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Whole Metagenome Shotgun Sequencing

Insights into all phenotypic, genotypic and other variable features of the microbiome
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Why profile microbial genomes?

Profiling of whole microbial genomes leads to a detailed taxonomic classification of all bacteria and other microorganisms in your sample. You can make the distinction up to species and subspecies level when the total DNA is analyzed instead of solely the V4 region of the 16S ribosomal gene.

Mirjam Rademaker Whole Metagenome Shotgun Sequencing
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Advantages of whole metagenome sequencing service

Depending on your research question and purity of your sample, our scientists can provide you with the optimal method to visualize the microbiome and their traits. For example, antibiotics resistance cassettes can be directly linked to the (sub)species. Resistant bacteria can be detected with a high accuracy and sensitivity, which is especially important for clinical applications.

  • Best taxonomic classification option due to the alignment of the whole genome
  • Classification down to species and subspecies level
  • Linking of phenotypic features with species
  • Publication-ready figures

Whole Metagenome Shotgun Sequencing Resources



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Service workflow

Data analysis

GenomeScan BioIT experts have set up data-analysis pipelines for efficient processing of whole metagenome sequencing data, either for short-read or long-read sequencing. Sequential steps include data trimming and preparation for alignment to the NCBI reference database to determine the characteristics and relative abundancies of different microbial populations. Depending on your research question, the bio-informatics specialist will generate a report with ready-to-present data.

The basis of the report consists of a comprehensive table containing the various microbes that were detected. It displays the taxonomic rank, genome size and number of reads that classifies the various microorganisms. Krona-plots provide an interactive tool to visualize the composition of the sample.

Short or long reads

At GenomeScan we can offer the choice between short (Illumina) and long-read (PacBio) sequencing. Illumina sequencing instruments reads short ~150 bp fragments, which allows for fast and high throughput analysis.

The PacBio Sequel sequences long stretches of DNA, up to 60 kb. Human or other eukaryotic DNA can be selectively removed before bacterial full genome profiling. Our scientists have designed a hybridization capture method to remove methylated DNA residues, which efficiently depletes the host DNA.

whole metagenome product specification Whole Metagenome Shotgun Sequencing
Service specifications

We have summarized key information about our whole metagenome sequencing service into a service specification sheet.

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Other Services

16S microbial profiling
Whole Exome Sequencing
Whole Genome Sequencing
Long read sequencing
Targeted proteomics panels

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