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Understanding the dynamics of microbial communities has gained much attention in recent years. Modern genomic technologies based on massive parallel DNA sequencing (Next Generation Sequencing) have opened a wide range of possibilities for genetic research on microbial genomes and communities. BaseClear offers complete solutions to study the collective genomes of microorganisms present in a sample. These studies are often referred to as metagenomics, but also as environmental genomics, ecogenomics or community genomics.

Genomic analysis can be applied to obtain information about the composition as well as the functional capabilities of an ecosystem. This allows the study of functional genes and gene clusters as well as provide insights into the organism’s phenotype. This for example can lead to a better understanding and advances of food fermentation processes. 


For '16S metagenomics' please refer to our Microbial diversity analysis page. 

Our whole genome sequencing (WGS) analysis protocol for metagenomics analysis generally involves sequencing on the Illumina MiSeq or HiSeq platform. In brief paired-end reads are assembled into metagenomes using an optimized in-house protocol. The resulting contigs are subject to so-called genome binning which aims to reconstruct complete genomes (as much complete as possible) and assigns these to the closest possible taxonomy . In addition a functional analysis is applied to detect ORFs and associated gene functions. Also it is possible to use a reference-guided approach (thus not de novo) which focuses on the presence or absence of genes/genomes (known prior to the start). Please ask our Product specialist Metagenomics for the available options and example projects. 

Our WGS-based analysis protocol includes a sophisticated workflow comprising a metagenome assembly, binning and taxonomic classification.

Delivered output:

  • De novo assembly of (binned) contigs
  • Taxonomy table containing a summary contig annotations and their relative abundance
  • Publication-ready figures and plots (barchart, piechart, cladogram)
  • Complete report including a summary of the classification results


While metagenomics provides a wealth of knowledge with respect to the functional potential of the sampled microbial community, it does not provide information about which of their genes are expressed. However, this can be achieved by metatranscriptomics and starts with the extraction of RNA. As total extracted RNA predominantly consists of ribosomal RNA (rRNA) that does not give information about the expression of functional genes, a rRNA depletion step is performed followed by library preparation and sequencing by paired-end sequencing on the HiSEQ Illumina platform.

BaseClear offers complete solutions for metatranscriptomic research, please contact our product specialist metagenomics (Tom van den Bogert) to discuss your project in detail. 

Meet Adalberto Costessi!

Adalberto is manager of our Next Generation sequencing (NGS) department and is also responsible for the development of new related technologies.


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