FAQs Next Generation Sequencing

• General FAQs for Next Generation Sequencing >>

The decision between amplicon sequencing and metagenome sequencing depends on your research objectives and the specific characteristics of your samples. Each method has its own strengths and limitations:

Amplicon sequencing (e.g., 16S rRNA, ITS):

• Ideal for taxonomic profiling across a large number of samples
• Cost-effective and suitable for detecting subtle differences between microbial communities
• Commonly used in case-control studies or for longitudinal sampling across different environments
• Limited to organisms targeted by specific primers and cannot provide functional insights

Metagenome sequencing (shotgun approach):

• Primer-independent and free from PCR biases, allowing a more accurate and comprehensive view of microbial diversity
• Detects both taxonomic and functional features, including genes and pathways
• Capable of identifying culturable and unculturable organisms across all domains of life
• Requires higher sequencing depth and greater computational resources

If your study requires broad taxonomic coverage, functional insights, or detection of viruses and rare taxa, metagenomics is likely the better option. For projects focused on comparative analysis across many samples with known target groups, amplicon sequencing may be more appropriate.

INVIEW Metagenome accepts a wide range of biological samples:

• Research samples of human origin, such as swabs, fecal samples, and lavage fluids
• Food samples for quality control and pathogen detection in an industrial environment (e.g. dairies, breweries, meat-processing and agriculture)
• Environmental samples from soil, water, or surface

Eurofins Genomics has extensive expertise in DNA isolation and metagenomic sequencing.

In host-associated samples (e.g., human skin, saliva), DNA extracted from the sample often includes a mixture of microbial and host (e.g., human) DNA. This is referred to as host contamination. High host contamination means a significant portion of your reads may not be useful for analyzing the microbiome

The appropriate sequencing depth for metagenomic studies depends largely on the complexity of the microbial community and the level of host DNA contamination in the sample.

• High-complexity communities (with many species at varying abundances) and samples with high host DNA content generally require greater sequencing depth to achieve reliable microbial detection and taxonomic resolution.
• Low-complexity samples or those with minimal host contamination may require fewer reads to obtain meaningful data.

If the ideal sequencing depth is unclear, we recommend performing a pilot sequencing run on a small number of representative samples to determine empirical requirements.

To account for host DNA contamination—which reduces the proportion of usable microbial reads—we increase sequencing depth accordingly. This ensures that enough microbial data is retained for robust analysis.

We base our recommendations on empirical evidence and industry best practices to ensure a minimum number of high-quality microbial reads. The goal is to retain enough usable data after removing host reads to support robust taxonomic and functional profiling.

Insufficient sequencing in high-host samples can lead to:

• Poor microbial taxonomic resolution
• Incomplete functional profiling
• Biases in comparative analysis
• Difficulty detecting low-abundance taxa

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.

Metagenomic analysis allows for the comprehensive identification of microorganisms without relying on taxonomic markers such as 16S rRNA. This approach enables the detection of both culturable and unculturable organisms, including:

• Bacteria
• Archaea
• Fungi
• Eukaryota
• DNA Viruses

While Eurofins Genomics has extensive experience in profiling human-associated microbiota, we have also successfully analyzed microbial communities from food, industrial, and environmental samples.

Yes, INVIEW Metagenome includes a guaranteed output of 10 million read pairs per sample.

If higher sequencing depth is required, additional read packages can be ordered upon request

INVIEW Metagenome Explore

This option is designed for broad taxonomic profiling of all organisms present in a microbiome. It includes 10 million read pairs, which is suitable for:

• Low-complexity metagenomes
• Gaining a broad overview of microbial genera in more complex communities

Explore is ideal for projects focused primarily on identifying which organisms are present, without requiring functional or resistance analysis. For deeper insight, additional sequencing depth can be achieved by ordering extra read packages.

INVIEW Metagenome Advance

This package includes comprehensive taxonomic analysis along with detailed insights into:

• Antibiotic resistance genes
• Functional profiling of microbial communities

Advance is tailored for complex metagenomes where both community structure and functional characteristics are of interest. Applications include:

• Detection and quantification of resistance factors in natural or clinical environments
• Analysis of biological functions and metabolic pathways within microbial communities

As with Explore, 10 million read pairs are included, with the option to add more if necessary. Please note that the required sequencing depth may vary significantly depending on sample complexity and host DNA contamination. In such cases, additional sequencing may be required to achieve robust and reliable results.