NEXT GENERATION SEQUENCING (NGS) SERVICES

Microbial Sequencing

In collaboration with Life and Brain GmbH, we offer complete solutions for microbiome analysis with a focus on the gut microbiome. Next-generation sequencing allows a more comprehensive assessment of the highly complex individual gut microbiota and its impact on essential functions such as colonisation resistance, digestive processes, nutrient absorption and also mucosal immunity. The new findings could improve our understanding of gut microbes in human health and disease.

We offer leading microbial sequencing on our Illumina and PacBio sequencing platforms. We provide standard and modified DNA extraction protocols from various sample types, amplicon sequencing (16S gene), shotgun metagenomics and genome sequencing. Other services are also available on request. Our aim is to provide a complete solution for (minimally) unbiased microbiome analysis, taking into account all sources of bias. Depending on the current workload and sample size, we
achieve a turnaround time of approximately 4 weeks.

Sampling & Logistics

Sampling and sample storage are critical steps in gut microbiota analysis. Sampling needs to be carried out consistently and stable storage needs to be ensured to avoid changing bacterial
composition. We recommend the use of a DNA/RNA stabiliser (for example: DNA/RNA shield, RNAprotect and other products). This ensures the stability of the samples over several weeks even at room temperature and inactivates infectious agents. Samples should be frozen and stored at -80°C as soon as possible. Samples must be shipped on dry ice if not stabilised. We can assist with sample collection and logistics if required.

Microbial DNA Preparation Services

For a wide range of sample materials we offer a choice of DNA extraction protocols. For faecal samples, we have established and validated our own modified high-throughput DNA
extraction protocol based on PerkinElmer Chemagen technology for reliable and complete results. We also offer a wide range of established DNA extraction kits from various
manufacturers including Qiagen, ZymoResearch, PerkinElmer and others. We have currently evaluated and used the Qiagen PowerFecal DNA Kit, Qiagen PowerFecal Pro DNA Kit, Qiagen PowerSoil DNA Kit, ZymoResearch ZymoBIOMICS DNA MIDI Kit, Magtivio MAgSi-DNA Stool Kit and PerkinElmer Chemagic DNA Stool Kit. Appropriate controls, including the various
microbiome standards, allow for optimal quality control.

16S Sequencing / Amplicon Sequencing

We offer amplification of the V1-V2 and V3-V4 regions on the Illumina MiSeq platform as part of our 16S sequencing service. Other regions such as V1-3 or V5-V6 can also be used on
request. In addition, we also offer the sequencing of the entire 16S gene (V1-V9 regions) on the PacBio Sequel platform. Our 16S sequencing provides up to species-level resolution. Phylogenetic coverage is determined by the 16S primers selected and the region of interest. The choice of 16S gene region of interest may vary depending on the study. We are happy to advise on this upon request. Sequencing libraries are generated after amplicon PCR using appropriate indexing kits. The maximum number of samples per run is 384 samples on the
Illumina MiSeq and 96 samples on the PacBio Sequel.

Shotgun Metagenomics

For more in-depth analysis, we offer whole genome sequencing (WGS). It provides strain- level resolution for prokaryotic and eukaryotic microorganisms (bacteria, archaea, viruses,
fungi, protists). Determining the functional genetic capacity of the microbiome is another advantage of shotgun metagenomics. Metabolic networks can be mapped and markers can
be studied in a targeted and efficient manner.

Overview:

	Targeted Microorganisms	Sequencing Platform
Targeted Sequencings: 16S short reads (V1-V2, V3-V4)	Bacteria, Archaea	Illumina MiSeq
Targeted Sequencing: ITS short reads	Fungi	Illumina MiSeq
Targeted Sequencing: 16S/ITS/18S long reads (V1-V9)	Bacteria, Archaea, Fungi	PacBio Sequel
Shotgun Metagenomics	Bacteria, Viruses, Fungi, Protists	Illumina NovaSeq

Submission Guidelines:

Feel free to contact us to start consultation on your project. A shipping form will be provided. Write an email to Jun. Prof. Marie-Christine Simon (mcsimon@uni-bonn.de) & Dr. Waldemar Seel (wseel@uni-bonn.de)