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.
Whole Metagenome Shotgun Sequencing
Insights into all phenotypic, genotypic and other variable features of the microbiome
Why profile microbial genomes?
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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
Service workflow
1. Initial meeting
When you consider using one of our services, our scientific team will help choosing the optimal project design. Each service can be customized by adding options. You will receive an overview of project budget and deliverables, so you can make an informed choice. Once you return your Purchase Order form, your project manager will contact you to discuss the next steps.
2. Sample delivery
Sample specifications for whole metagenome sequencing are:
Purified genomic DNA
- Validated input PCR free: ≥ 50ng / sample
- Minimum volume: 15μL / sample
- Quality: HMW DNA, column or bead purified
3. Sample entry QC
After sample arrival, an entry QC is performed to determine if the sample quality is sufficient so we can guarantee the data outcome stated in your quotation. You will receive a report with sample QC results to inform you of our findings before proceeding further. Samples that fail QC can be replaced by spare samples delivered in the same shipment or sent at a later stage.
4. Library prep/QC and sequencing
The library resulting from sample preparation goes into a library QC step to ensure sufficient material per sample and the right library size. Sequencing on Illumina NovaSeq 6000 (PE150):
- Standard read depth 7.5 Gb / sample
- Unique Molecular Identifiers
- Unique dual indexing
5. Data QC
The raw data that is generated by the sequencer must be divided to obtain one data file per sample. This is called demultiplexing.
Your project manager checks the data quality by analyzing the quality metrics of the run. Final inspection of the data takes place and the dataset is transferred onto a hard disk.
6. Reporting
You receive your Project Report together with your data. It contains an overview of the experimental methods used, sample specifications, and a summary of all technical information for publication. Deliverables:
- TAT: 2-3 weeks after successful sample QC
- FastQ files via secure e-transfer
- Quality score Q30 of ≥80% for PE150 reads
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.
Service specifications
We have summarized key information about our whole metagenome sequencing service into a service specification sheet.
Let's get the conversation started for your next NGS project
Please either fill in below or email us directly at info@genomescan.nl
and we will get in touch with you to discuss your requirements
