Shotgun Metagenomics

Introduction to Shotgun Metagenomics

Our shotgun metagenomics services allow detailed characterization of entire microbial communities, enabling precise sub-species/strain-level and functional annotation of the microbiome.

In shotgun metagenomics, DNA from a sample is fragmented in a random manner followed by next-generation sequencing (NGS). This generates primer-independent and unbiased sequencing data, which can be analyzed using various reference-based and reference-free methods. Shotgun metagenomics targets all DNA material in a sample and produces relative abundance information for all genes, functions and organisms including bacteria, fungi, archaea, and viruses (phages).

Introduction to Metagenomic Species (MGS) Concept

We base our shotgun metagenomics analyses on the metagenomic species (MGS) concept, which facilitates high-resolution metagenomics analysis, far beyond classical reference-based approaches.

While classical reference-based methods rely on comparisons to the limited number of available reference genomes, the MGS approach allows identification and profiling of microbial species independent of reference sequences. The technique was published by our CSO, Dr. H. Bjørn Nielsen et al. in Nature Biotechnology (2014) and utilizes co-abundant binning of genes across a large collection of deep sequenced metagenomic samples to identify species. Since then, the method has been refined and sequencing technologies have improved allowing accurate profiling at subspecies level.

At Clinical Microbiomics, we offer our clients microbiome analyses that take advantage of our MGS catalogues. The MGS catalogues have been extensively annotated for taxonomy and functional potential using both EggNOG and KEGG. In the typical human gut microbiome sample our gene catalogue accounts for more than 90% of the microbiome sequence reads, which greatly supersedes the typical 25-40% representation seen for reference-based approaches. Moreover, the MGS profiling provides substantially increased detection sensitivity and abundance accuracy.

Metagenomics Applications

• Research and discovery across a wide variety of human health areas including gut, oral, vaginal and skin health.
• Analysis of clinical studies for linking the microbiome to clinical outcomes in drug, probiotic and nutritional intervention studies
• Analysis of potential microbiome factors determining responders and non-responders in clinical studies
• Microbiome biomarker discovery
• Microbiome data mining for identifying disease-associated strains
• Analysis of antibiotic resistance genes in clinical studies (resistome analysis)
• Engraftment and colonization analysis for fecal microbial transplant (FMT) studies and probiotic studies

Our Metagenomics Services and Solutions

Sample Preparation - We offer DNA extraction for metagenomics projects, performed under highly controlled and traceable conditions in our advanced, Copenhagen-based, ISO17025 certified laboratory. We have specialized low-input protocols for low biomass samples such as skin samples.

Sequencing - DNA sequencing is performed using Illumina-based shotgun metagenomics sequencing at highly competitive prices, even for deep sequenced samples.

Data Analysis - We have vast in-house metagenomics data analysis experience with state-of-the-art bioinformatic approaches, including:

• multi-omics integration
• advanced statistical modelling
• machine learning
• antibiotic resistance genes (resistome)
• SNV-based strain tracking
• Responder/non-responder models
• FMT/probiotic persistence probability
• Phage discovery, and much more.

Customized Solutions - We offer de-novo discovery of microbes based on the samples from your study. This advanced and computational heavy procedure, based on the MGS concept, allows you to circumvent the limitations of standard reference-based approaches only describing the microbes that have previously been described (e.g. with reference genomes). Accordingly, we offer to identify new cohort-specific species for describing the full microbial diversity of your samples.

Our Experience

At Clinical Microbiomics we have extensive experience managing shotgun metagenomics projects and offer complete and validated in-house workflows from sample preparation to metagenomic sequencing to bioinformatics, biostatistics and tailored data analysis. Our highly experienced scientific team and MGS bioinformatics platform will give you the highest taxonomical (species/strain) and functional resolution (genes) possible. Your project will be overseen by one of our experienced metagenomics study directors who will follow every step of the project workflow, ensuring that quality is consistently at the highest level. You will always be able to contact the study director for direct insights in to the day-to-day processing of your samples.