approaches. This can be done during preclinical research on laboratory models or in a later stage during clinical research on patients or healthy volunteers. BaseClear offers a complete microbiome analysis solution. We can facilitate the entire process, including:

  • Sampling solutions and transport
  • DNA and/or RNA extraction
  • Sequencing
  • Visualization of the microbial profiles
  • Biostatistics
  • Sharing results with participants
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Technical approach for microbial community analysis studies

The technical approach for microbial diversity studies is usually based on PCR amplification of specifc genes followed by Next Generation sequencing. The generated sequence data is compared to microbial sequencing databases. We also offer complete downstream bioinformatics solutions. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies. Taxonomic classification is performed using an in-house protocol. The standard output includes a comprehensive table containing all taxonomies found and their counts, but also a number of publication-ready figures which allow an easy (graphical) interpretation of the findings (e.g. a cladogram, pie chart and bar chart). The results can also be easily viewed and compared in an interactive manner using our unique online Genome Explorer.

Extended advice on the project setup and in-depth downstream analysis are available. Depending on your research questions and available budget, we can give advice on the best possible strategy that guarantees an optimal output.

Easy-to-interpret tables and figures

Our microbial diversity analysis protocol includes the generation of easy-to-interpret tables and figures. For example the taxonomic pie chart displayed in the figure provides a clear overview of the taxonomic classifications and relative abundance. Alternatively taxonomic data can be easily (and interactively) explored with zoomable Krona pie chart.

Delivered output for microbial community analysis projects

  • Taxonomy table containing a summary of all read-annotations and their relative abundance.
  • Publication-ready figures and plots (bar chart, pie chart, cladogram).
  • Microbial profiling analysis report containing a summary of the annotation results.
  • Access to our Genome Explorer which allows interactive analyses of the results.
BaseClear Krona chart microbial communty 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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