Metagenomics & amplicon profiling

BaseClear offers dedicated metagenomics services to answer two fundamental questions in microbiome studies – “what microbial species are there?” and “which molecular functions are they performing?”

Metagenomics analysis allows the exploration of the diversity, composition and functional capacity of microbial communities. With the development of next-generation sequencing technologies and advances in bioinformatics and biostatistics, studying metagenomic communities delivers increasingly valuable data and insights. Our experts are happy to discuss the details and best technical approach that can be used to answer the research questions on your next metagenomics and amplicon profiling projects.

Functional Metagenomics Analysis

Our advanced metagenomics analysis pipeline includes data QC, optional host filtering, de novo assembly, gene prediction, and annotation. We quantify gene abundance and detect antimicrobial resistance genes (AMR) and virulence factors.

Key features:

  • High-throughput analysis for human and non-human metagenomic data
  • Supports diverse clinical trial projects with various sample sizes and microbiomes
  • Tailored workflows cover all life domains, viruses, and phages

Validated workflow backed by industry benchmarks

Commercial applications:

  • Clinical trials (human/animal)
  • Industrial enzyme discovery
  • Probiotic identification
  • Studying probiotic impacts on gut microbiome



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Taxonomic Analysis

We offer a rapid and accurate method for profiling taxonomic abundance in metagenome samples. Our assembly-free pipeline utilizes dedicated databases tailored for specific applications such as infant, pathogen, human skin, bovine rumen, poultry, and swine microbiomes. These databases are customizable upon request. Following taxonomic classification, we generate abundance tables for microorganisms per sample.

How are we unique?

    • Validated databases covering viruses, archaea, bacteria, and eukaryotes
    • Rapid taxonomic classification for large clinical trials
    • High sensitivity and accurate abundance estimation
    • Detailed reports from domain to species level, including strain-level classification
    • Incorporation of metagenome-assembled genomes (MAGs) boosts classification rates
      • Infant microbiome database reduces unclassified reads to <10%
      • Bovine rumen database lowers unclassified reads from >72% to <30%

Microbial profiling

BaseClear offers microbial profiling solutions to determine the composition of bacteria, Archaea and fungi in your samples. This can be applied to a broad range of samples, including food, probiotics, water, microbiome, biofilm, fermentation and soil. Our bacterial and fungal profiling services are based on Next-Generation Sequencing (NGS) technology. To analyse the bacteria in your samples we use 16S profiling technology. To identify and quantify the fungi in your samples we use ITS profiling technology.

Why choose our microbial profiling service?

BaseClear is specialized in microbial profiling of both environmental and microbiota samples. We process for instance soil, food, probiotics, faecal and skin samples. With our 16S/ITS profiling service we identify thousands of bacteria and fungi in your sample. With our fungal and bacterial profiling also non-cultivable microorganisms are identified. Our microbial profiling in an extremely fast method for screening of complex microbial communities.

The experimental design for these kind of projects is crucial. Our PhD-level specialists can help determine the best strategy for your project for most reliable results.


16S & ITS Sequencing

BaseClear offers microbial profiling through PCR amplification of 16S genes for bacteria and ITS genes for fungi, followed by sequencing. Data is compared against microbial databases and analyzed using our proprietary tool, Genome Explorer. Our bioinformatics solutions cover standard 16S and/or ITS amplicon analysis for taxonomic classification. Illumina MiSeq reads are merged, aligned against a 16S database, and classified using our protocol. We provide project setup advice and extensive downstream analysis.

Depending on your needs and budget, we use Illumina HiSeq or PacBio SMRT platforms for shorter or longer reads. Typically, we generate Illumina MiSeq paired-end reads, merged into pseudo-reads for comprehensive coverage (e.g., V3-V4 region). Results include taxonomic tables and publication-ready figures (cladogram, pie chart, bar chart). Our online Genome Explorer facilitates interactive result comparison.

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