Understanding the dynamics of microbial communities has gained much attention in recent years. Modern genomic technologies based on Next-Generation Sequencing (NGS) have opened a wide range of possibilities for microbial identification and diversity studies. BaseClear offers complete microbial profiling solutions to extract DNA from your samples and the means to determine the composition of bacteria, Archaea and fungi. This can be applied to a broad range of samples, including food, probiotics, water, microbiome, biofilm, fermentation and soil.

Why choose our microbial diversity analysis service?

  • BaseClear is specialized in microbial diversity studies for environmental (e.g. food, water and soil) and microbiota (e.g. faeces, skin) samples
  • With our fungal and bacterial community analysis service you can identify thousands of microorganisms in one analysis
  • Our bacterial 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. Our BiaNomics business unit 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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Sharing results with participants

Technical approach for fungal and bacterial profiling

The technical approach for microbial diversity studies is usually based on PCR amplification of housekeeping or functional genes followed by sequencing. For bacterial profling usually the 16S region is used, for fungal profiling the ITS region. The generated data is compared to microbial sequencing databases. Data analysis is performed by our in-house developed tool: the BaseClear Genome Explorer.

BaseClear offers complete bioinformatics solutions for microbial profiling analysis. Standard solutions for microbial profiling include 16S and/or ITS amplicon analysis for taxonomic classification and relative frequencies. Illumina MiSeq reads are merged into overlapping pseudo-reads and subsequently aligned against a 16S database. Taxonomic classification is performed using an in-house protocol. Extended advice on the project setup and in-depth downstream analysis are available.

For bacterial diversity analysis alternatively also the Illumina HiSeq and PacBio SMRT platforms can be used to generate shorter and longer reads, respectively. Depending on your research question and available budget, BaseClear can offer the best possible strategy that guarantees an optimal output. In most cases Illumina MiSeq paired-end reads are generated which are merged into overlapping pseudo-reads using our bioinformatics analysis pipeline. In this manner a relatively long stretch of the 16S rRNA gene can be covered (e.g. the V3-V4 region). Subsequently each read is aligned against a 16S rRNA gene database for taxonomic classification.

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.

Flowchart microbial profiling

Easy-to-interpret tables and figures

Our bacterial 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 profiling projects

  • Taxonomy table containing a summary of all read-annotations and their relative abundance.
  • Publication-ready figures and plots (bar chart, pie chart, cladogram).
  • Bacterial profiling analysis report containing a summary of the 16S annotation results.
  • Access to our Genome Explorer which allows interactive analyses of the results.
BaseClear Krona chart microbial communty analysis

Related services

Meet Tom van den Bogert!

Tom is responsible for metagenomics and microbial profiling projects, which are based on our next generation sequencing technologies, and the development of related approaches.

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