The right answers to frequently asked questions
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What kind of samples can be used?
In general all kind of (DNA) samples can be used for metagenome profiling such as:
- samples of human origin (swaps, feces, lavage)
- food samples for quality control of microorganisms and pathogen detection in an industrial setting (dairies, breweries, meat-processing and agricultural facilities)
- environmental samples
Eurofins Genomics is particularly well-experienced in DNA isolation and sequencing of stool samples.
How much starting material is required?
For information on quantity and concentration required for specific library preparation methods please refer to your quote or contact us. For optimal results we generally require >100 ng of double-stranded, purified DNA (total amount depends on the proportion of microbial DNA in the sample). Please note that the DNA has to be RNA-free with an OD 260/280 >1.8 and OD 260/230 >2.0.
What data will I receive?
Eurofins Genomics will deliver tables (tsv, txt) listing all genera present in the analysed sample and the respective read counts. In addition, you receive all raw sequencing data.
Operational Taxonomic Units (OTUs), which are classified by BLAST analysis against appropriate databases, are represented in a tabular form including taxonomic identification. Only the best hits are considered for OTU assignment.
What is the necessary coverage for metagenome analysis?
The required sequencing depth for successful metagenome sequencing mainly depends on the complexity of the sample (number and representation of individual species) and the level of expected host contamination. Samples of high complexity with high background levels of host DNA require more coverage than samples of reduced complexity and with lower host DNA contamination levels. In case of doubt we recommend performing a pilot on a sub-set of samples to determine the required sequencing coverage.
Do you guarantee a certain sequencing output?
Yes, Inview Metagenome Explore comes with guaranteed 10 million read-pairs. Additional read packages can be ordered separately.
Which organisms can be detected?
Metagenomics analysis permits the identification of microorganisms independent of taxonomic genetic markers. The approach enables the identification of culturable and unculturable organisms, such as bacteria, archaea, viruses, as well as simple eukaryotes including fungi and protists. Although Eurofins Genomics has the most expertise in profiling human microbiota, we have also successfully identified microbial community members from food, industrial and environmental samples.
How do I choose between targeted amplicon sequencing and metagenome sequencing?
Both amplicon and metagenome sequencing have their own advantages and disadvantages.
Your method of choice should be selected based on your research aim. Generally, the successful outcome of a project depends on several factors such as community composition, the abundance of other close species or strains and sequencing coverage depth.
Amplicon sequencing offers suitable assessment of taxonomic composition and diversity of a large number of samples. As you have more power to detect subtle differences between microbial communities, the method is beneficial for statistical comparisons, such as for case control studies or for sampling environments over time.
Metagenomic sequencing is free of taxon-specific PCR biases due to the primer sets used. This enables more accurate representations of the analysed microbiota and more dependable estimations of species abundance levels. Metagenomics analysis can also help elucidate both taxonomic as well as functional characteristics of a given sample.
What is the difference between Inview Metagenome Explore and Inview Metagenome Advance?
Inview Metagenome Explore is a great product for the general taxonomic profiling of all organisms present in a given microbiome. The included 10 million read pairs are suitable for analysis of low complexity metagenomes, as well as for a broad overview of genera in complex metagenomes. A deeper sequencing coverage can be accomplished by adding additional read packages.
Inview Metagenome Advance offers detailed assessment of antibiotic resistance and community function, in addition to taxonomic characterisation. The product is ideal for profiling of complex metagenomes. For a deeper sequencing coverage than the included 10 million read pairs additional read packages can be added. The service can help quantify functional processes in a particular community or detect numerous resistance factors in an undisturbed natural environment.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH