Next Generation Sequencing (NGS) Services

Microbial sequencing

We offer leading microbial sequencing on our Illumina and PacBio sequencing platforms. We provide stock and modified DNA extraction protocols from various samples types, amplicon sequencing (16S gene), shotgun metagenomics, and genome sequencing. Other services can also be inquired. Our goal is to deliver a complete solution for (minimal) unbiased Microbiome analysis, by taking all sources of bias into account. Depending on the current workload and sample size, we achieve a turnaround of about 4 weeks.

In cooperation with Life and Brain Gmbh we offer complete solutions for microbiome analysis, with a focus on the gut microbiome. Next-generation sequencing allows for a more comprehensive assessment of the highly complex individual intestinal microbiota and its effect on essential tasks such as colonization resistance, digestive processes, absorption of nutrients, and also mucosal immunity. The new insight might improve our understanding of the gut microbes in human health and disease. 

Sampling & logistics

Sampling and storage are critical steps for gut microbiota analysis. Sampling must be standardized and samples should be completely stabilized during storage to prevent bias in the results. Samples should be frozen and storage at -80 °C as soon as possible. Samples must be shipped on dry ice. If required, we can assist with sample collection and logistics. 

Microbial DNA preparation services: 

We offer a selection of different DNA extraction protocols for a wide range of sample materials. For fecal samples we established and validated our own modified high throughput DNA extraction protocol based on the PerkinElmer Chemagen technology for reliable and complete results. In addition, we also provide a wide selection of established DNA extraction kits from various manufacturers, e.g. Qiagen, ZymoResearch, PerkinElmer, … . We have currently evaluated und used Qiagen PowerFecal DNA Kit, Qiagen PowerFecal Pro DNA Kit, Qiagen PowerSoil DNA Kit, ZymoResearch ZymoBIOMICS DNA MIDI Kit, and PerkinElmer Chemagic DNA stool Kit. Appropriate controls, including the various Microbiome standards, allow for optimal quality control. DNA extraction marks a crucial step in microbiome analysis, since the analysis has no value if the DNA does not represent the actual microbial community. 

16S Sequencing / Amplicon Sequencing

We deliver up to species-level resolution with our 16S sequencing. The phylogenetic coverage is determined by the chosen 16S primers and its targeted region. Depending on the study performed, the choice of the 16S gene region of interest may vary. We are happy to offer advice on this matter on request. The primer sets used are critical for successful identification of all microorganisms. Our 16S sequencing service offer amplification of the V1-V2 and V3-V4 regions on the Illumina MiSeq platform. Other regions, such V1-3 or V5-V6, can also be used on request. In addition, we also offer sequencing of the entire 16S gene (V1-V9 regions) on the PacBio Sequel platform. 

PCR amplicons with multiple barcodes are generated and sequenced on either the Illumina MiSeq machine (paired-end mode) of length approx. 400-500 bp (300+300 bp with ~100-200 bp overlap) or of longer reads on the PacBio Sequel platform. Maximum samples per run are up to 384 (380 samples + 4 PCR controls) for MiSeq or 96 (92 samples + 4 PCR controls) for Sequel. Libraries are prepared according to the 16S metagenome library preparation protocols of the named manufacturers (Illumina, PacBio). 

Shotgun Metagenomics

Use for identification with the highest precision and sensitivity. It allows for strain-level resolution for all prokaryotic and eukaryotic microorganisms (bacteria, archaea, viruses, fungi, protists). The main advantage of shotgun metagenomics lies in the functional gene characterization of the investigated microbiome. Metabolism networks can be displayed and markers investigated in a targeted and efficient way. This approach allows also for the discovery of previously unknown microorganisms. 

Overview:

Submission Guidelines: 

Contact the Microbiome Manager to start consultation of your project. Shipping form will be provided.