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Metagenomic Sequencing

Metagenomic Sequencing is the culture-independent, high-throughput analysis of the bacterial, viral or fungal composition of environmental samples, such as food, soil, microbiota, etc. and can be divided in two main categories. One is to focus on specific marker genes for phylogenetic identification only. For this so-called targeted amplicon approach, the ribosomal small subunit RNA (16S rRNA) gene has emerged as the most used marker. Further markers may be other rRNA genes, Rubisco or the ITS region. Alternatively, the use of the entire DNA or RNA for sequencing is often referred to as shotgun Metagenomics or, in case of RNA, as Metatranscriptomics, offering a random representation of all extracted genomic sequences, giving insights into the metabolic profiles of these specific communities.

At IMGM, we use one of our Illumina devices to offer you prime quality sequencing data, enabling a comprehensive view into the diversity and abundance or functional gene composition of your microbial community of interest.

Phylogenetic Identification - Bacterial Diversity and Abundance

IMGM's flexible metagenomics amplicon sequencing service offers the choice between experimentally tested primer pairs for different variable regions alongside the 16S rRNA gene (see graph below). We also offer you a completely flexible choice for own primers depending on your targets and research aims.

Additional flexibility is given by the possibility to step into the analysis pipeline at your most convenient starting point, e.g. start directly with gDNA, preamplified PCR products or even sequencing-ready libraries. In case your project belongs to the category “off the beaten path”, IMGM has a long standing expertise with custom project design for metagenomics analyses.

For 16S/18S/23S and ITS we offer the analysis of microbial composition, diversity and abundance with up-to-date bioinformatics software tools. OTU clustering and phylogenetic classification as well as further steps like calculation of alpha and beta diversity is carried out with a diligent view on data quality. This enables you to easily extract conclusions from your experimental data and to directly use our data to publish your results.

enteralis™ - medical 16S amplicon metagenomics

enteralis is a turnkey solution for gut microbiome analysis. It helps customer to tackle crucial decisions during their microbiome analysis by providing the best available tools. We have developed our metagenomics service to a stable routine, offering fast turnaround times with validated high quality methods and extensive analysis even for single samples. IMGMs proven expertise with metagenomics projects also enables us to offer upscaled solutions for big studies.

Sample kits, medical guidance and reporting are provided by the medical experts from the MVZ Martinsried, holding vast expertise in human genetic and microbiological analyses. Sequencing analysis is performed at IMGM using validated protocols for human gut microbiome analysis. Bioinformatic analysis uses the 16S centroids method developed by Smartgene, which is used for microbial identification since 1998.

Sample results are depicted individually in clear graphics and interactive Krona charts. During analysis, sample data is being compared to an internal database containing also publicly available microbiome data. Alpha and beta-diversity metrics as well as graphical clustering were chosen to present the relationship of the sample results to other known results. All data is presented in a clear graphical report which helps to quickly pinpoint the characteristics of each sample.

For more details, please refer to our flyer on enteralis.

Improved metagenomic analysis using low error amplicon sequencing

IMGM has developed a method to lower the errors introduced by erroneous polymerase activity during amplification and library preparation or by inaccuracies during sequencing.

Using a molecular tagging technique to label the DNA template pool of a microbial community (see figure below, STEP 1), the whole template pool is amplified and sequenced (see figure below, STEP 2). Due to the unique barcode, clustering and building a consensus sequence of the initial DNA template is possible. Therefore, amplification and sequencing errors can be corrected using bioinformatics tools.

This low error amplification method enables a more precise picture of the actual composition of the analyzed community and thus opens otherwise non-thinkable perspectives for all metagenomic applications.

Metabolic Profiles - Functional Gene Composition

Shotgun Metagenomic Sequencing is performed to sequence the entire DNA or RNA within an environmental sample. Take advantage of IMGM's broad NGS technology spectrum to get exactly the data you are looking for, whether you have RNA or DNA samples, just a few or several hundred. Have a look at gene expression levels, find potential novel biocatalysts or enzymes, get evolutionary profiles of community function and structure or see interactions between microbial communities and their host.

A detailed description of the workflow of IMGM’s Metagenomics Services can be found here.

IMGM's professional Metagenomics Services include:

  • Selection from IMGM´s 16S primer portfolio or custom primers
  • Flexible starting point from DNA isolation to sequencing-ready library
  • Identification of the appropriate technical approach and platform
  • Professional sample processing throughout the workflow
  • Fast turnaround times and focus on high quality data
  • Detailed and comprehensive reporting of data and results
  • Dedicated service for medical/clinical samples


Go for enhanced analytical power!
Entrust IMGM with your next Metagenomics project.