The right answers to frequently asked questions
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What kind of samples can be used?
For Inview Metagenome Advance we accept clinical research samples of human origin (e.g. swaps, feces, lavage). Upon request many types of starting material can be used for whole metagenome analysis such as:
food samples for quality control and pathogen detection in an industrial environment (dairies, breweries, meat-processing and agricultural facilities)
Eurofins Genomics is particularly well-experienced in DNA isolation and sequencing of stool samples.
How much starting material is required?
For specific information on quantity and concentration requirements for specific library preparation methods please refer to your quote or contact us directly. For best results we typically 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 provide you with tables (tsv, txt) that list all genera present in your sample and the respective read counts. In addition, you will receive all raw sequencing data.
Operational Taxonomic Units (OTUs), which are classified by Kraken’s exact k-mer alignment algorithm and appropriate MiniKrakenDB database, are represented in table format with taxonomic identification.
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. Microbial communities 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 Advance 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 markers such as 16S rRNA. Metagenome sequencing enables the identification of both culturable and unculturable organisms, such as bacteria, archaea, fungi, protozoa and viruses. Although Eurofins Genomics is most experienced in profiling human microbiota, we have also successfully characterised 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 present distinct advantages as well as disadvantages. Your method of choice should be based on your research goal. The successful outcome of a project typically depends on several factors such as community composition, the abundance of closely-related species and sequencing depth.
Amplicon sequencing offers suitable taxonomic profiling of a large number of samples. The approach enables the detection of subtle differences between microbial communities, which makes the method beneficial for statistical comparisons, such as for case control studies or for sampling varying environments over time.
Metagenomic sequencing does not rely on a certain set of primers, which frees the method of taxon-specific PCR biases. This makes possible more accurate representations of the analysed microbiota and more dependable estimations species abundance. Metagenomics analysis can provide information on both the taxonomic as well as the functional characteristics of a given sample.
What is the difference between Inview Metagenome Explore and Inview Metagenome Advance?
Inview Metagenome Explore is a ideally suited for broad 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 provides 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 be applied to the quantification of functional processes in a particular community or to the detection of numerous resistance factors in an undisturbed natural environment. Please note that the required sequencing depth for successful metagenomic profiling is strongly influenced by the complexity and expected level of host contamination of the starting material. Therefore, additional sequencing effort could be necessary to obtain satisfactory results.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH